A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

about() - Method in class org.ginsim.gui.GUIManager

Show an "about" dialog

AboutDialog - Class in org.ginsim.gui.shell

"About dialog" for GINsim

AboutDialog() - Constructor for class org.ginsim.gui.shell.AboutDialog

This is the default constructor

AbstractDerivedGraph<V,E extends Edge<V>,AG extends Graph<AV,AE>,AV,AE extends Edge<AV>> - Class in org.ginsim.core.graph

Base class for graphs which need an associated graph.

AbstractDerivedGraph(GraphFactory) - Constructor for class org.ginsim.core.graph.AbstractDerivedGraph

AbstractGraph<V,E extends Edge<V>> - Class in org.ginsim.core.graph

Base class for graphs using a storage backend: it provides generic methods and storage abstraction.

AbstractGraph(GraphFactory) - Constructor for class org.ginsim.core.graph.AbstractGraph

Create a new graph with the default back-end.

AbstractGraphFactory<G extends Graph<?,?>> - Class in org.ginsim.core.graph

Base class for Graph Factories.

AbstractGraphFactory(Class, String) - Constructor for class org.ginsim.core.graph.AbstractGraphFactory

AbstractHelpCanvasEventManager - Class in org.ginsim.gui.graph.canvas.events

AbstractHelpCanvasEventManager(GraphCanvasRenderer) - Constructor for class org.ginsim.gui.graph.canvas.events.AbstractHelpCanvasEventManager

AbstractParameterPanel<G extends Graph,T> - Class in org.ginsim.gui.shell.editpanel

All parameter panels must extend this abstract class to be updated on selection changes

AbstractParameterPanel(GraphGUI<?, ?, ?>) - Constructor for class org.ginsim.gui.shell.editpanel.AbstractParameterPanel

AbstractParameterPanel(Graph<?, ?>) - Constructor for class org.ginsim.gui.shell.editpanel.AbstractParameterPanel

AbstractServiceGUI - Class in org.ginsim.gui.service

This class contains the weight used to order the services' actions in the menus The services must inherit from this class

AbstractServiceGUI() - Constructor for class org.ginsim.gui.service.AbstractServiceGUI

AbstractStackDialogHandler - Class in org.ginsim.gui.utils.dialog.stackdialog

AbstractStackDialogHandler() - Constructor for class org.ginsim.gui.utils.dialog.stackdialog.AbstractStackDialogHandler

AbstractStateSet - Class in org.ginsim.service.tool.avatar.domain

Abstract class enclosing a state-set
State-sets can be implemented in multiple ways (e.g.

AbstractStateSet() - Constructor for class org.ginsim.service.tool.avatar.domain.AbstractStateSet

AbstractTreeTableModel - Class in org.ginsim.gui.utils.widgets.treetable

An abstract implementation of the TreeTableModel interface, handling the list of listeners.

AbstractTreeTableModel(Object) - Constructor for class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

accept(File) - Method in class org.ginsim.commongui.utils.FileFormatFilter

accept(File) - Method in class org.ginsim.gui.shell.GsFileFilter

Accept all directories and files with the good extension.

action - Variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.ComponentAdapter

ACTION - Static variable in class org.ginsim.gui.utils.data.ColumnDefinition

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.graph.canvas.CanvasHelpAction

actionPerformed(EditAction) - Method in class org.ginsim.gui.graph.EditActionManager

Warn the manager that an action was performed.

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.RootPanel

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationCreatePanel

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.graph.view.style.EdgeRoutingPanel

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.graph.view.style.StyleTab

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.shell.actions.ExportAction

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.shell.actions.ImportAction

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.shell.actions.LayoutAction

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.utils.data.ListSelectionPanel

actionPerformed(ActionEvent, int) - Method in interface org.ginsim.gui.utils.data.MultiActionListener

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.utils.data.PropertyActionButton

actionPerformed(int, int) - Method in interface org.ginsim.gui.utils.data.TableActionListener

actionPerformed(ActionEvent) - Method in class org.ginsim.gui.utils.widgets.ButtonPopup

actionPerformed(ActionEvent) - Method in class org.ginsim.servicegui.export.petrinet.PetriNetExportAction

actionPerformed(ActionEvent) - Method in class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorCaptionFrame

actionPerformed(ActionEvent) - Method in class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorFrame

actionPerformed(ActionEvent) - Method in class org.ginsim.servicegui.tool.interactionanalysis.InteractionAnalysisFrame

actionPerformed(ActionEvent) - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphFrame

actionPerformed(ActionEvent) - Method in class org.ginsim.servicegui.tool.omddViz.OmddVizFrame

actionPerformed(ActionEvent) - Method in class org.ginsim.servicegui.tool.pathfinding.PathFindingFrame

activable(RegulatoryGraph, RegulatoryNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

ActivityLevel - Enum in org.ginsim.core.graph.regulatorygraph

add(T) - Method in class org.ginsim.common.utils.ArraySet

add(String, String) - Method in interface org.ginsim.common.utils.OpenHelper

Create a new link.

add(String, String) - Method in class org.ginsim.core.annotation.BiblioList

add(String, String) - Method in class org.ginsim.core.annotation.DatabaseInfo

add(String, String) - Method in class org.ginsim.core.annotation.HttpHelper

add(HierarchicalNode) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNodeSet

add() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

add(T) - Method in class org.ginsim.core.utils.data.ListenableNamedList

add(int, T) - Method in class org.ginsim.core.utils.data.ListenableNamedList

add(String, AbstractStateSet) - Method in class org.ginsim.service.tool.avatar.domain.CycleGraph

Adds a set of successor states from a state within the cycle

add(State) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Adds a state to the given state-set

add(State) - Method in class org.ginsim.service.tool.avatar.domain.Result

Adds a stable state to results

add(AbstractStateSet) - Method in class org.ginsim.service.tool.avatar.domain.Result

Adds a complex attractor (terminal cycle) to results

add(State, int) - Method in class org.ginsim.service.tool.avatar.domain.Result

Adds a stable state to results

add(AbstractStateSet, int) - Method in class org.ginsim.service.tool.avatar.domain.Result

Adds a complex attractor (terminal cycle) to results

add(State) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Adds a state to the given state-set

add() - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

add(int) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

add(SimulationParameters, int) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

add() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

add(int) - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserPathModel

add() - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicSearchPathConfig

add(int) - Method in class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

add(int) - Method in interface org.ginsim.servicegui.tool.pathfinding.PathFindingTableModel

add2path(DynamicNode) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

addActionListener(MultiActionListener) - Method in class org.ginsim.gui.utils.widgets.ButtonPopup

addActionListener(TableActionListener) - Method in class org.ginsim.gui.utils.widgets.EnhancedJTable

addAll(MDDStateSet) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Adds a set of states to the state-set

addAll(StateSet) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Adds a set of states to the state-set

addAllTheStatesInQueue() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Perform a mergeMultiple on all the omdd in the pile and the root.

addAllToNewSigma(Collection<HierarchicalNode>) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSetFactory

addAnchor(String, String) - Method in class org.ginsim.common.document.DocumentWriter

add a new anchor into the document.

addAttr(String, Color) - Method in class org.ginsim.common.xml.XMLWriter

Add a color attribute to the opened tag.

addAttr(String, String) - Method in class org.ginsim.common.xml.XMLWriter

add an attribute to the opened tag.

addAttributeTag(XMLWriter, String, int) - Method in class org.ginsim.core.io.parser.GINMLWriter

addAttributeTag(XMLWriter, String, boolean) - Method in class org.ginsim.core.io.parser.GINMLWriter

addAttributeTag(XMLWriter, String, String) - Method in class org.ginsim.core.io.parser.GINMLWriter

addAttributeTag(XMLWriter, String, Object) - Method in class org.ginsim.core.io.parser.GINMLWriter

addBlockClose(Graph, Object) - Method in class org.ginsim.gui.GUIManager

Block closing of the graph

addBlockEdit(Graph, Object) - Method in class org.ginsim.gui.GUIManager

block editing mode for the graph

addButton(JButton) - Method in class org.ginsim.gui.utils.data.ListEditionPanel

addButton(JButton) - Method in class org.ginsim.gui.utils.data.ListPanel

addButtonAction() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

addCall(String, int, int, Map, int, boolean) - Static method in class org.ginsim.common.xml.XMLHelper

Deprecated.

addCall(String, int, Map, CallMode) - Static method in class org.ginsim.common.xml.XMLHelper

addCall(String, int, int, Map, CallMode) - Static method in class org.ginsim.common.xml.XMLHelper

addCall(String, int, Map, int, boolean) - Static method in class org.ginsim.common.xml.XMLHelper

Deprecated.

addCall(String, int, Map) - Static method in class org.ginsim.common.xml.XMLHelper

addCategory(String, CSSStyle) - Method in class org.ginsim.core.graph.view.css.Selector

Declare a new category responding to this selector

addCellEditor(Class, TableCellEditor) - Method in class org.ginsim.gui.utils.widgets.EnhancedJTable

addCellRenderer(Class, Class) - Method in class org.ginsim.gui.utils.widgets.EnhancedJTable

addChild(HierarchicalNode) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSet

addChild(TreeElement, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

addChild(TreeElement, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

addChild(TreeElement, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeString

addChild(TreeElement, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeValue

addChildren(int, int, List<TreeNode>, int, int[], EdgeAttributesReader) - Method in class org.ginsim.core.graph.tree.TreeBuilder

addComplementaryNode(String, String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

addComplexContent(String, boolean) - Method in class org.ginsim.common.xml.XMLWriter

add a complex "text child", it will be enclosed into CDATA markers

addComponent(Component, int, int, int, int, double, double, int, int, int, int, int, int, int, int) - Method in class org.ginsim.gui.utils.widgets.GsPanel

addConstraint(NodeInfo, byte) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

Add a constraint to a clause

addContent(String) - Method in class org.ginsim.common.xml.XMLWriter

add a "text child"

addCumulative(State) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Adds a state to the state-set (whenever the given state is already present within the state-set, the probability of the state to be inserted is added to the original state in the state-set)

addCumulative(State) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Adds a state to the state-set (whenever the given state is already present within the state-set, the probability of the state to be inserted is added to the original state in the state-set)

addDefinition(Object) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetList

addEdge(E) - Method in class org.ginsim.core.graph.AbstractGraph

Add an edge to this graph structure.

addEdge(V, V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

addEdge(V, V, E) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

addEdge(DynamicNode, DynamicNode, boolean) - Method in interface org.ginsim.core.graph.dynamicgraph.DynamicGraph

add an edge between source and target

addEdge(DynamicNode, DynamicNode, boolean) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

addEdge(E) - Method in interface org.ginsim.core.graph.GraphModel

Add an edge to this graph structure.

addEdge(HierarchicalNode, HierarchicalNode) - Method in interface org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraph

add an edge between source and target

addEdge(HierarchicalNode, HierarchicalNode) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

add an edge between source and target

addEdge(NodeReducedData, NodeReducedData) - Method in interface org.ginsim.core.graph.reducedgraph.ReducedGraph

add an edge to this graph.

addEdge(NodeReducedData, NodeReducedData) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

add an edge to this graph.

addEdge(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

addEdge(RegulatoryEdge) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

Adds the GsEdgeIndex to the interaction

addEdge(RegulatoryNode, RegulatoryNode, RegulatoryEdgeSign) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Add a signed edge

addEdge(RegulatoryNode, RegulatoryNode, RegulatoryEdgeSign) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

addEdge(Graph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

addEdge(RegulatoryEdgeSign, Graph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

addEdge(RegulatoryEdgeSign, int, Graph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

addEdge(TreeNode, TreeNode, int) - Method in interface org.ginsim.core.graph.tree.Tree

add an edge between source and target

addEdge(TreeNode, TreeNode, int) - Method in class org.ginsim.core.graph.tree.TreeImpl

add an edge between source and target

addEdge(EditActionManager, V, V) - Method in class org.ginsim.gui.graph.AddEdgeAction

addEdge(String, String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

AddEdgeAction<V,E extends Edge<V>> - Class in org.ginsim.gui.graph

AddEdgeAction(String, String) - Constructor for class org.ginsim.gui.graph.AddEdgeAction

AddEdgeAction(String) - Constructor for class org.ginsim.gui.graph.AddEdgeAction

addEdgeInBackend(E) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

Add an edge in the JGraphT Graph

addEdgeInBackend(E) - Method in interface org.ginsim.core.graph.GraphBackend

Add an edge to the graph.

AddEdgeInGraphCanvasEventManager - Class in org.ginsim.gui.graph.canvas.events

AddEdgeInGraphCanvasEventManager(GraphCanvasRenderer) - Constructor for class org.ginsim.gui.graph.canvas.events.AddEdgeInGraphCanvasEventManager

addEdgesToSelection(Collection<E>) - Method in class org.ginsim.gui.graph.GraphSelection

Add the edges in l to the list of selected edges

addEdgeStyle() - Method in class org.ginsim.core.graph.view.style.StyleManager

Create a new edge style.

addEdgeTo(HierarchicalNode) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Add an edge between to a node

addEdgeToSelection(E) - Method in class org.ginsim.gui.graph.GraphSelection

addEditButtons(JToolBar) - Method in class org.ginsim.gui.graph.EditActionManager

Fill the toolbar with buttons matching the available edit actions.

addEditEntries(JMenu, GraphGUI<?, ?, ?>) - Static method in class org.ginsim.gui.shell.callbacks.EditCallBack

Create and populate an Edit menu

addEmptyExpression(byte, RegulatoryNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

addEmptyParameter(byte, RegulatoryNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

addEntity(String, String) - Static method in class org.ginsim.common.xml.XMLHelper

addExpression(byte, RegulatoryNode, BooleanParser) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

addExpression(JTree, byte, RegulatoryNode, String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

addExpression(byte, RegulatoryNode, String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryParser

addField(Component, GenericPropertyInfo, int) - Method in class org.ginsim.gui.utils.data.GenericPropertyEditorPanel

addField(Component, GenericPropertyInfo, int) - Method in interface org.ginsim.gui.utils.data.GenericPropertyHolder

addField(Component, GenericPropertyInfo, int) - Method in class org.ginsim.gui.utils.data.PropertySwitch

addFile() - Method in class org.ginsim.core.annotation.BiblioList

addFile(String) - Method in class org.ginsim.core.annotation.BiblioList

addFixedPerturbation(NodeInfo, int) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

Add a perturbation to fix a component.

addFormatedContent(String, boolean) - Method in class org.ginsim.common.xml.XMLWriter

add a "text child", already formated: should _NOT_ be escaped

addGraphGUIListener(GraphGUIListener<G, V, E>) - Method in class org.ginsim.gui.graph.BaseGraphGUI

addGraphGUIListener(GraphGUIListener<G, V, E>) - Method in interface org.ginsim.gui.graph.GraphGUI

Register a GraphGUIListener

addGraphListener(G, GraphListener<G>) - Method in class org.ginsim.core.graph.GSGraphManager

addHelperClass(String, OpenHelper) - Static method in class org.ginsim.common.utils.OpenUtils

Register a protocol handler.

addHelperClassAlias(String, String) - Static method in class org.ginsim.common.utils.OpenUtils

Add an alias for an existing handler.

addImage(BufferedImage, String) - Method in class org.ginsim.common.document.DocumentWriter

addInitialState(int, byte[]) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

addInitialState(byte[]) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

addInitState(String, Map) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

addInline(L, String) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

addInputToTransition(String, String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

addLink(String, String) - Method in class org.ginsim.common.document.DocumentWriter

add a new link into the document.

addLink(String, Graph) - Method in class org.ginsim.core.annotation.Annotation

addLinkToCurRef(String, String) - Method in class org.ginsim.core.annotation.BiblioList

addListener(ObjectPropertyEditorUI) - Method in class org.ginsim.gui.utils.data.ObjectEditor

addListListener(GenericListListener) - Method in class org.ginsim.core.utils.data.ListenableNamedList

addLogicalParameter(LogicalParameter, boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

addLogicalParameter(LogicalParameter, boolean) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

Adds the specified interaction I to the interactions of the node

addMapping(RegulatoryNode, List<RegulatoryNode>, IntegrationFunction) - Method in class org.ginsim.service.tool.composition.IntegrationFunctionMapping

addMask(int, int) - Static method in class org.ginsim.common.utils.MaskUtils

Add a mask to a value.

addMessage(String) - Method in exception org.ginsim.common.application.GsException

addMissingFormats() - Static method in class org.ginsim.core.service.FormatSupportService

Trigger the creation of automatic wrappers for all available formats.

addMissingRefWarning(String) - Method in class org.ginsim.core.annotation.BiblioList

addModel(Simulation, String) - Static method in class org.ginsim.service.tool.avatar.service.AvatarServiceFacade

addModel(Simulation, String) - Static method in class org.ginsim.service.tool.avatar.service.FirefrontServiceFacade

addModel(Simulation, String) - Static method in class org.ginsim.service.tool.avatar.service.MonteCarloServiceFacade

addModel(StatefulLogicalModel) - Method in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

addModel(StatefulLogicalModel) - Method in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

addModel(StatefulLogicalModel) - Method in class org.ginsim.service.tool.avatar.simulation.MonteCarloSimulation

addModel(StatefulLogicalModel) - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

addMultiplePerturbation(List<Perturbation>) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

addNeighbour(int, int) - Method in class org.ginsim.service.tool.composition.GenericTopology

Specifies that module neighindex2 is a neighbour of module neighindex1, but not the other way around.

addNeighbour(int, int) - Method in interface org.ginsim.service.tool.composition.Topology

Specifies that module neighindex2 is a neighbour of module neighindex1, but not the other way around.

addNeighbour(int, int) - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

addNeighbour(int, int) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

addNeighbour(int, int) - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

addNewEdge(String, String, byte, RegulatoryEdgeSign) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

add an edge from textual parameters (for the parser).

addNewEdge(String, String, byte, String) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

add an edge from textual parameters (for the parser).

addNewEdge(String, String, byte, String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

addNewEdge(String, String, byte, RegulatoryEdgeSign) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

addNewNode(String, String, byte) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

add a node from textual parameters (for the parser).

addNewNode(String, String, byte) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

addNode(V) - Method in class org.ginsim.core.graph.AbstractGraph

Add a node to this graph structure

addNode(V) - Method in interface org.ginsim.core.graph.GraphModel

Add a node to this graph structure

addNode() - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

addNode() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

addNode(RegulatoryNode) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

addNode(EditActionManager, int, int) - Method in class org.ginsim.gui.graph.AddNodeAction

addNode(SimulationQueuedState) - Method in class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

addNode(SimulationQueuedState) - Method in interface org.ginsim.service.tool.reg2dyn.helpers.SimulationHelper

addNode(SimulationQueuedState) - Method in class org.ginsim.service.tool.reg2dyn.helpers.STGSimulationHelper

addNode(SimulationQueuedState) - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.STGLimitedSimulationHelper

addNode(String, String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

AddNodeAction<V> - Class in org.ginsim.gui.graph

AddNodeAction(String, NodeAttributesReader) - Constructor for class org.ginsim.gui.graph.AddNodeAction

AddNodeAction(String, NodeAttributesReader, String) - Constructor for class org.ginsim.gui.graph.AddNodeAction

addNodeInBackend(V) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

Add a vertex in the JGraphT graph

addNodeInBackend(V) - Method in interface org.ginsim.core.graph.GraphBackend

Add a node to the graph.

AddNodeInGraphCanvasEventManager - Class in org.ginsim.gui.graph.canvas.events

AddNodeInGraphCanvasEventManager(GraphCanvasRenderer) - Constructor for class org.ginsim.gui.graph.canvas.events.AddNodeInGraphCanvasEventManager

addNodesToSelection(Collection<V>) - Method in class org.ginsim.gui.graph.GraphSelection

Add the nodes in l to the list of selected nodes

addNodeStyle() - Method in class org.ginsim.core.graph.view.style.StyleManager

Create a new node style.

addNodeToSelection(V) - Method in class org.ginsim.gui.graph.GraphSelection

addObject(Graph, String, Object) - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

Allow to associate objects with a graph to retrieve them later.

addOracle(Map<String, List<byte[]>>) - Method in class org.ginsim.service.tool.avatar.params.AvatarStateStore

Adds an oracle as a set of named state-patterns

addOracle(NamedStateList) - Method in class org.ginsim.service.tool.avatar.params.AvatarStateStore

addOutput(int) - Method in class org.colomoto.biolqm.io.avatar.AvatarClause

Adds the output value given the inputted restrictions

addOutputPaths(Collection<String>, Collection<String>, double) - Method in class org.ginsim.service.tool.avatar.domain.ApproximateFinalPaths

addOutputPaths(Collection<String>, Collection<String>, double[][]) - Method in class org.ginsim.service.tool.avatar.domain.ApproximateFinalPaths

addOutputPaths(Collection<String>, Collection<String>, double) - Method in class org.ginsim.service.tool.avatar.domain.ExhaustiveFinalPaths

addOutputPaths(Collection<String>, Collection<String>, double[][]) - Method in class org.ginsim.service.tool.avatar.domain.ExhaustiveFinalPaths

addOutputPaths(Collection<String>, Collection<String>, double) - Method in interface org.ginsim.service.tool.avatar.domain.FinalPaths

Creates transitions with uniform probability from a given cycle to its exits

addOutputPaths(Collection<String>, Collection<String>, double[][]) - Method in interface org.ginsim.service.tool.avatar.domain.FinalPaths

Inserts transitions from a given cycle to its exits

addOutputToTransition(String, String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

addPanel(Component, String) - Method in class org.ginsim.gui.utils.data.ListEditionPanel

addParam(byte, RegulatoryNode, String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryParser

addPlot(String, BufferedImage) - Method in class org.ginsim.service.tool.avatar.domain.Result

Adds a plotted chart to results

addPosition(int, int, int, int, int, int, int) - Method in class org.ginsim.gui.utils.data.GenericPropertyInfo

addPosition(int, int) - Method in class org.ginsim.gui.utils.data.GenericPropertyInfo

addProperties(Object[]) - Method in class org.ginsim.common.document.DocumentStyle

Add all the properties to the style

addProperty(String, Object) - Method in class org.ginsim.common.document.DocumentStyle

Add a property with a value to the current style

addProperty(String, String, Object) - Method in class org.ginsim.common.document.DocumentStyle

Add a property with a value to the style

addRangePerturbation(NodeInfo, int, int) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

Add a perturbation to fix the value of a component in a range.

addRecentFile(String) - Static method in class org.ginsim.common.application.OptionStore

Add file path to recent file list.

addRef(String) - Method in class org.ginsim.core.annotation.BiblioList

addRegulation(int) - Method in class org.ginsim.gui.graph.regulatorygraph.MultiEdgeEditPanel

addRegulatorPerturbation(NodeInfo, NodeInfo, int) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

Add a perturbation to fix a component.

addRestriction(String, int) - Method in class org.colomoto.biolqm.io.avatar.AvatarClause

Adds a restriction

addSecondaryPanel(Component, String) - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

addSon(ParamTreeElement, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

addSon(ParamTreeElement, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

addSourceNode(String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

addState(byte[], int) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Add the state directly to the stateSet.

addState(byte[], int) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Add state to the set with status
If the state was already there, the old status remains.
NB: use updateStatus to change the status.

addState(String, int) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Add state to the set with status
If the state was already there, the old status remains.
NB: use updateStatus to change the status.

addState(byte[]) - Method in class org.ginsim.gui.utils.data.SimpleStateListTableModel

addState(byte[]) - Method in class org.ginsim.service.tool.simulation.STGSimulation

addStateList(NamedStateList, NamedStateList, NamedStateList) - Method in class org.ginsim.service.tool.avatar.params.AvatarStateStore

Adds a list of named states of common and input components

addStates(List<byte[]>) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Add states to the set with status 1
If the states were already there, their old status remains.
NB: use updateStatus to change the status.

addStateToThePile(byte[]) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Add a new state to the pile.

addStyle(String) - Method in class org.ginsim.common.document.DocumentStyle

Create a new style identified by value.
The current style is set to it.

addStyleSheet(StyleSheet) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheet

addSupportedClass(Class, Class) - Static method in class org.ginsim.gui.utils.data.GenericPropertyEditorPanel

addTab(EditTab) - Method in class org.ginsim.gui.shell.editpanel.EditPanel

Add an editing tab.

addTableRow(String[]) - Method in class org.ginsim.common.document.DocumentWriter

Open a new table row and new table cells with the content of the array

addTabToEditPanel(EditTab) - Method in class org.ginsim.gui.shell.MainFrame

Add a given EditTab to the edit panel

addTag(String) - Method in class org.ginsim.common.xml.XMLWriter

add (i.e.

addTag(String, String[], String) - Method in class org.ginsim.common.xml.XMLWriter

add (i.e.

addTag(String, String[]) - Method in class org.ginsim.common.xml.XMLWriter

add (i.e.

addTagWithContent(String, Object) - Method in class org.ginsim.common.xml.XMLWriter

add (i.e.

addTagWithContent(String, String) - Method in class org.ginsim.common.xml.XMLWriter

add (i.e.

addTempPanel(Component) - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

addTimeout(TimeoutObject, long) - Static method in class org.ginsim.common.callable.Timeout

add a new timeout waiter object

addtoannotation(Annotation, Annotation) - Method in class org.ginsim.service.tool.graphcomparator.RegulatoryGraphComparator

addToNewSigma(HierarchicalNode) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSetFactory

addTransition(byte[], byte[]) - Method in class org.ginsim.service.tool.simulation.STGSimulation

addTransition(String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

addTreeModelListener(TreeModelListener) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

addTreeModelListener(TreeModelListener) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

addValue(byte) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

addValue(TreeValue) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

addVertex() - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

addVertex(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

addViewListener(GraphViewListener) - Method in class org.ginsim.core.graph.AbstractGraph

addViewListener(GraphViewListener) - Method in interface org.ginsim.core.graph.Graph

Add a listener for view change events.

addVisible(RegulatoryNode) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

AdjacencyList - Class in org.ginsim.johnsonCycles

Calculates the adjacency-list for a given adjacency-matrix.

AdjacencyList() - Constructor for class org.ginsim.johnsonCycles.AdjacencyList

AdjacencyMatrixWidget - Class in org.ginsim.servicegui.tool.composition

Widget to specify module topology

AdjacencyMatrixWidget(CompositionSpecificationDialog) - Constructor for class org.ginsim.servicegui.tool.composition.AdjacencyMatrixWidget

affectedSelectors - Variable in class org.ginsim.core.graph.view.css.CascadingStyleSheet

algorithm - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

Alias - Annotation Type in org.ginsim.core.service

Annotate a service with an alias to define a short name (to be used in script mode for example)

alias - Variable in class org.ginsim.core.service.ServiceClassInfo

ALL - Static variable in class org.ginsim.service.tool.circuit.CircuitDescr

allData - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanParser

allnodes - Variable in class org.ginsim.service.tool.avatar.params.AvatarStateStore

AllSelector - Class in org.ginsim.core.graph.view.css

A simple selector with two categories to select all the nodes or all the edges.

AllSelector() - Constructor for class org.ginsim.core.graph.view.css.AllSelector

alpha - Variable in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

minimum probability of a state to be considered relevant

amanager - Variable in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

AnchorSelector - Class in org.ginsim.gui.graph.view.style

Custom widget to select the anchor of self-edges

AnchorSelector(EdgeRoutingPanel) - Constructor for class org.ginsim.gui.graph.view.style.AnchorSelector

AND - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

AND - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

animate(JFrame, DynamicGraph) - Static method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

AnimatorUI - Class in org.ginsim.servicegui.tool.regulatorygraphanimation

UI for the animator plugin.

AnimatorUI(JFrame, RegulatoryAnimator) - Constructor for class org.ginsim.servicegui.tool.regulatorygraphanimation.AnimatorUI

Annotation - Class in org.ginsim.core.annotation

Generic annotation: some free text and a list of urls.

Annotation() - Constructor for class org.ginsim.core.annotation.Annotation

create an empty annotation.

AnnotationLink - Class in org.ginsim.core.annotation

A link in an annotation.

AnnotationLink(String, Graph) - Constructor for class org.ginsim.core.annotation.AnnotationLink

AnnotationPanel - Class in org.ginsim.gui.annotation

Panel to edit annotations

AnnotationPanel() - Constructor for class org.ginsim.gui.annotation.AnnotationPanel

This method initializes

appendToComment(String) - Method in class org.ginsim.core.annotation.Annotation

Add the string containing the comments to the end of the actual comments.

apply(Graph, CascadingStyleSheetManager) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheet

Apply this css on a graph using a CascadingStyleSheetManager Note this css needs to be compiled before

apply(Collection, NodeAttributesReader, Collection, EdgeAttributesReader, CascadingStyleSheetManager) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheet

apply(AttributesReader) - Method in class org.ginsim.core.graph.view.css.CSSEdgeStyle

apply(AttributesReader) - Method in class org.ginsim.core.graph.view.css.CSSNodeStyle

apply(AttributesReader) - Method in interface org.ginsim.core.graph.view.css.CSSStyle

Apply the style to an element using its GsAttributesReader

apply() - Method in class org.ginsim.gui.annotation.AnnotationPanel

apply() - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

apply() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

apply() - Method in class org.ginsim.gui.utils.data.HelpedListEditorUI

apply() - Method in class org.ginsim.gui.utils.data.MinMaxEditor

apply() - Method in interface org.ginsim.gui.utils.data.ObjectPropertyEditorUI

apply() - Method in class org.ginsim.gui.utils.data.PropertyActionButton

apply() - Method in class org.ginsim.gui.utils.data.PropertySwitch

apply() - Method in class org.ginsim.gui.utils.data.SpinEditor

apply() - Method in class org.ginsim.gui.utils.widgets.BooleanEditor

apply() - Method in class org.ginsim.gui.utils.widgets.StatusTextField

apply(LogicalModel) - Method in class org.ginsim.service.tool.modelreduction.ReductionConfig

applyComment() - Method in class org.ginsim.gui.annotation.AnnotationPanel

applyEdgeStyle(Collection<E>, EdgeStyle<V, E>) - Method in class org.ginsim.core.graph.view.style.StyleManager

Apply a style to a group of edges.

applyEdgeStyle(E, EdgeStyle<V, E>) - Method in class org.ginsim.core.graph.view.style.StyleManager

Apply a style to a single edge.

applyEdgeVisualSettings(Edge<?>, StyleManager, EdgeAttributesReader, NodeAttributesReader, String, Attributes) - Static method in class org.ginsim.core.io.parser.GinmlHelper

we are reading edge visual settings from a ginml file, apply them on the current edge.

applyEditor() - Method in class org.ginsim.gui.utils.data.models.MaxSpinModel

applyEditor() - Method in class org.ginsim.gui.utils.data.models.MinSpinModel

applyNewGraph(RegulatoryNode, Map) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

applyNewGraph(RegulatoryNode, Map) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

Apply all the logical parameters from this list to the clone node (from the new graph)

applyNewMaxValue(byte, RegulatoryGraph, List) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

applyNewMaxValue(byte) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

applyNodeStyle(Collection<V>, NodeStyle<V>) - Method in class org.ginsim.core.graph.view.style.StyleManager

Apply a style to a group of nodes.

applyNodeStyle(V, NodeStyle<V>) - Method in class org.ginsim.core.graph.view.style.StyleManager

Apply a style to a single node.

applyNodeVisualSettings(NodeAttributesReader, StyleManager, String, Attributes) - Static method in class org.ginsim.core.io.parser.GinmlHelper

we are reading node visual settings from a ginml file, apply them on the current node.

applyOnEdge(Selector, Object, EdgeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Apply a selector on an edge using its attribute reader.

applyOnEdge(CSSEdgeStyle, Object, EdgeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Apply a style on an edge using its attribute reader.

applyOnNode(Selector, Object, NodeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Apply a selector on a node using its attribute reader.

applyOnNode(CSSNodeStyle, Object, NodeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Apply a style on an edge using its attribute reader.

applySelectorOnEdges(Selector, Collection, EdgeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Apply one selector on each edges from a collection If you want to apply several selector, use applySelectorsOnEdges instead.

applySelectorOnNodes(Selector, Collection, NodeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Apply one selector on each nodes from a collection If you want to apply several selector, use applySelectorsOnNodes instead.

applySelectorsOnEdges(List, Collection, EdgeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Apply all the selectors in cascade on each edges If you want to apply only one selector, use applySelectorOnEdges instead.

applySelectorsOnNodes(List, Collection, NodeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Apply all the selectors in cascade on each nodes If you want to apply only one selector, use applySelectorOnNodes instead.

applyStyleForEdge(Object, AttributesReader) - Method in class org.ginsim.core.graph.view.css.Selector

Apply the style to an edge using an attributesReder for a category id or null if the category doesn't exist.

applyStyleForNode(Object, AttributesReader) - Method in class org.ginsim.core.graph.view.css.Selector

Apply the style to a node using an attributesReder for a category id or null if the category doesn't exist.

approxDepth - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

maximum depth for the approximate rewiring strategy

ApproximateFinalPaths - Class in org.ginsim.service.tool.avatar.domain

Approximate representation of the probabilities of the transitions within and going out of a cycle.
Useful when assuming that the transitions to the states out of a cycle are equiprobable (Uniform transitions).

ApproximateFinalPaths() - Constructor for class org.ginsim.service.tool.avatar.domain.ApproximateFinalPaths

Creates an empty cycle

arcs - Variable in class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

areCompatibleStableStatesDiscernible() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

AReg2GPConfig - Class in org.ginsim.servicegui.tool.regulatorygraphanimation

Export a path in the state transition graph to gnuplot scripts.

AReg2GPConfig(JFrame, List, List) - Constructor for class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPConfig

AReg2GPModel - Class in org.ginsim.servicegui.tool.regulatorygraphanimation

tableModel to configure gene state blockers

AReg2GPModel(List, boolean[]) - Constructor for class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPModel

areNeighbours(int, int) - Method in class org.ginsim.service.export.cadp.CADPWriter

Method determines whether modules Mi and Mj are neighbours (this relation is not necessarily symmetrical

areNeighbours(int, int) - Method in class org.ginsim.service.tool.composition.GenericTopology

Method determining whether one module in neighbour of another in the defined Topology

areNeighbours(int, int) - Method in interface org.ginsim.service.tool.composition.Topology

Method determining whether one module in neighbour of another in the defined Topology

areNeighbours(int, int) - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

areNeighbours(int, int) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

areNeighbours(int, int) - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

areTransientCompacted() - Method in interface org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraph

Return true if the transients are compacted into component by their atteignability of attractors.

areTransientCompacted() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

Return true if the transients are compacted into component by their atteignability of attractors.

arg - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TUnaryOperator

args - Variable in class org.ginsim.ScriptLauncher

Arguments passed to the script

ArraySet<T> - Class in org.ginsim.common.utils

A sorted set, based on an ArrayList.

ArraySet() - Constructor for class org.ginsim.common.utils.ArraySet

asImage() - Method in interface org.ginsim.service.tool.avatar.utils.GINsimPlot

associate(RegulatoryNode, PriorityClass) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

associate(RegulatoryNode, PriorityClass, PriorityClass) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

associated(Graph, String) - Method in class org.ginsim.ScriptLauncher

Get (existing) associated data

associated(Graph<?, ?>, String, boolean) - Method in class org.ginsim.ScriptLauncher

Get or create associated data.

associatedGraph - Variable in class org.ginsim.core.graph.AbstractDerivedGraph

associatedID - Variable in class org.ginsim.core.graph.AbstractDerivedGraph

associationValid(RegulatoryGraph, DynamicGraph) - Static method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

Test if an association between a regulatory graph and a state transition graph is valid: all what we can do is checking the node-order to see if they obviously differ (by size of node's name).

ASYNCHRONOUS - Static variable in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

this class is asynchronous

ASYNCHRONOUS - Static variable in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetList

atEnd - Variable in enum org.ginsim.common.xml.CallMode

atom() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

atStart - Variable in enum org.ginsim.common.xml.CallMode

attractorsCount - Variable in class org.ginsim.service.tool.avatar.domain.Result

Number of occurrences per attractor

attractorsDepths - Variable in class org.ginsim.service.tool.avatar.domain.Result

Depth of attractors (from a well-defined portion of the state space)

attractorsLowerBound - Variable in class org.ginsim.service.tool.avatar.domain.Result

Lower probability bound of attractors

attractorsUpperBound - Variable in class org.ginsim.service.tool.avatar.domain.Result

Upper probability bound of attractors

attributes - Variable in class org.ginsim.core.graph.AbstractGraph

AttributesReader - Interface in org.ginsim.core.graph.view

autoscroll(Point) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.GsJTree

avaAproxDepth - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

avaDepth - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

AvaException - Exception in org.ginsim.service.tool.avatar.utils

Exception associated with the behavior of Avatar simulations

AvaException(String) - Constructor for exception org.ginsim.service.tool.avatar.utils.AvaException

Creates a new Avatar exception with a dedicated message

AvaException(String, Throwable) - Constructor for exception org.ginsim.service.tool.avatar.utils.AvaException

Creates a new Avatar exception with a detail message and nested exception

avaKeepTrans - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

AvaMath - Class in org.ginsim.service.tool.avatar.utils

Facilities associated with simplistic mathematical functions

AvaMath() - Constructor for class org.ginsim.service.tool.avatar.utils.AvaMath

AvaMatrix - Class in org.ginsim.service.tool.avatar.utils

Facilities to manipulate matrices (focus on the inversion procedure)

AvaMatrix() - Constructor for class org.ginsim.service.tool.avatar.utils.AvaMatrix

avaMaxPSize - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

avaMaxRewiringSize - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

avaMinCycle - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

avaMinTran - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

AvaOptions - Class in org.ginsim.service.tool.avatar.utils

Functions to extract values from text commands

AvaOptions() - Constructor for class org.ginsim.service.tool.avatar.utils.AvaOptions

AvaParameterEditionPanel - Class in org.ginsim.servicegui.tool.avatar.parameters

Panel to edit, add and remove the context of a simulation (parameters, states and changes to the model)

AvaParameterEditionPanel(AvatarConfigFrame, RegulatoryGraph, AvatarParameterList) - Constructor for class org.ginsim.servicegui.tool.avatar.parameters.AvaParameterEditionPanel

Creates the left panel to manage parameterizations

avaRuns - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

avaStrategy - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

AvatarClause - Class in org.colomoto.biolqm.io.avatar

Defines an Avatar clause (how the state of a component changes as a function of its regulators)

AvatarClause() - Constructor for class org.colomoto.biolqm.io.avatar.AvatarClause

AvatarConfigFrame - Class in org.ginsim.servicegui.tool.avatar

Main panel for displaying the all of the context associated with avatar simulations

AvatarConfigFrame(RegulatoryGraph, JFrame) - Constructor for class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

Creates the panel with avatar-based simulations from the current graph

AvatarLogicalModelActionDialog - Class in org.ginsim.servicegui.tool.avatar

Class for managing contextual aspects associated with the main panel (including the responsibility to update the applicable perturbations and reductions to the input model)

AvatarLogicalModelActionDialog(RegulatoryGraph, Frame, String, int, int) - Constructor for class org.ginsim.servicegui.tool.avatar.AvatarLogicalModelActionDialog

Creates the necessary context to instantiate the panel of avatar simulations

AvatarLogicalModelException - Exception in org.colomoto.biolqm.io.avatar

Exception associated with the loading and exportation of Avatar files

AvatarLogicalModelException(String) - Constructor for exception org.colomoto.biolqm.io.avatar.AvatarLogicalModelException

Creates a new Avatar exception with a dedicated message

AvatarLogicalModelException(String, Throwable) - Constructor for exception org.colomoto.biolqm.io.avatar.AvatarLogicalModelException

Creates a new Avatar exception with a detail message and nested exception

AvatarMDDSimulation - Class in org.ginsim.service.tool.avatar.simulation.others

Avatar simulation for the discovery of point and complex attractors.
Class providing all the functionalities to explore STGs, extend and rewire cycles.

AvatarMDDSimulation() - Constructor for class org.ginsim.service.tool.avatar.simulation.others.AvatarMDDSimulation

Instantiates an Avatar simulation based on a logical model

AvatarPanel - Class in org.ginsim.servicegui.tool.avatar.algopanels

Class for managing the panel for Avatar simulations

AvatarPanel() - Constructor for class org.ginsim.servicegui.tool.avatar.algopanels.AvatarPanel

Instantiates the context of a simulation panel

AvatarParameterList - Class in org.ginsim.service.tool.avatar.params

Stores the context of simulations (parameters and changes to the input model)

AvatarParameterList(Graph<RegulatoryNode, RegulatoryMultiEdge>, AvatarParameters) - Constructor for class org.ginsim.service.tool.avatar.params.AvatarParameterList

AvatarParameters - Class in org.ginsim.service.tool.avatar.params

Serializable context of a simulation (parameters, oracles and initial states)

AvatarParameters() - Constructor for class org.ginsim.service.tool.avatar.params.AvatarParameters

Creates an empty context

AvatarParametersHelper - Class in org.ginsim.servicegui.tool.avatar.parameters

Helper for loading, unloading and displaying a list of simulation parameters

AvatarParametersHelper(AvaParameterEditionPanel) - Constructor for class org.ginsim.servicegui.tool.avatar.parameters.AvatarParametersHelper

Instantiates a helper using the panel of parameters to display, load or unload

AvatarParametersManager - Class in org.ginsim.service.tool.avatar.params

Saves and opens the context of a simulation

AvatarParametersManager() - Constructor for class org.ginsim.service.tool.avatar.params.AvatarParametersManager

Instantiates a manager to save and load the context of simulations

AvatarResults - Class in org.ginsim.servicegui.tool.avatar

Facilities to run and kill simulations and display their results

AvatarResults(Simulation, JTextArea, AvatarConfigFrame, boolean, StatefulLogicalModel, File, File, File, File, JButton, JButton) - Constructor for class org.ginsim.servicegui.tool.avatar.AvatarResults

Creates the necessary context to run a simulation and display its results

AvatarService - Class in org.ginsim.service.tool.avatar.service

Provider of Avatar services in GINsim

AvatarService() - Constructor for class org.ginsim.service.tool.avatar.service.AvatarService

AvatarServiceFacade - Class in org.ginsim.service.tool.avatar.service

Facade of an Avatar simulation.
Instantiates an Avatar simulation from arguments within a command line, provides soundness checks, and outputs statistics and help tips.

AvatarServiceFacade() - Constructor for class org.ginsim.service.tool.avatar.service.AvatarServiceFacade

AvatarServiceGUI - Class in org.ginsim.servicegui.tool.avatar

GUI for the avatar simulation services

AvatarServiceGUI() - Constructor for class org.ginsim.servicegui.tool.avatar.AvatarServiceGUI

AvatarSimulation - Class in org.ginsim.service.tool.avatar.simulation

Avatar simulation for the discovery of point and complex attractors.
Class providing all the functionalities to explore STGs, extend and rewire cycles.

AvatarSimulation() - Constructor for class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

Instantiates an Avatar simulation

AvatarSimulation.AvatarStrategy - Enum in org.ginsim.service.tool.avatar.simulation

enum specifying the different behavioral strategies of Avatar

AvatarStateStore - Class in org.ginsim.service.tool.avatar.params

List of named states that maintains the initial states and oracles for a given simulation

AvatarStateStore(List<byte[]>, RegulatoryGraph) - Constructor for class org.ginsim.service.tool.avatar.params.AvatarStateStore

Creates a named state store given a set of states and the current graph

AvatarStateStore(RegulatoryGraph) - Constructor for class org.ginsim.service.tool.avatar.params.AvatarStateStore

AvatarStateStore(List<byte[]>, List<byte[]>, List<byte[]>, RegulatoryGraph) - Constructor for class org.ginsim.service.tool.avatar.params.AvatarStateStore

Creates a named state store given a set of states from common and input components and the current graph

AvatarStateStore(List<byte[]>, String[], List<byte[]>, String[], List<byte[]>, String[], RegulatoryGraph) - Constructor for class org.ginsim.service.tool.avatar.params.AvatarStateStore

Creates a named state store given a set of states, their names and the current graph

AvatarStateStore(List<RegulatoryNode>, List<RegulatoryNode>, List<RegulatoryNode>, NamedStateList, NamedStateList, NamedStateList) - Constructor for class org.ginsim.service.tool.avatar.params.AvatarStateStore

Creates a named state store based on node info and the list of named states for common and input components

AvatarUtils - Class in org.colomoto.biolqm.io.avatar

Facilities for the management of logical models for simulations

AvatarUtils() - Constructor for class org.colomoto.biolqm.io.avatar.AvatarUtils

avaTau - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

B

BACKEND - Static variable in class org.ginsim.service.tool.stablestates.StableStatesService

backendSelectionUpdated(List<V>, List<E>) - Method in class org.ginsim.gui.graph.GraphSelection

Set the selection.

background - Variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

BACKGROUND - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

backgroundSCCGraph(Graph, TaskListener) - Method in class org.ginsim.service.tool.scc.SCCGraphService

Compute the SCC graph in background.

BaseAction - Class in org.ginsim.gui.shell.actions

this class is used for all actions, it will lookup for an internationalized string for the name and the tooltip

BaseAction(String, ImageIcon, String, KeyStroke, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.BaseAction

BaseAction(String, String, String, KeyStroke, Integer, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.BaseAction

BaseAction(String, ImageIcon, String, KeyStroke, Integer, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.BaseAction

BaseGraphGUI<G extends Graph<V,E>,V,E extends Edge<V>> - Class in org.ginsim.gui.graph

Abstract class providing generic parts of a Graph GUI.

BaseGraphGUI(G, GraphGUIHelper<G, V, E>, boolean) - Constructor for class org.ginsim.gui.graph.BaseGraphGUI

BaseSimulationFrame - Class in org.ginsim.servicegui.tool.reg2dyn

BaseSimulationFrame(RegulatoryGraph, Frame, String, int, int) - Constructor for class org.ginsim.servicegui.tool.reg2dyn.BaseSimulationFrame

BaseSimulationUpdater - Class in org.ginsim.service.tool.reg2dyn.updater

This is the part of the simulation in charge for generating the following states.

BaseSimulationUpdater(LogicalModel) - Constructor for class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

BaseSimulationUpdater(ModelHelper) - Constructor for class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

BaseSTGLayout - Class in org.ginsim.service.layout

Base class for layouts working on State Transition Graphs.

BaseSTGLayout() - Constructor for class org.ginsim.service.layout.BaseSTGLayout

BaseStyle<S extends Style> - Class in org.ginsim.core.graph.view.style

BaseStyle(S, String) - Constructor for class org.ginsim.core.graph.view.style.BaseStyle

baseStyle - Variable in class org.ginsim.core.graph.view.style.BaseStyleOverride

BaseStyleOverride<S extends Style> - Class in org.ginsim.core.graph.view.style

BaseStyleOverride(S) - Constructor for class org.ginsim.core.graph.view.style.BaseStyleOverride

BasicGraphAssociatedManager<T> - Class in org.ginsim.core.graph.objectassociation

Base class to create managers for associated objects.

BasicGraphAssociatedManager(String, String[], Class) - Constructor for class org.ginsim.core.graph.objectassociation.BasicGraphAssociatedManager

BasicProgressListener<T> - Class in org.ginsim.common.callable

Simple implementation of ProgressListener, to retrieve the result and extend.

BasicProgressListener() - Constructor for class org.ginsim.common.callable.BasicProgressListener

bcancel - Variable in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

bclose - Variable in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

beginNewSigma() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSetFactory

beta - Variable in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

minimum residual probability in F to stop simulation

Bezier - Class in org.ginsim.core.graph.view

Interpolates given points by a bezier curve.

Bezier(List<Point>) - Constructor for class org.ginsim.core.graph.view.Bezier

Creates a new Bezier curve.

BG_NORMAL - Static variable in class org.ginsim.gui.graph.dynamicgraph.DynamicItemCellRenderer

BG_SEL - Static variable in class org.ginsim.gui.graph.dynamicgraph.DynamicItemCellRenderer

BiblioList - Class in org.ginsim.core.annotation

Bibliography: list of bibliographic entries.

BiblioList(Graph<?, ?>, boolean) - Constructor for class org.ginsim.core.annotation.BiblioList

BiblioManager - Class in org.ginsim.core.annotation

Associated data manager to save and restore bibliographies.

BiblioManager() - Constructor for class org.ginsim.core.annotation.BiblioManager

BiolayoutEncoder - Class in org.ginsim.service.export.struct

BiolayoutEncoder() - Constructor for class org.ginsim.service.export.struct.BiolayoutEncoder

biolayoutExport(Graph, Collection<Edge<?>>, String) - Method in class org.ginsim.service.export.struct.GraphStructureExportService

Encode the graph to struct output

blacklistFormat(LogicalModelFormat) - Static method in class org.ginsim.core.service.FormatSupportService

Blacklist a format to prevent the creation of an automatic wrapper for it.

blueHues - Static variable in class org.ginsim.common.utils.ColorPalette

An array of blue hues, all the blue web colors plus the greenish blues Teal, MediumAquamarine...

BNetFormatService - Class in org.ginsim.service.format

GINsim export service for the BoolNet format.

BNetFormatService() - Constructor for class org.ginsim.service.format.BNetFormatService

BooleanEditor - Class in org.ginsim.gui.utils.widgets

BooleanEditor() - Constructor for class org.ginsim.gui.utils.widgets.BooleanEditor

BooleanFunctionTreeEditor - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

BooleanFunctionTreeEditor(JTree, DefaultTreeCellRenderer) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeEditor

BooleanFunctionTreePanel - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

BooleanFunctionTreePanel(Object, JTree, boolean, int) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

BooleanFunctionTreeRenderer - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

BooleanFunctionTreeRenderer(int, PanelFactory) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeRenderer

BooleanGene - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction

BooleanGene() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanGene

booleanize(LogicalModel) - Method in class org.ginsim.service.tool.modelbooleanizer.ModelBooleanizerService

BooleanParser - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction

BooleanParser(Collection<RegulatoryMultiEdge>) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

BooleanParser(Collection<RegulatoryMultiEdge>, boolean) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

BooleanTreeNodeFactory - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction

BooleanTreeNodeFactory(String, String, TBooleanParser) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanTreeNodeFactory

BoolNetFormatServiceGUI - Class in org.ginsim.servicegui.format

GUI Action to export model to the BoolNet format

BoolNetFormatServiceGUI() - Constructor for class org.ginsim.servicegui.format.BoolNetFormatServiceGUI

BoolsimFormatService - Class in org.ginsim.service.format

GINsim export service for the boolsim format.

BoolsimFormatService() - Constructor for class org.ginsim.service.format.BoolsimFormatService

BoolsimFormatServiceGUI - Class in org.ginsim.servicegui.format

GUI Action to export model to the boolsim format

BoolsimFormatServiceGUI() - Constructor for class org.ginsim.servicegui.format.BoolsimFormatServiceGUI

border - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

border - Variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

border - Variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

BORDER - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

BOTH - Static variable in class org.ginsim.common.xml.XMLHelper

BOTH - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

breadthFirst - Variable in class org.ginsim.service.tool.reg2dyn.Simulation

breadthFirst - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

brun - Variable in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

btrans - Variable in class org.ginsim.service.tool.avatar.domain.State

build(GenericPropertyHolder) - Method in class org.ginsim.gui.utils.data.GenericPropertyInfo

buildActions(GraphGUI<?, ?, ?>, JMenuBar, JToolBar) - Method in interface org.ginsim.gui.shell.FrameActionManager

buildActions(GraphGUI<?, ?, ?>, JMenuBar, JToolBar) - Method in class org.ginsim.gui.shell.MainFrameActionManager

buildFunctions(ParamTreeNode, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

buildFunctions(Hashtable, String, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafValue

buildHashCode() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNodeSet

Initialize the value of the hashCode from the content of the set.

busyPlaying() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AnimatorUI

inform the user that the animator is playing.

Button - Class in org.ginsim.gui.utils.widgets

Button(String) - Constructor for class org.ginsim.gui.utils.widgets.Button

Button(String, int, int, int, int) - Constructor for class org.ginsim.gui.utils.widgets.Button

buttonPanel - Variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

ButtonPopup - Class in org.ginsim.gui.utils.widgets

ButtonPopup(String, boolean, List) - Constructor for class org.ginsim.gui.utils.widgets.ButtonPopup

C

CADPCommonWriter - Class in org.ginsim.service.export.cadp

Writer class for common.lnt including general functions and type definitions, based on the maximum value of the multi-valued components, if any are referred to in the model specification

CADPCommonWriter(CADPExportConfig) - Constructor for class org.ginsim.service.export.cadp.CADPCommonWriter

CADPExportConfig - Class in org.ginsim.service.export.cadp

Class containing all the information required for the specification of the composition to be provided via LTS abstraction and minimisation using CADP

CADPExportConfig(RegulatoryGraph) - Constructor for class org.ginsim.service.export.cadp.CADPExportConfig

CADPExportConfigPanel - Class in org.ginsim.servicegui.export.cadp

Main dialog for CADP export

CADPExportConfigPanel(CADPExportConfig, CADPExportAction) - Constructor for class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

CADPExportService - Class in org.ginsim.service.export.cadp

GINsim export service for CADP including: LOTOS NT specifications, (common, module and integration), EXP specifications (synchronization vectors), SVL script, MCL properties and README file

CADPExportService() - Constructor for class org.ginsim.service.export.cadp.CADPExportService

CADPExportServiceGUI - Class in org.ginsim.servicegui.export.cadp

CADP Export Service

CADPExportServiceGUI() - Constructor for class org.ginsim.servicegui.export.cadp.CADPExportServiceGUI

CADPExpWriter - Class in org.ginsim.service.export.cadp

Class generating the EXP file which specifies the synchronization vectors

CADPExpWriter(CADPExportConfig) - Constructor for class org.ginsim.service.export.cadp.CADPExpWriter

CADPIntegrationWriter - Class in org.ginsim.service.export.cadp

CADPIntegrationWriter(CADPExportConfig) - Constructor for class org.ginsim.service.export.cadp.CADPIntegrationWriter

CADPIntegrationWriter.IntegrationProcessWriter - Class in org.ginsim.service.export.cadp

CADPMclWriter - Class in org.ginsim.service.export.cadp

Class generating an MCL file for each global stable state

CADPMclWriter(CADPExportConfig, List<byte[]>) - Constructor for class org.ginsim.service.export.cadp.CADPMclWriter

CADPModuleWriter - Class in org.ginsim.service.export.cadp

Class that produces the LOTOS NT specification of a single Logical Regulatory Module

CADPModuleWriter(CADPExportConfig, String) - Constructor for class org.ginsim.service.export.cadp.CADPModuleWriter

CADPModuleWriter(CADPExportConfig) - Constructor for class org.ginsim.service.export.cadp.CADPModuleWriter

CADPModuleWriter.FunctionWriter - Class in org.ginsim.service.export.cadp

CADPModuleWriter.RuleWriter - Class in org.ginsim.service.export.cadp

CADPReadMeWriter - Class in org.ginsim.service.export.cadp

Class generating the dynamic README file for the CADP export bundle

CADPReadMeWriter(CADPExportConfig) - Constructor for class org.ginsim.service.export.cadp.CADPReadMeWriter

CADPSvlWriter - Class in org.ginsim.service.export.cadp

Class generating the SVL for the CADP export bundle

CADPSvlWriter(CADPExportConfig) - Constructor for class org.ginsim.service.export.cadp.CADPSvlWriter

CADPWriter - Class in org.ginsim.service.export.cadp

Class providing methods supporting all writers of CADP specifications

CADPWriter(CADPExportConfig) - Constructor for class org.ginsim.service.export.cadp.CADPWriter

CADPWriter.GateWriter - Class in org.ginsim.service.export.cadp

CADPWriter.InitialStateWriter - Class in org.ginsim.service.export.cadp

CADPWriter.StateVarWriter - Class in org.ginsim.service.export.cadp

calculateComplexAttractor(StateSet, List<StateSet>, PriorityQueue<StateSet>) - Method in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

Calculates a complex attractor based on the knowledge of previous incarnations

calculateComplexAttractor(List<MDDStateSet>, int) - Method in class org.ginsim.service.tool.avatar.simulation.others.AvatarMDDSimulation

Calculates a complex attractor based on the knowledge of previous incarnations

CallDescription - Class in org.ginsim.common.xml

Define how to handle a given tag while parsing an XML document with the XMLHelper.

CallDescription(int, int, CallMode) - Constructor for class org.ginsim.common.xml.CallDescription

Describes how to deal with a tag when parsing a XML file

CallMode - Enum in org.ginsim.common.xml

Define when to call the handler for an XML tag.

callTarget(Object) - Method in class org.ginsim.common.application.OSXAdapter

canAddInline() - Method in class org.ginsim.gui.utils.data.ListPanelHelper

canApplyNewMaxValue(RegulatoryNode, byte, List, List) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

canApplyNewMaxValue(RegulatoryNode, byte, List, List) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

canApplyNewMaxValue(byte, List, List) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

canBeSaved() - Method in class org.ginsim.gui.graph.BaseGraphGUI

canBeSaved() - Method in interface org.ginsim.gui.graph.GraphGUI

Indicates if the type of graph associated to the GraphGUI can be saved or not

cancel() - Method in class org.ginsim.commongui.dialog.ResultsDialog

cancel() - Method in interface org.ginsim.gui.graph.canvas.CanvasEventManager

cancel() - Method in class org.ginsim.gui.graph.canvas.events.AddEdgeInGraphCanvasEventManager

cancel() - Method in class org.ginsim.gui.graph.canvas.events.AddNodeInGraphCanvasEventManager

cancel() - Method in class org.ginsim.gui.graph.canvas.events.GraphSelectionCanvasEventManager

cancel() - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

cancel() - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

cancel() - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

cancel() - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

close the circuit search/analyse dialog.

cancel() - Method in class org.ginsim.servicegui.tool.interactionanalysis.InteractionAnalysisFrame

cancel() - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphFrame

cancel() - Method in class org.ginsim.servicegui.tool.pathfinding.PathFindingFrame

cancel() - Method in class org.ginsim.servicegui.tool.reg2dyn.SingleSimulationFrame

cancel() - Method in class org.ginsim.servicegui.tool.stateinregulatorygraph.StateInRegGraphFrame

canClose(Graph) - Method in class org.ginsim.gui.GUIManager

Verify if it is allowed to close the graph can be closed

canCopyPaste() - Method in class org.ginsim.gui.graph.BaseGraphGUI

canCopyPaste(DynamicGraph) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

canCopyPaste() - Method in interface org.ginsim.gui.graph.GraphGUI

Does this graph type support copy/paste actions?

canCopyPaste(G) - Method in interface org.ginsim.gui.graph.GraphGUIHelper

Does this graph type support copy/paste actions?

canCopyPaste(HierarchicalTransitionGraph) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

canCopyPaste(ReducedGraph) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

canCopyPaste(RegulatoryGraph) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

canCopyPaste(TrapSpaceInclusionDiagram) - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

canCopyPaste(Tree) - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

canCreate() - Method in class org.ginsim.gui.utils.data.ListPanelHelper

canEditImmediately(EventObject) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeEditor

canExport() - Method in class org.ginsim.core.service.FormatSupportService

canExport(RegulatoryGraph) - Method in class org.ginsim.gui.service.FormatSupportServiceGUI

canExportModel(RegulatoryGraph) - Method in class org.ginsim.core.service.FormatSupportService

canFilter - Variable in class org.ginsim.gui.utils.data.ListPanelHelper

canImport() - Method in class org.ginsim.core.service.FormatSupportService

canMoveItems(int[]) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetList

canOrder - Variable in class org.ginsim.gui.utils.data.ListPanelHelper

canRemove() - Method in class org.ginsim.gui.utils.data.ListPanelHelper

CanvasEventManager - Interface in org.ginsim.gui.graph.canvas

CanvasGraphGUIImpl<G extends Graph<V,E>,V,E extends Edge<V>> - Class in org.ginsim.gui.graph.canvas

CanvasGraphGUIImpl(G, GraphGUIHelper<G, V, E>, boolean) - Constructor for class org.ginsim.gui.graph.canvas.CanvasGraphGUIImpl

CanvasHelpAction - Class in org.ginsim.gui.graph.canvas

CanvasHelpAction(SimpleCanvas) - Constructor for class org.ginsim.gui.graph.canvas.CanvasHelpAction

CanvasRenderer - Interface in org.ginsim.gui.graph.canvas

Generic interface for Canvas renderer: all drawing and object selection happens here.

cards - Variable in class org.ginsim.gui.utils.data.ListPanel

cascade - Variable in class org.ginsim.core.graph.view.css.CascadingStyleSheet

CascadingStyleSheet - Class in org.ginsim.core.graph.view.css

This class represent the CSS object itself

CascadingStyleSheet() - Constructor for class org.ginsim.core.graph.view.css.CascadingStyleSheet

Create and initialize the collections of the CSS

CascadingStyleSheetManager - Class in org.ginsim.core.graph.view.css

CascadingStyleSheetManager(boolean) - Constructor for class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

CAT_COMPLEX - Static variable in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

CAT_EDGES - Static variable in class org.ginsim.core.graph.view.css.AllSelector

CAT_IN - Static variable in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

CAT_NODES - Static variable in class org.ginsim.core.graph.view.css.AllSelector

categories() - Method in class org.ginsim.core.graph.view.css.Selector

A collection of all the categories this selector respond to.

cb_simplify - Variable in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

CENTER - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

CFG_ASYNC - Static variable in class org.ginsim.service.export.nusmv.NuSMVConfig

CFG_COMPLETE - Static variable in class org.ginsim.service.export.nusmv.NuSMVConfig

CFG_PCLASS - Static variable in class org.ginsim.service.export.nusmv.NuSMVConfig

CFG_SYNC - Static variable in class org.ginsim.service.export.nusmv.NuSMVConfig

changed - Variable in class org.ginsim.service.tool.graphcomparator.ComparedItemInfo

CHANGED - Static variable in class org.ginsim.service.tool.graphcomparator.GraphComparatorStyleProvider

changed(boolean) - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicSearchPathConfig

notify that the path constraints have changed.

changeNodeId(Object, String) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

changeNodeId(Object, String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

ChangeType - Enum in org.ginsim.core.graph.dynamicgraph

Define the types of changes in the transition from one state to another.

changeType - Variable in class org.ginsim.core.graph.dynamicgraph.DynamicEdge

characters(char[], int, int) - Method in class org.ginsim.common.xml.XMLHelper

if curVal is not null, read characters will be appended there.

charHeight - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

chart - Variable in class org.ginsim.service.tool.avatar.simulation.Simulation

ChartGNUPlot - Class in org.ginsim.service.tool.avatar.utils

Plotting facilities using JavaPlot library

ChartGNUPlot() - Constructor for class org.ginsim.service.tool.avatar.utils.ChartGNUPlot

charts - Variable in class org.ginsim.service.tool.avatar.domain.Result

Charts to be plotted

charWidth - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

check(CircuitAlgo, List) - Method in class org.ginsim.service.tool.circuit.CircuitDescr

check if this circuit is functional.

checkEdge(RegulatoryEdge, int[], int, int) - Method in class org.ginsim.service.tool.circuit.CircuitAlgo

childs - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

childsCount - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

An array indicating for each node in the nodeOrder their count of childs.

CircuitAlgo - Class in org.ginsim.service.tool.circuit

analyse circuits to detect their functionality/functional range.

CircuitAlgo(RegulatoryGraph, boolean) - Constructor for class org.ginsim.service.tool.circuit.CircuitAlgo

CircuitAlgo(RegulatoryGraph, Perturbation, boolean) - Constructor for class org.ginsim.service.tool.circuit.CircuitAlgo

CircuitAlgo.subReport - Class in org.ginsim.service.tool.circuit

CircuitAnalyser - Class in org.ginsim.service.tool.circuit

A Task for circuit analysis: returns a list of circuits with functionality contexts.

CircuitAnalyser(RegulatoryGraph, Perturbation, boolean) - Constructor for class org.ginsim.service.tool.circuit.CircuitAnalyser

CircuitAnalyser(RegulatoryGraph, Perturbation, boolean, List<CircuitDescrInTree>) - Constructor for class org.ginsim.service.tool.circuit.CircuitAnalyser

CircuitConfigureSearch - Class in org.ginsim.servicegui.tool.circuit

configure the circuit-search.

CircuitConfigureSearch(CircuitFrame, CircuitSearchStoreConfig, List) - Constructor for class org.ginsim.servicegui.tool.circuit.CircuitConfigureSearch

create the configuration window.

circuitDesc - Variable in class org.ginsim.service.tool.circuit.FunctionalityContext

CircuitDescr - Class in org.ginsim.service.tool.circuit

CircuitDescr() - Constructor for class org.ginsim.service.tool.circuit.CircuitDescr

CircuitDescrInTree - Class in org.ginsim.service.tool.circuit

CircuitDescrInTree(CircuitDescr, boolean, int) - Constructor for class org.ginsim.service.tool.circuit.CircuitDescrInTree

CircuitFrame - Class in org.ginsim.servicegui.tool.circuit

configuration/status frame for circuit search/analyse

CircuitFrame(JFrame, Graph<?, ?>) - Constructor for class org.ginsim.servicegui.tool.circuit.CircuitFrame

This is the default constructor

CircuitGUIStatus - Enum in org.ginsim.servicegui.tool.circuit

CircuitSearcher - Class in org.ginsim.service.tool.circuit

Find circuits in a graph.

CircuitSearcher(RegulatoryGraph) - Constructor for class org.ginsim.service.tool.circuit.CircuitSearcher

CircuitSearcher(RegulatoryGraph, CircuitSearchStoreConfig) - Constructor for class org.ginsim.service.tool.circuit.CircuitSearcher

CircuitSearchStoreConfig - Class in org.ginsim.service.tool.circuit

store configuration of circuit search.

CircuitSearchStoreConfig(List<RegulatoryNode>) - Constructor for class org.ginsim.service.tool.circuit.CircuitSearchStoreConfig

CircuitService - Class in org.ginsim.service.tool.circuit

CircuitService() - Constructor for class org.ginsim.service.tool.circuit.CircuitService

CircuitServiceGUI - Class in org.ginsim.servicegui.tool.circuit

main method for the circuit service

CircuitServiceGUI() - Constructor for class org.ginsim.servicegui.tool.circuit.CircuitServiceGUI

cl - Variable in class org.ginsim.core.service.ServiceClassInfo

CLEANUP - Static variable in class org.ginsim.service.tool.circuit.FunctionalityCleanupOperator

cleanupContext(int, int[]) - Method in class org.ginsim.service.tool.circuit.CircuitAlgo

Remove constraint on the members from a functionality context.

cleanupDup() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

cleanupInteraction() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

cleanupInteraction() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

update logical parameters when an interaction is deleted.

cleanupInteractionForNewGraph(Map) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

clear() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

clear() - Method in class org.ginsim.service.tool.circuit.CircuitDescr

clearChilds() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

clearEdgeRouting(E) - Method in class org.ginsim.core.graph.view.style.StyleManager

clearOffscreen() - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

Throw away the cached image.

clearTree() - Method in class org.ginsim.core.graph.tree.TreeBuilder

Remove all the vertices from the tree

click(Point, boolean) - Method in interface org.ginsim.gui.graph.canvas.CanvasEventManager

click(Point, boolean) - Method in class org.ginsim.gui.graph.canvas.events.AddEdgeInGraphCanvasEventManager

click(Point, boolean) - Method in class org.ginsim.gui.graph.canvas.events.AddNodeInGraphCanvasEventManager

click(Point, boolean) - Method in class org.ginsim.gui.graph.canvas.events.GraphSelectionCanvasEventManager

click(Point, boolean) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

click(int, int) - Method in class org.ginsim.gui.utils.widgets.EnhancedJTable

clone() - Method in class org.ginsim.core.annotation.Annotation

clone() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

clone(ListOfPerturbations, Map<NodeInfo, NodeInfo>, Map<Perturbation, Perturbation>) - Method in interface org.ginsim.core.graph.regulatorygraph.perturbation.Perturbation

Copy the perturbation to a new graph (in particular to a reduced version of the current graph)

clone(ListOfPerturbations, Map<NodeInfo, NodeInfo>, Map<Perturbation, Perturbation>) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationFixed

clone(ListOfPerturbations, Map<NodeInfo, NodeInfo>, Map<Perturbation, Perturbation>) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationMultiple

clone(ListOfPerturbations, Map<NodeInfo, NodeInfo>, Map<Perturbation, Perturbation>) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationRange

clone(ListOfPerturbations, Map<NodeInfo, NodeInfo>, Map<Perturbation, Perturbation>) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationRegulator

clone(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

clone(RegulatoryGraph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

clone() - Method in class org.ginsim.core.graph.view.css.CSSEdgeStyle

clone() - Method in class org.ginsim.core.graph.view.css.CSSNodeStyle

clone() - Method in interface org.ginsim.core.graph.view.css.CSSStyle

clone(AvatarStateStore) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.CompleteStatePanel

Clones the state panel based on a named store

clone() - Method in class org.ginsim.service.tool.avatar.params.AvatarStateStore

clone() - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

clone() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

clone() - Method in class org.ginsim.service.tool.reg2dyn.updater.DeterministicSimulationUpdater

clone() - Method in class org.ginsim.service.tool.reg2dyn.updater.GenericSimulationUpdater

cloneForState(byte[]) - Method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

cloneForState(byte[]) - Method in class org.ginsim.service.tool.reg2dyn.updater.DeterministicSimulationUpdater

cloneForState(byte[]) - Method in class org.ginsim.service.tool.reg2dyn.updater.GenericSimulationUpdater

cloneForState(byte[]) - Method in interface org.ginsim.service.tool.reg2dyn.updater.SimulationUpdater

close() - Method in class org.ginsim.common.document.DocumentWriter

Close every element open then close the document

close() - Method in class org.ginsim.common.xml.XMLWriter

Close the writer: all open tags and the underlying outputstream.

close(Graph) - Method in class org.ginsim.core.graph.GSGraphManager

Remove all the server side association to the graph

close(Graph) - Method in class org.ginsim.gui.GUIManager

Unmemorize the relationship between a graph and its GraphGUI and Frame

close() - Method in class org.ginsim.gui.shell.AboutDialog

close() - Method in class org.ginsim.gui.shell.MainFrame

close the window without exiting: ie close if it's not the last window

close() - Method in class org.ginsim.gui.shell.StartupDialog

close() - Method in class org.ginsim.gui.utils.dialog.stackdialog.AbstractStackDialogHandler

close() - Method in interface org.ginsim.gui.utils.dialog.stackdialog.StackDialogHandler

close() - Method in class org.ginsim.gui.utils.widgets.Frame

close() - Method in class org.ginsim.gui.WhatToDoWithGraph

close() - Method in class org.ginsim.servicegui.layout.MultidimensionLayoutGUI

close() - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewer

close() - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicSearchPathConfig

close() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AnimatorUI

close() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPConfig

close the config window.

closeEmptyGraphs() - Method in class org.ginsim.gui.GUIManager

Close all the windows of graphs that are empty

closeEvent() - Method in class org.ginsim.commongui.dialog.SimpleDialog

closeList() - Method in class org.ginsim.common.document.DocumentWriter

Close a list.

closeListItem() - Method in class org.ginsim.common.document.DocumentWriter

Close a list item.

closeNotification() - Method in interface org.ginsim.gui.notifications.NotificationSource

closeNotification() - Method in class org.ginsim.gui.shell.MainFrame

Close the top notification by set invisible the notification panel and updating it if another Notification is in the queue

closeParagraph() - Method in class org.ginsim.common.document.DocumentWriter

Close a paragraph

closeStartupDialog() - Method in class org.ginsim.gui.GUIManager

closeTable() - Method in class org.ginsim.common.document.DocumentWriter

Close a table

closeTableCell() - Method in class org.ginsim.common.document.DocumentWriter

Close a table cell

closeTableRow() - Method in class org.ginsim.common.document.DocumentWriter

Close a table row

closeTag() - Method in class org.ginsim.common.xml.XMLWriter

close the currently opened tag.

closeUntil(int) - Method in class org.ginsim.common.document.DocumentWriter

Close every opened element until we are in the correct position in the tree

CNetFormatService - Class in org.ginsim.service.format

GINsim export service for the CNET format used by the BNS tool.

CNetFormatService() - Constructor for class org.ginsim.service.format.CNetFormatService

CNetFormatServiceGUI - Class in org.ginsim.servicegui.format

GUI Action to export model to the CNET format

CNetFormatServiceGUI() - Constructor for class org.ginsim.servicegui.format.CNetFormatServiceGUI

codingLongStates(BigInteger[]) - Static method in class org.ginsim.service.tool.avatar.domain.Dictionary

Loads the hash function: sum of the Cartesian product between the given parameter and a given state

codingShortStates(long[]) - Static method in class org.ginsim.service.tool.avatar.domain.Dictionary

Loads the hash function: sum of the Cartesian product between the given parameter and a given state

COLOR - Static variable in class org.ginsim.common.document.DocumentStyle

COLOR - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

color - Variable in enum org.ginsim.core.notification.NotificationType

ColorableItem - Interface in org.ginsim.gui.utils.widgets

in a JList or a JTable, this Object can "choose" its background color.

ColoredCellRenderer - Class in org.ginsim.servicegui.tool.stablestates

custom cell renderer to colorize cells

ColoredCellRenderer() - Constructor for class org.ginsim.servicegui.tool.stablestates.ColoredCellRenderer

colorize(Graph<?, ?>) - Method in class org.ginsim.core.graph.view.css.Colorizer

Apply the selector on all the edges and nodes of the graph If you apply the style only on a known subset of edges/nodes, surcharging this method to be more specific could be more efficient.

colorizeGraph(int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

colorize the regulatory graph according to the selected element.

Colorizer - Class in org.ginsim.core.graph.view.css

Do some generic work to colorize properly a graph, given a selector.

Colorizer(Selector) - Constructor for class org.ginsim.core.graph.view.css.Colorizer

Construct the colorizer from a selector and a graph.

ColorizerPanel - Class in org.ginsim.gui.graph.view.style

JPanel to control the colorization of a graph via a GUI.

ColorizerPanel(String, Graph<?, ?>) - Constructor for class org.ginsim.gui.graph.view.style.ColorizerPanel

Create a ColorizerPanel containing the colorizeButton.

ColorizerPanel(Graph<?, ?>) - Constructor for class org.ginsim.gui.graph.view.style.ColorizerPanel

Create a ColorizerPanel containing the colorizeButton but no initialColorizationCheckbox.

ColorPalette - Class in org.ginsim.common.utils

Some pre-defined color palettes and methods to help generating new ones or manipulating colors in general.

ColorPalette() - Constructor for class org.ginsim.common.utils.ColorPalette

ColorProperty - Class in org.ginsim.core.graph.view.style

ColorProperty(String, boolean) - Constructor for class org.ginsim.core.graph.view.style.ColorProperty

ColorProperty(String) - Constructor for class org.ginsim.core.graph.view.style.ColorProperty

ColumnDefinition - Class in org.ginsim.gui.utils.data

Describe a column for use in a ListPanel

ColumnDefinition(String, Class, boolean, int) - Constructor for class org.ginsim.gui.utils.data.ColumnDefinition

ColumnDefinition(String, Class, boolean) - Constructor for class org.ginsim.gui.utils.data.ColumnDefinition

COLUMNS - Static variable in class org.ginsim.servicegui.tool.reg2dyn.ListOfSimulationParametersHelper

COLUMNS - Static variable in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

combine(MDDManager, int, int) - Method in class org.ginsim.service.tool.circuit.ContextMergeOperator

combine(MDDManager, int, int) - Method in class org.ginsim.service.tool.circuit.FunctionalityCleanupOperator

combine(MDDManager, int, int) - Method in class org.ginsim.service.tool.circuit.FunctionalityMergeOperator

CompactStateSet - Class in org.ginsim.service.tool.avatar.domain

Representation of a state-set recurring to a compact set of patterns defining the internal states

CompactStateSet(List<NodeInfo>) - Constructor for class org.ginsim.service.tool.avatar.domain.CompactStateSet

Creates an empty state-set

CompactStateSet(String, List<NodeInfo>, AbstractStateSet) - Constructor for class org.ginsim.service.tool.avatar.domain.CompactStateSet

Creates a state-set with the given list of states and their probability of occurrence

CompactStateSet(String, List<NodeInfo>, List<byte[]>) - Constructor for class org.ginsim.service.tool.avatar.domain.CompactStateSet

Creates a state-set with the given list of states and their probability of occurrence

compare(String, String) - Method in class org.ginsim.service.tool.avatar.utils.NaturalOrderComparator

compare(State, State) - Method in class org.ginsim.service.tool.avatar.utils.StateProbComparator

compare(StateSet, StateSet) - Method in class org.ginsim.service.tool.avatar.utils.StateSetComparator

comparedEdges - Variable in class org.ginsim.service.tool.graphcomparator.GraphComparatorResult

ComparedItemInfo<T> - Class in org.ginsim.service.tool.graphcomparator

Hold information on an item in a compared graph: allow to associated extra information to the ComparedItemStatus.

ComparedItemInfo(T, T, T) - Constructor for class org.ginsim.service.tool.graphcomparator.ComparedItemInfo

comparedNodes - Variable in class org.ginsim.service.tool.graphcomparator.GraphComparatorResult

compareEdges(RegulatoryMultiEdge, RegulatoryMultiEdge) - Method in class org.ginsim.service.tool.graphcomparator.RegulatoryGraphComparator

compareTo(Object) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

compareTo(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

compareTo(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

compareTo(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionListElement

compareTo(Object) - Method in class org.ginsim.core.notification.Notification

Compare the notification to the given object.

compile(String, RegulatoryGraph, RegulatoryNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

compile(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanParser

compile() - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheet

Compile the CSS, allowing it to be applied.

complete(Simulation) - Method in class org.ginsim.service.tool.avatar.params.AvatarParameters

Updates the context with the parameters of a given simulation

CompleteStatePanel - Class in org.ginsim.gui.graph.regulatorygraph.initialstate

Extension of original initial state panel in order to support oracles and cloning

CompleteStatePanel(NamedStateList, NamedStateList, NamedStateList, boolean) - Constructor for class org.ginsim.gui.graph.regulatorygraph.initialstate.CompleteStatePanel

Creates a complete state panel from a given list of states

complexAttractorPatterns - Variable in class org.ginsim.service.tool.avatar.domain.Result

Pattern representation of complex attractors

complexAttractors - Variable in class org.ginsim.service.tool.avatar.domain.Result

Complex attractors (terminal cycles)

ComponentAdapter - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd

ComponentAdapter(GlassPane, String) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.ComponentAdapter

componentHidden(ComponentEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeRenderer

componentMoved(ComponentEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeRenderer

componentResized(ComponentEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeRenderer

componentShown(ComponentEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeRenderer

CompositionConfig - Class in org.ginsim.service.tool.composition

Class representing the specification of parameters for the Composition service

CompositionConfig() - Constructor for class org.ginsim.service.tool.composition.CompositionConfig

CompositionConfigDialog - Class in org.ginsim.servicegui.tool.composition

The composition dialog

CompositionContext - Interface in org.ginsim.servicegui.tool.composition.integrationgrammar

Interface to provide semantic information to integration grammar parsing tree traversals

CompositionContextImpl - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

CompositionContextImpl(CompositionSpecificationDialog, List<NodeInfo>) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.CompositionContextImpl

CompositionPanel - Class in org.ginsim.servicegui.tool.composition

Main panel for composition dialog

CompositionService - Class in org.ginsim.service.tool.composition

Module composition service

CompositionService() - Constructor for class org.ginsim.service.tool.composition.CompositionService

CompositionServiceGUI - Class in org.ginsim.servicegui.tool.composition

Register the Composition Service

CompositionServiceGUI() - Constructor for class org.ginsim.servicegui.tool.composition.CompositionServiceGUI

CompositionSpecificationDialog - Interface in org.ginsim.servicegui.tool.composition

Interface for the Specification of Composition Parameters

compute(Collection<Integer>) - Method in class org.ginsim.service.tool.composition.IntegrationFunction.IntegrationFunctionReification

computeChange(byte[], byte[]) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.DecisionOnEdge

Compute the changes of a given edge (source, target)

computeComposedGraph(RegulatoryGraph, CompositionConfig) - Method in class org.ginsim.service.tool.composition.CompositionService

computeReachableStates(StatefulLogicalModel) - Static method in class org.ginsim.service.tool.avatar.simulation.Reachable

Method to find all the reachable states from a given portion of the state space

computeWidthPerDepthFromRegGraph() - Method in class org.ginsim.core.graph.tree.TreeBuilder

concreteIntegrationProcess() - Method in class org.ginsim.service.export.cadp.CADPIntegrationWriter.IntegrationProcessWriter

concreteIntegrationProcessName(RegulatoryNode, int) - Method in class org.ginsim.service.export.cadp.CADPWriter

concreteProcessName(int) - Method in class org.ginsim.service.export.cadp.CADPWriter

ConfidenceInterval - Class in org.ginsim.service.tool.avatar.utils

Statistical facilities to compute confidence intervals

ConfidenceInterval() - Constructor for class org.ginsim.service.tool.avatar.utils.ConfidenceInterval

configure() - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationSelectionPanel

configure() - Method in class org.ginsim.gui.utils.data.ListSelectionPanel

configure(NodeAttributesReader, int, int, int, int, int) - Method in interface org.ginsim.service.layout.LayoutAlgo

set some parameters for the layout, getting ready to place all nodes.

configure(NodeAttributesReader, int, int, int, int, int) - Method in class org.ginsim.service.layout.LevelLayout

configure(NodeAttributesReader, int, int, int, int, int) - Method in class org.ginsim.service.layout.RingLayout

configure() - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionConfigSelectionPanel

configure() - Method in class org.ginsim.servicegui.tool.reg2dyn.PrioritySelectionPanel

conjunction() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

conjunctionWith(IntegrationFunctionClause) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

ConnectivityServiceGUI - Class in org.ginsim.servicegui.tool.scc

register the scc service

ConnectivityServiceGUI() - Constructor for class org.ginsim.servicegui.tool.scc.ConnectivityServiceGUI

ConnectivityStyleProvider - Class in org.ginsim.service.tool.scc

Color a graph according to its connected components.

ConnectivityStyleProvider(List<NodeReducedData>, Graph) - Constructor for class org.ginsim.service.tool.scc.ConnectivityStyleProvider

constraints - Variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

contained(NamedStateList, List<byte[]>) - Static method in class org.ginsim.service.tool.avatar.simulation.MDDUtils

contains(byte[]) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Indicates if the HierarchicalNode contains a state by searching both the pile and the omdd

contains(byte[]) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Test if the set contains state that is, if its status is not 0

contains(State) - Method in class org.ginsim.service.tool.avatar.domain.AbstractStateSet

Checks whether a given state is contained in the state-set

contains(State) - Method in class org.ginsim.service.tool.avatar.domain.CompactStateSet

contains(State) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

contains(String) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Deprecated.

contains(State) - Method in class org.ginsim.service.tool.avatar.domain.Result

Checks whether a stable state is stored

contains(State) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

contains(String) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Checks whether a given state (based on its key) is in the state-set

containsEdge(V, V) - Method in class org.ginsim.core.graph.AbstractGraph

containsEdge(E) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

containsEdge(V, V) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

containsEdge(V, V) - Method in interface org.ginsim.core.graph.GraphBackend

containsEdge(V, V) - Method in interface org.ginsim.core.graph.GraphModel

containsFunction() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

containsLink(AnnotationLink) - Method in class org.ginsim.core.annotation.Annotation

containsLink(String) - Method in class org.ginsim.core.annotation.Annotation

containsNode(V) - Method in class org.ginsim.core.graph.AbstractGraph

containsNode(V) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

containsNode(V) - Method in interface org.ginsim.core.graph.GraphBackend

containsNode(V) - Method in interface org.ginsim.core.graph.GraphModel

containsNode(TreeNode) - Method in interface org.ginsim.core.graph.tree.Tree

Indicates if the tree contains a node

containsNode(TreeNode) - Method in class org.ginsim.core.graph.tree.TreeImpl

Indicates if the tree contains a node

containsParameter() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

containsRoot() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

containsState(byte[]) - Method in interface org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueItem

containsState(byte[]) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueSCC

containsState(byte[]) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

containsValue() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

containsVertex(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

contentChanged() - Method in interface org.ginsim.core.utils.data.GenericListListener

contentChanged() - Method in class org.ginsim.service.tool.avatar.params.AvatarParameterList

contentChanged() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

ContextExtractor - Class in org.ginsim.service.tool.circuit

Extract functionality context for one interaction.

ContextExtractor(MDDManager) - Constructor for class org.ginsim.service.tool.circuit.ContextExtractor

contextIndex - Variable in class org.ginsim.service.tool.circuit.FunctionalityContext

ContextMergeOperator - Class in org.ginsim.service.tool.circuit

This operation combines functionality contexts.

ContextMergeOperator() - Constructor for class org.ginsim.service.tool.circuit.ContextMergeOperator

convergence - Variable in class org.ginsim.service.tool.avatar.domain.Result

Convergence

copiedSubGraph - Static variable in class org.ginsim.gui.shell.callbacks.EditCallBack

copy(Style) - Method in class org.ginsim.core.graph.view.style.BaseStyle

copy(Style) - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

copy(Style) - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

copy(Style) - Method in interface org.ginsim.core.graph.view.style.Style

Copy properties from an existing style.

COPY - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.TreeMenu

copy() - Method in class org.ginsim.service.tool.avatar.domain.ExhaustiveFinalPaths

copy_to(SimulationParameters, Map) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

copyEdge(DynamicGraph, DynamicEdge) - Method in class org.ginsim.service.tool.graphcomparator.DynamicGraphComparator

copyEdge(G, E) - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

copyEdge(RegulatoryGraph, RegulatoryMultiEdge) - Method in class org.ginsim.service.tool.graphcomparator.RegulatoryGraphComparator

copyFrom(Annotation) - Method in class org.ginsim.core.annotation.Annotation

copyFrom(EdgeAttributesReader) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

copyFrom(NodeAttributesReader) - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

copyFrom(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

copyFrom(boolean[]) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

copyFrom(EdgeAttributesReader) - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

copyFrom(NodeAttributesReader) - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

copyLine(int) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

copyNode(DynamicGraph, DynamicNode) - Method in class org.ginsim.service.tool.graphcomparator.DynamicGraphComparator

copyNode(G, V) - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

copyNode(RegulatoryGraph, RegulatoryNode) - Method in class org.ginsim.service.tool.graphcomparator.RegulatoryGraphComparator

copyNodeStyles(RegulatoryGraph, RegulatoryGraph) - Method in class org.ginsim.service.tool.modelbooleanizer.ModelBooleanizerService

copyStateRow() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

copyView(Graph<V, E>, ViewCopyHelper<Graph<V, E>, V, E>) - Method in class org.ginsim.core.graph.AbstractGraph

copyView(Graph<V, E>, ViewCopyHelper<Graph<V, E>, V, E>) - Method in interface org.ginsim.core.graph.Graph

Transfer view settings from a related graph.

create() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphFactory

create(List<?>) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphFactory

create() - Method in interface org.ginsim.core.graph.GraphFactory

Create a new graph of the type factory is managing

create() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphFactory

create(List<NodeInfo>, boolean) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphFactory

create() - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphFactory

create(Graph) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphFactory

create() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphFactory

create() - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceTreeFactory

create(TrapSpaceList) - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceTreeFactory

create() - Method in class org.ginsim.core.graph.tree.TreeFactory

create(TreeBuilder) - Method in class org.ginsim.core.graph.tree.TreeFactory

create() - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationCreatePanel

create(L, Object) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

create() - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

create(String) - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewer

CREATE_1_FUNCTION - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.TreeMenu

CREATE_N_FUNCTIONS - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.TreeMenu

createAtom(String, String, String, String) - Static method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification

createAtom(String, String, String, String, String) - Static method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification

createAtom(IntegrationFunctionSpecification.IntegrationExpression) - Static method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification

createColorPaletteByHue(int, float, float, float, float) - Static method in class org.ginsim.common.utils.ColorPalette

Generate a color palette with colors in a restricted range of Hue and Brightness.

createColorPaletteByRange(int, float, float) - Static method in class org.ginsim.common.utils.ColorPalette

Create a palette of color by varying the hue for nbcolors steps

createColorPaletteByRange(int) - Static method in class org.ginsim.common.utils.ColorPalette

createColorProperty(String) - Static method in class org.ginsim.core.graph.view.style.StyleProperty

createConjunction(IntegrationFunctionSpecification.IntegrationExpression, IntegrationFunctionSpecification.IntegrationExpression) - Static method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification

createDefaultEdgeStyle(G) - Method in class org.ginsim.core.graph.AbstractGraphFactory

createDefaultEdgeStyle(DynamicGraph) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphFactory

createDefaultEdgeStyle(G) - Method in interface org.ginsim.core.graph.GraphFactory

createDefaultEdgeStyle(RegulatoryGraph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphFactory

createDefaultEdgeStyle(Tree) - Method in class org.ginsim.core.graph.tree.TreeFactory

createDefaultNodeStyle(G) - Method in class org.ginsim.core.graph.AbstractGraphFactory

createDefaultNodeStyle(DynamicGraph) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphFactory

createDefaultNodeStyle(G) - Method in interface org.ginsim.core.graph.GraphFactory

createDefaultNodeStyle(HierarchicalTransitionGraph) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphFactory

createDefaultNodeStyle(RegulatoryGraph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphFactory

createDefaultNodeStyle(Tree) - Method in class org.ginsim.core.graph.tree.TreeFactory

createDiagramFromOmdd(int) - Method in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

createDiagramFromOmdd() - Method in class org.ginsim.core.graph.tree.TreeBuilderFromMDD

createDisjunction(IntegrationFunctionSpecification.IntegrationExpression, IntegrationFunctionSpecification.IntegrationExpression) - Static method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification

createEdge(V, V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

createGeneratedName(String, File) - Static method in class org.ginsim.common.utils.TempDir

Creates a temp directory with a generated name (given a certain prefix) in a given directory.

createNamed(String, File) - Static method in class org.ginsim.common.utils.TempDir

Creates a temp directory with a given name in a given directory.

createNegation(IntegrationFunctionSpecification.IntegrationExpression) - Static method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification

createOperand(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanTreeNodeFactory

createOperand(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNodeFactory

createOperator(String, Stack) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNodeFactory

createReport(String, Map<String, String>) - Method in class org.ginsim.ScriptLauncher

Create a report file, this creates the file and DocumentWriter, don't forget to close it.

createSimpleStrokedShape(Shape) - Method in class org.ginsim.core.graph.view.SimpleStroke

createStateSet() - Method in interface org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraph

createStateSet() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

createStrokedShape(Shape) - Method in class org.ginsim.core.graph.view.SimpleStroke

createStyle() - Method in class org.ginsim.gui.graph.view.style.StyleTab

createTransferable(JComponent) - Method in class org.ginsim.gui.utils.widgets.TableHeaderTransferHandler

Create a Transferable to use as the source for a data transfer.

createTreeFromOmdd(int) - Method in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

createTreeFromOmdd() - Method in class org.ginsim.core.graph.tree.TreeBuilderFromMDD

createUI(JComponent) - Static method in class org.ginsim.commongui.utils.VerticalLabelUI

cs - Variable in class org.ginsim.core.graph.view.css.Colorizer

CSS_BACKGROUND - Static variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

CSS_BORDER - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSS_BORDER - Static variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

CSS_BORDER_RAISED - Static variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

CSS_BORDER_SIMPLE - Static variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

CSS_BORDER_STRONG - Static variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

CSS_FOREGROUND - Static variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

CSS_LINECOLOR - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSS_LINEEND - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSS_LINEEND_DUAL - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSS_LINEEND_NEGATIVE - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSS_LINEEND_POSITIVE - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSS_LINEEND_UNKNOWN - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSS_SHAPE - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSS_SHAPE - Static variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

CSS_SHAPE_CURVE - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSS_SHAPE_ELLIPSE - Static variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

CSS_SHAPE_RECTANGLE - Static variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

CSS_SHAPE_STRAIGHT - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSS_TEXTCOLOR - Static variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

CSSEdgeStyle - Class in org.ginsim.core.graph.view.css

EdgeStyle store some graphical attributes of an edge Attributes : - lineColor : the line color = any Color - shape : the style of the edge = straight or curve - lineEnd : the line end = positive, negative, double or unknown

CSSEdgeStyle() - Constructor for class org.ginsim.core.graph.view.css.CSSEdgeStyle

A new style from the with all values to NULL

CSSEdgeStyle(Color) - Constructor for class org.ginsim.core.graph.view.css.CSSEdgeStyle

CSSEdgeStyle(Color, EdgeEnd, int, float) - Constructor for class org.ginsim.core.graph.view.css.CSSEdgeStyle

A new style from the scratch

CSSEdgeStyle(EdgeAttributesReader) - Constructor for class org.ginsim.core.graph.view.css.CSSEdgeStyle

A new style from a GsAttributesReader areader

CSSEdgeStyle(CSSEdgeStyle) - Constructor for class org.ginsim.core.graph.view.css.CSSEdgeStyle

A new style copied from another

CSSNodeStyle - Class in org.ginsim.core.graph.view.css

NodeStyle store some graphical attributes of a node Attributes : - background : the color for the background = any Color - foreground : the color for the text and the border = any Color - border : the style of the border = simple, raised or strong - shape : the shape = ellipse or rectangle

CSSNodeStyle() - Constructor for class org.ginsim.core.graph.view.css.CSSNodeStyle

A new style from the with all values to NULL

CSSNodeStyle(Color, Color, Color, NodeBorder, NodeShape) - Constructor for class org.ginsim.core.graph.view.css.CSSNodeStyle

A new style from the scratch

CSSNodeStyle(NodeAttributesReader) - Constructor for class org.ginsim.core.graph.view.css.CSSNodeStyle

A new style from a GsAttributesReader areader

CSSNodeStyle(CSSNodeStyle) - Constructor for class org.ginsim.core.graph.view.css.CSSNodeStyle

A new style copied from another

CSSStyle - Interface in org.ginsim.core.graph.view.css

Style are dedicated to store some graphical attributes of graphical elements like node and edges

CSSSyntaxException - Exception in org.ginsim.core.graph.view.css

CSSSyntaxException() - Constructor for exception org.ginsim.core.graph.view.css.CSSSyntaxException

CSSSyntaxException(String) - Constructor for exception org.ginsim.core.graph.view.css.CSSSyntaxException

CSSSyntaxException(String, String, int) - Constructor for exception org.ginsim.core.graph.view.css.CSSSyntaxException

CSSSyntaxException(Throwable) - Constructor for exception org.ginsim.core.graph.view.css.CSSSyntaxException

CSSSyntaxException(String, Throwable) - Constructor for exception org.ginsim.core.graph.view.css.CSSSyntaxException

cur_state - Variable in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

CURRENT_OS - Static variable in enum org.ginsim.common.application.CurrentOS

CurrentOS - Enum in org.ginsim.common.application

Detect the current Operating System and provide the information in an easier way for some OS-dependent operations.

curval - Variable in class org.ginsim.common.xml.XMLHelper

if set to other than null, characters will be stored here

curve - Variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

customStyleProvider(RegulatoryGraph) - Method in class org.ginsim.service.export.image.ImageExportService

CUT - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.TreeMenu

cycle - Variable in class org.ginsim.service.tool.avatar.domain.ExhaustiveFinalPaths

CycleGraph - Class in org.ginsim.service.tool.avatar.domain

Class with functionalities to explore a cycle of states

CycleGraph(List<String>) - Constructor for class org.ginsim.service.tool.avatar.domain.CycleGraph

Creates a cycle

CytoscapeEncoder - Class in org.ginsim.service.export.struct

CytoscapeEncoder() - Constructor for class org.ginsim.service.export.struct.CytoscapeEncoder

cytoscapeExport(RegulatoryGraph, String) - Method in class org.ginsim.service.export.struct.GraphStructureExportService

Run the Cytoscape export by instantiating and calling a CytoscapeEncoder

D

damage(Object) - Method in class org.ginsim.core.graph.AbstractGraph

damage() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

damage(Object) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

damage() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

damage(Object) - Method in interface org.ginsim.core.graph.GraphBackend

Declare an object visual setting change

damage() - Method in interface org.ginsim.core.graph.view.AttributesReader

The current item will be changed: mark its current area as damaged if needed.

damage(Rectangle) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

damageCanvas(Rectangle) - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

Mark a part of the canvas as needing to be redrawn.

damageItem(Object) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

Mark an item as needing redraw.

data - Variable in class org.ginsim.gui.utils.data.GenericPropertyInfo

data - Variable in class org.ginsim.gui.utils.data.SimpleStateListTableModel

A list of state : byte[]

DatabaseInfo - Class in org.ginsim.core.annotation

MIRIAM-based OpenHelper: open MIRIAM URNs MIRIAM provides a list of biological databases and the identifiers.org webservice to open generic links (Database, identifier pairs) in these databases (supporting mirrors)

DatabaseInfo(String, String) - Constructor for class org.ginsim.core.annotation.DatabaseInfo

dataFlavors - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

dataFlavorsList - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

DataViewer - Class in org.ginsim.servicegui.tool.dataviewer

Let the user manage the objects associated to a graph.

DataViewer(Graph<?, ?>) - Constructor for class org.ginsim.servicegui.tool.dataviewer.DataViewer

DataViewerServiceGUI - Class in org.ginsim.servicegui.tool.dataviewer

GUI to view the associated objects.

DataViewerServiceGUI() - Constructor for class org.ginsim.servicegui.tool.dataviewer.DataViewerServiceGUI

ddmanager - Variable in class org.ginsim.core.graph.tree.TreeBuilderFromMDD

debug() - Static method in class org.ginsim.common.application.LogManager

print the log in System.out

debug(Object) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append msg to the end of the line

debug(int, Object) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append msg to the end of the line if mask match the debug mask

debug(int) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append msg to the end of the line

debug(int, int) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append msg to the end of the line if mask match the debug mask

debug(boolean) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append msg to the end of the line

debug(int, boolean) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append msg to the end of the line if mask match the debug mask

debug(double) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append msg to the end of the line

debug(int, double) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append msg to the end of the line if mask match the debug mask

debug(long) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append msg to the end of the line

debug(int, long) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append msg to the end of the line if mask match the debug mask

debug - Static variable in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

debug_collection(Collection) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append the content of the collection to the end of the line if mask match the debug mask

debug_collection(int, Collection) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append the content of the collection to the end of the line if mask match the debug mask

debug_collection(Object[]) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append the content of the collection to the end of the line if mask match the debug mask

debug_collection(int, Object[]) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append the content of the collection to the end of the line if mask match the debug mask

debug_collection(int[]) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append the content of the collection to the end of the line if mask match the debug mask

debug_collection(int, int[]) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append the content of the collection to the end of the line if mask match the debug mask

debug_collection(double[]) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append the content of the collection to the end of the line if mask match the debug mask

debug_collection(int, double[]) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append the content of the collection to the end of the line if mask match the debug mask

debug_collection(boolean[]) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append the content of the collection to the end of the line if mask match the debug mask

debug_collection(int, boolean[]) - Static method in class org.ginsim.common.application.LogManager

print the log in System.out and append the content of the collection to the end of the line if mask match the debug mask

DEC_PLACES - Static variable in class org.colomoto.biolqm.io.avatar.AvatarUtils

DecisionAnalysis - Class in org.ginsim.servicegui.tool.decisionanalysis

Labels a given set of edges from an HTG with the updated genes of their corresponding edges in the STG.

DecisionAnalysis(LogicalModel, HierarchicalTransitionGraph, SimulationParameters) - Constructor for class org.ginsim.servicegui.tool.decisionanalysis.DecisionAnalysis

DecisionAnalysisFrame - Class in org.ginsim.servicegui.tool.decisionanalysis

DecisionAnalysisFrame(JFrame, HierarchicalTransitionGraph, RegulatoryGraph) - Constructor for class org.ginsim.servicegui.tool.decisionanalysis.DecisionAnalysisFrame

DecisionAnalysisServiceGUI - Class in org.ginsim.servicegui.tool.decisionanalysis

DecisionAnalysisServiceGUI() - Constructor for class org.ginsim.servicegui.tool.decisionanalysis.DecisionAnalysisServiceGUI

DecisionOnEdge - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

Store a label that represent the genes that are updated between two states source, and target.

DecisionOnEdge(HierarchicalTransitionGraph, HierarchicalNode, HierarchicalNode, List<NodeInfo>) - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.DecisionOnEdge

deepCopy(Tree) - Method in class org.ginsim.core.graph.tree.TreeNode

DEFAULT_ALPHA - Static variable in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

DEFAULT_HEIGHT - Static variable in class org.ginsim.core.graph.view.style.NodeStyleImpl

DEFAULT_PROPERTIES - Static variable in class org.ginsim.core.graph.view.style.EdgeStyleImpl

DEFAULT_PROPERTIES - Static variable in class org.ginsim.core.graph.view.style.NodeStyleImpl

DEFAULT_URL_DTD_FILE - Static variable in class org.ginsim.core.io.parser.GinmlHelper

default URL of the DTD

DEFAULT_WIDTH - Static variable in class org.ginsim.core.graph.view.style.NodeStyleImpl

DefaultDialogSize - Class in org.ginsim.commongui.dialog

Simple structure to store and remember the default size of a dialog.

DefaultDialogSize(String, int, int) - Constructor for class org.ginsim.commongui.dialog.DefaultDialogSize

DefaultDynamicEdgeStyle - Class in org.ginsim.core.graph.dynamicgraph

Default style for edges in the State Transition Graph.

DefaultDynamicEdgeStyle() - Constructor for class org.ginsim.core.graph.dynamicgraph.DefaultDynamicEdgeStyle

DefaultDynamicNodeStyle - Class in org.ginsim.core.graph.dynamicgraph

Default style for nodes in the State Transition Graph.

DefaultDynamicNodeStyle(DynamicGraph) - Constructor for class org.ginsim.core.graph.dynamicgraph.DefaultDynamicNodeStyle

defaultFont - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

DefaultHTGNodeStyle - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

Default style for the HTG.

DefaultHTGNodeStyle(HierarchicalTransitionGraph) - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.DefaultHTGNodeStyle

defaultPalette - Static variable in class org.ginsim.common.utils.ColorPalette

defaultPalette2 - Static variable in class org.ginsim.common.utils.ColorPalette

defaultPalette3 - Static variable in class org.ginsim.common.utils.ColorPalette

DefaultRegulatoryEdgeStyle - Class in org.ginsim.core.graph.regulatorygraph

Default style for edge of regulatory graphs.

DefaultRegulatoryEdgeStyle() - Constructor for class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryEdgeStyle

DefaultRegulatoryNodeStyle - Class in org.ginsim.core.graph.regulatorygraph

DefaultRegulatoryNodeStyle() - Constructor for class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryNodeStyle

defaultStyle - Variable in class org.ginsim.core.graph.view.style.BaseStyleOverride

DefaultTableHeaderCellRenderer - Class in org.ginsim.commongui.utils

A default cell renderer for a JTableHeader.

DefaultTableHeaderCellRenderer() - Constructor for class org.ginsim.commongui.utils.DefaultTableHeaderCellRenderer

Constructs a DefaultTableHeaderCellRenderer.

DefaultTreeEdgeStyle - Class in org.ginsim.core.graph.tree

DefaultTreeEdgeStyle() - Constructor for class org.ginsim.core.graph.tree.DefaultTreeEdgeStyle

DefaultTreeNodeStyle - Class in org.ginsim.core.graph.tree

DefaultTreeNodeStyle() - Constructor for class org.ginsim.core.graph.tree.DefaultTreeNodeStyle

DEFINITION - Static variable in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionAsynchronous

DEFINITION - Static variable in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionComplete

DEFINITION - Static variable in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSynchronous

degreeOf(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

del(int) - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserPathModel

del() - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicSearchPathConfig

del(int) - Method in class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

del(int) - Method in interface org.ginsim.servicegui.tool.pathfinding.PathFindingTableModel

DELETE - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.TreeMenu

delete(String) - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewer

DeleteAction - Class in org.ginsim.gui.graph

DeleteAction(Graph<?, ?>) - Constructor for class org.ginsim.gui.graph.DeleteAction

deleted(int[]) - Method in interface org.ginsim.common.utils.ListReorderListener

deleted(int[]) - Method in class org.ginsim.core.annotation.Annotation

deleteDirectory(File) - Static method in class org.ginsim.common.utils.IOUtils

Remove all files and directory from the given path

deleteNotification(Notification) - Method in interface org.ginsim.core.notification.NotificationListener

Receive a notification from the NotificationManager and remove it from the notification list

deleteNotification(Notification) - Method in class org.ginsim.gui.shell.MainFrame

Remove the given notification from the queue

deleteParameter() - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

delete the selected row in the table

deleteRow(int) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

delete a row

deleteStateRow() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

deleteStyle(Style) - Method in class org.ginsim.core.graph.view.style.StyleManager

deleteStyle() - Method in class org.ginsim.gui.graph.view.style.StyleTab

deliverLogs() - Static method in class org.ginsim.common.application.LogManager

Produce a zip file containing the log files and returns the path to the file

delLink(String, Graph) - Method in class org.ginsim.core.annotation.Annotation

depth - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

The current depth in the dfs.

depth - Variable in class org.ginsim.service.tool.reg2dyn.htg.TarjanSimulation

The current depth in the dfs.

depth - Variable in class org.ginsim.service.tool.reg2dyn.SimulationQueuedState

depth - Variable in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

deriveValidId(String) - Static method in class org.ginsim.common.xml.XMLWriter

description - Variable in class org.ginsim.core.annotation.DatabaseInfo

DetailedErrorNotification - Class in org.ginsim.core.notification.detailed

DetailedErrorNotification(Object, String, String) - Constructor for class org.ginsim.core.notification.detailed.DetailedErrorNotification

DetailedInformationNotification - Class in org.ginsim.core.notification.detailed

DetailedInformationNotification(Object, String, String) - Constructor for class org.ginsim.core.notification.detailed.DetailedInformationNotification

DetailedNotification - Interface in org.ginsim.core.notification.detailed

DetailedWarningNotification - Class in org.ginsim.core.notification.detailed

DetailedWarningNotification(Object, String, String) - Constructor for class org.ginsim.core.notification.detailed.DetailedWarningNotification

DeterministicSimulationUpdater - Class in org.ginsim.service.tool.reg2dyn.updater

Wrap LogicalModel's updater API into GINsim.

DeterministicSimulationUpdater(DeterministicUpdater) - Constructor for class org.ginsim.service.tool.reg2dyn.updater.DeterministicSimulationUpdater

developer_mode - Static variable in class org.ginsim.Launcher

True if the developers extras (toolkit menu, under-developement...) should be enabled

dfa6 - Variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

DFA6(BaseRecognizer) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer.DFA6

dialog - Variable in class org.ginsim.gui.utils.data.ListSelectionPanel

Dictionary - Class in org.ginsim.service.tool.avatar.domain

Class responsible for the efficient calculus of the hash code of a given state

Dictionary() - Constructor for class org.ginsim.service.tool.avatar.domain.Dictionary

dirPrefix - Variable in class org.ginsim.common.document.DocumentWriter

disabledEdition(List<NamedState>) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

disjunction() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

dispose() - Method in class org.ginsim.gui.shell.MainFrame

some things to do before destroying the window TODO: check if this is actually needed

dispose() - Method in class org.ginsim.gui.utils.widgets.Frame

divideWindow(boolean) - Method in class org.ginsim.gui.shell.MainFrame

change the attribute panel position.

do_simulation() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

Run the simulation, handle exception and build the graph.

do_simulation() - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.LimitedSimulation

do_simulation() - Method in class org.ginsim.service.tool.reg2dyn.Simulation

doAdd(ActionEvent) - Method in class org.ginsim.gui.utils.data.ListPanel

doAddAnchor(String, String) - Method in class org.ginsim.common.document.DocumentWriter

doAddAnchor(String, String) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doAddAnchor(String, String) - Method in class org.ginsim.common.document.OOoDocumentWriter

doAddAnchor(String, String) - Method in class org.ginsim.common.document.WikiDocumentWriter

doAddAnchor(String, String) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doAddImage(BufferedImage, String) - Method in class org.ginsim.common.document.DocumentWriter

doAddImage(BufferedImage, String) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doAddImage(BufferedImage, String) - Method in class org.ginsim.common.document.OOoDocumentWriter

doAddImage(BufferedImage, String) - Method in class org.ginsim.common.document.WikiDocumentWriter

doAddImage(BufferedImage, String) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doAddLink(String, String) - Method in class org.ginsim.common.document.DocumentWriter

doAddLink(String, String) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doAddLink(String, String) - Method in class org.ginsim.common.document.OOoDocumentWriter

doAddLink(String, String) - Method in class org.ginsim.common.document.WikiDocumentWriter

doAddLink(String, String) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doBuildNext() - Method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

doBuildNext() - Method in class org.ginsim.service.tool.reg2dyn.updater.SynchronousSimulationUpdater

doCancel() - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

doCancel() - Method in class org.ginsim.servicegui.tool.stablestates.StableStateSwingUI

doCancel() - Method in class org.ginsim.servicegui.tool.trapspace.TrapSpaceSwingUI

doChaos(boolean, boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

doClone() - Method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

doClone() - Method in class org.ginsim.service.tool.reg2dyn.updater.SynchronousSimulationUpdater

doClose() - Method in class org.ginsim.commongui.dialog.ResultsDialog

doClose() - Method in class org.ginsim.commongui.dialog.SimpleDialog

doClose() - Method in class org.ginsim.gui.shell.SearchFrame

doClose() - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

doClose() - Method in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

doClose() - Method in class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorCaptionFrame

doClose() - Method in class org.ginsim.servicegui.tool.interactionanalysis.InteractionAnalysisFrame

doClose() - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphFrame

doCloseDocument() - Method in class org.ginsim.common.document.DocumentWriter

doCloseDocument() - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doCloseDocument() - Method in class org.ginsim.common.document.OOoDocumentWriter

doCloseDocument() - Method in class org.ginsim.common.document.WikiDocumentWriter

doCloseDocument() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doCloseList() - Method in class org.ginsim.common.document.DocumentWriter

doCloseList() - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doCloseList() - Method in class org.ginsim.common.document.OOoDocumentWriter

doCloseList() - Method in class org.ginsim.common.document.WikiDocumentWriter

doCloseList() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doCloseListItem() - Method in class org.ginsim.common.document.DocumentWriter

doCloseListItem() - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doCloseListItem() - Method in class org.ginsim.common.document.OOoDocumentWriter

doCloseListItem() - Method in class org.ginsim.common.document.WikiDocumentWriter

doCloseListItem() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doCloseParagraph() - Method in class org.ginsim.common.document.DocumentWriter

doCloseParagraph() - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doCloseParagraph() - Method in class org.ginsim.common.document.OOoDocumentWriter

doCloseParagraph() - Method in class org.ginsim.common.document.WikiDocumentWriter

doCloseParagraph() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doCloseTable() - Method in class org.ginsim.common.document.DocumentWriter

doCloseTable() - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doCloseTable() - Method in class org.ginsim.common.document.OOoDocumentWriter

doCloseTable() - Method in class org.ginsim.common.document.WikiDocumentWriter

doCloseTable() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doCloseTableCell() - Method in class org.ginsim.common.document.DocumentWriter

doCloseTableCell() - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doCloseTableCell() - Method in class org.ginsim.common.document.OOoDocumentWriter

doCloseTableCell() - Method in class org.ginsim.common.document.WikiDocumentWriter

doCloseTableCell() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doCloseTableRow() - Method in class org.ginsim.common.document.DocumentWriter

doCloseTableRow() - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doCloseTableRow() - Method in class org.ginsim.common.document.OOoDocumentWriter

doCloseTableRow() - Method in class org.ginsim.common.document.WikiDocumentWriter

doCloseTableRow() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doColorize(Graph<?, ?>) - Method in class org.ginsim.core.graph.view.css.Colorizer

Initialise the CascadingStyle to handle the original style save at the first call.

doColorize() - Method in class org.ginsim.gui.graph.view.style.ColorizerPanel

Perform the colorization of the graph, update the button name accordingly

doColorize() - Method in class org.ginsim.gui.graph.view.style.StyleColorizerCheckbox

Perform the colorization of the graph, update the button name accordingly

doCreate(Graph) - Method in class org.ginsim.core.annotation.BiblioManager

doCreate(Graph) - Method in interface org.ginsim.core.graph.objectassociation.GraphAssociatedObjectManager

create the associated object for a graph

doCreate(Graph) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesManager

doCreate(Graph) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationManager

doCreate(Object) - Method in class org.ginsim.gui.utils.data.ListPanel

doCreate(L, Object) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

doCreate(Graph) - Method in class org.ginsim.service.tool.avatar.params.AvatarParametersManager

doCreate(String, int) - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

doCreate(Graph) - Method in class org.ginsim.service.tool.modelreduction.ReductionConfigManager

doCreate(Graph) - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalMappingManager

doCreate(Graph) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParametersManager

doCreate(AvatarParameterList, Object) - Method in class org.ginsim.servicegui.tool.avatar.parameters.AvatarParametersHelper

doCreate(SimulationParameterList, Object) - Method in class org.ginsim.servicegui.tool.reg2dyn.ListOfSimulationParametersHelper

doCreate(PrioritySetDefinition, Object) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionHelper

doCreate(PrioritySetList, Object) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

doCreateMeta(String, String) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doCreateMeta(String, String) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

DOCTYPE - Static variable in class org.ginsim.core.io.parser.GinmlHelper

documentProperties - Variable in class org.ginsim.common.document.DocumentWriter

DocumentStyle - Class in org.ginsim.common.document

DocumentStyle contain a generic representation of the style for a document
A DocumentStyle is a map of styles identified by their name (like the class in HTML), followed by a map of couples (property, value) and the function to manipulate them.

DocumentStyle() - Constructor for class org.ginsim.common.document.DocumentStyle

documentStyles - Variable in class org.ginsim.common.document.DocumentWriter

DocumentWriter - Class in org.ginsim.common.document

DocumentWriter is an abstract class designed to help writing documents.

DocumentWriter() - Constructor for class org.ginsim.common.document.DocumentWriter

DocumentWriterFactory - Interface in org.ginsim.common.document

A factory to create document writer instances.

doesDocumentSupportExtra(String) - Method in class org.ginsim.common.document.DocumentWriter

Indicate if the current document support a specific extra

doExport(RegulatoryGraph, String, ExportAction<?>) - Method in class org.ginsim.gui.service.FormatSupportServiceGUI

doExport(String) - Method in class org.ginsim.gui.shell.actions.ExportAction

Main export function: will be called after the target file was selected

doExport(String) - Method in class org.ginsim.servicegui.export.documentation.LRGDocumentationAction

doExport(String) - Method in class org.ginsim.servicegui.export.petrinet.PetriNetExportAction

doGetFileFilter() - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

doImport(String) - Method in class org.ginsim.gui.service.FormatSupportServiceGUI

doImport(String) - Method in class org.ginsim.gui.shell.actions.ImportAction

Main import function: will be called after the target file was selected

doIt(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.FunctionsCreator

doLayout(boolean, boolean, boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.CompleteStatePanel

doLayout(boolean, boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

doLayout(ActionEvent) - Method in class org.ginsim.gui.shell.actions.LayoutAction

doMerge(Graph<V, E>) - Method in class org.ginsim.core.graph.AbstractGraph

Specialized method that execute the merging of the given graph with the current one Must be override at specialized graph level

doMerge(Graph) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

doMerge(Graph) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

not used for this kind of graph: it has no meaning

doMerge(Graph) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

doMerge(Graph<RegulatoryNode, RegulatoryMultiEdge>) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

doMerge(Graph<TrapSpaceNode, TrapSpaceInclusion>) - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceTreeImpl

doMerge(Graph<TreeNode, TreeEdge>) - Method in class org.ginsim.core.graph.tree.TreeImpl

doMoveUp() - Method in class org.ginsim.gui.utils.data.ListPanel

doOpen(InputStream, Graph) - Method in class org.ginsim.core.annotation.BiblioManager

doOpen(InputStream, Graph) - Method in interface org.ginsim.core.graph.objectassociation.GraphAssociatedObjectManager

open associated object.

doOpen(InputStream, Graph) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesManager

doOpen(InputStream, Graph) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationManager

doOpen(InputStream, Graph) - Method in class org.ginsim.service.tool.avatar.params.AvatarParametersManager

doOpen(InputStream, Graph) - Method in class org.ginsim.service.tool.modelreduction.ReductionConfigManager

doOpen(InputStream, Graph) - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalMappingManager

doOpen(InputStream, Graph) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParametersManager

doOpenHeader(int, String, String) - Method in class org.ginsim.common.document.DocumentWriter

doOpenHeader(int, String, String) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doOpenHeader(int, String, String) - Method in class org.ginsim.common.document.OOoDocumentWriter

doOpenHeader(int, String, String) - Method in class org.ginsim.common.document.WikiDocumentWriter

doOpenHeader(int, String, String) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doOpenList(String, boolean) - Method in class org.ginsim.common.document.DocumentWriter

doOpenList(String, boolean) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doOpenList(String, boolean) - Method in class org.ginsim.common.document.OOoDocumentWriter

doOpenList(String, boolean) - Method in class org.ginsim.common.document.WikiDocumentWriter

doOpenList(String, boolean) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doOpenListItem() - Method in class org.ginsim.common.document.DocumentWriter

doOpenListItem() - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doOpenListItem() - Method in class org.ginsim.common.document.OOoDocumentWriter

doOpenListItem() - Method in class org.ginsim.common.document.WikiDocumentWriter

doOpenListItem() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doOpenParagraph(String) - Method in class org.ginsim.common.document.DocumentWriter

doOpenParagraph(String) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doOpenParagraph(String) - Method in class org.ginsim.common.document.OOoDocumentWriter

doOpenParagraph(String) - Method in class org.ginsim.common.document.WikiDocumentWriter

doOpenParagraph(String) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doOpenTable(String, String, String[]) - Method in class org.ginsim.common.document.DocumentWriter

doOpenTable(String, String, String[]) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doOpenTable(String, String, String[]) - Method in class org.ginsim.common.document.OOoDocumentWriter

doOpenTable(String, String, String[]) - Method in class org.ginsim.common.document.WikiDocumentWriter

doOpenTable(String, String, String[]) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doOpenTableCell(int, int, boolean, String) - Method in class org.ginsim.common.document.DocumentWriter

doOpenTableCell(int, int, boolean, String) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doOpenTableCell(int, int, boolean, String) - Method in class org.ginsim.common.document.OOoDocumentWriter

doOpenTableCell(int, int, boolean, String) - Method in class org.ginsim.common.document.WikiDocumentWriter

doOpenTableCell(int, int, boolean, String) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doOpenTableRow(String) - Method in class org.ginsim.common.document.DocumentWriter

doOpenTableRow(String) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doOpenTableRow(String) - Method in class org.ginsim.common.document.OOoDocumentWriter

doOpenTableRow(String) - Method in class org.ginsim.common.document.WikiDocumentWriter

doOpenTableRow(String) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doRemove(ListOfPerturbations, int[]) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationPanelListHelper

doRemove(L, int[]) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

doRemove(AvatarParameterList, int[]) - Method in class org.ginsim.servicegui.tool.avatar.parameters.AvatarParametersHelper

doRemove(SimulationParameterList, int[]) - Method in class org.ginsim.servicegui.tool.reg2dyn.ListOfSimulationParametersHelper

doRemove(PrioritySetDefinition, int[]) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionHelper

doRemove(PrioritySetList, int[]) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

doSave(OutputStreamWriter, Collection<V>, Collection<E>) - Method in class org.ginsim.core.graph.AbstractGraph

save implementation for a specific graph type.

doSave(OutputStreamWriter, Graph) - Method in class org.ginsim.core.graph.objectassociation.BasicGraphAssociatedManager

doSave(OutputStreamWriter, Graph) - Method in interface org.ginsim.core.graph.objectassociation.GraphAssociatedObjectManager

save the object associated with this graph.

doSave(OutputStreamWriter, Graph) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesManager

doSave(OutputStreamWriter, Graph) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationManager

doSave(OutputStreamWriter, Graph) - Method in class org.ginsim.service.tool.avatar.params.AvatarParametersManager

doSave(OutputStreamWriter, Graph) - Method in class org.ginsim.service.tool.modelreduction.ReductionConfigManager

doSave(OutputStreamWriter, Graph) - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalMappingManager

doSave(OutputStreamWriter, Graph) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParametersManager

doSaveGnuPlotArrowPath(File, File, List, List, boolean[]) - Static method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPConfig

doSaveGnuPlotMultiPath(File, File, List, List, boolean[]) - Static method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPConfig

doSetState() - Method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

doSetState() - Method in class org.ginsim.service.tool.reg2dyn.updater.SynchronousSimulationUpdater

doSetValueAt(Object, int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

doSetValueAt(Object, int, int) - Method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

doSpecialisedComparison() - Method in class org.ginsim.service.tool.graphcomparator.DynamicGraphComparator

doSpecialisedComparison() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

doSpecialisedComparison() - Method in class org.ginsim.service.tool.graphcomparator.RegulatoryGraphComparator

Dotify - Interface in org.ginsim.core.io.parser

Indicates a class can be dumped into dot (graphviz language) Thanks to Aurelien for his brilliant idea for the name of this interface

DOWN - Static variable in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

doWriteStyles() - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doWriteStyles() - Method in class org.ginsim.common.document.OOoDocumentWriter

doWriteStyles() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

doWriteText(String, boolean) - Method in class org.ginsim.common.document.DocumentWriter

doWriteText(String, boolean) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

doWriteText(String, boolean) - Method in class org.ginsim.common.document.OOoDocumentWriter

doWriteText(String, boolean) - Method in class org.ginsim.common.document.WikiDocumentWriter

doWriteText(String, boolean) - Method in class org.ginsim.common.document.XHTMLDocumentWriter

dragDropEnd(DragSourceDropEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.DropListener

dragDropEnd(DragSourceDropEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsDragSourceListener

dragEnter(DropTargetDragEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.DropListener

dragEnter(DragSourceDragEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsDragSourceListener

dragExit(DropTargetEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.DropListener

dragExit(DragSourceEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsDragSourceListener

dragged(Point) - Method in interface org.ginsim.gui.graph.canvas.CanvasEventManager

dragged(Point) - Method in class org.ginsim.gui.graph.canvas.events.AddEdgeInGraphCanvasEventManager

dragged(Point) - Method in class org.ginsim.gui.graph.canvas.events.AddNodeInGraphCanvasEventManager

dragged(Point) - Method in class org.ginsim.gui.graph.canvas.events.GraphSelectionCanvasEventManager

dragged(Point) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

dragGestureRecognized(DragGestureEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsDragGestureListener

dragOver(DropTargetDragEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.DropListener

dragOver(DragSourceDragEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsDragSourceListener

DragStatus - Enum in org.ginsim.gui.graph.canvas.events

drop(TreeElement) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

drop(TreeElement) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

drop(DropTargetDropEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.DropListener

dropable - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

dropActionChanged(DropTargetDragEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.DropListener

dropActionChanged(DragSourceDragEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsDragSourceListener

DropListener - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd

DropListener(LogicalFunctionTreePanel, GlassPane) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.DropListener

DUAL - Static variable in class org.ginsim.service.tool.circuit.CircuitDescr

DynamicAnalyserPathModel - Class in org.ginsim.servicegui.tool.dynamicanalyser

table model for the path constraint table.

DynamicAnalyserPathModel(DynamicGraph, List, List, DynamicSearchPathConfig) - Constructor for class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserPathModel

DynamicAnalyserPathModel - Class in org.ginsim.servicegui.tool.pathfinding

table model for the path constraint table.

DynamicAnalyserPathModel(DynamicGraph) - Constructor for class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

DynamicAnalyserServiceGUI - Class in org.ginsim.servicegui.tool.dynamicanalyser

offer some facilities to analyse the state transition graph.

DynamicAnalyserServiceGUI() - Constructor for class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserServiceGUI

DynamicEdge - Class in org.ginsim.core.graph.dynamicgraph

Edges in a state transition graph.

DynamicEdge(DynamicGraph, DynamicNode, DynamicNode) - Constructor for class org.ginsim.core.graph.dynamicgraph.DynamicEdge

DynamicGINMLWriter - Class in org.ginsim.core.graph.dynamicgraph

Save a STG in the GINML format.

DynamicGINMLWriter(DynamicGraph) - Constructor for class org.ginsim.core.graph.dynamicgraph.DynamicGINMLWriter

DynamicGraph - Interface in org.ginsim.core.graph.dynamicgraph

the dynamic (state transition) graph.

DynamicGraphComparator - Class in org.ginsim.service.tool.graphcomparator

Compare 2 DynamicGraph

DynamicGraphComparator(DynamicGraph, DynamicGraph) - Constructor for class org.ginsim.service.tool.graphcomparator.DynamicGraphComparator

DynamicGraphFactory - Class in org.ginsim.core.graph.dynamicgraph

Factory used to create dynamical graphs (STGs).

DynamicGraphFactory() - Constructor for class org.ginsim.core.graph.dynamicgraph.DynamicGraphFactory

DynamicGraphGUIHelper - Class in org.ginsim.gui.graph.dynamicgraph

DynamicGraphGUIHelper() - Constructor for class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

DynamicGraphImpl - Class in org.ginsim.core.graph.dynamicgraph

Implementation of dynamical graphs.

DynamicGraphImpl(List<NodeInfo>) - Constructor for class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

create a new DynamicGraph.

DynamicGraphImpl() - Constructor for class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

DynamicItemAttributePanel - Class in org.ginsim.gui.graph.dynamicgraph

basic info on a vertex of the state transition graph (ie state of the system)

DynamicItemAttributePanel(DynamicGraph) - Constructor for class org.ginsim.gui.graph.dynamicgraph.DynamicItemAttributePanel

DynamicItemCellRenderer - Class in org.ginsim.gui.graph.dynamicgraph

custom cell renderer to colorize cells

DynamicItemCellRenderer() - Constructor for class org.ginsim.gui.graph.dynamicgraph.DynamicItemCellRenderer

DynamicItemModel - Class in org.ginsim.gui.graph.dynamicgraph

table model to display a dynamic node or edge.

DynamicItemModel(DynamicGraph) - Constructor for class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

DynamicLayout3D - Class in org.ginsim.service.layout

Layout State Transition Graphs: place nodes on a cube according to activity levels

DynamicLayout3D() - Constructor for class org.ginsim.service.layout.DynamicLayout3D

DynamicLayoutMultidimention - Class in org.ginsim.service.layout

Layout State Transition Graphs: place nodes according to activity levels.

DynamicLayoutMultidimention(DynamicGraph, byte[], boolean, Color[]) - Constructor for class org.ginsim.service.layout.DynamicLayoutMultidimention

DynamicNode - Class in org.ginsim.core.graph.dynamicgraph

A node in a State Transition Graph (i.e.

DynamicNode(byte[]) - Constructor for class org.ginsim.core.graph.dynamicgraph.DynamicNode

DynamicNode(String) - Constructor for class org.ginsim.core.graph.dynamicgraph.DynamicNode

create a dynamicNode from it's id: the first character is ignored (must be a letter to be a valid id) each following character is parsed as int

DynamicParser - Class in org.ginsim.core.graph.dynamicgraph

Parse a GINML file containing a STG.

DynamicParser() - Constructor for class org.ginsim.core.graph.dynamicgraph.DynamicParser

DynamicParser(Set<String>, Attributes, String) - Constructor for class org.ginsim.core.graph.dynamicgraph.DynamicParser

DynamicPathItemCellRenderer - Class in org.ginsim.servicegui.tool.dynamicanalyser

modified cell renderer to highlight states not in the graph

DynamicPathItemCellRenderer(List) - Constructor for class org.ginsim.servicegui.tool.dynamicanalyser.DynamicPathItemCellRenderer

DynamicPathItemCellRenderer(boolean[]) - Constructor for class org.ginsim.servicegui.tool.dynamicanalyser.DynamicPathItemCellRenderer

DynamicPathItemCellRenderer(boolean[], List, Color, Color) - Constructor for class org.ginsim.servicegui.tool.dynamicanalyser.DynamicPathItemCellRenderer

DynamicSearchPathConfig - Class in org.ginsim.servicegui.tool.dynamicanalyser

UI to search a path in the dynamic graph.

DynamicSearchPathConfig(JFrame, DynamicGraph) - Constructor for class org.ginsim.servicegui.tool.dynamicanalyser.DynamicSearchPathConfig

get ready

dynamicUpdateValues() - Method in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

dynamicUpdateValues() - Method in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

dynamicUpdateValues() - Method in class org.ginsim.service.tool.avatar.simulation.MonteCarloSimulation

dynamicUpdateValues() - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

Updates a simulation with parameterizations dynamically fixed based on the properties of the input model

E

EAST - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

Edge<V> - Class in org.ginsim.core.graph

Base class for all edges: store the source and target nodes.

Edge(Graph<V, ?>, V, V) - Constructor for class org.ginsim.core.graph.Edge

create a edge.

edge - Variable in enum org.ginsim.core.graph.view.MovingEdgeType

EDGE_COLOR - Static variable in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

EdgeAnchor - Enum in org.ginsim.core.graph.view

EdgeAttributeReaderImpl<V,E extends Edge<V>> - Class in org.ginsim.core.graph.backend

a generic edgeAttributeReader storing data into a dedicated hashmap

EdgeAttributeReaderImpl(StyleManager<V, E>, GraphBackend<V, E>, NodeAttributesReader) - Constructor for class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

EdgeAttributesReader<V,E extends Edge<V>> - Interface in org.ginsim.core.graph.view

graphic info on an edge.

EdgeCount() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

EdgeEnd - Enum in org.ginsim.core.graph.view

Available markers for arrow ends.

EdgePattern - Enum in org.ginsim.core.graph.view

EdgeRoutingPanel - Class in org.ginsim.gui.graph.view.style

The panel showing edge routing options.

EdgeRoutingPanel(StyleManager) - Constructor for class org.ginsim.gui.graph.view.style.EdgeRoutingPanel

edgeSet() - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

edgesOf(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

EdgeStyle<V,E extends Edge<V>> - Interface in org.ginsim.core.graph.view.style

Define the visual parameters of an edge.

EdgeStyleImpl<V,E extends Edge<V>> - Class in org.ginsim.core.graph.view.style

Simple implementation for EdgeStyle.

EdgeStyleImpl() - Constructor for class org.ginsim.core.graph.view.style.EdgeStyleImpl

EdgeStyleImpl(String, EdgeStyle<V, E>) - Constructor for class org.ginsim.core.graph.view.style.EdgeStyleImpl

EdgeStyleOverride<V,E extends Edge<V>> - Class in org.ginsim.core.graph.view.style

EdgeStyleOverride(EdgeStyle<V, E>) - Constructor for class org.ginsim.core.graph.view.style.EdgeStyleOverride

EdgeViewInfo<V,E extends Edge<V>> - Interface in org.ginsim.core.graph.view

Store basic view information on an edge: intermediate points and optional style.

EdgeViewInfoImpl<V,E extends Edge<V>> - Class in org.ginsim.core.graph.backend

EdgeViewInfoImpl() - Constructor for class org.ginsim.core.graph.backend.EdgeViewInfoImpl

edit(Collection, Collection<Edge>) - Method in class org.ginsim.gui.graph.view.style.StyleTab

editable - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

editable - Variable in class org.ginsim.gui.utils.data.ColumnDefinition

EditAction - Class in org.ginsim.gui.graph

Minimalistic description of the available edit types for a Graph.

EditAction(EditMode, String) - Constructor for class org.ginsim.gui.graph.EditAction

EditAction(EditMode, String, String) - Constructor for class org.ginsim.gui.graph.EditAction

EditActionManager - Class in org.ginsim.gui.graph

Manage the available interactive edition action.

EditActionManager(GraphGUI, List<EditAction>) - Constructor for class org.ginsim.gui.graph.EditActionManager

Create an action manager with a list of specific edit actions

editButtonPressed() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

EditCallBack - Class in org.ginsim.gui.shell.callbacks

Callbacks for the "File" menu

EditCallBack() - Constructor for class org.ginsim.gui.shell.callbacks.EditCallBack

edited - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

EDITME - Static variable in class org.ginsim.gui.utils.data.ColumnDefinition

EditMode - Enum in org.ginsim.gui.graph

Available interactive edition modes.

editor - Variable in class org.ginsim.gui.utils.data.GenericPropertyInfo

EditPanel - Class in org.ginsim.gui.shell.editpanel

Tabbed panel which follows the current selection.

EditPanel(GraphGUI<?, ?, ?>) - Constructor for class org.ginsim.gui.shell.editpanel.EditPanel

EditTab - Interface in org.ginsim.gui.shell.editpanel

Simple interface for edition panels.

ElementaryCyclesSearch - Class in org.ginsim.johnsonCycles

Searchs all elementary cycles in a given directed graph.

ElementaryCyclesSearch(boolean[][], Object[]) - Constructor for class org.ginsim.johnsonCycles.ElementaryCyclesSearch

Constructor.

encode(Graph, Collection<Edge<?>>, String) - Method in class org.ginsim.service.export.struct.BiolayoutEncoder

Encode the graph to struct output

encode(RegulatoryGraph, String) - Method in class org.ginsim.service.export.struct.CytoscapeEncoder

Encode the RegulatoryGraph graph into a file named filename

encode(Graph, Collection<Object>, Collection<Edge<?>>, String) - Method in class org.ginsim.service.export.struct.GraphvizEncoder

Encode the graph to graphviz output

endAnim() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

stop the animator, restore colors...

endElement(String, String, String) - Method in class org.ginsim.common.xml.XMLHelper

endElement(int) - Method in class org.ginsim.common.xml.XMLHelper

endElement(String, String, String) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicParser

endElement(String, String, String) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphParser

endElement(String, String, String) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphParser

endElement(int) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationParser

endElement(String, String, String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryParser

endElement(String, String, String) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParametersParser

ENDING - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

endNewSigma() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSetFactory

ENDONLY - Static variable in class org.ginsim.common.xml.XMLHelper

endSimu(Graph, Exception) - Method in class org.ginsim.service.tool.composition.ReductionStub

endSimulation() - Method in class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

endSimulation() - Method in interface org.ginsim.service.tool.reg2dyn.helpers.SimulationHelper

endSimulation() - Method in class org.ginsim.service.tool.reg2dyn.helpers.STGSimulationHelper

enforceBorder() - Method in interface org.ginsim.core.graph.view.style.NodeStyle

enforceBorder() - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

enforceBorder() - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

enforceColor() - Method in interface org.ginsim.core.graph.view.style.EdgeStyle

enforceColor() - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

enforceColor() - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

enforceColors() - Method in interface org.ginsim.core.graph.view.style.NodeStyle

enforceColors() - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

enforceColors() - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

enforceEnding() - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryEdgeStyle

enforceEnding() - Method in interface org.ginsim.core.graph.view.style.EdgeStyle

enforceEnding() - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

enforceEnding() - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

enforcePattern() - Method in class org.ginsim.core.graph.dynamicgraph.DefaultDynamicEdgeStyle

enforcePattern() - Method in interface org.ginsim.core.graph.view.style.EdgeStyle

enforcePattern() - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

enforcePattern() - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

enforceShape() - Method in interface org.ginsim.core.graph.view.style.NodeStyle

enforceShape() - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

enforceShape() - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

enforceSize() - Method in interface org.ginsim.core.graph.view.style.NodeStyle

enforceSize() - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

enforceSize() - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

enforceWidth() - Method in interface org.ginsim.core.graph.view.style.EdgeStyle

enforceWidth() - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

enforceWidth() - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

EnhancedJTable - Class in org.ginsim.gui.utils.widgets

A "better" JTable with some often needed customizations.

EnhancedJTable() - Constructor for class org.ginsim.gui.utils.widgets.EnhancedJTable

EnhancedJTable(TableModel) - Constructor for class org.ginsim.gui.utils.widgets.EnhancedJTable

EnhancedListCellRenderer - Class in org.ginsim.gui.utils.widgets

modified listCellRenderer: highlight some rows.

EnhancedListCellRenderer() - Constructor for class org.ginsim.gui.utils.widgets.EnhancedListCellRenderer

Empty constructor if you add GsColorable Objects to your list

ensureEdgeViewInfo(E) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

ensureEdgeViewInfo(E) - Method in interface org.ginsim.core.graph.GraphBackend

Get raw view information for an edge, create it if needed.

ensureParagraph() - Method in class org.ginsim.common.document.DocumentWriter

Open a new paragraph if we are in a paragraph.

ensureStoreEdge(Edge) - Method in class org.ginsim.core.graph.view.GraphicalAttributesStore

Deprecated.

ensureStoreNode(Object) - Method in class org.ginsim.core.graph.view.GraphicalAttributesStore

Deprecated.

EnumAlgorithm - Enum in org.ginsim.service.tool.avatar.service

ENUMBER - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

ENUMBER - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

EnumProperty - Class in org.ginsim.core.graph.view.style

EnumProperty(String, Enum[]) - Constructor for class org.ginsim.core.graph.view.style.EnumProperty

EnumProperty(String, Enum[], boolean) - Constructor for class org.ginsim.core.graph.view.style.EnumProperty

EOF - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

EOF - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

EPSILON - Variable in class org.ginsim.core.graph.dynamicgraph.DynamicNode

equals(Object) - Method in class org.ginsim.common.utils.FileFormatDescription

equals(Object) - Method in class org.ginsim.core.annotation.AnnotationLink

equals(Object) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicNode

equals(Object) - Method in class org.ginsim.core.graph.reducedgraph.NodeReducedData

equals(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

equals(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionListElement

equals(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

equals(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

equals(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafValue

equals(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

equals(Object) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

Compare the object to the given one, using the internal NodeInfo.

equals(Object) - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceNode

equals(Object) - Method in class org.ginsim.core.graph.tree.TreeNode

equals(Object) - Method in class org.ginsim.core.graph.view.style.BaseStyle

equals(Color, Color) - Static method in class org.ginsim.core.graph.view.style.NodeStyleImpl

equals(Object) - Method in class org.ginsim.core.utils.data.HashSetForSet

equals(Object) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

ereader - Variable in class org.ginsim.core.graph.view.GraphicalAttributesStore

Deprecated.

eReader - Variable in class org.ginsim.core.io.parser.GINMLWriter

error(Object) - Static method in class org.ginsim.common.application.LogManager

Log an error.

error(SAXParseException) - Method in class org.ginsim.common.xml.XMLHelper

errorDisplay(String, Exception) - Static method in class org.ginsim.servicegui.tool.avatar.AvatarResults

Displays a message of error whenever a simulation is not successfully executed

ErrorNotification - Class in org.ginsim.core.notification

ErrorNotification(Object, String) - Constructor for class org.ginsim.core.notification.ErrorNotification

escape(Object) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

escape() - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

EStatus - Enum in org.ginsim.core.service

Possible status for services.

eval() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanParser

eval() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

evaluate(int, byte[][]) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionEvaluation

ExceptionNotification - Class in org.ginsim.core.notification

ExceptionNotification(Object, String, Exception) - Constructor for class org.ginsim.core.notification.ExceptionNotification

ExhaustiveFinalPaths - Class in org.ginsim.service.tool.avatar.domain

Exhaustive representation of the probabilities of the transitions within and going out of a cycle

ExhaustiveFinalPaths() - Constructor for class org.ginsim.service.tool.avatar.domain.ExhaustiveFinalPaths

Creates an empty cycle

exhaustiveUpdater - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

exit() - Method in class org.ginsim.gui.GUIManager

exit - Variable in class org.ginsim.service.tool.avatar.simulation.Simulation

exit() - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

exitProbs - Variable in class org.ginsim.service.tool.avatar.domain.ExhaustiveFinalPaths

export(RegulatoryGraph, String) - Method in class org.ginsim.core.service.FormatSupportService

export(LogicalModel, String) - Method in class org.ginsim.core.service.FormatSupportService

export(LogicalModel, StreamProvider) - Method in class org.ginsim.core.service.FormatSupportService

export(CADPExportConfig, String) - Method in class org.ginsim.service.export.cadp.CADPExportService

Exports the necessary files for CADP

export(RegulatoryGraph, String) - Method in class org.ginsim.service.export.documentation.LRGDocumentationService

export(GenericDocumentFormat, String) - Method in class org.ginsim.service.export.documentation.LRGDocumentationWriter

export(NuSMVConfig, File) - Method in class org.ginsim.service.export.nusmv.NuSMVExportService

export(PRISMConfig, File) - Method in class org.ginsim.service.export.prism.PRISMExportService

export(RegulatoryGraph, String) - Method in class org.ginsim.service.export.reggraph.RegGraphExportService

export(SATConfig, File) - Method in class org.ginsim.service.export.sat.SATExportService

export(RegulatoryGraph, String) - Method in class org.ginsim.service.format.sbml.SBMLqualService

Convenience method to export without having to configure anything.

export(SBMLQualConfig, String) - Method in class org.ginsim.service.format.sbml.SBMLqualService

Perform the SBML export, using the JSBML-based encoder from LogicalModel.

export() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPConfig

do the export.

export_tip - Variable in class org.ginsim.gui.service.FormatSupportServiceGUI

ExportAction<G extends Graph> - Class in org.ginsim.gui.shell.actions

ExportAction(G, String, String, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.ExportAction

exportAnnotation(SBase, Annotation) - Method in class org.ginsim.service.format.sbml.SBMLqualService

exportPNG(Graph<?, Edge<?>>, String) - Method in class org.ginsim.service.export.image.ImageExportService

Export a model view as PNG image.

exportPNG(Graph<?, Edge<?>>, String, int) - Method in class org.ginsim.service.export.image.ImageExportService

Export a model view as PNG image.

exportSVG(Graph, String) - Method in class org.ginsim.service.export.image.ImageExportService

Export the graph to a SVG file

exportSVG(Graph, StyleProvider, String) - Method in class org.ginsim.service.export.image.ImageExportService

Export the graph to a SVG file

exportSVG(Graph, Collection, Collection<Edge>, String) - Method in class org.ginsim.service.export.image.ImageExportService

Export the graph to a SVG file

expression() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

extend(Rectangle) - Method in class org.ginsim.gui.graph.canvas.SimpleDimension

extendCycle(State, StateSet, StateSet, StateSet, int, int, Map<String, Integer>, int) - Method in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

Method for extending cycles before rewiring

extendCycle(State, MDDStateSet, MDDStateSet, int, int, Map<String, Integer>, int) - Method in class org.ginsim.service.tool.avatar.simulation.others.AvatarMDDSimulation

Method for extending cycles before rewiring

extendSelectionToIncomingEdges() - Method in class org.ginsim.gui.graph.GraphSelection

Add all the incoming edges of the selected nodes to the list of selected edges

extendSelectionToIncomingNodes() - Method in class org.ginsim.gui.graph.GraphSelection

Add all the incoming nodes of the selected nodes to the list of selected nodes

extendSelectionToInternalEdges() - Method in class org.ginsim.gui.graph.GraphSelection

Add all the edges between the selected nodes to the list of selected edges

extendSelectionToOutgoingEdges() - Method in class org.ginsim.gui.graph.GraphSelection

Add all the outgoing edges of the selected nodes to the list of selected edges

extendSelectionToOutgoingNodes() - Method in class org.ginsim.gui.graph.GraphSelection

Add all the outgoing nodes of the selected nodes to the list of selected nodes

extension - Variable in class org.ginsim.common.utils.FileFormatDescription

F

factory - Variable in class org.ginsim.common.document.GenericDocumentFormat

The documentWriter to instanciate to write a document of this type (eg.

FACTORY - Static variable in class org.ginsim.common.document.LaTeXDocumentWriter

FACTORY - Static variable in class org.ginsim.common.document.OOoDocumentWriter

FACTORY - Static variable in class org.ginsim.common.document.XHTMLDocumentWriter

fallback - Variable in class org.ginsim.core.graph.view.style.IntegerProperty

FALSE - Static variable in class org.ginsim.service.tool.circuit.CircuitDescr

ffAlpha - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

ffBeta - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

ffDepth - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

ffMaxExpand - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

FileCallBack - Class in org.ginsim.gui.shell.callbacks

Callbacks for the "File" menu

FileCallBack() - Constructor for class org.ginsim.gui.shell.callbacks.FileCallBack

FileFormatDescription - Class in org.ginsim.common.utils

Simple description of a file format.

FileFormatDescription(String, String) - Constructor for class org.ginsim.common.utils.FileFormatDescription

FileFormatFilter - Class in org.ginsim.commongui.utils

FileFilter using a (List of) FileFormatDescription.

FileFormatFilter(FileFormatDescription) - Constructor for class org.ginsim.commongui.utils.FileFormatFilter

FileFormatFilter(List<FileFormatDescription>) - Constructor for class org.ginsim.commongui.utils.FileFormatFilter

filename - Variable in class org.ginsim.service.tool.avatar.domain.Result

Fine name

FileSelectionHelper - Class in org.ginsim.gui.shell

FileSelectionHelper() - Constructor for class org.ginsim.gui.shell.FileSelectionHelper

fillExtraValues(byte[], byte[]) - Method in interface org.ginsim.core.graph.dynamicgraph.TransitionGraph

Retrieve the values for all extra components for a given state.

fillExtraValues(byte[], byte[]) - Method in class org.ginsim.core.graph.dynamicgraph.TransitionGraphImpl

fillMenu(JMenu, Graph) - Static method in class org.ginsim.gui.shell.callbacks.SelectionCallBack

FILTER_NO_SYNCHRONOUS - Static variable in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

FinalPaths - Interface in org.ginsim.service.tool.avatar.domain

Interface for the storage transitions within and going-out of a state-set
Transitions can be represented in multiple ways (e.g.

findPatterns() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTree

findUniqueName(String) - Method in class org.ginsim.core.utils.data.NamedList

Pick a name (for a new object)

fireAdded(T, int) - Method in class org.ginsim.core.utils.data.ListenableNamedList

fireAdmissibleIntegrationFunctionsChange() - Method in class org.ginsim.servicegui.tool.composition.IntegrationFunctionWidget

fireAdmissibleIntegrationFunctionsChange(RegulatoryNode) - Method in class org.ginsim.servicegui.tool.composition.IntegrationFunctionWidget

fireChanged() - Method in class org.ginsim.core.utils.data.ListenableNamedList

FirefrontMDDSimulation - Class in org.ginsim.service.tool.avatar.simulation.others

Firefront simulation for the quasi-exact analysis of point attractors

FirefrontMDDSimulation() - Constructor for class org.ginsim.service.tool.avatar.simulation.others.FirefrontMDDSimulation

Instantiates a Firefront simulation based on a logical model

FirefrontPanel - Class in org.ginsim.servicegui.tool.avatar.algopanels

Class for managing the panel for Firefront simulations

FirefrontPanel() - Constructor for class org.ginsim.servicegui.tool.avatar.algopanels.FirefrontPanel

Instantiates the context of a simulation panel

FirefrontServiceFacade - Class in org.ginsim.service.tool.avatar.service

Facade of a Firefront simulation.
Instantiates a Firefront simulation from arguments within a command line, provides soundness checks, and outputs statistics and help tips.

FirefrontServiceFacade() - Constructor for class org.ginsim.service.tool.avatar.service.FirefrontServiceFacade

FirefrontSimulation - Class in org.ginsim.service.tool.avatar.simulation

Firefront simulation for the quasi-exact analysis of point attractors

FirefrontSimulation() - Constructor for class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

Instantiates a Firefront simulation

fireGraphChange(GraphChangeType, Object) - Method in class org.ginsim.core.graph.AbstractGraph

fireGraphChange(GraphChangeType, Object) - Method in interface org.ginsim.core.graph.Graph

The graph has changed, all listeners will be notified.

fireGraphChange(G, GraphChangeType, Object) - Method in class org.ginsim.core.graph.GSGraphManager

fireGraphClose() - Method in class org.ginsim.gui.graph.BaseGraphGUI

fireGraphClose() - Method in interface org.ginsim.gui.graph.GraphGUI

Warn the listeners that the graph will be closed

fireInitialStatesUpdate() - Method in class org.ginsim.servicegui.export.cadp.InitialStatesWidget

fireIntegrationFunctionsChanged() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

fireIntegrationMappingChange() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

fireIntegrationMappingChange() - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

fireIntegrationMappingChange() - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

fireMetaChange() - Method in class org.ginsim.core.graph.AbstractGraph

fireRemoved(T, int) - Method in class org.ginsim.core.utils.data.ListenableNamedList

fireSelectionChange() - Method in class org.ginsim.gui.graph.BaseGraphGUI

fireTreeNodesChanged(Object, Object[], int[], Object[]) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

fireTreeNodesInserted(Object, Object[], int[], Object[]) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

fireTreeNodesRemoved(Object, Object[], int[], Object[]) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

fireTreeStructureChanged(TreeElement) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

fireTreeStructureChanged(Object, Object[], int[], Object[]) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

fireUserUpdate(Graph<?, ?>, String, String, String) - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

Signal that a data user has been updated (removed or renamed)

fireUserUpdate(Graph<?, ?>, String, String) - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

Signal that a data user has been updated (removed or renamed)

fireViewUpdated() - Method in class org.ginsim.gui.graph.canvas.VirtualScrollPane

first - Variable in class org.ginsim.service.tool.graphcomparator.ComparedItemInfo

firstStatesToString() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Return a string representation of the first state in the node.

firstStatesToString() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Return a String representation of a state in the set (the first in the pile or the first reach in the omdd)

fixedSize - Variable in class org.ginsim.gui.utils.data.ColumnDefinition

FixedSizePanel - Class in org.ginsim.servicegui.tool.avatar.others

Panel with fixed size

FixedSizePanel(int, int) - Constructor for class org.ginsim.servicegui.tool.avatar.others.FixedSizePanel

Creates a panel with the inputted width and height

flush() - Method in class org.ginsim.core.graph.view.css.Selector

By default this does nothing but subclasses of Selector could use this function to free the cache of category<=>object.

flushCache() - Method in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

focusGained(FocusEvent) - Method in class org.ginsim.gui.utils.widgets.StatusTextField

focusLost(FocusEvent) - Method in class org.ginsim.gui.utils.widgets.StatusTextField

FOLLOW_10_in_atom134 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_10_in_atom165 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_10_in_atom201 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_10_in_atom232 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_11_in_atom152 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_11_in_atom189 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_11_in_atom225 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_11_in_atom238 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_12_in_atom140 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_12_in_atom146 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_12_in_atom171 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_12_in_atom177 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_12_in_atom183 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_12_in_atom207 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_12_in_atom213 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_12_in_atom219 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_AND_in_conjunction102 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_atom_in_atom249 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_atom_in_conjunction106 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_atom_in_conjunction99 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_conjunction_in_disjunction66 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_conjunction_in_disjunction73 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_disjunction_in_expression46 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ENUMBER_in_atom138 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ENUMBER_in_atom144 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ENUMBER_in_atom150 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ENUMBER_in_atom169 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ENUMBER_in_atom175 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ENUMBER_in_atom181 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ENUMBER_in_atom187 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ENUMBER_in_atom205 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ENUMBER_in_atom211 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ENUMBER_in_atom217 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_expression_in_atom236 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_expression_in_eval25 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ID_in_atom132 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ID_in_atom163 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_ID_in_atom199 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_NOT_in_atom245 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_OR_in_disjunction69 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FOLLOW_RANGE_in_atom223 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

FONT_SIZE - Static variable in class org.ginsim.common.document.DocumentStyle

foreground - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

foreground - Variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

FOREGROUND - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

formalIntegrationFunction() - Method in class org.ginsim.service.export.cadp.CADPIntegrationWriter.IntegrationProcessWriter

formalIntegrationFunctionName(RegulatoryNode, int, IntegrationFunction) - Method in class org.ginsim.service.export.cadp.CADPWriter

formalIntegrationProcess() - Method in class org.ginsim.service.export.cadp.CADPIntegrationWriter.IntegrationProcessWriter

formalIntegrationProcessName(RegulatoryNode, int, IntegrationFunction) - Method in class org.ginsim.service.export.cadp.CADPWriter

formalProcessName(String) - Method in class org.ginsim.service.export.cadp.CADPWriter

format - Variable in class org.ginsim.core.service.FormatSupportService

FORMAT - Static variable in class org.ginsim.servicegui.format.sbml.SBMLqualServiceGUI

FormatSupportService<F extends org.colomoto.biolqm.io.LogicalModelFormat> - Class in org.ginsim.core.service

Generic service to support format implemented in LogicalModel.

FormatSupportService(F) - Constructor for class org.ginsim.core.service.FormatSupportService

FormatSupportServiceGUI<S extends FormatSupportService> - Class in org.ginsim.gui.service

Generic GUI integration service for formats providers.

FormatSupportServiceGUI(String, S, FileFormatDescription) - Constructor for class org.ginsim.gui.service.FormatSupportServiceGUI

frame - Variable in class org.ginsim.gui.shell.editpanel.AbstractParameterPanel

Frame - Class in org.ginsim.gui.utils.widgets

Frame(String, int, int) - Constructor for class org.ginsim.gui.utils.widgets.Frame

frame - Variable in class org.ginsim.service.tool.reg2dyn.Simulation

FrameActionManager - Interface in org.ginsim.gui.shell

Manager for the list of actions available in a GUI.

fromString(String[]) - Static method in class org.ginsim.core.graph.view.css.CSSEdgeStyle

Create a new style from an array of strings

fromString(String[]) - Static method in class org.ginsim.core.graph.view.css.CSSNodeStyle

Create a new style from an array of strings

FTableInteractionModel - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction

FTableInteractionModel(RegulatoryNode) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.FTableInteractionModel

FUNC_DUAL - Static variable in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisAlgo

FUNC_NEGATIVE - Static variable in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisAlgo

FUNC_NON - Static variable in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisAlgo

FUNC_POSITIVE - Static variable in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisAlgo

FUNCTION_FLAVOR - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

FUNCTIONAL - Static variable in class org.ginsim.service.tool.circuit.CircuitDescr

FunctionalityCleanupOperator - Class in org.ginsim.service.tool.circuit

Cleanup functionality contexts to remove constraint on the circuit members

FunctionalityContext - Class in org.ginsim.service.tool.circuit

FunctionalityContext(CircuitDescr, int) - Constructor for class org.ginsim.service.tool.circuit.FunctionalityContext

FunctionalityMergeOperator - Class in org.ginsim.service.tool.circuit

Merge functionality contexts.

FunctionEditorModel - Interface in org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree

FunctionPanel - Interface in org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree

FunctionPanelImpl - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

FunctionPanelImpl(LogicalFunctionPanel, TreeElement, JTree, boolean, int, boolean) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

FunctionsCreator - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function

FunctionsCreator(RegulatoryGraph, Collection<LogicalParameter>, RegulatoryNode) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.FunctionsCreator

FunctionWriter(List<RegulatoryNode>, CADPWriter.StateVarWriter) - Constructor for class org.ginsim.service.export.cadp.CADPModuleWriter.FunctionWriter

G

GateWriter(List<RegulatoryNode>) - Constructor for class org.ginsim.service.export.cadp.CADPWriter.GateWriter

GenericDocumentFormat - Class in org.ginsim.common.document

This class contain metadata about each kind of document like id, extension, filter and its class.

GenericDocumentFormat(DocumentWriterFactory, String, String) - Constructor for class org.ginsim.common.document.GenericDocumentFormat

Define a new generic document format.

GenericGraphAction - Class in org.ginsim.gui.shell.actions

GenericGraphAction(Graph<?, ?>, String, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.GenericGraphAction

GenericGraphAction(Graph<?, ?>, String, String, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.GenericGraphAction

GenericGraphAction(Graph<?, ?>, String, ImageIcon, String, KeyStroke, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.GenericGraphAction

GenericListListener - Interface in org.ginsim.core.utils.data

GenericPropertyEditorPanel - Class in org.ginsim.gui.utils.data

A panel to edit the properties of an object.

GenericPropertyEditorPanel(ObjectEditor) - Constructor for class org.ginsim.gui.utils.data.GenericPropertyEditorPanel

GenericPropertyHolder - Interface in org.ginsim.gui.utils.data

GenericPropertyInfo - Class in org.ginsim.gui.utils.data

All we need to know about a property

GenericPropertyInfo(ObjectEditor, int, String, Class) - Constructor for class org.ginsim.gui.utils.data.GenericPropertyInfo

GenericSimulationUpdater - Class in org.ginsim.service.tool.reg2dyn.updater

Wrap LogicalModel's updater API into GINsim.

GenericSimulationUpdater(MultipleSuccessorsUpdater) - Constructor for class org.ginsim.service.tool.reg2dyn.updater.GenericSimulationUpdater

GenericTopology - Class in org.ginsim.service.tool.composition

Represents the topological relationships between Logical Regulatory Modules being composed.

GenericTopology(int) - Constructor for class org.ginsim.service.tool.composition.GenericTopology

The topology

get(String) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

Deprecated.

get(Class<S>) - Static method in class org.ginsim.core.service.GSServiceManager

Get a service directly, i.e.

get(String) - Static method in class org.ginsim.core.service.GSServiceManager

Get a service directly, i.e.

get(int) - Method in class org.ginsim.core.utils.data.ValueList

get(LogicalModel, ProgressListener<Graph>, SimulationParameters) - Method in class org.ginsim.service.tool.reg2dyn.Reg2DynService

get_size() - Method in class org.ginsim.service.tool.stableregions.PNGraph

getActionLabels() - Method in class org.ginsim.gui.utils.data.ListPanelHelper

getActionNew() - Static method in class org.ginsim.gui.shell.callbacks.FileCallBack

getActionOpen() - Static method in class org.ginsim.gui.shell.callbacks.FileCallBack

getActions() - Static method in class org.ginsim.gui.shell.callbacks.HelpCallBack

getActionsRecent() - Static method in class org.ginsim.gui.shell.callbacks.FileCallBack

getActivesEdges(int) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

get the active(s) Edge(s) of the interaction at the row row.

getAdjacencyList(boolean[][]) - Static method in class org.ginsim.johnsonCycles.AdjacencyList

Calculates a adjacency-list for a given array of an adjacency-matrix.

getAdjacencyList(int) - Method in class org.ginsim.johnsonCycles.StrongConnectedComponents

This method returns the adjacency-structure of the strong connected component with the least vertex in a subgraph of the original graph induced by the nodes {s, s + 1, ..., n}, where s is a given node.

getAdjList() - Method in class org.ginsim.johnsonCycles.SCCResult

getAliases() - Method in class org.ginsim.core.graph.objectassociation.BasicGraphAssociatedManager

getAliases() - Method in interface org.ginsim.core.graph.objectassociation.GraphAssociatedObjectManager

Get the aliases under which the object used to be saved (zip name in old files)

getAllComponents() - Method in class org.ginsim.service.export.cadp.CADPWriter

getAllData() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanParser

getAllEdges(V, V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getAllFormats() - Static method in class org.ginsim.common.document.GenericDocumentFormat

getAllGraphs() - Method in class org.ginsim.core.graph.GSGraphManager

Return the list of registered graphs

getAllIStateList() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

getAllParams() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

getAllStateList() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

getAnchor() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

getAnchor() - Method in class org.ginsim.core.graph.backend.EdgeViewInfoImpl

getAnchor() - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

getAnchor() - Method in interface org.ginsim.core.graph.view.EdgeViewInfo

getAnchor() - Method in class org.ginsim.gui.graph.view.style.AnchorSelector

getAnnotation() - Method in class org.ginsim.core.graph.AbstractGraph

Give access to the annotation associated with this graph.

getAnnotation() - Method in interface org.ginsim.core.graph.GraphModel

Give access to the annotation associated with this graph.

getAnnotation() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

getAnnotation() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

get notes on this gene.

getArgs() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBinaryOperator

getArgs() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperator

getArgs() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TUnaryOperator

getArgs() - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

getArgs() - Method in class org.ginsim.gui.utils.data.ObjectEditor

getAssociatedGraph() - Method in class org.ginsim.core.graph.AbstractDerivedGraph

getAssociatedGraph() - Method in interface org.ginsim.core.graph.GraphAssociation

Given access to the graph that has been associated to the current graph

getAssociatedGraphID() - Method in class org.ginsim.core.graph.AbstractDerivedGraph

getAssociatedGraphID() - Method in interface org.ginsim.core.graph.GraphAssociation

getAsStringList() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionList

getAsynchronousInstance(LogicalModel) - Static method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

getAttributes() - Method in class org.ginsim.core.graph.AbstractGraph

getAttributes() - Method in interface org.ginsim.core.graph.Graph

Retrieve graph-level attributes

getAttributes() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getAttributeValueWithDefault(Attributes, String, String) - Static method in class org.ginsim.common.xml.XMLHelper

getAutoscrollInsets() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.GsJTree

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.gui.service.FormatSupportServiceGUI

getAvailableActions(Graph<?, ?>) - Static method in class org.ginsim.gui.service.GSServiceGUIManager

Give access to the list of GUI actions provided by the available services for the given graph type

getAvailableActions(Graph<?, ?>) - Method in interface org.ginsim.gui.service.ServiceGUI

Give access to the list of the actions that the service provides for the given graph.

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.gui.service.SimpleServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.export.cadp.CADPExportServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.export.documentation.LRGDocumentationServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.export.image.ImageExportServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.export.maboss.MaBoSSExportServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.export.nusmv.NuSMVExportServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.export.petrinet.PetriNetExportServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.export.prism.PRISMExportServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.export.reggraph.RegGraphExportServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.export.sat.SATExportServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.export.struct.GraphStructureExportServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.format.ginml.GINMLFormatServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.layout.LayoutServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.avatar.AvatarServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.circuit.CircuitServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.composition.CompositionServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewerServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.decisionanalysis.DecisionAnalysisServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.interactionanalysis.InteractionAnalysisServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.modelbooleanizer.ModelBooleanizerServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.modelreversion.ModelReversionServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.omddViz.OmddVizServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.pathfinding.PathFindingServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.polytopesViz.PolytopesVizServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.reg2dyn.limitedSimulation.LimitedSimulationServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.reg2dyn.Reg2DynServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryGraphAnimationServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.regulatorytreefunction.RegulatoryFunctionTreeServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.scc.ConnectivityServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.stableregions.StableRegionsServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.stablestates.StableStatesServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.stateinregulatorygraph.StateInRegulatoryGraphServiceGUI

getAvailableActions(Graph<?, ?>) - Method in class org.ginsim.servicegui.tool.trapspace.TrapSpaceServiceGUI

getAvailableServices() - Static method in class org.ginsim.core.service.GSServiceManager

Give access to the list of available GsServices

getBackground(DynamicNode) - Method in class org.ginsim.core.graph.dynamicgraph.DefaultDynamicNodeStyle

getBackground(HierarchicalNode) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.DefaultHTGNodeStyle

getBackground(TreeNode) - Method in class org.ginsim.core.graph.tree.DefaultTreeNodeStyle

getBackground(V) - Method in interface org.ginsim.core.graph.view.style.NodeStyle

getBackground(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getBackground(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

getBackgroundColor() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getBackgroundColor() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

getBaseline(JComponent, int, int) - Method in class org.ginsim.commongui.utils.VerticalLabelUI

Overridden to always return -1, since a vertical label does not have a meaningful baseline.

getBaselineResizeBehavior(JComponent) - Method in class org.ginsim.commongui.utils.VerticalLabelUI

Overridden to always return Component.BaselineResizeBehavior.OTHER, since a vertical label does not have a meaningful baseline

getBCGIntegrationFilename(RegulatoryNode, int) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getBCGIntegrationFileName(RegulatoryNode, int) - Method in class org.ginsim.service.export.cadp.CADPWriter

getBCGModelFilename(int) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getBCGModelFileName(int) - Method in class org.ginsim.service.export.cadp.CADPWriter

getBoolValue(String, String[]) - Static method in class org.ginsim.service.tool.avatar.utils.AvaOptions

Checks whether a given parameter is present

getBorder() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getBorder() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

getBounds() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

getBounds() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getBounds() - Method in interface org.ginsim.core.graph.view.AttributesReader

get the boundary rectangle for the selected item.

getBounds() - Method in interface org.ginsim.gui.graph.canvas.CanvasRenderer

Get the (virtual) size of the area needed to paint all objects in this renderer.

getBounds() - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

getBuffer() - Method in class org.ginsim.common.xml.XMLWriter

If toBuffer has previously been called, stop saving to buffer.

getByName(String) - Method in class org.ginsim.core.utils.data.NamedList

getCachedEdgeAttributeReader() - Method in class org.ginsim.core.graph.AbstractGraph

getCachedNodeAttributeReader() - Method in class org.ginsim.core.graph.AbstractGraph

getCaretPosition() - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanel

getCaretPosition() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

getCategory(Object) - Method in class org.ginsim.core.graph.view.css.Selector

Return the category corresponding to the object obj or null if it doesn't respond to any.

getCategoryForEdge(Object) - Method in class org.ginsim.core.graph.view.css.AllSelector

getCategoryForEdge(Object) - Method in class org.ginsim.core.graph.view.css.Selector

Return the category corresponding to the object obj or null if it doesn't respond to any.

getCategoryForEdge(Object) - Method in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

getCategoryForNode(Object) - Method in class org.ginsim.core.graph.view.css.AllSelector

getCategoryForNode(Object) - Method in class org.ginsim.core.graph.view.css.Selector

Return the category corresponding to the object obj or null if it doesn't respond to any.

getCategoryForNode(Object) - Method in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

getCellEditorValue() - Method in class org.ginsim.gui.utils.widgets.treetable.JTreeTable.TreeTableCellEditor

getChange(byte[]) - Method in class org.ginsim.service.layout.BaseSTGLayout

Find the first change between two states.

getChild(HierarchicalNode) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSet

getChild(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

getChild(Object, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

getChildCount() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

getChildCount(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

getChildCount(int) - Method in class org.ginsim.service.tool.circuit.CircuitDescr

getChildInterface(Class, Class) - Static method in class org.ginsim.common.utils.IntrospectionUtils

Return the deeper interface that inherits from the base interface

getChildrenWithSingleNode(int, int) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Creates a state where only a single component is initialized (others as -1)

getChilds() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

getChildsCount() - Method in interface org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraph

getChildsCount() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

return an array indicating for each node in the nodeOrder their count of childs.

getChildsCount() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Return An array indicating such that childsCount[i] indicates the maxValue of the i-th gene

getCircuit() - Method in class org.ginsim.service.tool.circuit.CircuitDescrInTree

getCircuitAnalyser(RegulatoryGraph) - Method in class org.ginsim.service.tool.circuit.CircuitService

getCircuitAnalyser(RegulatoryGraph, boolean) - Method in class org.ginsim.service.tool.circuit.CircuitService

getCircuitAnalyser(RegulatoryGraph, Perturbation, boolean) - Method in class org.ginsim.service.tool.circuit.CircuitService

getCircuits(List<NodeReducedData>) - Method in class org.ginsim.service.tool.circuit.CircuitSearcher

getCircuitSearcher(RegulatoryGraph, CircuitSearchStoreConfig) - Method in class org.ginsim.service.tool.circuit.CircuitService

getColor(DynamicEdge) - Method in class org.ginsim.core.graph.dynamicgraph.DefaultDynamicEdgeStyle

getColor(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryEdgeStyle

getColor(TreeEdge) - Method in class org.ginsim.core.graph.tree.DefaultTreeEdgeStyle

getColor(E) - Method in interface org.ginsim.core.graph.view.style.EdgeStyle

getColor(E) - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

getColor(E) - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

getColor() - Method in interface org.ginsim.gui.utils.widgets.ColorableItem

getColorCode(Color) - Static method in class org.ginsim.common.utils.ColorPalette

Convert a 8-bit Color into a CSS-like string (without the #).
Exemple : Color(255,127,0) -> "FF7F00"

getColorFromCode(String) - Static method in class org.ginsim.common.utils.ColorPalette

get a Color corresponding to a given color code.

getColorizer() - Method in class org.ginsim.service.tool.polytopesViz.PolytopesService

getColumnClass(int) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

getColumnClass(int) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

getColumnClass(int) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

getColumnClass(int) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

getColumnClass(int) - Method in interface org.ginsim.gui.utils.widgets.treetable.TreeTableModel

Returns the type for column number column.

getColumnClass(int) - Method in class org.ginsim.gui.utils.widgets.treetable.TreeTableModelAdapter

getColumnClass(int) - Method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

getColumnClass(int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPModel

getColumnCount() - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

getColumnCount() - Method in class org.ginsim.gui.graph.dynamicgraph.StableTableModel

getColumnCount() - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTableModel

getColumnCount() - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphTableModel

getColumnCount() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

getColumnCount() - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

getColumnCount() - Method in class org.ginsim.gui.utils.data.SimpleStateListTableModel

getColumnCount() - Method in interface org.ginsim.gui.utils.widgets.treetable.TreeTableModel

Returns the number of available column.

getColumnCount() - Method in class org.ginsim.gui.utils.widgets.treetable.TreeTableModelAdapter

getColumnCount() - Method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

getColumnCount() - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserPathModel

getColumnCount() - Method in class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

getColumnCount() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPModel

getColumnCount() - Method in class org.ginsim.servicegui.tool.trapspace.TrapSpaceTableModel

getColumnName(int) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

getColumnName(int) - Method in class org.ginsim.gui.graph.dynamicgraph.StableTableModel

getColumnName(int) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTableModel

getColumnName(int) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphTableModel

getColumnName(int) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

getColumnName(int) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

getColumnName(int) - Method in class org.ginsim.gui.utils.data.SimpleStateListTableModel

getColumnName(int) - Method in interface org.ginsim.gui.utils.widgets.treetable.TreeTableModel

Returns the name for column number column.

getColumnName(int) - Method in class org.ginsim.gui.utils.widgets.treetable.TreeTableModelAdapter

getColumnName(int) - Method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

getColumnName(int) - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserPathModel

getColumnName(int) - Method in class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

getColumnName(int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPModel

getColumnName(int) - Method in class org.ginsim.servicegui.tool.trapspace.TrapSpaceTableModel

getColumns() - Method in class org.ginsim.gui.utils.data.ListPanelHelper

getColumns() - Method in class org.ginsim.servicegui.tool.avatar.parameters.AvatarParametersHelper

getColumns() - Method in class org.ginsim.servicegui.tool.reg2dyn.ListOfSimulationParametersHelper

getColumns() - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionHelper

getColumns() - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

getColumnSortOrder(JTable, int) - Static method in class org.ginsim.commongui.utils.DefaultTableHeaderCellRenderer

getComment() - Method in class org.ginsim.core.annotation.Annotation

return the String containing the comments.

getCommonModuleName() - Static method in class org.ginsim.service.export.cadp.CADPWriter

getCompactStates() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

getCompactString() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

getCompanion(ListEditionPanel<Perturbation, ListOfPerturbations>) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationPanelListHelper

getCompanion(ListEditionPanel<T, L>) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

getCompanion(ListEditionPanel<AvatarParameters, AvatarParameterList>) - Method in class org.ginsim.servicegui.tool.avatar.parameters.AvatarParametersHelper

getCompanion(ListEditionPanel<SimulationParameters, SimulationParameterList>) - Method in class org.ginsim.servicegui.tool.reg2dyn.ListOfSimulationParametersHelper

getCompanion(ListEditionPanel<PriorityClass, PrioritySetDefinition>) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionHelper

getCompanion(ListEditionPanel<UpdaterDefinition, PrioritySetList>) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

getCompatibleReducedStableStates() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getCompatibleStableStates() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getCompatibleStableStates() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

getComponent() - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

getComponent() - Method in interface org.ginsim.gui.graph.canvas.VirtualScrollable

Get the component for this view.

getComponent() - Method in class org.ginsim.gui.graph.dynamicgraph.StateTransitionGraphEditor

getComponent() - Method in interface org.ginsim.gui.graph.GUIEditor

getComponent() - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalGraphEditor

getComponent() - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryEdgeEditor

getComponent() - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

getComponent() - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeMainPanel

getComponent() - Method in class org.ginsim.gui.graph.tree.TreeActionPanel

getComponent() - Method in class org.ginsim.gui.graph.view.style.StyleTab

getComponent() - Method in class org.ginsim.gui.shell.editpanel.AbstractParameterPanel

getComponent() - Method in interface org.ginsim.gui.shell.editpanel.EditTab

getComponent() - Method in class org.ginsim.gui.shell.editpanel.MainEditTab

getComponent() - Method in class org.ginsim.gui.utils.data.ObjectEditor

getComponentCount() - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

getComponentCount() - Method in interface org.ginsim.gui.graph.dynamicgraph.StateTableModel

getComponentName(int) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

getComponentName(int) - Method in interface org.ginsim.gui.graph.dynamicgraph.StateTableModel

getComponentName() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationAtom

getComponents(Graph) - Method in class org.ginsim.service.tool.scc.SCCGraphService

getConfidenceInterval(int, double) - Static method in class org.ginsim.service.tool.avatar.utils.ConfidenceInterval

Computes the confidence interval "lowerboud,upperbound"

getConfig(LogicalModel) - Method in class org.ginsim.service.export.nusmv.NuSMVExportService

getConfig() - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

getConfigPanel(ExportAction, RegulatoryGraph) - Method in class org.ginsim.gui.service.FormatSupportServiceGUI

getConfigPanel() - Method in class org.ginsim.gui.shell.actions.ExportAction

getConfigPanel(ExportAction, RegulatoryGraph) - Method in class org.ginsim.servicegui.format.sbml.SBMLqualServiceGUI

getConfigPanel() - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

getConstraintValue(NodeInfo) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

getConstrastedForegroundColor(Color) - Static method in class org.ginsim.common.utils.ColorPalette

Return black or white to contrast with the given background

getContent() - Method in class org.ginsim.core.graph.reducedgraph.NodeReducedData

getContentString() - Method in class org.ginsim.core.graph.reducedgraph.NodeReducedData

getContext() - Method in interface org.ginsim.core.graph.regulatorygraph.MDDContext

getContext() - Method in class org.ginsim.service.tool.circuit.CircuitDescr

getContext(int, MDDVariable) - Method in class org.ginsim.service.tool.circuit.ContextExtractor

getContext(int, MDDVariable, int, int) - Method in class org.ginsim.service.tool.circuit.ContextExtractor

getContext() - Method in class org.ginsim.service.tool.circuit.FunctionalityContext

getConvergence(double[][], List<String>, int, String, String, String) - Static method in class org.ginsim.service.tool.avatar.utils.ChartGNUPlot

Creates a chart based on the convergence of probabilities per attractor

getCreateTypes() - Method in class org.ginsim.gui.utils.data.ListPanelHelper

getCreateTypes() - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

getCSS() - Method in class org.ginsim.core.graph.dynamicgraph.DefaultDynamicEdgeStyle

getCSS() - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryEdgeStyle

getCSS() - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

getCSS() - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

getCSS() - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getCSS() - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

getCSS() - Method in interface org.ginsim.core.graph.view.style.Style

define the style as CSS rules.

getCSS() - Method in interface org.ginsim.core.graph.view.style.StyleProvider

getCSS() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGCustomStyleProvider

getCSS() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGStateStyleProvider

getCSSClass(DynamicEdge) - Method in class org.ginsim.core.graph.dynamicgraph.DefaultDynamicEdgeStyle

getCSSClass(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryEdgeStyle

getCSSClass(E) - Method in interface org.ginsim.core.graph.view.style.EdgeStyle

get the CSS class(es) used by a specific edge.

getCSSClass(E) - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

getCSSClass(E) - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

getCSSClass(V) - Method in interface org.ginsim.core.graph.view.style.NodeStyle

get the CSS class(es) used by a specific node.

getCSSClass(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getCSSClass(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

getCSSNameSuffix() - Method in class org.ginsim.core.graph.view.style.BaseStyle

getCurrentDefinition() - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionPanel

getCurrentFlavor() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

getCurrentNode() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.FunctionsCreator

getCurrentStyle() - Method in class org.ginsim.common.document.DocumentStyle

Return the current style

getCurrentText() - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanel

getCurrentText() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

getCustomProperty(StyleProperty) - Method in class org.ginsim.core.graph.dynamicgraph.DefaultDynamicEdgeStyle

getCustomProperty(StyleProperty) - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryEdgeStyle

getCustomProperty(StyleProperty) - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

getCustomProperty(StyleProperty) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getCycles() - Method in class org.ginsim.service.tool.stableregions.PNGraph

getDamageBounds(Object) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

getDash() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

getDash() - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

set the edge as dashed.

getData() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionList

getData() - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanData

getDataManagerInfo(Class) - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

getDefaultColor(RegulatoryEdgeSign) - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryEdgeStyle

getDefaultColor(ActivityLevel) - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryNodeStyle

getDefaultEdgeStyle() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

getDefaultEdgeStyle() - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

Get the default style used for the edges in this graph.

getDefaultEdgeStyle() - Method in class org.ginsim.core.graph.view.style.StyleManager

Retrieve the default style for edges

getDefaultNodeStyle() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getDefaultNodeStyle() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

Get the default style for the nodes in this graph.

getDefaultNodeStyle() - Method in class org.ginsim.core.graph.view.style.StyleManager

Retrieve the default style for nodes

getDefaultSize() - Method in class org.ginsim.gui.utils.dialog.stackdialog.AbstractStackDialogHandler

getDefaultSize() - Method in interface org.ginsim.gui.utils.dialog.stackdialog.StackDialogHandler

getDefaultSize() - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewer

getDelegates() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

getDelegates() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

getDepth() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

getDepth() - Method in class org.ginsim.core.graph.tree.TreeNode

getDescr(List<NodeInfo>) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

Describe this parameter.

getDescription() - Method in class org.ginsim.commongui.utils.FileFormatFilter

getDescription() - Method in interface org.ginsim.core.graph.regulatorygraph.perturbation.Perturbation

Get a human-readable description of the perturbation

getDescription() - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationFixed

getDescription() - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationMultiple

getDescription() - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationRange

getDescription() - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationRegulator

getDescription() - Method in class org.ginsim.gui.shell.GsFileFilter

getDescription() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer.DFA6

getDetail() - Method in class org.ginsim.common.xml.ParsingWarningReport

getDetails() - Method in class org.ginsim.core.notification.detailed.DetailedErrorNotification

Returns the notification details

getDetails() - Method in class org.ginsim.core.notification.detailed.DetailedInformationNotification

Returns the notification details

getDetails() - Method in interface org.ginsim.core.notification.detailed.DetailedNotification

getDetails() - Method in class org.ginsim.core.notification.detailed.DetailedWarningNotification

Returns the notification details

getDialog() - Method in class org.ginsim.gui.utils.data.ListEditionPanel

getDialog() - Method in class org.ginsim.servicegui.tool.avatar.others.IndexableActionListener

getDiffGraph() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

Return a merge graph colored to indicates vertices and edges parent graph.

getDiffGraph() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparatorResult

Return the new graph created for the comparison

getDiffStates(DynamicNode, DynamicNode) - Method in class org.ginsim.service.layout.BaseSTGLayout

Construct the | bit operator for a table of byte.

getDimension() - Method in class org.ginsim.core.graph.AbstractGraph

getDimension() - Method in interface org.ginsim.core.graph.Graph

Get the global bounds of the graph.

getDisplayName(V) - Method in class org.ginsim.core.graph.AbstractGraph

getDisplayName(V) - Method in interface org.ginsim.core.graph.Graph

Retrieve the name to use when displaying a graph node.

getDisplayName(RegulatoryNode) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getDisplayName() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

getDNFForm(int, List) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTree

getDocumentExtra(String) - Method in class org.ginsim.common.document.DocumentWriter

Get a documentExtra

getDocumentWriter() - Method in interface org.ginsim.common.document.DocumentWriterFactory

Create a document writer.

getDoubleValue(String, String[]) - Static method in class org.ginsim.service.tool.avatar.utils.AvaOptions

Get the double value of a given parameter

getDynamic() - Method in class org.ginsim.service.tool.localgraph.LocalGraphConfig

getDynamicGraph() - Method in class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

getDynamicGraph() - Method in interface org.ginsim.service.tool.reg2dyn.helpers.SimulationHelper

getDynamicGraph() - Method in class org.ginsim.service.tool.reg2dyn.helpers.STGSimulationHelper

getEdge(V, V) - Method in class org.ginsim.core.graph.AbstractGraph

getEdge(V, V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getEdge(V, V) - Method in interface org.ginsim.core.graph.GraphBackend

getEdge(V, V) - Method in interface org.ginsim.core.graph.GraphModel

getEdge(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

getEdge() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionListElement

getEdge(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

getEdge(int) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

getEdge() - Method in class org.ginsim.gui.graph.regulatorygraph.IncomingEdgeListModel

get the list of incoming edge

getEdgeAnchor(E) - Method in class org.ginsim.core.graph.view.style.StyleManager

getEdgeAttributeReader() - Method in class org.ginsim.core.graph.AbstractGraph

getEdgeAttributeReader() - Method in interface org.ginsim.core.graph.Graph

Give access to the attribute reader of edges

getEdgeCount() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

getEdgeCurved(E) - Method in class org.ginsim.core.graph.view.style.StyleManager

getEdgeEditionPanel() - Method in class org.ginsim.gui.graph.BaseGraphGUI

getEdgeEditionPanel(DynamicGraph) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

getEdgeEditionPanel() - Method in interface org.ginsim.gui.graph.GraphGUI

getEdgeEditionPanel(G) - Method in interface org.ginsim.gui.graph.GraphGUIHelper

Create an edition panel for edges.

getEdgeEditionPanel(HierarchicalTransitionGraph) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

getEdgeEditionPanel(ReducedGraph) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

getEdgeEditionPanel(RegulatoryGraph) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

getEdgeEditionPanel(TrapSpaceInclusionDiagram) - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

getEdgeEditionPanel(Tree) - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

getEdgeFactory() - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getEdgeForThreshold(int) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

getEdgeIndexes() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

getEdgeName(int) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

getEdges() - Method in class org.ginsim.core.graph.AbstractGraph

getEdges() - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

getEdges() - Method in interface org.ginsim.core.graph.GraphBackend

getEdges() - Method in interface org.ginsim.core.graph.GraphModel

getEdges() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

getEdgesCount() - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getEdgeSource(E) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getEdgeStyle(String) - Method in class org.ginsim.core.graph.view.style.StyleManager

Retrieve an edge style based on its name.

getEdgeStyle(E, EdgeStyle<V, E>) - Method in interface org.ginsim.core.graph.view.style.StyleProvider

Get the style used for an edge.

getEdgeStyle(Edge, EdgeStyle) - Method in class org.ginsim.service.tool.graphcomparator.GraphComparatorStyleProvider

getEdgeStyle(Edge, EdgeStyle) - Method in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisStyleProvider

getEdgeStyle(RegulatoryMultiEdge, EdgeStyle<RegulatoryNode, RegulatoryMultiEdge>) - Method in class org.ginsim.service.tool.localgraph.LocalGraphStyleProvider

getEdgeStyle(Edge, EdgeStyle) - Method in class org.ginsim.service.tool.scc.ConnectivityStyleProvider

getEdgeStyle(RegulatoryMultiEdge, EdgeStyle<RegulatoryNode, RegulatoryMultiEdge>) - Method in class org.ginsim.servicegui.tool.lrgcolorizer.LRGPatternStyleProvider

getEdgeStyle(Edge, EdgeStyle) - Method in class org.ginsim.servicegui.tool.pathfinding.PathStyleProvider

getEdgeStyle(RegulatoryMultiEdge, EdgeStyle<RegulatoryNode, RegulatoryMultiEdge>) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGCustomStyleProvider

getEdgeStyle(RegulatoryMultiEdge, EdgeStyle<RegulatoryNode, RegulatoryMultiEdge>) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGStateStyleProvider

getEdgeStyle(DynamicEdge, EdgeStyle<DynamicNode, DynamicEdge>) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.STGPathStyleProvider

getEdgeStyles() - Method in class org.ginsim.core.graph.view.style.StyleManager

Get the list of all edge styles

getEdgeSupplier() - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getEdgeTarget(E) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getEdgeViewInfo(E) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

getEdgeViewInfo(E) - Method in interface org.ginsim.core.graph.GraphBackend

Get raw view information for an edge.

getEdgeWeight(E) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getEditActionManager() - Method in class org.ginsim.gui.graph.BaseGraphGUI

getEditActionManager() - Method in interface org.ginsim.gui.graph.GraphGUI

getEditActions(DynamicGraph) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

getEditActions(G) - Method in interface org.ginsim.gui.graph.GraphGUIHelper

getEditActions(HierarchicalTransitionGraph) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

getEditActions(ReducedGraph) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

getEditActions(RegulatoryGraph) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

getEditActions(TrapSpaceInclusionDiagram) - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

getEditActions(Tree) - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

getEditingRow() - Method in class org.ginsim.gui.utils.widgets.treetable.JTreeTable

getEditingTabLabel() - Method in class org.ginsim.gui.graph.BaseGraphGUI

getEditingTabLabel(DynamicGraph) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

getEditingTabLabel() - Method in interface org.ginsim.gui.graph.GraphGUI

getEditingTabLabel(G) - Method in interface org.ginsim.gui.graph.GraphGUIHelper

Retrieve the Title used for the selection edition tab

getEditingTabLabel(HierarchicalTransitionGraph) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

getEditingTabLabel(ReducedGraph) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

getEditingTabLabel(RegulatoryGraph) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

getEditingTabLabel(TrapSpaceInclusionDiagram) - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

getEditingTabLabel(Tree) - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

getEdition() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

getEditionPanel() - Method in class org.ginsim.servicegui.tool.avatar.parameters.AvaParameterEditionPanel

Accesses the left panel for editing the context of simulations

getEditorModel() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

getEditPanel(L, StackDialog) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

getElementaryCycles() - Method in class org.ginsim.johnsonCycles.ElementaryCyclesSearch

Returns List::List::Object with the Lists of nodes of all elementary cycles in the graph.

getElementAt(int) - Method in class org.ginsim.gui.graph.regulatorygraph.IncomingEdgeListModel

getElementAt(int) - Method in class org.ginsim.gui.utils.data.models.ValueListComboModel

getElementAt(int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

getEnding(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryEdgeStyle

getEnding(E) - Method in interface org.ginsim.core.graph.view.style.EdgeStyle

getEnding(E) - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

getEnding(E) - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

getErrorBars(Map<String, List<Integer>>, Map<String, String>, String, String, String) - Static method in class org.ginsim.service.tool.avatar.utils.ChartGNUPlot

Creates a chart with statistics on the depth for a list of attractors

getException() - Method in class org.ginsim.core.notification.ExceptionNotification

getExistingNode(V) - Method in class org.ginsim.core.graph.AbstractGraph

getExistingNode(V) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

getExistingNode(V) - Method in interface org.ginsim.core.graph.GraphBackend

getExistingNode(V) - Method in interface org.ginsim.core.graph.GraphModel

getExitProbs(String, int) - Method in class org.ginsim.service.tool.avatar.domain.CycleGraph

Computes the exit probabilities associated with the given state

getExitStateSet() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Returns the states accessible from the state-set

getExitStateSet() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Returns the states accessible from the state-set

getExpFilename() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getExpFileName() - Method in class org.ginsim.service.export.cadp.CADPWriter

getExportType() - Method in class org.ginsim.service.export.sat.SATConfig

getExtension() - Method in interface org.ginsim.gui.graph.GraphOptionPanel

getExtension() - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphOptionPanel

getExtensionList() - Method in class org.ginsim.commongui.utils.FileFormatFilter

getExtensionList() - Method in class org.ginsim.gui.shell.GsFileFilter

Returns the array of available extensions for this filter

getExtraCount() - Method in class org.ginsim.common.xml.ParsingWarning

getExtraNames() - Method in interface org.ginsim.core.graph.dynamicgraph.TransitionGraph

Get the list of known extra components names.

getExtraNames() - Method in class org.ginsim.core.graph.dynamicgraph.TransitionGraphImpl

getFactory() - Static method in class org.ginsim.gui.graph.GraphGUIHelperFactory

Method providing access to the factory instance

getFileFilter() - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

Provide the file filter to apply to a file chooser

getFileFilter() - Method in interface org.ginsim.gui.graph.GraphGUIHelper

Provide the file filter to apply to a file chooser

getFileFilter() - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

Provide the file filter to apply to a file chooser

getFileFilter() - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

Provide the file filter to apply to a file chooser

getFileFilter() - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

getFileFilter() - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

getFileFilter() - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

Provide the file filter to apply to a file chooser

getFileFilter() - Method in class org.ginsim.gui.service.FormatSupportServiceGUI

getFileFilter() - Method in class org.ginsim.gui.shell.actions.ExportAction

Get the file filter to be used for this export.

getFileFilter() - Method in class org.ginsim.gui.shell.actions.ImportAction

Get the file filter to be used for this import.

getFileFilter() - Method in class org.ginsim.servicegui.export.documentation.LRGDocumentationAction

getFileFilter() - Method in class org.ginsim.servicegui.export.petrinet.PetriNetExportAction

getFileMenu(Graph<?, ?>, JMenu, JMenu) - Static method in class org.ginsim.gui.shell.callbacks.FileCallBack

Create and populate a File menu.

getFirstChangeIndex() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicEdge

get the coordinate of the first change between the two states.

getFirstLine() - Method in class org.ginsim.common.xml.ParsingWarning

getFirstState() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Accesses the first state in the state-set (useful to iterate and remove)

getFirstState() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Accesses the first state in the state-set (useful to iterate and remove)

getFirstValue(NodeInfo) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

getFixedPropagationUsers() - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

getForeground() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

getForeground(V) - Method in interface org.ginsim.core.graph.view.style.NodeStyle

getForeground(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getForeground(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

getForegroundColor() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getForegroundColor() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

getFormat(String) - Static method in class org.ginsim.common.utils.FileFormatDescription

Retrieve a format by id.

getFormat(Class<C>, String) - Static method in class org.ginsim.common.utils.FileFormatDescription

Retrieve a subclassing format by ID.

getFormats(Class<C>) - Static method in class org.ginsim.common.utils.FileFormatDescription

Retrieve all formats of a given subclass.

getFrame(Graph) - Method in class org.ginsim.gui.GUIManager

Give access to the Frame corresponding to the given Graph

getFrame() - Method in class org.ginsim.servicegui.tool.avatar.others.IndexableActionListener

getFrame() - Method in class org.ginsim.servicegui.tool.omddViz.OmddVizFrame

getFreeChildren(int) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Creates a state (int array) where components are initialized as -1

getFreeState(int) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Creates a state (byte array) where components are initialized as -1

getFreeValues() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

getFromPos(int) - Static method in enum org.ginsim.core.graph.regulatorygraph.RegulatoryEdgeSign

getFunctions() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTree

getFunctions() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

getG1() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

Return the first graph to compare

getG2() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

Return the second graph to compare

getGateWriter() - Method in class org.ginsim.service.export.cadp.CADPWriter

getGINMLWriter() - Method in class org.ginsim.core.graph.AbstractGraph

getGINMLWriter() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

getGINMLWriter() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

getGINMLWriter() - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

getGINMLWriter() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getGrammarFileName() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

getGrammarFileName() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

getGraph() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicParser

getGraph() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphParser

getGraph() - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphParser

getGraph() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

getGraph() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.FunctionsCreator

getGraph() - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

getGraph() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryParser

getGraph() - Method in class org.ginsim.core.io.parser.GinmlParser

getGraph() - Method in class org.ginsim.core.io.parser.GsXMLHelper

getGraph() - Method in class org.ginsim.gui.graph.BaseGraphGUI

getGraph() - Method in interface org.ginsim.gui.graph.GraphGUI

getGraph() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getGraph() - Method in class org.ginsim.service.export.prism.PRISMConfig

getGraph() - Method in class org.ginsim.service.export.sat.SATConfig

getGraph() - Method in class org.ginsim.service.format.ginml.GINMLFormatConfig

getGraph() - Method in class org.ginsim.service.format.sbml.SBMLQualConfig

getGraph() - Method in class org.ginsim.service.tool.localgraph.LocalGraphConfig

getGraph() - Method in class org.ginsim.service.tool.simulation.STGSimulation

getGraph() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

getGraph() - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

getGraph() - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

getGraph() - Method in class org.ginsim.servicegui.tool.pathfinding.PathFindingFrame

getGraph1Name() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparatorResult

Get the name of the first graph

getGraph2Name() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparatorResult

Get the name of the second graph

getGraphBackend(Graph) - Static method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

getGraphClass() - Method in class org.ginsim.core.graph.AbstractGraphFactory

getGraphClass() - Method in interface org.ginsim.core.graph.GraphFactory

Return the class of graph this factory is managing

getGraphClass() - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphFactory

getGraphClass() - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

getGraphClass() - Method in interface org.ginsim.gui.graph.GraphGUIHelper

Get the graph class the helper helps to manage

getGraphClass() - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

getGraphClass() - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

getGraphClass() - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

getGraphClass() - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

getGraphClass() - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

getGraphComponent() - Method in class org.ginsim.gui.graph.canvas.CanvasGraphGUIImpl

getGraphComponent() - Method in interface org.ginsim.gui.graph.GraphGUI

getGraphFactories() - Method in class org.ginsim.core.graph.GSGraphManager

getGraphFromAttractor(DynamicGraph, AbstractStateSet, LogicalModel) - Static method in class org.ginsim.service.tool.avatar.simulation.SimulationUtils

Generates a drawable dynamic graph from a complex attractor

getGraphFromAttractor(ReducedGraph, StateSet, LogicalModel) - Static method in class org.ginsim.service.tool.avatar.simulation.SimulationUtils

Generates a drawable reduced graph from a complex attractor

getGraphFromPath(String) - Method in class org.ginsim.core.graph.GSGraphManager

Return the graph associated to the given file path, if it exists

getGraphGUI(Graph) - Method in class org.ginsim.gui.GUIManager

Give access to the GraphGUI corresponding to the given Graph

getGraphGUIHelper(Class<?>) - Method in class org.ginsim.gui.graph.GraphGUIHelperFactory

Give access to the GraphGUIHelper corresponding to the given graph class

getGraphGUIHelper(Graph) - Method in class org.ginsim.gui.graph.GraphGUIHelperFactory

Give access to the GraphGUIHelper corresponding to the given graph

getGraphicPanel() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

getGraphName() - Method in class org.ginsim.core.graph.AbstractGraph

Give access to the name of the graph

getGraphName() - Method in interface org.ginsim.core.graph.GraphModel

Give access to the name of the graph

getGraphPath(Graph) - Method in class org.ginsim.core.graph.GSGraphManager

Return the path of the file the graph has been loaded from or saved to (if it exists)

getGraphsInfo() - Method in class org.ginsim.core.graph.GSGraphManager

getGraphType() - Method in class org.ginsim.core.graph.AbstractGraphFactory

getGraphType() - Method in interface org.ginsim.core.graph.GraphFactory

Return the type of graph this factory is managing

getGraphType() - Method in class org.ginsim.core.graph.GSGraphManager

getGraphType() - Method in class org.ginsim.core.graph.objectassociation.BasicGraphAssociatedManager

getGraphType() - Method in interface org.ginsim.core.graph.objectassociation.GraphAssociatedObjectManager

Get the type of graph handled by this data manager.

getGraphZipName() - Method in class org.ginsim.core.graph.AbstractGraph

Return the zip extension for the graph type

getGraphZipName() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

Return the zip extension for the graph type

getGraphZipName() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

getGraphZipName() - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

Return the zip extension for the graph type

getGraphZipName() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getGravity() - Method in exception org.ginsim.common.application.GsException

get the gravity of the error, this should be one of GRAVITY_INFO, GRAVITY_NORMAL or GRAVITY_ERROR.

getHeight() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getHeight() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

getHeight(V) - Method in interface org.ginsim.core.graph.view.style.NodeStyle

getHeight(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getHeight(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

getHeight() - Method in class org.ginsim.gui.graph.canvas.SimpleDimension

getHelp() - Method in class org.ginsim.service.tool.avatar.service.AvatarServiceFacade

Provides help on the parameters of avatar simulations

getHelp() - Method in class org.ginsim.service.tool.avatar.service.FirefrontServiceFacade

Provides help on the parameters of firefront simulations

getHelp() - Method in class org.ginsim.service.tool.avatar.service.MonteCarloServiceFacade

Provides help on the parameters of Monte Carlo simulations

getHelper(Object) - Static method in class org.ginsim.common.utils.OpenUtils

Get the registered helper for a given "protocol"

getHelper() - Method in class org.ginsim.core.annotation.AnnotationLink

getHelper() - Static method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationPanelListHelper

getHelper(Object) - Method in class org.ginsim.gui.guihelpers.GUIHelperManager

getHNodeForState(byte[]) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNodeSet

Iterate over all the DynamicalHierarchicalNode in the HashSet and test if it contains state using the function contains(state) of HierarchicalNode

getHTMLComment() - Method in class org.ginsim.core.annotation.Annotation

getHTMLData() - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Fetch the data in a text/html format

getIcon(JTable, int) - Method in class org.ginsim.commongui.utils.DefaultTableHeaderCellRenderer

Overloaded to return an icon suitable to the primary sorted column, or null if the column is not the primary sort key.

getIcon(JTable, int) - Method in class org.ginsim.commongui.utils.VerticalTableHeaderCellRenderer

Overridden to return a rotated version of the sort icon.

getIcon() - Method in class org.ginsim.gui.graph.EditAction

getIcon(String) - Static method in class org.ginsim.gui.shell.actions.BaseAction

getId() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicNode

getId() - Method in class org.ginsim.core.graph.reducedgraph.NodeReducedData

getId(int) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

get the id of the corresponding subedge.

getId() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

getID() - Method in class org.ginsim.gui.shell.actions.ExportAction

getID() - Method in class org.ginsim.gui.shell.actions.ImportAction

getIdentifer() - Method in class org.ginsim.core.graph.view.css.Selector

Return the identifier for this selector

getIdentityChildren(int) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Creates an identity node array (e.g.

getImage(String) - Static method in class org.ginsim.commongui.utils.ImageLoader

getImageIcon(String) - Static method in class org.ginsim.commongui.utils.ImageLoader

getImagePath(String) - Static method in class org.ginsim.commongui.utils.ImageLoader

getIn() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

getIncomingEdges(V) - Method in class org.ginsim.core.graph.AbstractGraph

getIncomingEdges(V) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

getIncomingEdges(V) - Method in interface org.ginsim.core.graph.GraphBackend

getIncomingEdges(V) - Method in interface org.ginsim.core.graph.GraphModel

getInCycle(HierarchicalNodeSet, List) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

Retrieve the real SCC containing the state.

getIndex() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionListElement

getIndex(RegulatoryEdge) - Method in class org.ginsim.gui.graph.regulatorygraph.IncomingEdgeListModel

get the index in list of a GsEdgeIndex

getIndex() - Method in interface org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueItem

getIndex() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueSCC

getIndex() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

getIndexForGUI() - Method in enum org.ginsim.core.graph.regulatorygraph.RegulatoryEdgeSign

getIndexof(String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

get the index of the subedge having a given id

getIndexOf(Object) - Method in class org.ginsim.gui.utils.data.models.ValueListComboModel

getIndexOfChild(Object, Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

getIndexOfChild(Object, Object) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

getInfluencedInputs(RegulatoryNode) - Method in class org.ginsim.service.export.cadp.CADPWriter

getInfluencedInputs(RegulatoryNode) - Method in class org.ginsim.service.tool.composition.IntegrationFunctionMapping

Returns the list of input components whose value is influenced by the given proper component

getInfluencedModuleInputs(RegulatoryNode, int) - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

getInfluencedModuleInputs(RegulatoryNode, int) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

getInfluencedModuleInputs(RegulatoryNode, int) - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

getInfoPanel() - Method in class org.ginsim.gui.graph.BaseGraphGUI

getInfoPanel(DynamicGraph) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

getInfoPanel() - Method in interface org.ginsim.gui.graph.GraphGUI

getInfoPanel(G) - Method in interface org.ginsim.gui.graph.GraphGUIHelper

Create an Information Panel

getInfoPanel(HierarchicalTransitionGraph) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

getInfoPanel(ReducedGraph) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

getInfoPanel(RegulatoryGraph) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

getInfoPanel(TrapSpaceInclusionDiagram) - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

getInfoPanel(Tree) - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

getInitialState() - Method in interface org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateStore

getInitialState() - Method in class org.ginsim.service.export.cadp.CADPWriter

getInitialState() - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

getInitialState() - Method in class org.ginsim.service.export.prism.PRISMConfig

getInitialState() - Method in class org.ginsim.service.export.sat.SATConfig

getInitialState() - Method in class org.ginsim.service.format.sbml.SBMLQualConfig

getInitialState() - Method in class org.ginsim.service.tool.avatar.params.AvatarStateStore

getInitialState() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

getInitialState() - Method in class org.ginsim.service.tool.simulation.SimulationParameter

getInitialState() - Method in class org.ginsim.servicegui.export.petrinet.PetriNetExportAction

getInitialStates() - Method in interface org.colomoto.biolqm.StatefulLogicalModel

Gets the set of initial states defining a portion of the state-space

getInitialStates() - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

getInitialStates() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesHandler

getInitialStates() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getInitialStates() - Method in class org.ginsim.servicegui.export.cadp.InitialStatesWidget

getInitialStates() - Method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

getInitialStateWriter() - Method in class org.ginsim.service.export.cadp.CADPWriter

getInitialWeight() - Method in class org.ginsim.gui.service.FormatSupportServiceGUI

getInitialWeight() - Method in interface org.ginsim.gui.service.ServiceGUI

Give a weight for the service, as defined by the developer.

getInitialWeight() - Method in class org.ginsim.gui.service.SimpleServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.export.cadp.CADPExportServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.export.documentation.LRGDocumentationServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.export.image.ImageExportServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.export.maboss.MaBoSSExportServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.export.nusmv.NuSMVExportServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.export.petrinet.PetriNetExportServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.export.prism.PRISMExportServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.export.reggraph.RegGraphExportServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.export.sat.SATExportServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.export.struct.GraphStructureExportServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.format.ginml.GINMLFormatServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.layout.LayoutServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.avatar.AvatarServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.circuit.CircuitServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.composition.CompositionServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewerServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.decisionanalysis.DecisionAnalysisServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.interactionanalysis.InteractionAnalysisServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.modelbooleanizer.ModelBooleanizerServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.modelreversion.ModelReversionServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.omddViz.OmddVizServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.pathfinding.PathFindingServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.polytopesViz.PolytopesVizServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.reg2dyn.limitedSimulation.LimitedSimulationServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.reg2dyn.Reg2DynServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryGraphAnimationServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.regulatorytreefunction.RegulatoryFunctionTreeServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.scc.ConnectivityServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.stableregions.StableRegionsServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.stablestates.StableStatesServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.stateinregulatorygraph.StateInRegulatoryGraphServiceGUI

getInitialWeight() - Method in class org.ginsim.servicegui.tool.trapspace.TrapSpaceServiceGUI

getInitStatesIterator() - Method in class org.ginsim.service.tool.reg2dyn.Simulation

getInputConfigs() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesHandler

getInputNodes() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesHandler

getInputSelectorOrNull(RegulatoryGraph, PatternHolder) - Static method in class org.ginsim.gui.graph.regulatorygraph.initialstate.PatternSelectionPanel

getInputState() - Method in interface org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateStore

getInputState() - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

getInputState() - Method in class org.ginsim.service.export.prism.PRISMConfig

getInputState() - Method in class org.ginsim.service.export.sat.SATConfig

getInputState() - Method in class org.ginsim.service.format.sbml.SBMLQualConfig

getInputState() - Method in class org.ginsim.service.tool.avatar.params.AvatarStateStore

getInputState() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

getInputState() - Method in class org.ginsim.service.tool.simulation.SimulationParameter

getInputState() - Method in class org.ginsim.servicegui.export.petrinet.PetriNetExportAction

getInsets() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

getInsets() - Method in class org.ginsim.gui.utils.widgets.Button

getInsets() - Method in class org.ginsim.gui.utils.widgets.GsButton

getInstance() - Static method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphFactory

getInstance() - Static method in class org.ginsim.core.graph.GSGraphManager

getInstance() - Static method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphFactory

getInstance() - Static method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

getInstance() - Static method in class org.ginsim.core.graph.reducedgraph.ReducedGraphFactory

getInstance() - Static method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphFactory

getInstance() - Static method in class org.ginsim.core.graph.tree.TreeFactory

Return an instance of this TreeFactory.

getInstance() - Static method in class org.ginsim.gui.guihelpers.GUIHelperManager

getInstance() - Static method in class org.ginsim.gui.GUIManager

Give access to the manager singleton

getInstance(LogicalModel, PrioritySetDefinition) - Static method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

getIntegrationFunction() - Method in class org.ginsim.service.tool.composition.RegulatoryIntegration

getIntegrationFunctionComputer(IntegrationFunction) - Static method in enum org.ginsim.service.tool.composition.IntegrationFunction

getIntegrationFunctionForInput(RegulatoryNode) - Method in class org.ginsim.service.export.cadp.CADPWriter

getIntegrationFunctionForInput(RegulatoryNode) - Method in class org.ginsim.service.tool.composition.IntegrationFunctionMapping

getIntegrationInitialStateWriter(List<Map.Entry<RegulatoryNode, Integer>>) - Method in class org.ginsim.service.export.cadp.CADPWriter

getInteraction(int) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

Returns the interaction at the specified position index

getInteractions() - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

get all interactions

getInteractionsModel() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

getIntersection(Rectangle, Point, boolean, float) - Static method in class org.ginsim.core.graph.view.ViewHelper

Get the bounding box point to connect a box with an external point.

getIntersection(Rectangle, Point) - Static method in class org.ginsim.core.graph.view.ViewHelper

getIntValue(int) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

getIntValue(int) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

getIntValue(int) - Method in class org.ginsim.gui.graph.view.style.StyleEditor

getIntValue(int) - Method in class org.ginsim.gui.utils.data.ObjectEditor

getIntValue(String, String[]) - Static method in class org.ginsim.service.tool.avatar.utils.AvaOptions

Get the integer value of a given parameter

getInvalidComponentSpecification() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionVerification

getIStateList() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

getKey() - Method in class org.ginsim.service.tool.avatar.domain.AbstractStateSet

Returns the unique identifier of the state-set
If two state-sets have the same states they share the same key

getKey() - Method in class org.ginsim.servicegui.tool.avatar.others.IndexableActionListener

getKeys() - Method in class org.ginsim.service.tool.avatar.domain.AbstractStateSet

getKeys() - Method in class org.ginsim.service.tool.avatar.domain.CompactStateSet

getKeys() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Returns a collection with the keys of the states in the state-set

getKeys() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Returns a collection with the keys of the states in the state-set

getKeySet() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

getLabel() - Method in class org.ginsim.core.graph.tree.TreeNode

getLabelProgression() - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

This method initializes labelProgression

getLineColor() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

getLineColor() - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

getLineEnd() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

getLineEnd() - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

getLineWidth() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

getLineWidth() - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

getLink(String, String) - Method in interface org.ginsim.common.utils.OpenHelper

Create a standard link for this protocol-based link.

getLink(Object, Object) - Static method in class org.ginsim.common.utils.OpenUtils

Get a standard link (URI) for a given (protocol,value) pair

getLink(int) - Method in class org.ginsim.core.annotation.Annotation

get the vector of url

getLink() - Method in class org.ginsim.core.annotation.AnnotationLink

getLink(String, String) - Method in class org.ginsim.core.annotation.BiblioList

getLink(String, String) - Method in class org.ginsim.core.annotation.DatabaseInfo

getLink(String, String) - Method in class org.ginsim.core.annotation.HttpHelper

getLinkList() - Method in class org.ginsim.core.annotation.Annotation

getList() - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationSelectionPanel

getList() - Method in class org.ginsim.gui.utils.data.ListEditionPanel

getList() - Method in class org.ginsim.gui.utils.data.ListPanel

getList() - Method in class org.ginsim.gui.utils.data.ListSelectionPanel

getList() - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionConfigSelectionPanel

getList() - Method in class org.ginsim.servicegui.tool.reg2dyn.PrioritySelectionPanel

getListFromArray(T[]) - Static method in class org.ginsim.common.utils.ListTools

Create a list based on an array

getListPanel(L) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

getListVisible() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getListVisible() - Method in class org.ginsim.service.export.cadp.CADPWriter

getLNTIntegrationFilename() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getLNTIntegrationFileName() - Method in class org.ginsim.service.export.cadp.CADPWriter

getLNTModelFilename() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getLNTModelFileName() - Method in class org.ginsim.service.export.cadp.CADPWriter

getLoader() - Method in class org.ginsim.core.graph.GINsimFormat

getLog() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparatorResult

get the content of the log

getLogicalParameters() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

getLongDesc() - Method in enum org.ginsim.core.graph.regulatorygraph.RegulatoryEdgeSign

getLongId() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

getLongInfo(String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

getLow_index() - Method in interface org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueItem

getLow_index() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueSCC

getLow_index() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

getLowestNodeId() - Method in class org.ginsim.johnsonCycles.SCCResult

getLowLevelComponentFromName(String, int) - Method in interface org.ginsim.servicegui.tool.composition.integrationgrammar.CompositionContext

Obtain a NodeInfo from the name it had in the original module and an instance identification

getLowLevelComponentFromName(String, int) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.CompositionContextImpl

getLowLevelComponents() - Method in interface org.ginsim.servicegui.tool.composition.integrationgrammar.CompositionContext

getLowLevelComponents() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.CompositionContextImpl

getMainComponent() - Method in class org.ginsim.gui.utils.dialog.stackdialog.AbstractStackDialogHandler

getMainComponent() - Method in interface org.ginsim.gui.utils.dialog.stackdialog.StackDialogHandler

getMainComponent() - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewer

getMainEditionPanel() - Method in class org.ginsim.gui.graph.BaseGraphGUI

getMainEditionPanel(DynamicGraph) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

getMainEditionPanel() - Method in interface org.ginsim.gui.graph.GraphGUI

getMainEditionPanel(G) - Method in interface org.ginsim.gui.graph.GraphGUIHelper

Create an edition panel for the graph itself.

getMainEditionPanel(HierarchicalTransitionGraph) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

getMainEditionPanel(ReducedGraph) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

getMainEditionPanel(RegulatoryGraph) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

getMainEditionPanel(TrapSpaceInclusionDiagram) - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

getMainEditionPanel(Tree) - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

getMainMenu() - Static method in class org.ginsim.gui.shell.callbacks.FileCallBack

getMainPanel() - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

getMainPanel() - Method in class org.ginsim.servicegui.tool.avatar.AvatarLogicalModelActionDialog

getMainPanel() - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

getMainPanel() - Method in class org.ginsim.servicegui.tool.decisionanalysis.DecisionAnalysisFrame

getMainPanel() - Method in class org.ginsim.servicegui.tool.reg2dyn.limitedSimulation.LimitedSimulationFrame

getManagedClasses() - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

Give access to the list of classes for which object managers are registered

getManager() - Static method in class org.ginsim.core.notification.NotificationManager

Give access to the manager instance

getManager() - Method in class org.ginsim.service.tool.circuit.CircuitAlgo

getManager() - Method in class org.ginsim.service.tool.circuit.CircuitAnalyser

getManualSize() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

getMap() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

getMappedInputs() - Method in class org.ginsim.service.export.cadp.CADPWriter

getMappedInputs() - Method in class org.ginsim.service.tool.composition.IntegrationFunctionMapping

getMappedNodes() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

getMappedNodes() - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

getMappedNodes() - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

getMappedToModuleArguments(RegulatoryNode, int) - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

getMappedToModuleArguments(RegulatoryNode, int) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

getMappedToModuleArguments(RegulatoryNode, int) - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

getMapping() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getMapping() - Method in class org.ginsim.service.tool.composition.CompositionConfig

getMapping() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

getMapping() - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

getMapping() - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

getMapping() - Method in class org.ginsim.servicegui.tool.composition.IntegrationFunctionWidget

Builds the integration function mapping object from current selections

getMasterObject() - Method in class org.ginsim.gui.utils.data.ObjectEditor

getMax() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

getMax(int) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

getMaxAsString() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

getMaxDepth() - Method in class org.ginsim.core.graph.tree.TreeBuilder

getMaxDepth() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

getMaxDistance() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationAtom

getMaximumSize(JComponent) - Method in class org.ginsim.commongui.utils.VerticalLabelUI

Returns a Dimension appropriate for vertical rendering

getMaxName() - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

getMaxNeighbours() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationAtom

getMaxNodes() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

getMaxTerminal() - Method in class org.ginsim.core.graph.tree.TreeBuilder

getMaxValue() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

getMaxValue() - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

getMaxValues() - Method in class org.ginsim.gui.utils.data.SimpleStateListTableModel

getMaxValues(List<RegulatoryNode>) - Method in class org.ginsim.service.layout.BaseSTGLayout

Retrieve the maximal values of all components.

getMaxValueTable() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

getMCLPropertyFileName(List<byte[]>) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getMCLPropertyFileName(List<byte[]>) - Method in class org.ginsim.service.export.cadp.CADPWriter

getMDD(RegulatoryGraph, RegulatoryNode, MDDManager) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

Build a MDD corresponding to this parameter (using the new MDD toolkit)

getMDD(RegulatoryGraph, MDDManager) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

Experimental: Get the MDD for this node function using the new MDD toolkit.

getMDD(IntegrationFunctionSpecification.IntegrationExpression, int) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionMDDFactory

getMDD(IntegrationFunctionSpecification.IntegrationExpression, int, boolean) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionMDDFactory

getMDDFactory() - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Construct a MDDFactory associated to the nodes of this graph

getMDDFactory() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getMDDs(MDDManager) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Construct MDD representation of the logical functions of the nodes of this graph.

getMDDs(MDDManager) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getMenu() - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemAttributePanel

getMenu() - Method in interface org.ginsim.gui.shell.editpanel.EditTab

getMessage() - Method in exception org.ginsim.common.application.GsException

get the message associated with the exception.

getMessage() - Method in class org.ginsim.common.xml.ParsingWarning

getMessage() - Method in class org.ginsim.common.xml.ParsingWarningReport

getMessage() - Method in class org.ginsim.core.notification.Notification

Get the message describing this notification.

getMin() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

getMin(int) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

getMinDistance() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationAtom

getMinimumSize(JComponent) - Method in class org.ginsim.commongui.utils.VerticalLabelUI

Returns a Dimension appropriate for vertical rendering

getMinName() - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

getMinNeighbours() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationAtom

getMinValue() - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

getMode() - Method in interface org.ginsim.core.graph.tree.Tree

getMode() - Method in class org.ginsim.core.graph.tree.TreeImpl

getMode() - Method in class org.ginsim.gui.graph.EditAction

getMode() - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

getModel() - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Get a ready-to-be-used model (list of nodes and functions, no graph structure)

getModel(NodeOrderer) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Get a ready-to-be-used model (list of nodes and functions, no graph structure)

getModel(NodeOrderer, boolean) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Get a ready-to-be-used model (list of nodes and functions, no graph structure)

getModel() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getModel(NodeOrderer) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getModel(NodeOrderer, boolean) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getModel() - Method in class org.ginsim.service.export.cadp.CADPWriter

getModel() - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

getModel() - Method in class org.ginsim.service.export.prism.PRISMConfig

getModel() - Method in class org.ginsim.service.export.sat.SATConfig

getModel() - Method in class org.ginsim.service.format.ginml.GINMLFormatConfig

getModelName() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getModelName() - Method in class org.ginsim.service.export.cadp.CADPWriter

getModelReducer(RegulatoryGraph) - Method in class org.ginsim.service.tool.modelreduction.ModelReductionService

getModelReducer(LogicalModel) - Method in class org.ginsim.service.tool.modelreduction.ModelReductionService

getModelReverser(LogicalModel) - Method in class org.ginsim.service.tool.modelreversion.ModelReversionService

getModifiedPoints(NodeAttributesReader, EdgeAttributesReader, Edge<?>, List<Point>) - Static method in class org.ginsim.core.graph.view.ViewHelper

getMouseListener() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

getMouseMotionListener() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

getMovingPoints(MovingEdgeType, int, int, NodeAttributesReader, EdgeAttributesReader, Edge<?>) - Static method in class org.ginsim.core.graph.view.ViewHelper

Get the routing points for an edge which is affected by a move preview.

getMovingRows(int, int[]) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

when moving a selection of class, they must move with other class of the same priority.

getMovingType(boolean, boolean, boolean) - Static method in enum org.ginsim.core.graph.view.MovingEdgeType

getName() - Method in interface org.colomoto.biolqm.StatefulLogicalModel

Returns the model's name (by default the associated filename)

getName() - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

getName() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

getName() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

get the long name of the node.

getName() - Method in class org.ginsim.core.graph.view.style.BaseStyle

getName() - Method in class org.ginsim.core.graph.view.style.BaseStyleOverride

getName() - Method in interface org.ginsim.core.graph.view.style.Style

getName() - Method in interface org.ginsim.core.utils.data.NamedObject

getName() - Method in class org.ginsim.gui.graph.EditAction

getName() - Method in class org.ginsim.gui.utils.data.models.SpinModel

getName() - Method in class org.ginsim.service.tool.avatar.params.AvatarParameters

getName() - Method in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

getName() - Method in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

getName() - Method in class org.ginsim.service.tool.avatar.simulation.MonteCarloSimulation

getName() - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

getName() - Method in class org.ginsim.service.tool.modelreduction.ReductionConfig

getName() - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

getName() - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

getName() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

getName() - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionAsynchronous

getName() - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionComplete

getName() - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSequential

getName() - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSynchronous

getNames(boolean) - Method in class org.ginsim.service.tool.avatar.params.AvatarStateStore

Gathers all the names of the stored states

getNbArgs() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBinaryOperator

getNbArgs() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperator

getNbArgs() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TUnaryOperator

getNbEdge() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

getNbFunctions() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

getNbSons() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

getNbSons() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

getNegatedExpression() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationNegation

getNeighbourIndices(int) - Method in class org.ginsim.service.tool.composition.GenericTopology

Returns a vector containing the indices of neighbouring modules

getNeighbourIndices(int) - Method in interface org.ginsim.service.tool.composition.Topology

getNeighbourIndices(int, int) - Method in interface org.ginsim.servicegui.tool.composition.integrationgrammar.CompositionContext

Get neighbours at an exact distance

getNeighbourIndices(int, int, int) - Method in interface org.ginsim.servicegui.tool.composition.integrationgrammar.CompositionContext

getNeighbourIndices(int, int, int) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.CompositionContextImpl

getNeighbourIndices(int, int) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.CompositionContextImpl

getNewBufferedImage() - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

getNewEdge(V, V) - Method in class org.ginsim.gui.graph.AddEdgeAction

getNewGraph() - Method in class org.ginsim.core.graph.GSGraphManager

Create a new (RegulatoryGraph)

getNewGraph(Class<C>) - Method in class org.ginsim.core.graph.GSGraphManager

Create a new default graph of the given class

getNewGraph(Class<C>, Object...) - Method in class org.ginsim.core.graph.GSGraphManager

getNewIterator() - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.SimulationConstraint

Return a new iterator for the given state space.

getNewNode() - Method in class org.ginsim.gui.graph.AddNodeAction

getNewSelector(String) - Static method in class org.ginsim.core.graph.view.css.Selector

return a new selector corresponding to an identifier

getNextMaxValue() - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

try to increase the max value

getNextMinValue() - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

try to increase the min value

getNextValue() - Method in class org.ginsim.gui.graph.regulatorygraph.NodeMaxValueSpinModel

getNextValue() - Method in class org.ginsim.gui.utils.data.models.MaxSpinModel

getNextValue() - Method in class org.ginsim.gui.utils.data.models.MinSpinModel

getNode() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

getNode() - Method in class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

getNode() - Method in interface org.ginsim.service.tool.reg2dyn.helpers.SimulationHelper

getNode() - Method in class org.ginsim.service.tool.reg2dyn.helpers.STGSimulationHelper

getNodeAttributeReader() - Method in class org.ginsim.core.graph.AbstractGraph

getNodeAttributeReader() - Method in interface org.ginsim.core.graph.Graph

Give access to the attribute reader of vertices

getNodeBorder(V) - Method in interface org.ginsim.core.graph.view.style.NodeStyle

getNodeBorder(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getNodeBorder(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

getNodeByName(String) - Method in class org.ginsim.core.graph.AbstractGraph

Give access to the node named with the given name

getNodeByName(String) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

Give access to the vertex named with the given name

getNodeByName(String) - Method in interface org.ginsim.core.graph.GraphBackend

Give access to the node named with the given name

getNodeByName(String) - Method in interface org.ginsim.core.graph.GraphModel

Give access to the node named with the given name

getNodeCount() - Method in class org.ginsim.core.graph.AbstractGraph

getNodeCount() - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

getNodeCount() - Method in interface org.ginsim.core.graph.GraphBackend

getNodeCount() - Method in interface org.ginsim.core.graph.GraphModel

Return the number of node in this graph

getNodeEditionPanel() - Method in class org.ginsim.gui.graph.BaseGraphGUI

getNodeEditionPanel(DynamicGraph) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

getNodeEditionPanel() - Method in interface org.ginsim.gui.graph.GraphGUI

getNodeEditionPanel(G) - Method in interface org.ginsim.gui.graph.GraphGUIHelper

Create an edition panel for nodes.

getNodeEditionPanel(HierarchicalTransitionGraph) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

getNodeEditionPanel(ReducedGraph) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

getNodeEditionPanel(RegulatoryGraph) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

getNodeEditionPanel(TrapSpaceInclusionDiagram) - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

getNodeEditionPanel(Tree) - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

getNodeForState(byte[]) - Method in interface org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraph

Return the Node with the given state

getNodeForState(byte[]) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

getNodeInfo() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

getNodeInfos() - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

getNodeInfos() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getNodeName(int) - Method in class org.ginsim.core.graph.tree.TreeBuilder

Return the name of the node at level

getNodeName(int) - Method in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

getNodeName(int) - Method in class org.ginsim.core.graph.tree.TreeBuilderFromMDD

getNodeOrder() - Method in interface org.ginsim.core.graph.dynamicgraph.DynamicGraph

Return the node order as a list of String

getNodeOrder() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

Return the node order as a list of String

getNodeOrder() - Method in interface org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraph

Return the node order as a List of NodeInfo

getNodeOrder() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

Return the node order as a List of NodeInfo

getNodeOrder() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

getNodeOrder() - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Return the node order

getNodeOrder() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getNodeOrder(DynamicGraph, DynamicGraph) - Static method in class org.ginsim.service.tool.graphcomparator.DynamicGraphComparator

Return a common nodeOrder for g1 and g2.

getNodeOrder() - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

getNodeOrder() - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionPanel

getNodeOrderForSimulation() - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

getNodeOrderForSimulation() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getNodeOrderSize() - Method in class org.ginsim.core.graph.AbstractGraph

Return the size of the node order

getNodeOrderSize() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

Return the size of the node order

getNodeOrderSize() - Method in interface org.ginsim.core.graph.GraphModel

Return the size of the node order

getNodeOrderSize() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

Return the size of the node order

getNodeOrderSize() - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

Return 0 since no node order is defined on this king of graph

getNodeOrderSize() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getNodeOrderSize() - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceTreeImpl

getNodeOrderSize() - Method in class org.ginsim.core.graph.tree.TreeImpl

Return the size of the node order

getNodes() - Method in class org.ginsim.core.graph.AbstractGraph

getNodes() - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

getNodes() - Method in interface org.ginsim.core.graph.GraphBackend

getNodes() - Method in interface org.ginsim.core.graph.GraphModel

Return the Collection of the graph nodes

getNodes() - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

getNodes() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getNodes() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

getNodes() - Method in class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

getNodes() - Method in interface org.ginsim.servicegui.tool.pathfinding.PathFindingTableModel

getNodesByIncNumberRegulators(LogicalModel) - Method in class org.ginsim.service.export.nusmv.NodeInfoSorter

getNodeShape(HierarchicalNode) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.DefaultHTGNodeStyle

getNodeShape(RegulatoryNode) - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryNodeStyle

getNodeShape(TreeNode) - Method in class org.ginsim.core.graph.tree.DefaultTreeNodeStyle

getNodeShape(V) - Method in interface org.ginsim.core.graph.view.style.NodeStyle

getNodeShape(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getNodeShape(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

getNodeStyle(String) - Method in class org.ginsim.core.graph.view.style.StyleManager

Retrieve a node style based on its name.

getNodeStyle(V, NodeStyle<V>) - Method in interface org.ginsim.core.graph.view.style.StyleProvider

Get the style to use for a node.

getNodeStyle(Object, NodeStyle) - Method in class org.ginsim.service.tool.graphcomparator.GraphComparatorStyleProvider

getNodeStyle(Object, NodeStyle) - Method in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisStyleProvider

getNodeStyle(RegulatoryNode, NodeStyle<RegulatoryNode>) - Method in class org.ginsim.service.tool.localgraph.LocalGraphStyleProvider

getNodeStyle(Object, NodeStyle) - Method in class org.ginsim.service.tool.scc.ConnectivityStyleProvider

getNodeStyle(RegulatoryNode, NodeStyle<RegulatoryNode>) - Method in class org.ginsim.servicegui.tool.lrgcolorizer.LRGPatternStyleProvider

getNodeStyle(Object, NodeStyle) - Method in class org.ginsim.servicegui.tool.pathfinding.PathStyleProvider

getNodeStyle(RegulatoryNode, NodeStyle<RegulatoryNode>) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGCustomStyleProvider

getNodeStyle(RegulatoryNode, NodeStyle<RegulatoryNode>) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGStateStyleProvider

getNodeStyle(DynamicNode, NodeStyle<DynamicNode>) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.STGPathStyleProvider

getNodeStyles() - Method in class org.ginsim.core.graph.view.style.StyleManager

Get the list of all node styles

getNodesWithInputsAtEnd(LogicalModel) - Method in class org.ginsim.service.export.nusmv.NodeInfoSorter

getNodeViewInfo(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getNodeViewInfo(V) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

getNodeViewInfo(V) - Method in interface org.ginsim.core.graph.GraphBackend

Get the Raw view info for a node.

getNormalNodes() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesHandler

getNumberInstances() - Method in class org.ginsim.service.export.cadp.CADPWriter

getNumberInstances() - Method in class org.ginsim.service.tool.composition.GenericTopology

getNumberInstances() - Method in interface org.ginsim.service.tool.composition.Topology

getNumberInstances() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

getNumberInstances() - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

getNumberInstances() - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

getNumberNeighbours(int) - Method in class org.ginsim.service.tool.composition.GenericTopology

getNumberNeighbours(int) - Method in interface org.ginsim.service.tool.composition.Topology

getObject(Graph) - Method in class org.ginsim.core.graph.objectassociation.BasicGraphAssociatedManager

getObject(Graph) - Method in interface org.ginsim.core.graph.objectassociation.GraphAssociatedObjectManager

get the existing associated object for a graph

getObject(Graph, String, boolean) - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

Allow to associate objects with a graph to retrieve them later.

getObject(int) - Method in class org.ginsim.core.utils.data.ObjectStore

getObjectManager(String) - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

Give access to the Object manager in charge of the given object

getObjectManager(Class, String) - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

Give access to the Object manager in charge of the given object

getObjectManagerList() - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

Give access to the list of registered object managers that are not associated with a graph class

getObjectManagerList(Class) - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

Give access to the list of registered object managers for the given graph class

getObjectName() - Method in class org.ginsim.core.graph.objectassociation.BasicGraphAssociatedManager

getObjectName() - Method in interface org.ginsim.core.graph.objectassociation.GraphAssociatedObjectManager

getObjectUnderPoint(Point) - Method in interface org.ginsim.gui.graph.canvas.CanvasRenderer

Find the object under the provided point.

getObjectUnderPoint(Point) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

getOffset() - Method in interface org.ginsim.core.graph.view.ViewCopyHelper

Offset to move the last copied element.

getOffset() - Method in class org.ginsim.service.tool.modelreduction.ReconstructionTask

getOldEdges() - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

getOldNodes() - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

getomplementaryNode(String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

getOperandClassName() - Static method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

getOperands() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationOperation

getOperation() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationOperation

getOperators() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNodeFactory

getOperatorsAndParenthesis() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNodeFactory

getOption(String) - Static method in class org.ginsim.common.application.OptionStore

get the saved value of an option

getOption(String, T) - Static method in class org.ginsim.common.application.OptionStore

get the saved value of an option with a fallback value.

getOptionNames() - Method in class org.ginsim.core.notification.resolvable.ResolvableErrorNotification

getOptionNames() - Method in interface org.ginsim.core.notification.resolvable.ResolvableNotification

Provide the list of options for the resolution

getOptionNames() - Method in class org.ginsim.core.notification.resolvable.ResolvableWarningNotification

Returns the list of the associated resolution options

getOptionsName() - Method in class org.ginsim.core.notification.resolvable.InvalidFunctionResolution

getOptionsName() - Method in class org.ginsim.core.notification.resolvable.NotificationResolution

getOracleNames() - Method in class org.ginsim.service.tool.avatar.params.AvatarStateStore

getOracles() - Method in interface org.colomoto.biolqm.StatefulLogicalModel

Gets the stored oracles

getOracles() - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

getOracles() - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Accesses the oracles associated with the graph

getOracles() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getOracles() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.CompleteStatePanel

Updates the information on the state panel

getOracleState() - Method in class org.ginsim.service.tool.avatar.params.AvatarStateStore

getOrder(RegulatoryGraph) - Method in interface org.ginsim.core.graph.regulatorygraph.NodeOrderer

Pick an order for the components of a regulatory graph.

getOscillations() - Method in class org.ginsim.service.tool.stableregions.PNGraph

getOut() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

getOutgoingEdges(V) - Method in class org.ginsim.core.graph.AbstractGraph

getOutgoingEdges(V) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

getOutgoingEdges(V) - Method in interface org.ginsim.core.graph.GraphBackend

getOutgoingEdges(V) - Method in interface org.ginsim.core.graph.GraphModel

getOutput() - Method in class org.colomoto.biolqm.io.avatar.AvatarClause

Returns the target state of the regulated component

getOutputStrippingUsers() - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

getPanel(Object, StackDialog) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatesGUIHelper

getPanel(TreeElement, JTree, boolean, int, boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.PanelFactory

getPanel(ListOfPerturbations, StackDialog) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationGUIHelper

getPanel(T, StackDialog) - Method in interface org.ginsim.gui.guihelpers.GUIHelper

get a panel to edit this data

getPanel(ListOfReductionConfigs, StackDialog) - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionGUIHelper

getPanel(SimulationParameterList, StackDialog) - Method in class org.ginsim.servicegui.tool.reg2dyn.SimulationParametersGUIHelper

getPanelFactory() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeRenderer

getParameter(String) - Method in class org.ginsim.core.graph.tree.TreeBuilder

getParameter(int) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

getParameters() - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationParser

getParameters() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParametersParser

getParams(List<Integer>) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

getParent() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

getParent() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

getParent() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

getParent() - Method in class org.ginsim.core.graph.view.style.BaseStyle

getParent() - Method in class org.ginsim.core.graph.view.style.BaseStyleOverride

getParent() - Method in interface org.ginsim.core.graph.view.style.Style

getParentIndex() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

getParentIndex() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

getParentProperty(StyleProperty) - Method in class org.ginsim.core.graph.view.style.BaseStyle

getParentProperty(StyleProperty) - Method in class org.ginsim.core.graph.view.style.BaseStyleOverride

getParentProperty(StyleProperty) - Method in interface org.ginsim.core.graph.view.style.Style

getParser() - Method in class org.ginsim.core.graph.AbstractGraphFactory

getParser() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphFactory

getParser() - Method in interface org.ginsim.core.graph.GraphFactory

Return the class of the parser to use to read from file the type of graph the factory manager

getParser() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphFactory

getParser() - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphFactory

getParser() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphFactory

getParser() - Method in interface org.ginsim.core.graph.tree.Tree

getParser() - Method in class org.ginsim.core.graph.tree.TreeFactory

getParser() - Method in class org.ginsim.core.graph.tree.TreeImpl

getParserClass(String) - Method in class org.ginsim.core.graph.GSGraphManager

Search for the factory managing the given graph type and return the corresponding parser

getPath(TreeElement) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

getPath(byte, String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

getPath() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

getPaths(String) - Method in class org.ginsim.service.tool.avatar.domain.ApproximateFinalPaths

getPaths(String) - Method in class org.ginsim.service.tool.avatar.domain.ExhaustiveFinalPaths

getPaths(String) - Method in interface org.ginsim.service.tool.avatar.domain.FinalPaths

Returns the transitions to reachable exit states from a given state in the cycle

getPattern(DynamicEdge) - Method in class org.ginsim.core.graph.dynamicgraph.DefaultDynamicEdgeStyle

getPattern(Graph<DynamicNode, Edge<DynamicNode>>) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicNode

getPattern() - Method in interface org.ginsim.core.graph.regulatorygraph.namedstates.PatternHolder

getPattern() - Method in enum org.ginsim.core.graph.view.EdgePattern

getPattern(E) - Method in interface org.ginsim.core.graph.view.style.EdgeStyle

getPattern(E) - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

getPattern(E) - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

getPattern() - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

getPatternString(Graph<DynamicNode, Edge<DynamicNode>>) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicNode

getPclass(List<NodeInfo>) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

getPerturbation() - Method in interface org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationHolder

Retrieve the stored perturbation.

getPerturbation() - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationStore

getPerturbation() - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationUser

getPerturbation() - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

getPerturbation(SimulationParameters) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

getPerturbation() - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphFrame

getPerturbationPanel(ListOfPerturbations, StackDialog) - Static method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationGUIHelper

getPlainData() - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Fetch the data in a text/plain format.

getPNG(Graph<?, ?>, int) - Method in class org.ginsim.service.export.image.ImageExportService

getPnGraph() - Method in class org.ginsim.service.tool.stableregions.PNtoGraph

getPoint(int) - Method in class org.ginsim.core.graph.view.Bezier

Returns the bezier points at position i.

getPointCount() - Method in class org.ginsim.core.graph.view.Bezier

Returns the number of bezier points.

getPoints() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

getPoints() - Method in class org.ginsim.core.graph.backend.EdgeViewInfoImpl

getPoints() - Method in class org.ginsim.core.graph.view.Bezier

Returns the calculated bezier points.

getPoints() - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

getPoints() - Method in interface org.ginsim.core.graph.view.EdgeViewInfo

getPoints(Rectangle, Rectangle, List<Point>, int) - Static method in class org.ginsim.core.graph.view.ViewHelper

getPoints(NodeAttributesReader, EdgeAttributesReader, Edge<?>) - Static method in class org.ginsim.core.graph.view.ViewHelper

Route an edge: add automated intermediate points if needed, compute the points on the nodes bounding boxes.

getPParent() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

getPreferredSize(JComponent) - Method in class org.ginsim.commongui.utils.VerticalLabelUI

Returns a Dimension appropriate for vertical rendering

getPreferredSize() - Method in class org.ginsim.servicegui.tool.avatar.others.FixedSizePanel

getPreviousMaxValue() - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

try to decrease the max value

getPreviousMinValue() - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

try to decrease the min value

getPreviousValue() - Method in class org.ginsim.gui.graph.regulatorygraph.NodeMaxValueSpinModel

getPreviousValue() - Method in class org.ginsim.gui.utils.data.models.MaxSpinModel

getPreviousValue() - Method in class org.ginsim.gui.utils.data.models.MinSpinModel

getPriority(String) - Static method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNodeFactory

getPriorityClassDefinition() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

getProbability(State) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Returns the probability of a given state in the state-set

getProbability(State) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Returns the probability of a given state in the state-set

getProbableExitState(State) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Randomly accesses a probable exit state from a given state in the state-set

getProbableExitState(State) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Randomly accesses a probable exit state from a given state in the state-set

getProbableRandomState() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Selects a state by adequately considering the probabilities of the states in the state-set

getProbableRandomState() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Selects a state by adequately considering the probabilities of the states in the state-set

getProgression(List<double[]>, String, String, String) - Static method in class org.ginsim.service.tool.avatar.utils.ChartGNUPlot

Creates a chart based on the progression of probabilities per state-set (F, N, A)

getProperComponents() - Method in class org.ginsim.service.tool.composition.RegulatoryIntegration

getProperComponentsForInput(RegulatoryNode) - Method in class org.ginsim.service.export.cadp.CADPWriter

getProperComponentsForInput(RegulatoryNode) - Method in class org.ginsim.service.tool.composition.IntegrationFunctionMapping

getProperties() - Method in class org.ginsim.core.graph.dynamicgraph.DefaultDynamicEdgeStyle

getProperties() - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryEdgeStyle

getProperties() - Method in class org.ginsim.core.graph.view.style.BaseStyleOverride

getProperties() - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

getProperties() - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getProperties() - Method in interface org.ginsim.core.graph.view.style.Style

Retrieve all properties used by this style.

getProperties() - Method in class org.ginsim.gui.utils.data.ObjectEditor

getPropertiesForStyle(String) - Method in class org.ginsim.common.document.DocumentStyle

Return all the properties for a style

getPropertiesIteratorForStyle(String) - Method in class org.ginsim.common.document.DocumentStyle

Return an iterator over the properties for a style

getProperty(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

getProperty(StyleProperty) - Method in class org.ginsim.core.graph.view.style.BaseStyleOverride

getProperty(StyleProperty) - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

getProperty(StyleProperty) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getProperty(StyleProperty) - Method in interface org.ginsim.core.graph.view.style.Style

Retrieve the value of a property.

getProto() - Method in class org.ginsim.core.annotation.AnnotationLink

getRandomState(LogicalModel, List<byte[]>, boolean) - Static method in class org.ginsim.service.tool.avatar.simulation.SimulationUtils

Selects an initial state from a given pattern or state-set

getRawValue(int) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

getRawValue(int) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

getRawValue(int) - Method in class org.ginsim.gui.graph.view.style.StyleEditor

getRawValue() - Method in class org.ginsim.gui.utils.data.GenericPropertyInfo

getRawValue(int) - Method in class org.ginsim.gui.utils.data.ObjectEditor

getReady() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

getRealDepth(TreeNode) - Method in class org.ginsim.core.graph.tree.TreeBuilder

getRealDetph() - Method in class org.ginsim.core.graph.tree.TreeBuilder

getRealSize() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

getRecentFiles() - Static method in class org.ginsim.common.application.OptionStore

Get the list of recent files.

getReconstructionTask(LogicalModel, RegulatoryGraph) - Method in class org.ginsim.service.tool.modelreduction.ModelReductionService

Rebuild a regulatory graph from a reduced model.

getRectangle(Point, Point) - Static method in class org.ginsim.core.graph.view.ViewHelper

Get a rectangle given its two angle points.

getRectangle(int, int, int, int) - Static method in class org.ginsim.core.graph.view.ViewHelper

Get a rectangle given its two angle points.

getReducedCompatibleStableStates() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

getReducedGraph() - Method in class org.ginsim.service.tool.composition.ReductionStub

getReduction() - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

getReduction() - Method in interface org.ginsim.service.tool.modelreduction.ReductionHolder

Retrieve the stored reduction.

getReductionPanel(ListOfReductionConfigs) - Static method in class org.ginsim.servicegui.tool.modelreduction.ReductionGUIHelper

getReport() - Method in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisAlgoResult

getRestrictions() - Method in class org.colomoto.biolqm.io.avatar.AvatarClause

Returns the list of restrictions imposing a well-defined state in the current component

getResults() - Method in class org.ginsim.commongui.dialog.ResultsDialog

getReturnClassName() - Static method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

getRicherData(DataFlavor) - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

getRicherFlavors() - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Some subclasses will have flavors that are more descriptive than HTML or plain text.

getRoot() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

getRoot() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

getRoot() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

getRoot() - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

getRotationAngle(int, int) - Static method in class org.ginsim.core.graph.view.ViewHelper

Get the rotation angle between a vector and the horizontal axis.

getRowCount() - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

getRowCount() - Method in class org.ginsim.gui.graph.dynamicgraph.StableTableModel

getRowCount() - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTableModel

getRowCount() - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphTableModel

getRowCount() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

getRowCount() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.FTableInteractionModel

getRowCount() - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

getRowCount() - Method in class org.ginsim.gui.utils.data.SimpleStateListTableModel

getRowCount() - Method in class org.ginsim.gui.utils.widgets.treetable.TreeTableModelAdapter

getRowCount() - Method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

getRowCount() - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserPathModel

getRowCount() - Method in class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

getRowCount() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPModel

getRowCount() - Method in class org.ginsim.servicegui.tool.trapspace.TrapSpaceTableModel

getSaveMode() - Method in interface org.ginsim.gui.graph.GraphOptionPanel

getSaveMode() - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphOptionPanel

getSaveOptionPanel(DynamicGraph) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicGraphGUIHelper

Create a panel containing the option for graph saving

getSaveOptionPanel(G) - Method in interface org.ginsim.gui.graph.GraphGUIHelper

Create a panel containing the option for graph saving

getSaveOptionPanel(HierarchicalTransitionGraph) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

Create a panel containing the option for graph saving

getSaveOptionPanel(ReducedGraph) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

Create a panel containing the option for graph saving

getSaveOptionPanel(RegulatoryGraph) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

getSaveOptionPanel(TrapSpaceInclusionDiagram) - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

getSaveOptionPanel(Tree) - Method in class org.ginsim.gui.graph.tree.TreeGUIHelper

Create a panel containing the option for graph saving

getSaveString(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

getSaveVal() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanGene

getSCC() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueSCC

getSCCGraph(Graph) - Method in class org.ginsim.service.tool.scc.SCCGraphService

Compute the SCC of graph.

getSCCs(RegulatoryGraph) - Method in class org.ginsim.service.tool.stableregions.StableRegionsService

getScore() - Method in class org.ginsim.service.tool.circuit.CircuitDescrInTree

getSearcher(LogicalModel) - Method in class org.ginsim.service.tool.stablestates.StableStatesService

Deprecated.

This low-level API could change or be removed

getSearcher(RegulatoryGraph) - Method in class org.ginsim.service.tool.stablestates.StableStatesService

Deprecated.

This low-level API could change or be removed

getSelected() - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationSelectionPanel

getSelected() - Method in class org.ginsim.gui.utils.data.ListSelectionPanel

getSelected() - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionConfigSelectionPanel

getSelected() - Method in class org.ginsim.servicegui.tool.reg2dyn.PrioritySelectionPanel

getSelectedAction() - Method in class org.ginsim.gui.graph.EditActionManager

getSelectedArea() - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.FunctionEditorModel

getSelectedEdges() - Method in class org.ginsim.gui.graph.GraphSelection

getSelectedFile() - Method in class org.ginsim.gui.shell.actions.ExportAction

getSelectedFunction() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

getSelectedIndex() - Method in class org.ginsim.core.utils.data.ValueList

getSelectedInitialState() - Method in class org.ginsim.service.format.sbml.SBMLQualConfig

getSelectedInputState() - Method in class org.ginsim.service.format.sbml.SBMLQualConfig

getSelectedItem() - Method in class org.ginsim.gui.utils.data.ListEditionPanel

getSelectedItem() - Method in class org.ginsim.gui.utils.data.ListPanel

getSelectedItem() - Method in class org.ginsim.gui.utils.data.models.ValueListComboModel

getSelectedNodes() - Method in class org.ginsim.gui.graph.GraphSelection

getSelectedNodes() - Method in class org.ginsim.servicegui.export.cadp.VisibleComponentsWidget

getSelectedProperComponentsForInput(RegulatoryNode) - Method in class org.ginsim.servicegui.tool.composition.IntegrationFunctionWidget

getSelectedSet(Collection<NodeReducedData>) - Method in interface org.ginsim.core.graph.reducedgraph.ReducedGraph

getSelectedSet(Collection<NodeReducedData>) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

getSelectedStateList(boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

Get a list with the selected states

getSelection() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

getSelection() - Method in class org.ginsim.gui.graph.BaseGraphGUI

getSelection() - Method in interface org.ginsim.gui.graph.GraphGUI

Get an object to interact with the selection

getSelection(boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

getSelection() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

Get a boolean array defining the indexes of the selected states

getSelection() - Method in class org.ginsim.gui.utils.data.ListEditionPanel

getSelection() - Method in class org.ginsim.gui.utils.data.ListPanel

getSelectionPanel(Object, StackDialog) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatesGUIHelper

getSelectionPanel(ListOfPerturbations, StackDialog) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationGUIHelper

getSelectionPanel(T, StackDialog) - Method in interface org.ginsim.gui.guihelpers.GUIHelper

get a panel to select an item (for lists of elements)

getSelectionPanel(ListOfReductionConfigs, StackDialog) - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionGUIHelper

getSelectionPanel(SimulationParameterList, StackDialog) - Method in class org.ginsim.servicegui.tool.reg2dyn.SimulationParametersGUIHelper

getSelectionType() - Method in class org.ginsim.gui.graph.GraphSelection

getSelector() - Method in class org.ginsim.core.graph.view.css.Colorizer

getService(Class<S>) - Static method in class org.ginsim.core.service.GSServiceManager

Give access to the service by service class

getService(String) - Static method in class org.ginsim.core.service.GSServiceManager

Give access to the service by service name

getServicesInfo() - Static method in class org.ginsim.core.service.GSServiceManager

getServicesInfo() - Static method in class org.ginsim.gui.service.GSServiceGUIManager

getShape() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getShape() - Method in enum org.ginsim.core.graph.view.EdgeEnd

getShape() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

getShape(int, int, int, int) - Method in enum org.ginsim.core.graph.view.NodeShape

getShortDesc() - Method in enum org.ginsim.core.graph.regulatorygraph.RegulatoryEdgeSign

getShortDescForGUI() - Static method in enum org.ginsim.core.graph.regulatorygraph.RegulatoryEdgeSign

getShortDetail(String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

getShortDetail() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

getShortestPath(V, V) - Method in class org.ginsim.core.graph.AbstractGraph

getShortestPath(V, V) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

Find the shortest path between the two given vertices

getShortestPath(V, V) - Method in interface org.ginsim.core.graph.GraphBackend

Find the shortest path between the two given vertices

getShortestPath(V, V) - Method in interface org.ginsim.core.graph.GraphModel

Find the shortest path between the two given vertices

getShortId() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

getShortInfo(String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

getShortInfo() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

getSigma() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

return the set sigma

getSigmaImage() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSet

getSign() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

getSign() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

getSign(int) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

getSimulation(String) - Static method in class org.ginsim.service.tool.avatar.service.AvatarServiceFacade

Creates an avatar simulation from a string command

getSimulation(String[]) - Static method in class org.ginsim.service.tool.avatar.service.AvatarServiceFacade

Creates an avatar simulation from a given set of arguments

getSimulation(String) - Static method in class org.ginsim.service.tool.avatar.service.FirefrontServiceFacade

Creates a firefront simulation from a string command

getSimulation(String[]) - Static method in class org.ginsim.service.tool.avatar.service.FirefrontServiceFacade

Creates a firefront simulation from a given set of arguments

getSimulation(String) - Static method in class org.ginsim.service.tool.avatar.service.MonteCarloServiceFacade

Creates a montecarlo simulation from a string command

getSimulation(String[]) - Static method in class org.ginsim.service.tool.avatar.service.MonteCarloServiceFacade

Creates a Monte Carlo simulation from a given set of arguments

getSimulation(StatefulLogicalModel, boolean) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.AvatarPanel

getSimulation(StatefulLogicalModel, boolean) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.FirefrontPanel

getSimulation(StatefulLogicalModel, boolean) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.MonteCarloPanel

getSimulation(StatefulLogicalModel, boolean) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.SimulationPanel

Given contextual information, returns a simulation adequately parameterized according to the panel

getSimulationStrategyPanel() - Method in class org.ginsim.servicegui.tool.reg2dyn.SimulationParameterEditionPanel

getSize() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

getSize() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Gives the count of states in the diagram or INCONSISTENT_SIZE if the size is in inconsistent state.

getSize(TrapSpaceInclusionDiagram) - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceNode

getSize() - Method in class org.ginsim.core.utils.data.ObjectStore

getSize() - Method in class org.ginsim.gui.graph.regulatorygraph.IncomingEdgeListModel

getSize() - Method in class org.ginsim.gui.utils.data.models.ValueListComboModel

getSize() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

getSizeOrOverApproximation() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Gives the count of states in the diagram or its overapproximation if the size is in inconsistent state.

getSizeOrUpdate() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Gives the count of states in the diagram.
If the size is in inconsistent state, then call updateSize() before.

getSMax() - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

getSMin() - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

getSon(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

getSon(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

getSortKey(JTable, int) - Method in class org.ginsim.commongui.utils.DefaultTableHeaderCellRenderer

Returns the current sort key, or null if the column is unsorted.

getSource() - Method in class org.ginsim.core.graph.Edge

Get the source of this edge.

getSourceActions(JComponent) - Method in class org.ginsim.gui.utils.widgets.TableHeaderTransferHandler

getSourceEdge(E) - Method in interface org.ginsim.core.graph.view.ViewCopyHelper

Retrieve the equivalent edge from the source graph.

getSourceEdge(RegulatoryMultiEdge) - Method in class org.ginsim.service.tool.modelreduction.ReconstructionTask

getSourceNode(V) - Method in interface org.ginsim.core.graph.view.ViewCopyHelper

Retrieve the equivalent node from the source graph.

getSourceNode(RegulatoryNode) - Method in class org.ginsim.service.tool.modelreduction.ReconstructionTask

getStableActionName() - Static method in class org.ginsim.service.export.cadp.CADPWriter

getStableMotifs() - Method in class org.ginsim.service.tool.stableregions.PNGraph

getStableStates() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

getStartX() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GlassPane

getStartY() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GlassPane

getState(int) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

getState(int) - Method in class org.ginsim.gui.graph.dynamicgraph.StableTableModel

getState(int) - Method in interface org.ginsim.gui.graph.dynamicgraph.StateTableModel

getState(int) - Method in class org.ginsim.gui.utils.data.SimpleStateListTableModel

getState(byte[], int) - Method in class org.ginsim.service.layout.BaseSTGLayout

Get the level of a component

getState(String) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Returns a state given its key

getState(String) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Returns a state given its key

getState() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

getStateList() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

getStateList() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

Get the list of states

getStatePattern() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

Convert the internal lists of values into lists of ranges for use in bioLQM.

getStatePatterns(List<NodeInfo>, AbstractStateSet) - Static method in class org.ginsim.service.tool.avatar.simulation.MDDUtils

Infers a set of state patterns from a given set of states

getStates() - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Accesses the initial states associated with the graph

getStates() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getStates() - Method in class org.ginsim.service.tool.avatar.domain.CompactStateSet

Accesses the states in the state-set

getStates() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Returns a collection with the states in the state-set

getStates() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Returns a collection with the states in the state-set

getStates(NamedStatesHandler, List<NodeInfo>) - Static method in class org.ginsim.service.tool.avatar.simulation.MDDUtils

Returns a list of states given a handler for NamedStates and the ordered set of components

getStatesToHierarchicalNodes(DynamicGraph) - Static method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.LimitedSimulationService

getStateVarWriter() - Method in class org.ginsim.service.export.cadp.CADPWriter

getStatus(DynamicNode) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

getStatus(DynamicEdge) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

getStore() - Method in class org.ginsim.service.format.ginml.GINMLFormatConfig

getStreamForPath(String) - Static method in class org.ginsim.common.utils.IOUtils

Produces a FileInputStream initialized with the given path

getStreamForPath(Package, String) - Static method in class org.ginsim.common.utils.IOUtils

get an input stream for a file inside a given package.

getString(Object) - Method in class org.ginsim.core.graph.view.style.ColorProperty

getString(Object) - Method in class org.ginsim.core.graph.view.style.IntegerProperty

getString(Object) - Method in class org.ginsim.core.graph.view.style.StyleProperty

getString() - Method in class org.ginsim.service.export.image.SVGEncoder

getStrings(String[]) - Static method in class org.ginsim.common.application.Txt

Retrieve a group of strings at once.

getStringValue(int) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

getStringValue(int) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

getStringValue(int) - Method in class org.ginsim.gui.graph.view.style.StyleEditor

getStringValue() - Method in class org.ginsim.gui.utils.data.GenericPropertyInfo

getStringValue(int) - Method in class org.ginsim.gui.utils.data.ObjectEditor

getStringValue(String, String[]) - Static method in class org.ginsim.service.tool.avatar.utils.AvaOptions

Get the string value of a given parameter

getStronglyConnectedComponents() - Method in class org.ginsim.core.graph.AbstractGraph

Return a list of set of node, each set containing a strongly connected component of the graph

getStronglyConnectedComponents() - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

Return a list of set of vertex, each set containing a strongly connected component of the graph

getStronglyConnectedComponents() - Method in interface org.ginsim.core.graph.GraphBackend

Return a list of set of node, each set containing a strongly connected component of the graph

getStronglyConnectedComponents() - Method in interface org.ginsim.core.graph.GraphModel

Return a list of set of node, each set containing a strongly connected component of the graph

getStyle() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

getStyle() - Method in class org.ginsim.core.graph.backend.EdgeViewInfoImpl

getStyle() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getStyle(String) - Method in class org.ginsim.core.graph.view.css.Selector

Get the style for a category id or null if the category doesn't exist.

getStyle(Object) - Method in class org.ginsim.core.graph.view.css.Selector

Get the style for an object using getCategory to determine its category or null if the category doesn't exist or has no category If possible call getStyleForNode or getStyleForEdge, when you know the type of object

getStyle() - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

getStyle() - Method in interface org.ginsim.core.graph.view.EdgeViewInfo

getStyle() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

getStyle() - Method in interface org.ginsim.core.graph.view.NodeViewInfo

Get the style used to draw this node.

getStyle(RegulatoryGraph, byte[]) - Method in class org.ginsim.service.export.image.ImageExportService

getStyle(RegulatoryGraph, int[]) - Method in class org.ginsim.service.export.image.ImageExportService

getStyle(RegulatoryGraph, TrapSpace) - Method in class org.ginsim.service.export.image.ImageExportService

getStyle() - Method in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisAlgoResult

getStyleForEdge(Object) - Method in class org.ginsim.core.graph.view.css.Selector

Get the style for an edge using getCategory to determine its category or null if the category doesn't exist or has no category

getStyleForNode(Object) - Method in class org.ginsim.core.graph.view.css.Selector

Get the style for a node using getCategory to determine its category or null if the category doesn't exist or has no category

getStyleIterator() - Method in class org.ginsim.common.document.DocumentStyle

Return an iterator over the styles identifiers.

getStyleManager() - Method in class org.ginsim.core.graph.AbstractGraph

getStyleManager() - Method in interface org.ginsim.core.graph.Graph

Retrieve the style manager for this graph.

getStyleProvider() - Method in class org.ginsim.core.graph.view.style.StyleManager

Retrieve the current style provider.

getStyleProvider() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparatorResult

getStyleProvider(List<NodeReducedData>, Graph) - Method in class org.ginsim.service.tool.scc.SCCGraphService

getStyles() - Method in class org.ginsim.common.document.DocumentWriter

Get the styles of the document, and initialize them if needed.

getSubgraph(Collection<V>, Collection<E>) - Method in class org.ginsim.core.graph.AbstractGraph

Specialized method that build the sub-graph corresponding to the given lists of vertices and edges The returned graph contains clones of the given graph objects structured as they are in the current graph

getSubgraph(Collection, Collection) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

getSubgraph(Collection<V>, Collection<E>) - Method in interface org.ginsim.core.graph.GraphModel

Build a graph from the provided vertices and edges based on the current graph

getSubgraph(Collection<HierarchicalNode>, Collection<DecisionOnEdge>) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

Not used for this kind of graph: it's not interactively editable

getSubgraph(Collection, Collection) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

getSubgraph(Collection<RegulatoryNode>, Collection<RegulatoryMultiEdge>) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

getSubgraph(Collection<TrapSpaceNode>, Collection<TrapSpaceInclusion>) - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceTreeImpl

getSubgraph(Collection<TreeNode>, Collection<TreeEdge>) - Method in class org.ginsim.core.graph.tree.TreeImpl

getSuperInterfaces(Class) - Static method in class org.ginsim.common.utils.IntrospectionUtils

Return the list of all the interfaces (recursively) the given class implements

getSupportActions() - Static method in class org.ginsim.gui.shell.callbacks.HelpCallBack

getSupportClass(Class) - Static method in class org.ginsim.gui.utils.data.GenericPropertyEditorPanel

getSVG(Graph, StyleProvider) - Method in class org.ginsim.service.export.image.ImageExportService

Get a SVG representation of the graph with a custom style

getSVG(Graph) - Method in class org.ginsim.service.export.image.ImageExportService

Get a SVG representation of the graph

getSvlFilename() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getSymbol() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TAndOperator

getSymbol() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperator

getSymbol() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TNotOperator

getSymbol() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TOrOperator

getSynchronousInstance(LogicalModel) - Static method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.ginsim.gui.utils.widgets.treetable.JTreeTable.TreeTableCellEditor

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.ginsim.commongui.utils.DefaultTableHeaderCellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.ginsim.commongui.utils.MixedTableHeader

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemCellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalCellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.ginsim.gui.utils.widgets.treetable.JTreeTable.TreeTableCellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.ginsim.servicegui.export.cadp.ShowNonEditableStringCellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicPathItemCellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.ginsim.servicegui.tool.stablestates.ColoredCellRenderer

getTarget() - Method in class org.ginsim.core.graph.Edge

Get the target of this edge.

getTask(LogicalModel) - Static method in class org.ginsim.service.tool.stablestates.StableStatesService

getTask(RegulatoryGraph) - Method in class org.ginsim.service.tool.stablestates.StableStatesService

getTask(LogicalModel) - Method in class org.ginsim.service.tool.trapspace.TrapSpaceServiceWrapper

getTerminalWidth() - Method in class org.ginsim.core.graph.tree.TreeBuilder

getText() - Method in class org.ginsim.gui.utils.widgets.StatusTextField

getTextColor() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getTextColor(TreeNode) - Method in class org.ginsim.core.graph.tree.DefaultTreeNodeStyle

getTextColor() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

getTextColor(V) - Method in interface org.ginsim.core.graph.view.style.NodeStyle

getTextColor(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getTextColor(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

getThreshold() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationAtom

getTitle() - Method in exception org.ginsim.common.application.GsException

get a title for the error window.

getTitle() - Method in class org.ginsim.gui.graph.view.style.StyleTab

getTitle() - Method in interface org.ginsim.gui.shell.editpanel.EditTab

getTitle() - Method in class org.ginsim.gui.shell.editpanel.MainEditTab

getTitle() - Method in class org.ginsim.gui.utils.widgets.GsPanel

getTitle() - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalEditTab

getTokenNames() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

getToolTipText(MouseEvent) - Method in class org.ginsim.servicegui.tool.avatar.others.TitleToolTipPanel

getTopic() - Method in class org.ginsim.core.notification.Notification

Return the topic the notification is related to

getTopNotification() - Method in interface org.ginsim.gui.notifications.NotificationSource

getTopNotification() - Method in class org.ginsim.gui.shell.MainFrame

Return the most important notification (it is the head of the queue since the queue is ordered to have the most urgent notification on top).

getTopology() - Method in class org.ginsim.service.export.cadp.CADPExportConfig

getTopology() - Method in class org.ginsim.service.tool.composition.CompositionConfig

getTotalLevels() - Method in class org.ginsim.core.graph.tree.TreeBuilder

getTransferData(DataFlavor) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

getTransferData(DataFlavor) - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Returns an object which represents the data to be transferred.

getTransferDataFlavors() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

getTransferDataFlavors() - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Returns an array of DataFlavor objects indicating the flavors the data can be provided in.

getTransitionInputs(String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

getTransitionOutput(String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

getTransitions() - Method in class org.ginsim.service.tool.stableregions.PNGraph

getTree() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

getTreeCellEditorComponent(JTree, Object, boolean, boolean, boolean, int) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeEditor

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeRenderer

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.ginsim.gui.utils.widgets.EnhancedListCellRenderer

getTreeExpression() - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanel

getTreeExpression() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

getTreePanel() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

getType() - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getType() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

getType(Graph) - Method in class org.ginsim.core.graph.reducedgraph.NodeReducedData

Indicates the type of component.

getType() - Method in class org.ginsim.core.graph.tree.TreeNode

getType() - Method in class org.ginsim.core.notification.Notification

getTypeName(Graph) - Method in class org.ginsim.core.graph.reducedgraph.NodeReducedData

getUniformRandomState() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Selects a state assuming an uniform distribution of the probabilities of the states in the state-set

getUniformRandomState() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Selects a state assuming an uniform distribution of the probabilities of the states in the state-set

getUniqueId() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Return the long identifying this node "uniquely" (if in the range of long)

getUniqueId() - Method in class org.ginsim.core.graph.tree.TreeNode

getUnrecoverable() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSet

getUpdatePolicy() - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

getUpdater(LogicalModel) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

getUpdater(LogicalModel) - Method in interface org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinition

getUpdater(LogicalModel) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionAsynchronous

getUpdater(LogicalModel) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionComplete

getUpdater(LogicalModel) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSequential

getUpdater(LogicalModel) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSynchronous

getUpdaterForState(byte[]) - Method in class org.ginsim.service.tool.reg2dyn.Simulation

Create and initialize a SimulationUpdater for a given __state__.

getUpdatingMode() - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

getUpdatingMode() - Method in interface org.ginsim.service.tool.reg2dyn.priorityclass.UpdaterDefinitionStore

Retrieve the stored definition

getUpdatingMode() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

getUpperValue() - Method in class org.ginsim.gui.utils.widgets.RangeSlider

Returns the upper value in the range.

getUsedEdgeStyle(E) - Method in class org.ginsim.core.graph.view.style.StyleManager

Get the edge style stored in the graph.

getUsedNodeStyle(V) - Method in class org.ginsim.core.graph.view.style.StyleManager

Get the node style stored in the graph.

getUsedPerturbation(String) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

Retrieve the perturbation used by a specific user.

getUsedReduction(String) - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

getV_logicalParameters() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

getVal() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanGene

getVal() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperand

getVal(int) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

getValue() - Method in class org.ginsim.core.annotation.AnnotationLink

getValue() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanGene

getValue() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeValue

getValue() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

get value of the interaction

getValue() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TAndOperator

getValue() - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNode

getValue() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TNotOperator

getValue() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TOrOperator

getValue() - Method in class org.ginsim.core.graph.tree.TreeEdge

getValue() - Method in class org.ginsim.core.graph.tree.TreeNode

getValue(String) - Method in class org.ginsim.core.graph.view.style.ColorProperty

getValue(String) - Method in class org.ginsim.core.graph.view.style.EnumProperty

getValue(String) - Method in class org.ginsim.core.graph.view.style.IntegerProperty

getValue(String) - Method in class org.ginsim.core.graph.view.style.StyleProperty

getValue() - Method in class org.ginsim.gui.graph.dynamicgraph.StateTransitionGraphEditor

getValue() - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalGraphEditor

getValue() - Method in class org.ginsim.gui.graph.regulatorygraph.NodeMaxValueSpinModel

getValue(L, T, int) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

getValue() - Method in class org.ginsim.gui.utils.data.models.MaxSpinModel

getValue() - Method in class org.ginsim.gui.utils.data.models.MinSpinModel

getValue() - Method in interface org.ginsim.gui.utils.data.TextProperty

getValue() - Method in class org.ginsim.gui.utils.widgets.RangeSlider

Returns the lower value in the range.

getValue(PrioritySetDefinition, PriorityClass, int) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionHelper

getValueAt(int, int) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

getValueAt(int, int) - Method in class org.ginsim.gui.graph.dynamicgraph.StableTableModel

getValueAt(int, int) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTableModel

getValueAt(int, int) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphTableModel

getValueAt(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

getValueAt(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

getValueAt(int, int) - Method in class org.ginsim.gui.utils.data.SimpleStateListTableModel

getValueAt(Object, int) - Method in interface org.ginsim.gui.utils.widgets.treetable.TreeTableModel

Returns the value to be displayed for node node, at column number column.

getValueAt(int, int) - Method in class org.ginsim.gui.utils.widgets.treetable.TreeTableModelAdapter

getValueAt(int, int) - Method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

getValueAt(int, int) - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserPathModel

getValueAt(int, int) - Method in class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

getValueAt(int, int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPModel

getValueAt(int, int) - Method in class org.ginsim.servicegui.tool.trapspace.TrapSpaceTableModel

getValues() - Method in class org.ginsim.core.graph.view.style.EnumProperty

getVerboseLevel() - Static method in class org.ginsim.common.application.LogManager

Returns the verbose level actually set 0 = log; 1= info; 2 = trace

getVertex(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

Get an existing vertex.

getVertexSupplier() - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getViewEdgeStyle(E) - Method in class org.ginsim.core.graph.view.style.StyleManager

Get the edge style used for the view.

getViewMenu(JMenu) - Method in class org.ginsim.gui.graph.BaseGraphGUI

getViewMenu(JMenu) - Method in class org.ginsim.gui.graph.canvas.CanvasGraphGUIImpl

getViewMenu(JMenu) - Method in interface org.ginsim.gui.graph.GraphGUI

Fill the view menu with actions available on this graph GUI

getViewNodeStyle(V) - Method in class org.ginsim.core.graph.view.style.StyleManager

Get the node style used for the view.

getVInfoSet() - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

getVirtualDimension() - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

getVirtualDimension() - Method in interface org.ginsim.gui.graph.canvas.VirtualScrollable

Get the full virtual size of this widget.

getVisibleArea() - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

getVisibleArea() - Method in interface org.ginsim.gui.graph.canvas.VirtualScrollable

Get the part of the virtual size that is currently visible.

getWarnings() - Method in class org.ginsim.common.xml.XMLHelper

Get the list of warning encountered during parsing if any.

getWeight() - Method in class org.ginsim.gui.service.AbstractServiceGUI

getWeight() - Method in interface org.ginsim.gui.service.ServiceGUI

Give the real weight for the service.

getWeight() - Method in class org.ginsim.gui.shell.actions.BaseAction

getWidth() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getWidth() - Method in class org.ginsim.core.graph.tree.TreeNode

getWidth() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

getWidth(E) - Method in interface org.ginsim.core.graph.view.style.EdgeStyle

getWidth(E) - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

getWidth(E) - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

getWidth(V) - Method in interface org.ginsim.core.graph.view.style.NodeStyle

getWidth(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

getWidth(V) - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

getWidth() - Method in class org.ginsim.gui.graph.canvas.SimpleDimension

getWidth() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeRenderer

getWidthPerDepth() - Method in class org.ginsim.core.graph.tree.TreeBuilder

getWidthPerDepth_acc() - Method in class org.ginsim.core.graph.tree.TreeBuilder

getWidthPerDepth_acc(TreeNode) - Method in class org.ginsim.core.graph.tree.TreeBuilder

getWriter() - Method in class org.ginsim.common.document.GenericDocumentFormat

getX() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getX() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

getX() - Method in interface org.ginsim.core.graph.view.NodeViewInfo

Get the position of the node on the x axis

getY() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

getY() - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

getY() - Method in interface org.ginsim.core.graph.view.NodeViewInfo

Get the position of the node on the y axis

getZoomAction(BaseGraphGUI<?, ?, ?>, ZoomEffect) - Method in class org.ginsim.gui.graph.BaseGraphGUI

getZoomLevel() - Method in class org.ginsim.gui.graph.canvas.CanvasGraphGUIImpl

getZoomLevel() - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

getZoomLevel() - Method in interface org.ginsim.gui.graph.GraphGUI

GINMLFormatConfig - Class in org.ginsim.service.format.ginml

GINMLFormatConfig(RegulatoryGraph) - Constructor for class org.ginsim.service.format.ginml.GINMLFormatConfig

GINMLFormatConfigPanel - Class in org.ginsim.servicegui.format.ginml

GINMLFormatConfigPanel(GINMLFormatConfig, ExportAction) - Constructor for class org.ginsim.servicegui.format.ginml.GINMLFormatConfigPanel

GINMLFormatService - Class in org.ginsim.service.format.ginml

GINsim export service for the GINML (model-only) format.

GINMLFormatService() - Constructor for class org.ginsim.service.format.ginml.GINMLFormatService

GINMLFormatServiceGUI - Class in org.ginsim.servicegui.format.ginml

GINsim export service GUI for the GINML (model-only) format.

GINMLFormatServiceGUI() - Constructor for class org.ginsim.servicegui.format.ginml.GINMLFormatServiceGUI

GinmlHelper - Class in org.ginsim.core.io.parser

some help function to parse/write ginml files.

GinmlHelper() - Constructor for class org.ginsim.core.io.parser.GinmlHelper

GinmlParser - Class in org.ginsim.core.io.parser

Parser for GINML files.

GinmlParser() - Constructor for class org.ginsim.core.io.parser.GinmlParser

GINMLWriter<G extends Graph<V,E>,V,E extends Edge<V>> - Class in org.ginsim.core.io.parser

Base GINMLWriter class: it provides the common parts of a GINML file and hooks for specialised writers to add their graph-specific data.

GINMLWriter(G, String) - Constructor for class org.ginsim.core.io.parser.GINMLWriter

Create a GINML writer.

GINsimFormat - Class in org.ginsim.core.graph

GINsimFormat() - Constructor for class org.ginsim.core.graph.GINsimFormat

GINsimPlot - Interface in org.ginsim.service.tool.avatar.utils

glassPane - Variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.ComponentAdapter

GlassPane - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd

GlassPane() - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GlassPane

GNAFormatService - Class in org.ginsim.service.format

GINsim export service for the GNA (non-xml) format.

GNAFormatService() - Constructor for class org.ginsim.service.format.GNAFormatService

GNAFormatServiceGUI - Class in org.ginsim.servicegui.format

GUI Action to export model to the GNA (non-xml) format

GNAFormatServiceGUI() - Constructor for class org.ginsim.servicegui.format.GNAFormatServiceGUI

gnuplot() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AnimatorUI

gnuplotExport() - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicSearchPathConfig

Graph<V,E extends Edge<V>> - Interface in org.ginsim.core.graph

The main graph object in GINsim.

graph - Variable in class org.ginsim.core.io.parser.GINMLWriter

graph - Variable in class org.ginsim.gui.graph.BaseGraphGUI

graph - Variable in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

graph - Variable in class org.ginsim.gui.shell.actions.ExportAction

graph - Variable in class org.ginsim.gui.shell.actions.GenericGraphAction

graph - Variable in class org.ginsim.gui.shell.actions.LayoutAction

graph - Variable in class org.ginsim.gui.shell.editpanel.AbstractParameterPanel

graph - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

graph - Variable in class org.ginsim.servicegui.tool.circuit.CircuitFrame

graph_1 - Variable in class org.ginsim.service.tool.graphcomparator.GraphComparator

graph_2 - Variable in class org.ginsim.service.tool.graphcomparator.GraphComparator

graph_new - Variable in class org.ginsim.service.tool.graphcomparator.GraphComparator

GRAPH_ZIP_NAME - Static variable in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

GRAPH_ZIP_NAME - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

GRAPH_ZIP_NAME - Static variable in class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

GRAPH_ZIP_NAME - Static variable in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

graphAnnotation - Variable in class org.ginsim.core.graph.AbstractGraph

GraphAssociatedObjectManager<T> - Interface in org.ginsim.core.graph.objectassociation

Implement this interface to save/open objects associated to graph automatically.

GraphAssociation<AG extends Graph<AV,AE>,AV,AE extends Edge<AV>> - Interface in org.ginsim.core.graph

Defines a graph associated with the implementor of this interface.

GraphBackend<V,E extends Edge<V>> - Interface in org.ginsim.core.graph

Abstract definition of a graph backend to avoid leaking implementation details in the main classes.

GraphCanvasRenderer - Class in org.ginsim.gui.graph.canvas

GraphCanvasRenderer(Graph<?, ?>, SimpleCanvas, GraphSelection, EditActionManager) - Constructor for class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

graphChanged(GraphModel<?, ?>, GraphChangeType, Object) - Method in class org.ginsim.core.annotation.BiblioList

graphChanged(Graph, GraphChangeType, Object) - Method in class org.ginsim.core.graph.AbstractDerivedGraph

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

graphChanged(G, GraphChangeType, Object) - Method in interface org.ginsim.core.graph.GraphListener

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesHandler

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceTreeImpl

graphChanged(G, GraphChangeType, Object) - Method in class org.ginsim.gui.graph.BaseGraphGUI

graphChanged(GraphModel, GraphChangeType, Object) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

graphChanged(DynamicGraph, GraphChangeType, Object) - Method in class org.ginsim.gui.graph.dynamicgraph.StateTransitionGraphEditor

graphChanged(G, GraphChangeType, Object) - Method in interface org.ginsim.gui.graph.GraphGUIListener

The graph data was changed.

graphChanged(HierarchicalTransitionGraph, GraphChangeType, Object) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalGraphEditor

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationSelectionPanel

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

graphChanged(Graph, GraphChangeType, Object) - Method in class org.ginsim.gui.shell.editpanel.EditPanel

graphChanged(Graph, GraphChangeType, Object) - Method in class org.ginsim.gui.shell.MainFrame

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.service.tool.avatar.params.AvatarParameterList

GRAPH CHANGES ****

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

graphChanged(RegulatoryGraph, GraphChangeType, Object) - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionConfigSelectionPanel

graphChanged(Graph, GraphChangeType, Object) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

GraphChangeType - Enum in org.ginsim.core.graph

possible types of graph changes (edit events), used when firing and listening for change events.

graphClassName - Variable in class org.ginsim.core.io.parser.GINMLWriter

GraphComparator<V,E extends Edge<V>,G extends Graph<V,E>> - Class in org.ginsim.service.tool.graphcomparator

Compare two Graphs.

GraphComparator(G, G, G) - Constructor for class org.ginsim.service.tool.graphcomparator.GraphComparator

GraphComparatorCaptionFrame - Class in org.ginsim.servicegui.tool.graphcomparator

GraphComparatorCaptionFrame(GraphComparatorResult) - Constructor for class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorCaptionFrame

GraphComparatorFrame - Class in org.ginsim.servicegui.tool.graphcomparator

GraphComparatorFrame(JFrame, Graph) - Constructor for class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorFrame

GraphComparatorResult<V,E extends Edge<V>,G extends Graph<V,E>> - Class in org.ginsim.service.tool.graphcomparator

Contains the result of the comparison of two graphs graph_1 and graph_2 and the proper methods to handle the display of theses results

GraphComparatorResult(G, G, G) - Constructor for class org.ginsim.service.tool.graphcomparator.GraphComparatorResult

Create a new result

GraphComparatorService - Class in org.ginsim.service.tool.graphcomparator

GraphComparatorService() - Constructor for class org.ginsim.service.tool.graphcomparator.GraphComparatorService

GraphComparatorServiceGUI - Class in org.ginsim.servicegui.tool.graphcomparator

GraphComparatorServiceGUI() - Constructor for class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorServiceGUI

GraphComparatorStyleProvider - Class in org.ginsim.service.tool.graphcomparator

Provide styles for compared graphs.

GraphEventCascade - Interface in org.ginsim.core.graph

Interface for cascade changes: an object implementing this interface should be returned when a change triggers a cascade of other changes.

GraphFactory<G extends Graph<?,?>> - Interface in org.ginsim.core.graph

Factory to open or create specialised graph instances.

GRAPHFONT - Static variable in class org.ginsim.core.graph.view.ViewHelper

GraphGUI<G extends Graph<V,E>,V,E extends Edge<V>> - Interface in org.ginsim.gui.graph

Deal with the GUI view of a graph: get a component, provide access to selected items and view options.

graphGUIClosed(GraphGUI<G, V, E>) - Method in interface org.ginsim.gui.graph.GraphGUIListener

The GUI was closed.

graphGUIClosed(GraphGUI<RegulatoryGraph, RegulatoryNode, RegulatoryMultiEdge>) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationSelectionPanel

graphGUIClosed(GraphGUI) - Method in class org.ginsim.gui.shell.editpanel.EditPanel

graphGUIClosed(GraphGUI) - Method in class org.ginsim.gui.shell.MainFrame

graphGUIClosed(GraphGUI<RegulatoryGraph, RegulatoryNode, RegulatoryMultiEdge>) - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionConfigSelectionPanel

graphGUIClosed(GraphGUI) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

GraphGUIHelper<G extends Graph<V,E>,V,E extends Edge<V>> - Interface in org.ginsim.gui.graph

GUI-side helper for a graph type.

GraphGUIHelperFactory - Class in org.ginsim.gui.graph

This factory provides access to the GraphGUIHelper corresponding to a specific graph class The factory itself is managed as a singleton.

GraphGUIListener<G extends Graph<V,E>,V,E extends Edge<V>> - Interface in org.ginsim.gui.graph

Interface for objects which listen for Graph GUI events.

GraphicalAttributesStore - Class in org.ginsim.core.graph.view

Deprecated.

GraphicalAttributesStore(Graph) - Constructor for class org.ginsim.core.graph.view.GraphicalAttributesStore

Deprecated.

GraphListener<G extends GraphModel<?,?>> - Interface in org.ginsim.core.graph

Listen to graph edit events.

GraphModel<V,E extends Edge<V>> - Interface in org.ginsim.core.graph

Handle the basic structure of a graph.

graphName - Variable in class org.ginsim.core.graph.AbstractGraph

GraphOptionPanel - Interface in org.ginsim.gui.graph

offer save options to the user.

GraphSelection<V,E extends Edge<V>> - Class in org.ginsim.gui.graph

Manage the selection for a GraphGUI

GraphSelection(GraphGUI) - Constructor for class org.ginsim.gui.graph.GraphSelection

GraphSelectionCanvasEventManager - Class in org.ginsim.gui.graph.canvas.events

GraphSelectionCanvasEventManager(Graph<?, ?>, GraphCanvasRenderer, GraphSelection) - Constructor for class org.ginsim.gui.graph.canvas.events.GraphSelectionCanvasEventManager

graphSelectionChanged(GraphGUI<G, V, E>) - Method in interface org.ginsim.gui.graph.GraphGUIListener

The selection has changed.

graphSelectionChanged(GraphGUI<RegulatoryGraph, RegulatoryNode, RegulatoryMultiEdge>) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationSelectionPanel

graphSelectionChanged(GraphGUI) - Method in class org.ginsim.gui.shell.editpanel.EditPanel

graphSelectionChanged(GraphGUI) - Method in class org.ginsim.gui.shell.MainFrame

graphSelectionChanged(GraphGUI<RegulatoryGraph, RegulatoryNode, RegulatoryMultiEdge>) - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionConfigSelectionPanel

graphSelectionChanged(GraphGUI) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

GraphStructureExportService - Class in org.ginsim.service.export.struct

Export the structure of a graph to various formats: GraphViz, Biolayout, and cytoscape.

GraphStructureExportService() - Constructor for class org.ginsim.service.export.struct.GraphStructureExportService

GraphStructureExportServiceGUI - Class in org.ginsim.servicegui.export.struct

Export service to struct format

GraphStructureExportServiceGUI() - Constructor for class org.ginsim.servicegui.export.struct.GraphStructureExportServiceGUI

GraphViewListener - Interface in org.ginsim.core.graph

Listen to changes in a graph view.

GraphvizEncoder - Class in org.ginsim.service.export.struct

GraphvizEncoder() - Constructor for class org.ginsim.service.export.struct.GraphvizEncoder

graphvizExport(Graph, Collection<Object>, Collection<Edge<?>>, String) - Method in class org.ginsim.service.export.struct.GraphStructureExportService

GRAVITY_ERROR - Static variable in exception org.ginsim.common.application.GsException

really bad

GRAVITY_INFO - Static variable in exception org.ginsim.common.application.GsException

low gravity

GRAVITY_NORMAL - Static variable in exception org.ginsim.common.application.GsException

normal error

groupToggle(int[]) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

toggle the selection grouping: - if all selected items are part of the same group, it will be "ungrouped" - if selected items are part of several groups, they will be merged with the first one

groupToggle() - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionPanel

toggle the selection grouping: - if all selected items are part of the same group, it will be "ungrouped" - if selected items are part of several groups, they will be merged with the first one

GsButton - Class in org.ginsim.gui.utils.widgets

GsButton(String) - Constructor for class org.ginsim.gui.utils.widgets.GsButton

GsButton(ImageIcon) - Constructor for class org.ginsim.gui.utils.widgets.GsButton

GsButton(String, int, int, int, int) - Constructor for class org.ginsim.gui.utils.widgets.GsButton

GsDragGestureListener - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd

GsDragGestureListener(JTree, GsDragSourceListener, DropListener) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsDragGestureListener

GsDragSourceListener - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd

GsDragSourceListener(JTree, GlassPane) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsDragSourceListener

GsException - Exception in org.ginsim.common.application

When something bad happen, a GsException must be raised.

GsException(int, String) - Constructor for exception org.ginsim.common.application.GsException

create a GsException.

GsException(String, Exception) - Constructor for exception org.ginsim.common.application.GsException

GsException(int, Exception) - Constructor for exception org.ginsim.common.application.GsException

create a GsException.

GsException(int, String[]) - Constructor for exception org.ginsim.common.application.GsException

GsFileFilter - Class in org.ginsim.gui.shell

GINMLFilter.java filter the file to chose for saving/opening

GsFileFilter() - Constructor for class org.ginsim.gui.shell.GsFileFilter

GsFileFilter(FileFormatDescription) - Constructor for class org.ginsim.gui.shell.GsFileFilter

GsFileFilter(String[], String) - Constructor for class org.ginsim.gui.shell.GsFileFilter

GSGraphManager - Class in org.ginsim.core.graph

Manage registered graph types and handles graph creation (from scratch or through a parser).

GsJGraphtBaseGraph<V,E extends Edge<V>> - Class in org.ginsim.core.graph.backend

a "simple" jgrapht implementation using hashmap.

GsJGraphtBaseGraph() - Constructor for class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

GsJTree - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

GsJTree(TreeModel) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.GsJTree

GsPanel - Class in org.ginsim.gui.utils.widgets

GsPanel() - Constructor for class org.ginsim.gui.utils.widgets.GsPanel

GsPanel(String) - Constructor for class org.ginsim.gui.utils.widgets.GsPanel

GSServiceGUIManager - Class in org.ginsim.gui.service

This manager provides access to the ServiceGUI corresponding to a specific graph class The manager itself is managed as a singleton.

GSServiceGUIManager() - Constructor for class org.ginsim.gui.service.GSServiceGUIManager

GSServiceManager - Class in org.ginsim.core.service

This manager provides access to the GsServices corresponding to a specific graph class The manager itself is managed as a singleton.

GSServiceManager() - Constructor for class org.ginsim.core.service.GSServiceManager

GsTransferable - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd

GsTransferable(TreeElement[]) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

GsXMLHelper - Class in org.ginsim.core.io.parser

GsXMLHelper() - Constructor for class org.ginsim.core.io.parser.GsXMLHelper

guessEdgeStyle(String, Attributes) - Method in class org.ginsim.core.graph.view.style.StyleManager

Find an edge style corresponding to the desired attributes.

guessNodeStyle(String, Attributes) - Method in class org.ginsim.core.graph.view.style.StyleManager

Find a node style corresponding to the desired attributes.

gui - Variable in class org.ginsim.gui.shell.editpanel.AbstractParameterPanel

GUIEditor<T> - Interface in org.ginsim.gui.graph

An object in charge of graphical edition of an object type

GUIFor - Annotation Type in org.ginsim.gui.service

GUIHelper<T> - Interface in org.ginsim.gui.guihelpers

A GUIHelper provides a GUI for a given type of data.

GUIHelperManager - Class in org.ginsim.gui.guihelpers

GUIInfo - Class in org.ginsim.commongui.utils

Simple helper class to store some default settings

GUIInfo() - Constructor for class org.ginsim.commongui.utils.GUIInfo

GUIManager - Class in org.ginsim.gui

GUIManager() - Constructor for class org.ginsim.gui.GUIManager

GUIMessageUtils - Class in org.ginsim.commongui.dialog

Wrappers to create error and message dialogs.

GUIMessageUtils() - Constructor for class org.ginsim.commongui.dialog.GUIMessageUtils

H

HandledStackDialog - Class in org.ginsim.gui.utils.dialog.stackdialog

HandledStackDialog(StackDialogHandler) - Constructor for class org.ginsim.gui.utils.dialog.stackdialog.HandledStackDialog

HandledStackDialog(StackDialogHandler, Frame) - Constructor for class org.ginsim.gui.utils.dialog.stackdialog.HandledStackDialog

handles(String) - Method in class org.ginsim.core.graph.objectassociation.BasicGraphAssociatedManager

handles(String) - Method in interface org.ginsim.core.graph.objectassociation.GraphAssociatedObjectManager

Test if the key is a valid name for this data manager

hasChildren() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSet

hasConflict - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

hasConflict() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

hasConstraint(NodeInfo) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

hasEdge(LogicalFunctionListElement) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanGene

hasExits() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

hashCode() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicNode

hashcode() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

hashCode() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNodeSet

hashCode() - Method in class org.ginsim.core.graph.reducedgraph.NodeReducedData

hashCode() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

hashCode() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

hashCode() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafValue

hashCode() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

hashCode() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

hashCode() - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceNode

hashCode() - Method in class org.ginsim.core.utils.data.HashSetForSet

hashCode() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

HashSetForSet - Class in org.ginsim.core.utils.data

A regular HashSet's hashcode method depends on its content Therefore, if the content of a set change, its hashcode change.

HashSetForSet() - Constructor for class org.ginsim.core.utils.data.HashSetForSet

HashSetForSet(int) - Constructor for class org.ginsim.core.utils.data.HashSetForSet

hasMask(int, int) - Static method in class org.ginsim.common.utils.MaskUtils

Test if a value contains a mask.

hasNamedColumn() - Method in class org.ginsim.gui.utils.data.ListPanelHelper

hasNeighbours(int) - Method in class org.ginsim.service.export.cadp.CADPWriter

hasNeighbours(int) - Method in class org.ginsim.service.tool.composition.GenericTopology

hasNeighbours(int) - Method in interface org.ginsim.service.tool.composition.Topology

hasNeihgbours(int) - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

hasNeihgbours(int) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

hasNeihgbours(int) - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

hasNext() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesIterator

hasNext() - Method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

hasNext() - Method in class org.ginsim.service.tool.reg2dyn.updater.DeterministicSimulationUpdater

hasNext() - Method in class org.ginsim.service.tool.reg2dyn.updater.GenericSimulationUpdater

hasNext() - Method in class org.ginsim.servicegui.tool.modelreduction.TargetEdgesIterator

hasOracles() - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Checks whether the graph has oracles associated

hasOracles() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

hasOverlapping(StateSet) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Checks whether two state-sets share states

hasPaths() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

hasReverseEdge() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

hasReverseEdge() - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

Check if the graph also contains the reversed edge.

HEIGHT - Static variable in class org.ginsim.common.document.DocumentStyle

height - Variable in class org.ginsim.commongui.dialog.DefaultDialogSize

HEIGHT - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

help() - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

help() - Method in class org.ginsim.ScriptLauncher

Show some help about services and data available for scripts

HelpCallBack - Class in org.ginsim.gui.shell.callbacks

Here are the (few) callback for entry in the "help" menu

HelpCallBack() - Constructor for class org.ginsim.gui.shell.callbacks.HelpCallBack

HelpedList - Class in org.ginsim.gui.utils.data

Encapsulate a list and its helper to allow editing it as a generic property

HelpedList(ListPanelHelper) - Constructor for class org.ginsim.gui.utils.data.HelpedList

HelpedListEditorUI - Class in org.ginsim.gui.utils.data

HelpedListEditorUI() - Constructor for class org.ginsim.gui.utils.data.HelpedListEditorUI

helper - Variable in class org.ginsim.gui.utils.data.HelpedList

helper - Variable in class org.ginsim.gui.utils.data.ListPanel

helper - Variable in class org.ginsim.service.tool.reg2dyn.Simulation

HELPER - Static variable in class org.ginsim.servicegui.tool.reg2dyn.ListOfSimulationParametersHelper

HELPER - Static variable in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionHelper

HELPER - Static variable in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

helpOverlay(Graphics2D, Rectangle) - Method in interface org.ginsim.gui.graph.canvas.CanvasEventManager

helpOverlay(Graphics2D, Rectangle) - Method in class org.ginsim.gui.graph.canvas.events.AbstractHelpCanvasEventManager

helpOverlay(Graphics2D, Rectangle) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

HierarchicalCellRenderer - Class in org.ginsim.gui.graph.hierarchicaltransitiongraph

HierarchicalCellRenderer() - Constructor for class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalCellRenderer

HierarchicalEdgeParameterPanel - Class in org.ginsim.gui.graph.hierarchicaltransitiongraph

HierarchicalEdgeParameterPanel(HierarchicalTransitionGraph) - Constructor for class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalEdgeParameterPanel

HierarchicalGINMLWriter - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

Save a HTG in the GINML format.

HierarchicalGINMLWriter(HierarchicalTransitionGraph, boolean, String) - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalGINMLWriter

HierarchicalGraphEditor - Class in org.ginsim.gui.graph.hierarchicaltransitiongraph

HierarchicalGraphEditor(HierarchicalTransitionGraph) - Constructor for class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalGraphEditor

HierarchicalNode - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

Define the nodes of the Hierarchical Transition Graph.

HierarchicalNode(HierarchicalTransitionGraph) - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Default constructor.

HierarchicalNodeParameterPanel - Class in org.ginsim.gui.graph.hierarchicaltransitiongraph

HierarchicalNodeParameterPanel(HierarchicalTransitionGraph) - Constructor for class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalNodeParameterPanel

HierarchicalNodeSet - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

Define a set of nodes for the Hierarchical Transition Graph.
It is used to have an HashSet of HierarchicalNode.

HierarchicalNodeSet() - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNodeSet

HierarchicalSigmaSet - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

HierarchicalSigmaSet(HierarchicalNode, HierarchicalSigmaSet) - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSet

HierarchicalSigmaSetFactory - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

HierarchicalSigmaSetFactory() - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSetFactory

HierarchicalTableModel - Class in org.ginsim.gui.graph.hierarchicaltransitiongraph

HierarchicalTableModel(HierarchicalTransitionGraph) - Constructor for class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTableModel

HierarchicalTransitionGraph - Interface in org.ginsim.core.graph.hierarchicaltransitiongraph

Hierarchical Transition Graphs provide a compact representation of the dynamical behaviour.

HierarchicalTransitionGraphFactory - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

Factory for hierarchical transition graphs.

HierarchicalTransitionGraphFactory() - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphFactory

HierarchicalTransitionGraphGUIHelper - Class in org.ginsim.gui.graph.hierarchicaltransitiongraph

HierarchicalTransitionGraphGUIHelper() - Constructor for class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphGUIHelper

HierarchicalTransitionGraphImpl - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

Implementation of the HTG interface

HierarchicalTransitionGraphImpl() - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

create a new empty DynamicalHierarchicalGraph.

HierarchicalTransitionGraphImpl(List<NodeInfo>, boolean) - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

create a new DynamicalHierarchicalGraph with a nodeOrder.

HierarchicalTransitionGraphParser - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

Parse XML files defining hierarchical graphs.

HierarchicalTransitionGraphParser(Set<String>, Attributes, String) - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphParser

HierarchicalTransitionGraphParser() - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphParser

hook_edgeAttribute(XMLWriter, DynamicEdge) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGINMLWriter

hook_edgeAttribute(XMLWriter, DecisionOnEdge) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalGINMLWriter

hook_edgeAttribute(XMLWriter, Edge<NodeReducedData>) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGINMLWriter

hook_edgeAttribute(XMLWriter, RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGINMLWriter

hook_edgeAttribute(XMLWriter, E) - Method in class org.ginsim.core.io.parser.GINMLWriter

hook_graphAttribute(XMLWriter) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGINMLWriter

hook_graphAttribute(XMLWriter) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalGINMLWriter

hook_graphAttribute(XMLWriter) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGINMLWriter

hook_graphAttribute(XMLWriter) - Method in class org.ginsim.core.io.parser.GINMLWriter

hook_nodeAttribute(XMLWriter, DynamicNode) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGINMLWriter

hook_nodeAttribute(XMLWriter, HierarchicalNode) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalGINMLWriter

hook_nodeAttribute(XMLWriter, NodeReducedData) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGINMLWriter

hook_nodeAttribute(XMLWriter, RegulatoryNode) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGINMLWriter

hook_nodeAttribute(XMLWriter, V) - Method in class org.ginsim.core.io.parser.GINMLWriter

HORIZONTAL - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

hSW - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

htg - Variable in class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

htg - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

The HierarchicalTransitionGraph in construction

HTGSimulation - Class in org.ginsim.service.tool.reg2dyn.htg

Run a simulation to construct a HierarchicalTransitionGraph

HTGSimulation(LogicalModel, ProgressListener<Graph>, SimulationParameters) - Constructor for class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

HTGSimulationHelper - Class in org.ginsim.service.tool.reg2dyn.helpers

HTGSimulationHelper(LogicalModel, SimulationParameters) - Constructor for class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

HTGSimulationQueueItem - Interface in org.ginsim.service.tool.reg2dyn.htg

Interface of the items in the queue of the HTG simulation.

HTGSimulationQueueSCC - Class in org.ginsim.service.tool.reg2dyn.htg

HTGSimulationQueueSCC(HierarchicalNode, int, int) - Constructor for class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueSCC

Simple constructor.

HTGSimulationQueueState - Class in org.ginsim.service.tool.reg2dyn.htg

Used to represent the elements in the queue of the HTGSimulation

HTGSimulationQueueState(byte[], int, int) - Constructor for class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

Simple constructor.

htmlData - Variable in class org.ginsim.gui.utils.data.MyBasicTransferable

HttpHelper - Class in org.ginsim.core.annotation

OpenHelper for generic HTTP links.

HttpHelper() - Constructor for class org.ginsim.core.annotation.HttpHelper

hyperlinkUpdate(HyperlinkEvent) - Method in class org.ginsim.gui.shell.AboutDialog

I

iconditions - Variable in class org.ginsim.service.tool.avatar.domain.Result

Initial states associated with these results

id - Variable in class org.ginsim.common.utils.FileFormatDescription

ID - Variable in class org.ginsim.commongui.dialog.DefaultDialogSize

id - Variable in class org.ginsim.commongui.dialog.SimpleDialog

id - Variable in class org.ginsim.gui.utils.data.GenericPropertyInfo

ID - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

ID - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

IDENTICAL - Static variable in class org.ginsim.service.tool.graphcomparator.GraphComparatorStyleProvider

IDENTIFIER - Static variable in class org.ginsim.core.graph.view.css.AllSelector

identifier - Variable in class org.ginsim.core.graph.view.css.Selector

IDENTIFIER - Static variable in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

idExists(String) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

idExists(String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

ImageExportService - Class in org.ginsim.service.export.image

Export the graph view as image (PNG or SVG).

ImageExportService() - Constructor for class org.ginsim.service.export.image.ImageExportService

ImageExportServiceGUI - Class in org.ginsim.servicegui.export.image

GUI integration of the PNG and SVG exports.

ImageExportServiceGUI() - Constructor for class org.ginsim.servicegui.export.image.ImageExportServiceGUI

ImageLoader - Class in org.ginsim.commongui.utils

Load images from a list of image sources.

ImageLoader() - Constructor for class org.ginsim.commongui.utils.ImageLoader

imanager - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

import_tip - Variable in class org.ginsim.gui.service.FormatSupportServiceGUI

ImportAction - Class in org.ginsim.gui.shell.actions

ImportAction(String) - Constructor for class org.ginsim.gui.shell.actions.ImportAction

ImportAction(String, String) - Constructor for class org.ginsim.gui.shell.actions.ImportAction

ImportAction(String, ImageIcon, String, KeyStroke) - Constructor for class org.ginsim.gui.shell.actions.ImportAction

importAnnotation(RegulatoryGraph, SBase, Annotation) - Method in class org.ginsim.service.format.sbml.SBMLqualService

importFile(File) - Method in class org.ginsim.core.service.FormatSupportService

importFile(String) - Method in class org.ginsim.core.service.FormatSupportService

importLRG(String) - Method in class org.ginsim.core.service.FormatSupportService

importLRG(String) - Method in class org.ginsim.service.format.sbml.SBMLqualService

Return the graph built from the SBML file at the given path

importModel(LogicalModel) - Static method in class org.ginsim.core.graph.regulatorygraph.LogicalModel2RegulatoryGraph

Creates a new Regulatory graph, based on an existing logical model

importModel(LogicalModel, Collection<NodeInfo>) - Static method in class org.ginsim.core.graph.regulatorygraph.LogicalModel2RegulatoryGraph

Creates a new Regulatory graph, based on an existing logical model

incomingEdgeAdded(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

IncomingEdgeListModel - Class in org.ginsim.gui.graph.regulatorygraph

Model for JList containing a list GsDirectedEdge add display all regulaion data

IncomingEdgeListModel() - Constructor for class org.ginsim.gui.graph.regulatorygraph.IncomingEdgeListModel

default constructor

incomingEdgesOf(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

INCONSISTENT_SIZE - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

increment(State) - Method in class org.ginsim.service.tool.avatar.domain.Result

Increments the number of occurrences for a stable state (assumes the results contain the attractor)

increment(StateSet) - Method in class org.ginsim.service.tool.avatar.domain.Result

Increments the number of occurrences for a complex attractor (assumes the results contain the attractor)

incrementComplexAttractor(String, int) - Method in class org.ginsim.service.tool.avatar.domain.Result

inDegreeOf(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

index - Variable in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

index - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

The index of the next state found during the dfs.

index - Variable in class org.ginsim.service.tool.reg2dyn.htg.TarjanSimulation

The index of the next state found during the dfs.

IndexableActionListener - Class in org.ginsim.servicegui.tool.avatar.others

Action listener with internal state given by a key and a component

IndexableActionListener(String, JDialog) - Constructor for class org.ginsim.servicegui.tool.avatar.others.IndexableActionListener

Creates an action listener with internal state

IndexableActionListener(JFrame) - Constructor for class org.ginsim.servicegui.tool.avatar.others.IndexableActionListener

Creates an action listener with internal state

indexOf(Object) - Method in class org.ginsim.core.utils.data.ValueList

info(Object) - Static method in class org.ginsim.common.application.LogManager

Log an info.

InformationNotification - Class in org.ginsim.core.notification

InformationNotification(Object, String) - Constructor for class org.ginsim.core.notification.InformationNotification

inHitRegion(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreeEditor

init(String) - Static method in class org.ginsim.common.application.OptionStore

Initialise the option store: this should be called by the launcher once and only once.

init(Collection<LogicalParameter>, boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTree

init() - Method in class org.ginsim.core.graph.tree.TreeBuilder

This method is called before parsing the tree.

init() - Method in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

init() - Method in class org.ginsim.core.graph.tree.TreeBuilderFromManualOmdd

init() - Method in class org.ginsim.core.graph.tree.TreeBuilderFromRegulatoryGraph

init(ActionListener) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.TreeMenu

init() - Method in class org.ginsim.gui.utils.dialog.stackdialog.AbstractStackDialogHandler

init() - Method in class org.ginsim.service.export.cadp.CADPIntegrationWriter

init() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

init() - Method in class org.ginsim.servicegui.format.sbml.SBMLQualExportConfigPanel

initColorPalette(int) - Method in class org.ginsim.service.layout.DynamicLayout3D

Create a color palette by varying the hue.

initColorPalette(int) - Method in class org.ginsim.servicegui.layout.MultidimensionLayoutGUI

Create a color palette by variing the hue.

initDecal(byte[]) - Method in class org.ginsim.service.layout.DynamicLayout3D

initGUI(DynamicGraph) - Method in class org.ginsim.servicegui.layout.MultidimensionLayoutGUI

initialize() - Method in class org.ginsim.commongui.dialog.ResultsDialog

initialize(String, boolean) - Method in class org.ginsim.gui.utils.data.ListSelectionPanel

initialize(String, boolean, String, String) - Method in class org.ginsim.gui.utils.data.ListSelectionPanel

initialize() - Method in class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorCaptionFrame

initialize() - Method in class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorFrame

initialize() - Method in class org.ginsim.servicegui.tool.interactionanalysis.InteractionAnalysisFrame

initialize() - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphFrame

initialize() - Method in class org.ginsim.servicegui.tool.omddViz.OmddVizFrame

initialize() - Method in class org.ginsim.servicegui.tool.polytopesViz.PolytopesVizFrame

InitialStatePanel - Class in org.ginsim.gui.graph.regulatorygraph.initialstate

InitialStatePanel() - Constructor for class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

InitialStatePanel(NamedStatesHandler, boolean, String, String) - Constructor for class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

InitialStatePanel(NamedStatesHandler, boolean) - Constructor for class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

InitialStatePanel(Graph, boolean, String, String) - Constructor for class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

InitialStatePanel(Graph, boolean) - Constructor for class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

initialStates - Variable in class org.colomoto.biolqm.StatefulLogicalModelImpl

InitialStatesGUIHelper - Class in org.ginsim.gui.graph.regulatorygraph.initialstate

InitialStatesGUIHelper() - Constructor for class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatesGUIHelper

InitialStatesWidget - Class in org.ginsim.servicegui.export.cadp

Widget to specify the initial states of each module

InitialStatesWidget(CompositionSpecificationDialog) - Constructor for class org.ginsim.servicegui.export.cadp.InitialStatesWidget

InitialStateWriter(List<byte[]>, List<RegulatoryNode>) - Constructor for class org.ginsim.service.export.cadp.CADPWriter.InitialStateWriter

InitialStateWriter(List<byte[]>, List<Map.Entry<RegulatoryNode, Integer>>, boolean) - Constructor for class org.ginsim.service.export.cadp.CADPWriter.InitialStateWriter

initPanel - Variable in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

initRealDepth(int) - Method in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

Initialize the realDepth array, and max_terminal from an initial node, assuming regGraph is defined

initRealDepth(int) - Method in class org.ginsim.core.graph.tree.TreeBuilderFromManualOmdd

Initialize the realDepth array, and max_terminal from an initial node, assuming regGraph is defined

initRealDepth(int) - Method in class org.ginsim.core.graph.tree.TreeBuilderFromRegulatoryGraph

Initialize the realDepth array, and max_terminal from an initial node, assuming regGraph is defined

initStatesIterator - Variable in class org.ginsim.service.tool.reg2dyn.Simulation

InitStateTableModel - Class in org.ginsim.gui.graph.regulatorygraph.initialstate

model for the initState table.

InitStateTableModel(InitialStatePanel, NamedStateList, boolean) - Constructor for class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

simple constructor

inodes - Variable in class org.ginsim.service.tool.avatar.params.AvatarStateStore

inputPanel - Variable in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

inQueue - Variable in class org.ginsim.service.tool.reg2dyn.htg.TarjanSimulation

insert() - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityClassContentEditor

add genes to the selected class: they will be removed from their current class.

insertRight2Left() - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

Get the selected element in the right list (jL_IncomEdge), and insert them in the selected row in the left table (jSP_Table_Value)

InstanceSelectorWidget - Class in org.ginsim.servicegui.tool.composition

Widget to specify the number of model instances

InstanceSelectorWidget(CompositionSpecificationDialog) - Constructor for class org.ginsim.servicegui.tool.composition.InstanceSelectorWidget

InstanceSelectorWidget(CompositionSpecificationDialog, int, int) - Constructor for class org.ginsim.servicegui.tool.composition.InstanceSelectorWidget

instates - Variable in class org.ginsim.service.tool.avatar.params.AvatarStateStore

list of named states associated with input components

IntegerProperty - Class in org.ginsim.core.graph.view.style

IntegerProperty(String, boolean, int, int, int, int) - Constructor for class org.ginsim.core.graph.view.style.IntegerProperty

IntegerProperty(String, int, int, int, int) - Constructor for class org.ginsim.core.graph.view.style.IntegerProperty

IntegrationAtom(String, byte, int, int) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationAtom

IntegrationAtom(String, byte, int, int, int) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationAtom

IntegrationAtom(String, byte, int, int, int, int) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationAtom

IntegrationConjunction(IntegrationFunctionSpecification.IntegrationExpression, IntegrationFunctionSpecification.IntegrationExpression) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationConjunction

IntegrationDisjunction(IntegrationFunctionSpecification.IntegrationExpression, IntegrationFunctionSpecification.IntegrationExpression) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationDisjunction

IntegrationFunction - Enum in org.ginsim.service.tool.composition

The enumeration of all prototypical Integration functions

IntegrationFunction.IntegrationFunctionReification - Class in org.ginsim.service.tool.composition

IntegrationFunctionClause - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

A clause for the Integration Function, representing a conjunction of conditions

IntegrationFunctionClause() - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

IntegrationFunctionEvaluation - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationFunctionEvaluation(IntegrationFunctionSpecification.IntegrationExpression, CompositionContext) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionEvaluation

IntegrationFunctionMapping - Class in org.ginsim.service.tool.composition

The mapping of the input components

IntegrationFunctionMapping() - Constructor for class org.ginsim.service.tool.composition.IntegrationFunctionMapping

IntegrationFunctionMDDFactory - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationFunctionMDDFactory(CompositionContext, MDDManager) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionMDDFactory

IntegrationFunctionReification(IntegrationFunction) - Constructor for class org.ginsim.service.tool.composition.IntegrationFunction.IntegrationFunctionReification

IntegrationFunctionSpecification - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationFunctionSpecification() - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification

IntegrationFunctionSpecification.IntegrationAtom - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationFunctionSpecification.IntegrationConjunction - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationFunctionSpecification.IntegrationDisjunction - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationFunctionSpecification.IntegrationExpression - Interface in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationFunctionSpecification.IntegrationNegation - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationFunctionSpecification.IntegrationOperation - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationFunctionVerification - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationFunctionVerification(IntegrationFunctionSpecification.IntegrationExpression, CompositionContext) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionVerification

IntegrationFunctionWidget - Class in org.ginsim.servicegui.tool.composition

Widget to specify the Integration Function

IntegrationFunctionWidget(CompositionSpecificationDialog) - Constructor for class org.ginsim.servicegui.tool.composition.IntegrationFunctionWidget

IntegrationGrammarLexer - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationGrammarLexer() - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

IntegrationGrammarLexer(CharStream) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

IntegrationGrammarLexer(CharStream, RecognizerSharedState) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

IntegrationGrammarLexer.DFA6 - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationGrammarParser - Class in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationGrammarParser(TokenStream) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

IntegrationGrammarParser(TokenStream, RecognizerSharedState) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

IntegrationLogicalOperator - Enum in org.ginsim.servicegui.tool.composition.integrationgrammar

IntegrationNegation(IntegrationFunctionSpecification.IntegrationExpression) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationNegation

IntegrationOperation(IntegrationFunctionSpecification.IntegrationExpression, IntegrationFunctionSpecification.IntegrationExpression, IntegrationLogicalOperator) - Constructor for class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification.IntegrationOperation

IntegrationProcessWriter(Map.Entry<RegulatoryNode, Integer>, List<Map.Entry<RegulatoryNode, Integer>>, IntegrationFunction) - Constructor for class org.ginsim.service.export.cadp.CADPIntegrationWriter.IntegrationProcessWriter

InteractionAnalysisAlgo - Class in org.ginsim.service.tool.interactionanalysis

Search all the non functional interactions in the graph 'regGraph' and do some actions on them depending on the options (opt_*).

InteractionAnalysisAlgo() - Constructor for class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisAlgo

InteractionAnalysisAlgoResult - Class in org.ginsim.service.tool.interactionanalysis

This class is a simple container for the results of the algorithm : * The Style Provider * The InteractionAnalysisReport

InteractionAnalysisAlgoResult(StyleProvider, InteractionAnalysisReport) - Constructor for class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisAlgoResult

InteractionAnalysisFrame - Class in org.ginsim.servicegui.tool.interactionanalysis

InteractionAnalysisFrame(JFrame, RegulatoryGraph) - Constructor for class org.ginsim.servicegui.tool.interactionanalysis.InteractionAnalysisFrame

InteractionAnalysisReport - Class in org.ginsim.service.tool.interactionanalysis

A container class capable of exporting itself given a DocumentWriter Use the following structure : Map{ target :=> List[ SourceItem(source, level, reportItem(List[pathItem, pathItem, ....]), reportItem(List[pathItem, pathItem, ....]), ....), SourceItem(source, level, reportItem(List[pathItem, pathItem, ....]), reportItem(List[pathItem, pathItem, ....]), ....), SourceItem(source, level, reportItem(List[pathItem, pathItem, ....]), reportItem(List[pathItem, pathItem, ....]), ....) ], target :=> List[ SourceItem(source, level, reportItem(List[pathItem, pathItem, ....]), reportItem(List[pathItem, pathItem, ....]), ....), SourceItem(source, level, reportItem(List[pathItem, pathItem, ....]), reportItem(List[pathItem, pathItem, ....]), ....), SourceItem(source, level, reportItem(List[pathItem, pathItem, ....]), reportItem(List[pathItem, pathItem, ....]), ....) ] }

InteractionAnalysisReport() - Constructor for class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisReport

InteractionAnalysisService - Class in org.ginsim.service.tool.interactionanalysis

InteractionAnalysisService() - Constructor for class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisService

InteractionAnalysisServiceGUI - Class in org.ginsim.servicegui.tool.interactionanalysis

InteractionAnalysisServiceGUI() - Constructor for class org.ginsim.servicegui.tool.interactionanalysis.InteractionAnalysisServiceGUI

InteractionAnalysisStyleProvider - Class in org.ginsim.service.tool.interactionanalysis

Provide a style to view interaction analysis results on the graph.

interactionCount() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

Returns the number of the interaction in the node.

InteractionPanel - Class in org.ginsim.gui.graph.regulatorygraph

Panel to edit interaction of a gene

InteractionPanel(RegulatoryGraph) - Constructor for class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

This method initializes

InteractionStatus - Enum in org.ginsim.service.tool.interactionanalysis

interrupt() - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.LimitedSimulation

interrupt() - Method in class org.ginsim.service.tool.reg2dyn.Simulation

IntrospectionUtils - Class in org.ginsim.common.utils

Collection of static methods for common introspection tasks.

IntrospectionUtils() - Constructor for class org.ginsim.common.utils.IntrospectionUtils

InvalidFunctionResolution - Class in org.ginsim.core.notification.resolvable

InvalidFunctionResolution() - Constructor for class org.ginsim.core.notification.resolvable.InvalidFunctionResolution

inverseCommons(double[][]) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMatrix

Inverts a matrix using Commons library

inverseLa4J(double[][]) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMatrix

Inverts a matrix using La4J library

inverseSimpleEJML(double[][]) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMatrix

Inverts a matrix using EJML library

invertEdgesSelection() - Method in class org.ginsim.gui.graph.GraphSelection

Invert the selection of edges

invertNodesSelection() - Method in class org.ginsim.gui.graph.GraphSelection

Invert the selection of nodes

invertSelection() - Method in class org.ginsim.gui.graph.GraphSelection

Invert the selection of nodes and edges

invoke(Object, Method, Object[]) - Method in class org.ginsim.common.application.OSXAdapter

IOUtils - Class in org.ginsim.common.utils

Collection of helpers to open and parse files, or streams, allowing to access files inside jar archives from the JVM classpath.

IOUtils() - Constructor for class org.ginsim.common.utils.IOUtils

isActive(int, int) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

isActive(GraphSelection<?, ?>) - Method in class org.ginsim.gui.graph.view.style.StyleTab

isActive(GraphSelection<?, ?>) - Method in interface org.ginsim.gui.shell.editpanel.EditTab

isActive(GraphSelection<?, ?>) - Method in class org.ginsim.gui.shell.editpanel.MainEditTab

isActive(GraphSelection<?, ?>) - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalEditTab

isAssociationValid(Graph<?, ?>) - Method in class org.ginsim.core.graph.AbstractDerivedGraph

test if a graph can be associated with this one.

isAssociationValid(Graph<?, ?>) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

Indicates if the given graph can be associated to the current one

isAssociationValid(Graph<?, ?>) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

Indicates if the given graph can be associated to the current one

isAssociationValid(Graph<?, ?>) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

Indicates if the given graph can be associated to the current one

isAssociationValid(Graph<?, ?>) - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceTreeImpl

isBasal() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

isBasalValueDefined() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

isBranch() - Method in class org.ginsim.core.graph.tree.TreeNode

isCellEditable(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

isCellEditable(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

isCellEditable(int, int) - Method in class org.ginsim.gui.utils.data.SimpleStateListTableModel

isCellEditable(Object, int) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

By default, make the column with the Tree in it the only editable one.

isCellEditable(Object, int) - Method in interface org.ginsim.gui.utils.widgets.treetable.TreeTableModel

Indicates whether the the value for node node, at column number column is editable.

isCellEditable(int, int) - Method in class org.ginsim.gui.utils.widgets.treetable.TreeTableModelAdapter

isCellEditable(int, int) - Method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

isCellEditable(int, int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPModel

isColored() - Method in class org.ginsim.core.graph.view.css.Colorizer

isColorPercievedBright(Color) - Static method in class org.ginsim.common.utils.ColorPalette

Indicates if the given color is perceived bright

isCompatMode() - Method in class org.ginsim.core.graph.view.style.StyleManager

Check if the styles are disabled (for backward compatibility when saving).

isCompressed() - Method in interface org.ginsim.gui.graph.GraphOptionPanel

isCompressed() - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphOptionPanel

isCore - Variable in class org.ginsim.core.graph.view.style.StyleProperty

isCorrectMethod(Method, Object[]) - Method in class org.ginsim.common.application.OSXAdapter

isCurve() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

isCurve() - Method in class org.ginsim.core.graph.backend.EdgeViewInfoImpl

isCurve() - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

Is this edge curve? This only affects edges with intermediate points.

isCurve() - Method in interface org.ginsim.core.graph.view.EdgeViewInfo

isCycle() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

isCycle() - Method in interface org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueItem

isCycle() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueSCC

isCycle() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

isDataFlavorSupported(DataFlavor) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

isDataFlavorSupported(DataFlavor) - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Returns whether or not the specified data flavor is supported for this object.

isDirty() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

isDropable() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

isDup - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

isDup() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

isEditable() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

isEditable - Variable in class org.ginsim.gui.utils.data.GenericPropertyInfo

isEditAllowed() - Method in class org.ginsim.gui.graph.BaseGraphGUI

isEditAllowed() - Method in interface org.ginsim.gui.graph.GraphGUI

isEditAllowed(Graph) - Method in class org.ginsim.gui.GUIManager

Verify if edition is allowed on the graph

isEdited() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

isEmpty() - Method in class org.ginsim.core.annotation.Annotation

isEmpty() - Method in class org.ginsim.core.graph.AbstractGraph

isEmpty() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSetFactory

isEmpty() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesHandler

isEmpty() - Method in class org.ginsim.service.tool.avatar.domain.CompactStateSet

Checks whether there are states in the state-set

isEmpty() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Checks whether the state-set has states

isEmpty() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Checks whether the state-set has states

isError() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

isExtended() - Method in interface org.ginsim.gui.graph.GraphOptionPanel

isExtended() - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphOptionPanel

isFileWritable(String) - Static method in class org.ginsim.common.utils.IOUtils

Verify if the file at the given path can be opened in write mode

isFixedInputs() - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

isFunction(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

isGUI - Variable in class org.ginsim.service.tool.avatar.simulation.Simulation

whether a graphical or programmatic interface is being used (to store outputs)

isHTMLFlavor(DataFlavor) - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Returns whether or not the specified data flavor is an HTML flavor that is supported.

isHTMLSupported() - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Should the HTML flavors be offered? If so, the method getHTMLData should be implemented to provide something reasonable.

isImageReady() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GlassPane

isImplemented(IntegrationFunction) - Static method in enum org.ginsim.service.tool.composition.IntegrationFunction

isImpossible() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

isInput() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

isInteger(String) - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

Verify if the specified String is an integer

isLeaf() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

isLeaf() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

isLeaf(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

isLeaf() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

isLeaf() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

isLeaf() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperand

isLeaf() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperator

isLeaf() - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNode

isLeaf() - Method in class org.ginsim.core.graph.tree.TreeNode

isLeaf(Object) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

isManual(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

isManual(LogicalParameter) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

isMapped(RegulatoryNode) - Method in class org.ginsim.service.tool.composition.IntegrationFunctionMapping

isMapped(RegulatoryNode) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

isMappedTo(RegulatoryNode) - Method in class org.ginsim.service.tool.composition.IntegrationFunctionMapping

Indicates whether a proper components influence an integration functions

isMaxCompatible(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

isNameValid(int, String) - Method in class org.ginsim.core.utils.data.NamedList

isNormal() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

isOk() - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserPathModel

test if the entered states are valid (ie are in the graph)

isOk() - Method in class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

test if the entered states are valid (ie are in the graph)

isOneValue() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

isOscillation(Set<String>) - Method in class org.ginsim.service.tool.stableregions.PNGraph

isOutgoing(int) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

isOutput() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

isPlace(String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

isPlainFlavor(DataFlavor) - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Returns whether or not the specified data flavor is an plain flavor that is supported.

isPlainSupported() - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Should the plain text flavors be offered? If so, the method getPlainData should be implemented to provide something reasonable.

isPropagatingFixed(String) - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

isReduce() - Method in class org.ginsim.service.tool.composition.CompositionConfig

isRicherFlavor(DataFlavor) - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

isSaved() - Method in class org.ginsim.gui.graph.BaseGraphGUI

isSaved() - Method in interface org.ginsim.gui.graph.GraphGUI

Returns true if this graph has not been modified since the last change

isSelected() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

isSelected(NodeInfo) - Method in class org.ginsim.service.tool.modelreduction.ReductionConfig

isSelected(int, int) - Method in class org.ginsim.servicegui.tool.composition.AdjacencyMatrixWidget

isShowingMessage(Notification) - Method in class org.ginsim.gui.notifications.NotificationPanel

Test if this panel is currently showing the specified message.

isSingleState(byte[]) - Static method in class org.ginsim.service.tool.avatar.simulation.SimulationUtils

isSingleton() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSet

Indicates if the SigmaSet is a singleton (contains only one element), that is, if this HierarchicalSigmaSet's parent is not the root of the factory, ie.

isSizeConsistent() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Indicates if the size is in a consistent state, that is if it really reflect the number of state in the set, or only an overapproximation.

isStable() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicNode

is this a stable state ?

isStable() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

isStableMotif(Set<String>) - Method in class org.ginsim.service.tool.stableregions.PNGraph

isStateful() - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Checks whether the graph has states associated

isStateful() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

isStringFlavor(DataFlavor) - Method in class org.ginsim.gui.utils.data.MyBasicTransferable

Returns whether or not the specified data flavor is a String flavor that is supported.

isStrippingOutput(String) - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

isSymmetric() - Method in class org.ginsim.servicegui.tool.composition.AdjacencyMatrixWidget

istatesSelected - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

isTautological() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

isTerminal() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

isTransient() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

isTransient(Graph) - Method in class org.ginsim.core.graph.reducedgraph.NodeReducedData

isTransition(String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

isTrivial() - Method in class org.ginsim.core.graph.reducedgraph.NodeReducedData

isTrulyMapped(RegulatoryNode, int) - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

isTrulyMapped(RegulatoryNode, int) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

isTrulyMapped(RegulatoryNode, int) - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

isValid() - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.SimulationConstraint

Indicates if the space is valid for computation (not null & non empty)

isValidId(String) - Static method in class org.ginsim.common.xml.XMLWriter

Indicates if the given string is a valid GINsim ID (contains only a-z, A-Z, 0-9, "_" or "-" characters)

isValidValue(String) - Method in class org.ginsim.gui.graph.dynamicgraph.StateTransitionGraphEditor

isValidValue(String) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalGraphEditor

isValidValue(int, String) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

isValidValue(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

isValidValue(int, String) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

isValidValue(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

isValidValue(int, String) - Method in class org.ginsim.gui.graph.view.style.StyleEditor

isValidValue(int, int) - Method in class org.ginsim.gui.graph.view.style.StyleEditor

isValidValue(String) - Method in class org.ginsim.gui.utils.data.GenericPropertyInfo

isValidValue(int, String) - Method in class org.ginsim.gui.utils.data.ObjectEditor

isValidValue(int, int) - Method in class org.ginsim.gui.utils.data.ObjectEditor

isValidValue(String) - Method in interface org.ginsim.gui.utils.data.TextProperty

isWarning() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

item - Variable in class org.ginsim.service.tool.graphcomparator.ComparedItemInfo

itemAdded(Object, int) - Method in interface org.ginsim.core.utils.data.GenericListListener

itemAdded(Object, int) - Method in class org.ginsim.service.tool.avatar.params.AvatarParameterList

itemAdded(Object, int) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

itemRemoved(Object, int) - Method in interface org.ginsim.core.utils.data.GenericListListener

itemRemoved(Object, int) - Method in class org.ginsim.service.tool.avatar.params.AvatarParameterList

itemRemoved(Object, int) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

itemStateChanged(ItemEvent) - Method in class org.ginsim.gui.graph.view.style.StyleTab

itemStateChanged(ItemEvent) - Method in class org.ginsim.servicegui.tool.stablestates.StableStateSwingUI

iterator(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

J

jcbAlgorithm - Variable in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

selected simulation: Avatar, Firefront or Monte Carlo

JgraphtBackendImpl<V,E extends Edge<V>> - Class in org.ginsim.core.graph.backend

JSONDocumentationWriter - Class in org.ginsim.service.export.documentation

Export the documentation of a model into an interactive web page.

JSONDocumentationWriter(RegulatoryGraph, String) - Constructor for class org.ginsim.service.export.documentation.JSONDocumentationWriter

jTable - Variable in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

jtaOutput - Variable in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

JTreeTable - Class in org.ginsim.gui.utils.widgets.treetable

This example shows how to create a simple JTreeTable component, by using a JTree as a renderer (and editor) for the cells in a particular column in the JTable.

JTreeTable(TreeTableModel) - Constructor for class org.ginsim.gui.utils.widgets.treetable.JTreeTable

JTreeTable.TreeTableCellEditor - Class in org.ginsim.gui.utils.widgets.treetable

JTreeTable.TreeTableCellRenderer - Class in org.ginsim.gui.utils.widgets.treetable

jump(int, int, int[]) - Method in class org.ginsim.core.graph.tree.TreeBuilder

Try to jump over the skipped nodes between lastLevel and maxLevel and fill currentWidthPerDepth accordingly.

K

keepOracle - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

whether oracles should be kept between iterations

keepTransients - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

whether transient cycles should be kept between iterations

KEY - Static variable in class org.ginsim.core.annotation.BiblioManager

KEY - Static variable in class org.ginsim.core.graph.dynamicgraph.DynamicGraphFactory

KEY - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphFactory

KEY - Static variable in class org.ginsim.core.graph.reducedgraph.ReducedGraphFactory

KEY - Static variable in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesManager

KEY - Static variable in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationManager

KEY - Static variable in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphFactory

KEY - Static variable in class org.ginsim.core.graph.trapspacetree.TrapSpaceTreeFactory

key - Variable in class org.ginsim.core.graph.view.style.StyleProperty

key - Variable in enum org.ginsim.gui.graph.ZoomEffect

key - Variable in class org.ginsim.service.tool.avatar.domain.State

KEY - Static variable in class org.ginsim.service.tool.avatar.params.AvatarParametersManager

Manager identifier

key - Variable in class org.ginsim.service.tool.circuit.CircuitDescrInTree

KEY - Static variable in class org.ginsim.service.tool.modelreduction.ReductionConfigManager

KEY - Static variable in class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalMappingManager

KEY - Static variable in class org.ginsim.service.tool.reg2dyn.Reg2DynService

KEY - Static variable in class org.ginsim.service.tool.reg2dyn.SimulationParametersManager

keyPressed(KeyEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

keyPressed(KeyEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

keyPressed(KeyEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

keyPressed(KeyEvent) - Method in class org.ginsim.gui.utils.widgets.SeparatorComboBox

keyPressed(KeyEvent) - Method in class org.ginsim.gui.utils.widgets.StatusTextField

keyReleased(KeyEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

keyReleased(KeyEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

keyReleased(KeyEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

keyReleased(KeyEvent) - Method in class org.ginsim.gui.utils.widgets.SeparatorComboBox

keyReleased(KeyEvent) - Method in class org.ginsim.gui.utils.widgets.StatusTextField

keyTyped(KeyEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

keyTyped(KeyEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

keyTyped(KeyEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

keyTyped(KeyEvent) - Method in class org.ginsim.gui.utils.widgets.SeparatorComboBox

keyTyped(KeyEvent) - Method in class org.ginsim.gui.utils.widgets.StatusTextField

kill(boolean) - Method in class org.ginsim.servicegui.tool.avatar.AvatarResults

L

l_position - Variable in class org.ginsim.gui.utils.data.GenericPropertyInfo

Label - Class in org.ginsim.gui.utils.widgets

Label(String, int) - Constructor for class org.ginsim.gui.utils.widgets.Label

lastDraw - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

lastDraw - Variable in class org.ginsim.service.tool.reg2dyn.htg.TarjanSimulation

LaTeXDocumentWriter - Class in org.ginsim.common.document

LaTeX backend for DocumentWriter.

LaTeXDocumentWriter() - Constructor for class org.ginsim.common.document.LaTeXDocumentWriter

Launcher - Class in org.ginsim

Simple launcher: parse command line arguments, show some help, open files or run the script mode accordingly.

Launcher() - Constructor for class org.ginsim.Launcher

layout(DynamicGraph) - Method in class org.ginsim.service.layout.DynamicLayout3D

LayoutAction<G extends Graph<?,?>> - Class in org.ginsim.gui.shell.actions

LayoutAction(G, String) - Constructor for class org.ginsim.gui.shell.actions.LayoutAction

LayoutAction(G, String, String) - Constructor for class org.ginsim.gui.shell.actions.LayoutAction

LayoutAction(G, String, ImageIcon, String, KeyStroke) - Constructor for class org.ginsim.gui.shell.actions.LayoutAction

LayoutAlgo - Interface in org.ginsim.service.layout

Some common functions for our kind of layout algo.

layoutCL(JLabel, FontMetrics, String, Icon, Rectangle, Rectangle, Rectangle) - Method in class org.ginsim.commongui.utils.VerticalLabelUI

Transposes the view rectangles as appropriate for a vertical view before invoking the super method and copies them after they have been altered by SwingUtilities.layoutCompoundLabel(FontMetrics, String, Icon, int, int, int, int, Rectangle, Rectangle, Rectangle, int)

layoutIfNeeded(Graph<?, ?>) - Static method in class org.ginsim.gui.WhatToDoWithGraph

LayoutService - Class in org.ginsim.service.layout

This class contains different placement algorithms, two algorithms for the placement in level and two others for the placement on rings

LayoutService() - Constructor for class org.ginsim.service.layout.LayoutService

LayoutServiceGUI - Class in org.ginsim.servicegui.layout

LayoutServiceGUI() - Constructor for class org.ginsim.servicegui.layout.LayoutServiceGUI

LEAF_DEFAULT_DEPTH - Static variable in class org.ginsim.core.graph.tree.TreeNode

leafs - Static variable in class org.ginsim.core.graph.tree.TreeImpl

The tree pendant to OMDDNode.TERMINALS

leftArg - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBinaryOperator

length - Variable in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

LEVEL - Static variable in class org.ginsim.service.layout.LayoutService

LEVEL_INV - Static variable in class org.ginsim.service.layout.LayoutService

LevelLayout - Class in org.ginsim.service.layout

level placement of nodes

LevelLayout() - Constructor for class org.ginsim.service.layout.LevelLayout

LimitedSimulation - Class in org.ginsim.service.tool.reg2dyn.limitedsimulation

This is the main part of the simulation.

LimitedSimulation(LogicalModel, HierarchicalTransitionGraph, SimulationConstraint, SimulationParameters, ProgressListener<Graph>) - Constructor for class org.ginsim.service.tool.reg2dyn.limitedsimulation.LimitedSimulation

Constructs an empty dynamic graph

LimitedSimulationFrame - Class in org.ginsim.servicegui.tool.reg2dyn.limitedSimulation

LimitedSimulationFrame(JFrame, HierarchicalTransitionGraph, RegulatoryGraph) - Constructor for class org.ginsim.servicegui.tool.reg2dyn.limitedSimulation.LimitedSimulationFrame

LimitedSimulationService - Class in org.ginsim.service.tool.reg2dyn.limitedsimulation

LimitedSimulationService() - Constructor for class org.ginsim.service.tool.reg2dyn.limitedsimulation.LimitedSimulationService

LimitedSimulationServiceGUI - Class in org.ginsim.servicegui.tool.reg2dyn.limitedSimulation

LimitedSimulationServiceGUI() - Constructor for class org.ginsim.servicegui.tool.reg2dyn.limitedSimulation.LimitedSimulationServiceGUI

lineColor - Variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

lineEnd - Variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

LINEWIDTH - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

linkNode(TreeNode, TreeNode, int) - Method in class org.ginsim.core.graph.tree.TreeBuilder

Create an edge from source to target Also set the right color according to colorIndex, and the dashed line if the target is a leaf.

list - Variable in class org.ginsim.gui.utils.data.HelpedList

list - Variable in class org.ginsim.gui.utils.data.ListPanel

list_item_removed(SimulationParameters) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

LIST_TYPE - Static variable in class org.ginsim.common.document.DocumentStyle

ListEditionPanel<T,L extends List<T>> - Class in org.ginsim.gui.utils.data

ListEditionPanel(ListPanelHelper<T, L>, L, String, StackDialog, Object) - Constructor for class org.ginsim.gui.utils.data.ListEditionPanel

ListenableNamedList<T extends NamedObject> - Class in org.ginsim.core.utils.data

ListenableNamedList() - Constructor for class org.ginsim.core.utils.data.ListenableNamedList

listenerList - Variable in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

ListOfPerturbations - Class in org.ginsim.core.graph.regulatorygraph.perturbation

The list of perturbations associated to a regulatory graph.

ListOfPerturbations(RegulatoryGraph) - Constructor for class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

ListOfReductionConfigs - Class in org.ginsim.service.tool.modelreduction

store all simplification parameters and offer a mean to access them.

ListOfReductionConfigs(RegulatoryGraph) - Constructor for class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

ListOfSimulationParametersHelper - Class in org.ginsim.servicegui.tool.reg2dyn

Helper for displaying a list of simulation parameters.

ListPanel<T,L extends List<T>> - Class in org.ginsim.gui.utils.data

Generic UI to display the content of a list.

ListPanel(ListPanelHelper<T, L>, String) - Constructor for class org.ginsim.gui.utils.data.ListPanel

ListPanel(ListPanelHelper<T, L>, String, ListEditionPanel) - Constructor for class org.ginsim.gui.utils.data.ListPanel

ListPanelCompanion<T,L extends List<T>> - Interface in org.ginsim.gui.utils.data

Complete a ListPanel by providing additional panels reacting to the selection

ListPanelHelper<T,L extends List<T>> - Class in org.ginsim.gui.utils.data

Provide configuration and helper methods for a list panel.

ListPanelHelper() - Constructor for class org.ginsim.gui.utils.data.ListPanelHelper

ListReorderListener - Interface in org.ginsim.common.utils

ListSelectionPanel<T> - Class in org.ginsim.gui.utils.data

ListSelectionPanel(StackDialog, String) - Constructor for class org.ginsim.gui.utils.data.ListSelectionPanel

listSelectionUpdated(int[]) - Method in class org.ginsim.gui.utils.data.ListEditionPanel

listSelectionUpdated(int[]) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionPanel

call it when the user changes the class selection: update UI to match the selection

ListTools - Class in org.ginsim.common.utils

Basic tools for common list operations.

ListTools() - Constructor for class org.ginsim.common.utils.ListTools

LITMIT_ASK_QUESTION - Static variable in class org.ginsim.gui.WhatToDoWithGraph

load(String) - Method in class org.ginsim.ScriptLauncher

Open a graph from a file.

load(LogicalModel) - Method in class org.ginsim.ScriptLauncher

load(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.AvatarPanel

load(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.FirefrontPanel

load(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.MonteCarloPanel

load(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.SimulationPanel

Reads the fields of the panel and exports them into a set of parameters

load(AvatarConfigFrame) - Static method in class org.ginsim.servicegui.tool.avatar.parameters.AvatarParametersHelper

Creates a simulation context (parameters) using the fields from the main panel

loadEdgeStyle(StyleManager, EdgeAttributesReader, Attributes) - Static method in class org.ginsim.core.io.parser.GinmlHelper

Load style and intermediate points from GINML.

loadGINMLfile(String) - Method in class org.ginsim.gui.GUIManager

Load a graph from a GINML file and open a new frame for it.

loadNodeStyle(StyleManager, NodeAttributesReader, Attributes) - Static method in class org.ginsim.core.io.parser.GinmlHelper

Load node position and style from GINML

LocalGraph - Class in org.ginsim.service.tool.localgraph

Search all the non functional interactions in the graph 'g' and do some actions on them depending on the options (opt_*).

LocalGraph(RegulatoryGraph) - Constructor for class org.ginsim.service.tool.localgraph.LocalGraph

LocalGraph(RegulatoryGraph, List<byte[]>) - Constructor for class org.ginsim.service.tool.localgraph.LocalGraph

LocalGraphCategory - Enum in org.ginsim.service.tool.localgraph

LocalGraphConfig - Class in org.ginsim.service.tool.localgraph

LocalGraphConfig(RegulatoryGraph, DynamicGraph) - Constructor for class org.ginsim.service.tool.localgraph.LocalGraphConfig

LocalGraphFrame - Class in org.ginsim.servicegui.tool.localgraph

LocalGraphFrame(LocalGraphConfig) - Constructor for class org.ginsim.servicegui.tool.localgraph.LocalGraphFrame

LocalGraphService - Class in org.ginsim.service.tool.localgraph

LocalGraphService() - Constructor for class org.ginsim.service.tool.localgraph.LocalGraphService

LocalGraphServiceGUI - Class in org.ginsim.servicegui.tool.localgraph

LocalGraphServiceGUI() - Constructor for class org.ginsim.servicegui.tool.localgraph.LocalGraphServiceGUI

LocalGraphStyleProvider - Class in org.ginsim.service.tool.localgraph

LocalGraphStyleProvider(StyleManager<RegulatoryNode, RegulatoryMultiEdge>, Map<RegulatoryMultiEdge, LocalGraphCategory>, Map<RegulatoryNode, ActivityLevel>) - Constructor for class org.ginsim.service.tool.localgraph.LocalGraphStyleProvider

log - Variable in class org.ginsim.service.tool.avatar.domain.Result

Simulation log

log(String) - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

append the string 's' to the log

log(long) - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

append the long l to the log

log(int) - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

append the int i to the log

log(boolean) - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

append the boolean b to the log

log(Object) - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

append the object o to the log

LogicalFunctionList - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction

LogicalFunctionList() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionList

LogicalFunctionListElement - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction

LogicalFunctionListElement(RegulatoryMultiEdge, int) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionListElement

LogicalFunctionPanel - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction

LogicalFunctionPanel(RegulatoryGraph) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

LogicalFunctionTreePanel - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction

LogicalFunctionTreePanel(RegulatoryGraph, LogicalFunctionPanel) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

LogicalFunctionView - Interface in org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree

LogicalModel2RegulatoryGraph - Class in org.ginsim.core.graph.regulatorygraph

Create a RegulatoryGraph based on a LogicalModel.

LogicalModelActionDialog - Class in org.ginsim.gui.utils.dialog.stackdialog

LogicalModelActionDialog(RegulatoryGraph, Frame, String, int, int) - Constructor for class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

LogicalParameter - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction

the Class in which we store biological data for logical parameters (in the vertex)

LogicalParameter(int) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

Constructs an empty vector and set the value

LogicalParameter(List, int) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

LogicalParameterList - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction

LogicalParameterList() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

LogicalTruthTableFormatService - Class in org.ginsim.service.format

GINsim import/export service for the implicant table format.

LogicalTruthTableFormatService() - Constructor for class org.ginsim.service.format.LogicalTruthTableFormatService

LogManager - Class in org.ginsim.common.application

A simple helper class to log things in System.out or System.err The log schema is : lineNumber:className#methodName() msg\n eg.

LogManager() - Constructor for class org.ginsim.common.application.LogManager

logToHTMLString() - Method in class org.ginsim.service.tool.avatar.domain.Result

Serializes the log into HTML

LQM() - Method in class org.ginsim.ScriptLauncher

Grab a proxy to the bioLQM API

lrg - Variable in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

LRGCustomStyleProvider - Class in org.ginsim.servicegui.tool.regulatorygraphanimation

LRGCustomStyleProvider(RegulatoryGraph) - Constructor for class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGCustomStyleProvider

LRGDocumentationAction - Class in org.ginsim.servicegui.export.documentation

LRGDocumentationAction(RegulatoryGraph, GenericDocumentFormat, LRGDocumentationService) - Constructor for class org.ginsim.servicegui.export.documentation.LRGDocumentationAction

LRGDocumentationService - Class in org.ginsim.service.export.documentation

LRGDocumentationService() - Constructor for class org.ginsim.service.export.documentation.LRGDocumentationService

LRGDocumentationServiceGUI - Class in org.ginsim.servicegui.export.documentation

GenericDocumentExport is a plugin to export the documentation of a model into multiples document format.

LRGDocumentationServiceGUI() - Constructor for class org.ginsim.servicegui.export.documentation.LRGDocumentationServiceGUI

LRGDocumentationWriter - Class in org.ginsim.service.export.documentation

GenericDocumentExport is a plugin to export the documentation of a model into multiples document format.

LRGDocumentationWriter(RegulatoryGraph) - Constructor for class org.ginsim.service.export.documentation.LRGDocumentationWriter

LRGPatternStyleProvider - Class in org.ginsim.servicegui.tool.lrgcolorizer

LRGPatternStyleProvider(RegulatoryGraph) - Constructor for class org.ginsim.servicegui.tool.lrgcolorizer.LRGPatternStyleProvider

LRGStateStyleProvider - Class in org.ginsim.servicegui.tool.regulatorygraphanimation

LRGStateStyleProvider(RegulatoryGraph) - Constructor for class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGStateStyleProvider

LRMInitialStateModel - Class in org.ginsim.servicegui.export.cadp

Model for the specification of the initial states of the LRMs being composed

LRMInitialStateModel(InitialStatesWidget, CompositionSpecificationDialog) - Constructor for class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

Constructor

M

m_call - Variable in class org.ginsim.common.xml.XMLHelper

m_elt - Variable in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

m_helper - Static variable in class org.ginsim.common.utils.OpenUtils

m_helper - Static variable in class org.ginsim.core.annotation.AnnotationLink

m_initState - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

m_input - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

m_pattern - Static variable in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

m_right - Variable in class org.ginsim.gui.utils.data.ListPanelHelper

m_vertices - Variable in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

MaBoSSExportService - Class in org.ginsim.service.format

GINsim export service capable of encoding the working model into the MaBoSS format

MaBoSSExportService() - Constructor for class org.ginsim.service.format.MaBoSSExportService

MaBoSSExportServiceGUI - Class in org.ginsim.servicegui.export.maboss

GUI Action to export model to the MaBoSS format

MaBoSSExportServiceGUI() - Constructor for class org.ginsim.servicegui.export.maboss.MaBoSSExportServiceGUI

main(String[]) - Static method in class org.ginsim.johnsonCycles.StrongConnectedComponents

main(String[]) - Static method in class org.ginsim.johnsonCycles.TestCycles

main(String[]) - Static method in class org.ginsim.Launcher

The main "main" function, launching GINsin GUI or script handler.

MainEditTab - Class in org.ginsim.gui.shell.editpanel

MainEditTab(GraphGUI) - Constructor for class org.ginsim.gui.shell.editpanel.MainEditTab

MainFrame - Class in org.ginsim.gui.shell

GINsim's main frame shell.

MainFrame(GraphGUI) - Constructor for class org.ginsim.gui.shell.MainFrame

MainFrameActionManager - Class in org.ginsim.gui.shell

MainFrameActionManager() - Constructor for class org.ginsim.gui.shell.MainFrameActionManager

mainPanel - Variable in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

makeCommaList(List<String>) - Static method in class org.ginsim.service.export.cadp.CADPWriter

makeCommaList(List<String>, String) - Static method in class org.ginsim.service.export.cadp.CADPWriter

makeDNF(List, String, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

makeDNF(List, String, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafValue

makeDNF(List, String, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

makeDNFExpression(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.FunctionsCreator

makeFunctions(Hashtable, String, int, boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

makeFunctions(Hashtable, String, int, boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafValue

makeFunctions(Hashtable, String, int, boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

makePNGraph() - Method in class org.ginsim.service.tool.stableregions.PNtoGraph

makeTree(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.FunctionsCreator

makeUpdatedCommaList(List<String>, List<String>, String) - Static method in class org.ginsim.service.export.cadp.CADPWriter

mAND() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

mapState2Color(byte, Color) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGCustomStyleProvider

mapState2Color(byte, int, int, int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGCustomStyleProvider

markRemoved() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

MASK - Static variable in class org.ginsim.commongui.utils.GUIInfo

MASK - Static variable in interface org.ginsim.gui.shell.FrameActionManager

MaskUtils - Class in org.ginsim.common.utils

Manipulation of simple integer masks.

MaskUtils() - Constructor for class org.ginsim.common.utils.MaskUtils

master - Variable in class org.ginsim.gui.utils.data.ObjectEditor

match(String) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

match(String, PrioritySetDefinition) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

matches(Color, EdgePattern, int) - Method in interface org.ginsim.core.graph.view.style.EdgeStyle

matches(Color, EdgePattern, int) - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

matches(Color, EdgePattern, int) - Method in class org.ginsim.core.graph.view.style.EdgeStyleOverride

matches(NodeShape, Color, Color, Color, int, int) - Method in interface org.ginsim.core.graph.view.style.NodeStyle

matches(NodeShape, Color, Color, Color, int, int) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

matches(NodeShape, Color, Color, Color, int, int) - Method in class org.ginsim.core.graph.view.style.NodeStyleOverride

max - Variable in class org.ginsim.core.graph.view.style.IntegerProperty

max(List<Integer>) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMath

Returns the maximum of an integer list

max_depth - Variable in class org.ginsim.core.graph.tree.TreeBuilder

The level of the last depth (corresponding to the terminal node in widthPerDepth)

max_depth_reached - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

The current maximal depth of the dfs of the current initial state.

max_depth_reached - Variable in class org.ginsim.service.tool.reg2dyn.htg.TarjanSimulation

The current maximal depth of the dfs of the current initial state.

MAX_HEIGHT - Static variable in class org.ginsim.core.graph.view.style.NodeStyleImpl

max_terminal - Variable in class org.ginsim.core.graph.tree.TreeBuilder

Indicates the maximum count of terminal.

MAX_WIDTH - Static variable in class org.ginsim.core.graph.view.style.NodeStyleImpl

maxDepth - Variable in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

maximum depth

maxdepth - Variable in class org.ginsim.service.tool.reg2dyn.Simulation

maxdepth - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

maxExpand - Variable in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

maximum number of states to expand per iteration

maxlen - Variable in class org.ginsim.service.tool.circuit.CircuitSearchStoreConfig

MAXLEVEL - Static variable in interface org.ginsim.core.graph.dynamicgraph.DynamicGraph

maxnodes - Variable in class org.ginsim.service.tool.reg2dyn.Simulation

maxnodes - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

maxPSize - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

maximum number of visited transitions to stop expansion approximated by #states within the growing cycle times #exits

maxRewiringSize - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

maximum number of states within a cycle to be rewired

MaxSpinModel - Class in org.ginsim.gui.utils.data.models

model for a max spinbutton, depends on a GsMinMaxSpinModel

MaxSpinModel(MinMaxSpinModel) - Constructor for class org.ginsim.gui.utils.data.models.MaxSpinModel

maxSteps - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

maximum depth

maxSteps - Variable in class org.ginsim.service.tool.avatar.simulation.MonteCarloSimulation

maximum depth

maxTransientSize - Variable in class org.ginsim.service.tool.avatar.domain.Result

Transient cycles * public List transients;

MAXVALUE - Static variable in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

mcDepth - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

mcRuns - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

MDDContext - Interface in org.ginsim.core.graph.regulatorygraph

MDDStateSet - Class in org.ginsim.service.tool.avatar.domain

Default representation of a state-set recurring to a hash-map of states
States are efficiently stored and accessed using minimal keys

MDDStateSet(List<NodeInfo>) - Constructor for class org.ginsim.service.tool.avatar.domain.MDDStateSet

Creates an empty state-set

MDDStateSet(List<NodeInfo>, State) - Constructor for class org.ginsim.service.tool.avatar.domain.MDDStateSet

Creates a state-set with the given state

MDDStateSet(List<NodeInfo>, List<byte[]>) - Constructor for class org.ginsim.service.tool.avatar.domain.MDDStateSet

Creates a state-set with the given list of states

MDDStateSet(List<NodeInfo>, List<byte[]>, double) - Constructor for class org.ginsim.service.tool.avatar.domain.MDDStateSet

Creates a state-set with the given list of states and their probability of occurrence

MDDStateSet(List<NodeInfo>, MDDStateSet) - Constructor for class org.ginsim.service.tool.avatar.domain.MDDStateSet

Clones a given state-set

MDDUtils - Class in org.ginsim.service.tool.avatar.simulation

Facilities associated with simulation services.

MDDUtils() - Constructor for class org.ginsim.service.tool.avatar.simulation.MDDUtils

me - Variable in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

mean(List<Integer>) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMath

Returns the mean of an integer list

memory - Variable in class org.ginsim.service.tool.avatar.domain.Result

Simulation memory (Mbytes)

memory - Variable in class org.ginsim.service.tool.avatar.simulation.Simulation

mENUMBER() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

merge(SAXParseException) - Method in class org.ginsim.common.xml.ParsingWarning

merge(Graph<V, E>) - Method in class org.ginsim.core.graph.AbstractGraph

Launch the merge method on the specialized graph level, merging the current graph with the given one and fire a graph change event

merge(Graph<V, E>) - Method in interface org.ginsim.core.graph.GraphModel

Merge the provided graph with the current one

merge(HierarchicalNode, Collection<HierarchicalNode>, HierarchicalSigmaSetFactory, HierarchicalTransitionGraph) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Merge the slave (or its master) node into this (or its master).

merge(HierarchicalNode, HierarchicalNode) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSetFactory

merge(StatesSet) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Merge this set with the stateSet of the slaveNode.

merge(CSSStyle) - Method in class org.ginsim.core.graph.view.css.CSSEdgeStyle

merge(CSSStyle) - Method in class org.ginsim.core.graph.view.css.CSSNodeStyle

merge(CSSStyle) - Method in interface org.ginsim.core.graph.view.css.CSSStyle

Merge the defined attributes from the style s

merge(StyleProperty[], StyleProperty[]) - Static method in class org.ginsim.core.graph.view.style.StyleProperty

MERGE - Static variable in class org.ginsim.service.tool.circuit.FunctionalityMergeOperator

mergeContexts(int, int) - Method in class org.ginsim.service.tool.circuit.CircuitAlgo

Merge functionality contexts.

MESSAGE_ERROR - Static variable in class org.ginsim.gui.utils.widgets.Label

MESSAGE_NORMAL - Static variable in class org.ginsim.gui.utils.widgets.Label

MESSAGE_WARNING - Static variable in class org.ginsim.gui.utils.widgets.Label

messageLabel - Variable in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

META_AUTHOR - Static variable in class org.ginsim.common.document.DocumentWriter

META_CHANGED - Static variable in class org.ginsim.service.tool.graphcomparator.GraphComparatorStyleProvider

META_DATE - Static variable in class org.ginsim.common.document.DocumentWriter

META_DESCRIPTION - Static variable in class org.ginsim.common.document.DocumentWriter

META_GENERATOR - Static variable in class org.ginsim.common.document.DocumentWriter

META_KEYWORDS - Static variable in class org.ginsim.common.document.DocumentWriter

META_TITLE - Static variable in class org.ginsim.common.document.DocumentWriter

metaChanged - Variable in class org.ginsim.service.tool.graphcomparator.ComparedItemInfo

mID() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

milestone(Object) - Method in class org.ginsim.common.callable.BasicProgressListener

milestone(Object) - Method in interface org.ginsim.common.callable.ProgressListener

Inform about intermediate step or result.

milestone(Object) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

milestone(Object) - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

milestone(Object) - Method in class org.ginsim.servicegui.tool.reg2dyn.SingleSimulationFrame

min - Variable in class org.ginsim.core.graph.view.style.IntegerProperty

min(List<Integer>) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMath

Returns the minimum of an integer list

MIN_SIZE - Static variable in class org.ginsim.core.graph.view.style.NodeStyleImpl

minCSize - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

minimum cycle size for rewiring

minlen - Variable in class org.ginsim.service.tool.circuit.CircuitSearchStoreConfig

MinMaxEditor - Class in org.ginsim.gui.utils.data

MinMaxEditor() - Constructor for class org.ginsim.gui.utils.data.MinMaxEditor

MinMaxSpinModel - Interface in org.ginsim.gui.utils.data.models

GsMinMaxSpinModel: model controlling min and max spinbuttons

minMust - Variable in class org.ginsim.service.tool.circuit.CircuitSearchStoreConfig

MinSpinModel - Class in org.ginsim.gui.utils.data.models

model for a min spinbutton, depends on a GsMinMaxSpinModel

MinSpinModel(MinMaxSpinModel) - Constructor for class org.ginsim.gui.utils.data.models.MinSpinModel

minTransientSize - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

minimum size of a transient cycles to be stored

MINUS - Variable in class org.ginsim.core.graph.dynamicgraph.DynamicNode

MINUS_ONE_NODE - Static variable in class org.ginsim.core.graph.tree.TreeImpl

MiriamURNHelper - Class in org.ginsim.core.annotation

Parse the list of MIRIAM databases and add custom aliases for backward compatibility.

MiriamURNHelper() - Constructor for class org.ginsim.core.annotation.MiriamURNHelper

missingCategory(String) - Method in class org.ginsim.core.graph.view.css.Selector

Called when the category doesn't exist in the map.

missingCategory(String, AttributesReader) - Method in class org.ginsim.core.graph.view.css.Selector

Called when the category doesn't exist in the map.

missingCategory(String, CSSStyle) - Method in class org.ginsim.core.graph.view.css.Selector

Called when the category doesn't exist in the map.

MIXED_FLAVOR - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

MixedTableHeader - Class in org.ginsim.commongui.utils

MixedTableHeader(JTable, int) - Constructor for class org.ginsim.commongui.utils.MixedTableHeader

MixedTableHeader(JTable, int, int) - Constructor for class org.ginsim.commongui.utils.MixedTableHeader

mNOT() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

MODE_DIAGRAM - Static variable in class org.ginsim.core.graph.tree.TreeImpl

MODE_DIAGRAM_WITH_MULTIPLE_LEAFS - Static variable in class org.ginsim.core.graph.tree.TreeImpl

MODE_TREE - Static variable in class org.ginsim.core.graph.tree.TreeImpl

model - Variable in class org.ginsim.service.tool.avatar.simulation.Simulation

model - Variable in class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

ModelBooleanizerService - Class in org.ginsim.service.tool.modelbooleanizer

Model Booleanizer service.

ModelBooleanizerService() - Constructor for class org.ginsim.service.tool.modelbooleanizer.ModelBooleanizerService

ModelBooleanizerServiceGUI - Class in org.ginsim.servicegui.tool.modelbooleanizer

Main method to Booleanize a Multivalued model

ModelBooleanizerServiceGUI() - Constructor for class org.ginsim.servicegui.tool.modelbooleanizer.ModelBooleanizerServiceGUI

modelHelper - Variable in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

ModelReductionService - Class in org.ginsim.service.tool.modelreduction

ModelReductionService() - Constructor for class org.ginsim.service.tool.modelreduction.ModelReductionService

ModelReversionService - Class in org.ginsim.service.tool.modelreversion

Model reversion service.

ModelReversionService() - Constructor for class org.ginsim.service.tool.modelreversion.ModelReversionService

ModelReversionServiceGUI - Class in org.ginsim.servicegui.tool.modelreversion

Main method for the model reversion plugin

ModelReversionServiceGUI() - Constructor for class org.ginsim.servicegui.tool.modelreversion.ModelReversionServiceGUI

MonteCarloPanel - Class in org.ginsim.servicegui.tool.avatar.algopanels

Class for managing the panel for Monte Carlo simulations

MonteCarloPanel() - Constructor for class org.ginsim.servicegui.tool.avatar.algopanels.MonteCarloPanel

Instantiates the context of a simulation panel

MonteCarloServiceFacade - Class in org.ginsim.service.tool.avatar.service

Facade of a Monte Carlo simulation.
Instantiates a Monte Carlo simulation from arguments within a command line, provides soundness checks, and outputs statistics and help tips.

MonteCarloServiceFacade() - Constructor for class org.ginsim.service.tool.avatar.service.MonteCarloServiceFacade

MonteCarloSimulation - Class in org.ginsim.service.tool.avatar.simulation

Monte Carlo simulation for the analysis of point attractors

MonteCarloSimulation() - Constructor for class org.ginsim.service.tool.avatar.simulation.MonteCarloSimulation

Instantiates a Monte Carlo simulation

mOR() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

MotionAdapter - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd

MotionAdapter(GlassPane) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.MotionAdapter

mouseClicked(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

mouseClicked(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ParamPanel

mouseClicked(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

mouseClicked(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

mouseClicked(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

mouseClicked(MouseEvent) - Method in class org.ginsim.gui.graph.view.style.AnchorSelector

mouseDragged(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.MotionAdapter

mouseDragged(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ParamPanel

mouseDragged(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

mouseEntered(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

mouseEntered(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ParamPanel

mouseEntered(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

mouseEntered(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

mouseEntered(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

mouseEntered(MouseEvent) - Method in class org.ginsim.gui.graph.view.style.AnchorSelector

mouseExited(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

mouseExited(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ParamPanel

mouseExited(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

mouseExited(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

mouseExited(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

mouseExited(MouseEvent) - Method in class org.ginsim.gui.graph.view.style.AnchorSelector

mouseListener - Variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

mouseMotionListener - Variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

mouseMoved(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ParamPanel

mouseMoved(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

mousePressed(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.ComponentAdapter

mousePressed(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

mousePressed(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ParamPanel

mousePressed(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

mousePressed(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

mousePressed(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

mousePressed(MouseEvent) - Method in class org.ginsim.gui.graph.view.style.AnchorSelector

mouseReleased(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.ComponentAdapter

mouseReleased(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

mouseReleased(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ParamPanel

mouseReleased(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

mouseReleased(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

mouseReleased(MouseEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

mouseReleased(MouseEvent) - Method in class org.ginsim.gui.graph.view.style.AnchorSelector

move(int, int) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

move(int, int) - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

move(int, int) - Method in interface org.ginsim.core.graph.view.AttributesReader

Move the item.

move(int) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

moveData(L, int[], int) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

moveData(PrioritySetDefinition, int[], int) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionHelper

moveData(PrioritySetList, int[], int) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

moveDown() - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

move the selected items down

moveDown() - Method in class org.ginsim.servicegui.layout.MultidimensionLayoutGUI

moveElement(List, int, int, int[]) - Static method in class org.ginsim.common.utils.ListTools

moveElement(int, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

moveElementAt(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

moveElementAt(int, int) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

moveItems(List, int[], int) - Static method in class org.ginsim.common.utils.ListTools

Move some items in a list: swap position with other items.

moveLine(int[], int) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

Move the selection.

moveSelection(int[], int) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

moveUp() - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

move the selected items up

moveUp() - Method in class org.ginsim.servicegui.layout.MultidimensionLayoutGUI

MovingEdgeType - Enum in org.ginsim.core.graph.view

mRANGE() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

mT__10() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

mT__11() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

mT__12() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

mTokens() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

MultiActionListener - Interface in org.ginsim.gui.utils.data

MultidimensionLayoutGUI - Class in org.ginsim.servicegui.layout

MultidimensionLayoutGUI() - Constructor for class org.ginsim.servicegui.layout.MultidimensionLayoutGUI

MultiEdgeEditPanel - Class in org.ginsim.gui.graph.regulatorygraph

Panel to edit a regulation, and all included edges.

MultiEdgeEditPanel(RegulatoryGraph) - Constructor for class org.ginsim.gui.graph.regulatorygraph.MultiEdgeEditPanel

multiple - Variable in class org.ginsim.service.tool.reg2dyn.SimulationQueuedState

multiple - Variable in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

mutantAdded(Object) - Method in interface org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationListener

a mutant has been added.

mutantRemoved(Object) - Method in interface org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationListener

a mutant has been removed.

MyBasicTransferable - Class in org.ginsim.gui.utils.data

A transferable implementation for the default data transfer of some Swing components.

MyBasicTransferable(String, String) - Constructor for class org.ginsim.gui.utils.data.MyBasicTransferable

N

name - Variable in class org.colomoto.biolqm.StatefulLogicalModelImpl

name - Variable in class org.ginsim.core.annotation.DatabaseInfo

name - Variable in class org.ginsim.core.graph.view.style.BaseStyle

name - Variable in class org.ginsim.core.graph.view.style.StyleProperty

name - Variable in enum org.ginsim.gui.graph.ZoomEffect

name - Variable in class org.ginsim.gui.utils.data.GenericPropertyInfo

name - Variable in class org.ginsim.gui.utils.data.models.SpinModel

name - Variable in class org.ginsim.service.tool.avatar.domain.Result

Simulation name

name - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

name - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

NamedList<T extends NamedObject> - Class in org.ginsim.core.utils.data

Help handling a list of named objects

NamedList() - Constructor for class org.ginsim.core.utils.data.NamedList

NamedObject - Interface in org.ginsim.core.utils.data

NamedState - Class in org.ginsim.core.graph.regulatorygraph.namedstates

Defines a (set of) named state(s): a name associated to an activity pattern.

NamedState() - Constructor for class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

NamedStateList - Class in org.ginsim.core.graph.regulatorygraph.namedstates

A list of named States.

NamedStateList(List, boolean) - Constructor for class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

NamedStatesHandler - Class in org.ginsim.core.graph.regulatorygraph.namedstates

Store all available named states for a Regulatory Graph.

NamedStatesHandler(Graph<?, ?>) - Constructor for class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesHandler

NamedStatesIterator - Class in org.ginsim.core.graph.regulatorygraph.namedstates

Iterator giving all states defined in a list of named states.

NamedStatesIterator(List, NamedStateStore) - Constructor for class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesIterator

NamedStatesIterator(List, Map, Map) - Constructor for class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesIterator

NamedStatesManager - Class in org.ginsim.core.graph.regulatorygraph.namedstates

Manager for the named states associated data.

NamedStatesManager() - Constructor for class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesManager

NamedStateStore - Interface in org.ginsim.core.graph.regulatorygraph.namedstates

Store a reference to a group of named states.

nameState(byte[], List<?>) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

nameState(byte[], Object[]) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

nameState(byte[], RegulatoryGraph) - Method in class org.ginsim.ScriptLauncher

Deprecated.

nameStateInfo(byte[], Object[]) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

NaturalOrderComparator - Class in org.ginsim.service.tool.avatar.utils

NaturalOrderComparator() - Constructor for class org.ginsim.service.tool.avatar.utils.NaturalOrderComparator

nbinitialstates - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

nbinitialstates - Variable in class org.ginsim.service.tool.reg2dyn.htg.TarjanSimulation

nbnode - Variable in class org.ginsim.service.tool.reg2dyn.Simulation

needSaving(Graph) - Method in class org.ginsim.core.graph.objectassociation.BasicGraphAssociatedManager

needSaving(Graph) - Method in interface org.ginsim.core.graph.objectassociation.GraphAssociatedObjectManager

needSaving(Graph) - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalMappingManager

needssaving - Variable in enum org.ginsim.core.graph.GraphChangeType

NEGATIVE - Static variable in class org.ginsim.service.tool.circuit.CircuitDescr

NEW_LINE - Variable in class org.ginsim.common.document.DocumentWriter

NEW_LINE - Variable in class org.ginsim.common.document.LaTeXDocumentWriter

NEW_LINE - Variable in class org.ginsim.common.document.WikiDocumentWriter

NEW_LINE - Variable in class org.ginsim.common.document.XHTMLDocumentWriter

newFrame() - Method in class org.ginsim.gui.GUIManager

Create a new graph (of the default type, i.e.

newFrame(Graph) - Method in class org.ginsim.gui.GUIManager

Build a new frame for the given Graph by creating a suitable GraphGUI and memorize their relationship

newFrame(Graph, boolean) - Method in class org.ginsim.gui.GUIManager

Build a new frame for the given Graph by creating a suitable GraphGUI and memorize their relationship

newFromText(String) - Static method in class org.ginsim.core.graph.view.css.CascadingStyleSheet

Return a new CSS object from a text.

newLine() - Method in class org.ginsim.common.document.DocumentWriter

newLine() - Method in class org.ginsim.common.document.WikiDocumentWriter

newLine() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

newParagraph() - Method in class org.ginsim.common.document.DocumentWriter

Open a paragraph without a style

next() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesIterator

next - Variable in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

next() - Method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

next() - Method in class org.ginsim.service.tool.reg2dyn.updater.DeterministicSimulationUpdater

next() - Method in class org.ginsim.service.tool.reg2dyn.updater.GenericSimulationUpdater

next() - Method in class org.ginsim.servicegui.tool.modelreduction.TargetEdgesIterator

nextState() - Method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

nextState() - Method in class org.ginsim.service.tool.reg2dyn.updater.DeterministicSimulationUpdater

nextState() - Method in class org.ginsim.service.tool.reg2dyn.updater.GenericSimulationUpdater

nextState() - Method in interface org.ginsim.service.tool.reg2dyn.updater.SimulationUpdater

nextUid - Static variable in class org.ginsim.core.graph.tree.TreeNode

NOALIAS - Static variable in annotation type org.ginsim.core.service.Alias

NOCALL - Static variable in class org.ginsim.common.xml.XMLHelper

node - Variable in class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

node - Variable in class org.ginsim.service.tool.reg2dyn.helpers.STGSimulationHelper

node - Variable in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

node2Gate(RegulatoryNode, int) - Static method in class org.ginsim.service.export.cadp.CADPWriter

node2Gate(RegulatoryNode) - Static method in class org.ginsim.service.export.cadp.CADPWriter

node2StateVar(RegulatoryNode) - Static method in class org.ginsim.service.export.cadp.CADPWriter

node2SyncAction(RegulatoryNode, int, RegulatoryNode, int) - Static method in class org.ginsim.service.export.cadp.CADPWriter

NodeAttributeReaderImpl<V,E extends Edge<V>> - Class in org.ginsim.core.graph.backend

A generic nodeAttributeReader showing a unified view of default and node-specific styles (from the graph backend).

NodeAttributeReaderImpl(StyleManager<V, E>, Graph<V, E>, GraphBackend<V, E>) - Constructor for class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

NodeAttributesReader<V> - Interface in org.ginsim.core.graph.view

extract from graph graphic info on a node.

NodeBorder - Enum in org.ginsim.core.graph.view

nodeChange(byte[], int) - Method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

get change step for a gene

nodeFactory - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanParser

nodeForRow(int) - Method in class org.ginsim.gui.utils.widgets.treetable.TreeTableModelAdapter

NodeInfoSorter - Class in org.ginsim.service.export.nusmv

NodeInfoSorter() - Constructor for class org.ginsim.service.export.nusmv.NodeInfoSorter

NodeMaxValueSpinModel - Class in org.ginsim.gui.graph.regulatorygraph

model controlling spin buttons for base and max value of a RegulatoryNode

NodeMaxValueSpinModel(RegulatoryGraph) - Constructor for class org.ginsim.gui.graph.regulatorygraph.NodeMaxValueSpinModel

nodeOrder - Variable in class org.ginsim.core.graph.dynamicgraph.TransitionGraphImpl

nodeOrder - Variable in class org.ginsim.core.graph.tree.TreeBuilder

nodeOrder - Variable in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetList

NodeOrderer - Interface in org.ginsim.core.graph.regulatorygraph

Order the components of a regulatory graph.

NodeReducedData - Class in org.ginsim.core.graph.reducedgraph

Nodes in the graph of the strongly connected components.

NodeReducedData(String, Collection) - Constructor for class org.ginsim.core.graph.reducedgraph.NodeReducedData

NodeReducedData(String, List) - Constructor for class org.ginsim.core.graph.reducedgraph.NodeReducedData

NodeReducedData(String) - Constructor for class org.ginsim.core.graph.reducedgraph.NodeReducedData

nodes - Variable in class org.ginsim.service.tool.avatar.domain.Result

Names of components

nodes - Variable in class org.ginsim.service.tool.avatar.params.AvatarStateStore

nodeSet - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

A HashSet<HierarchicalNode> containg all the masters nodes.

NodeShape - Enum in org.ginsim.core.graph.view

NodeStyle<V> - Interface in org.ginsim.core.graph.view.style

Define the visual parameters of a node.

NodeStyleImpl<V> - Class in org.ginsim.core.graph.view.style

Simple implementation for NodeStyle.

NodeStyleImpl() - Constructor for class org.ginsim.core.graph.view.style.NodeStyleImpl

NodeStyleImpl(String, NodeStyle<V>) - Constructor for class org.ginsim.core.graph.view.style.NodeStyleImpl

NodeStyleOverride<V> - Class in org.ginsim.core.graph.view.style

NodeStyleOverride(NodeStyle<V>) - Constructor for class org.ginsim.core.graph.view.style.NodeStyleOverride

NodeViewInfo - Interface in org.ginsim.core.graph.view

Store for basic view information on nodes.

NONE - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

NONE - Static variable in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

normalizeColumns(double[][]) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMath

Normalizes the columns of a matrix

NORTH - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

NORTHEAST - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

NORTHWEST - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

NOT - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

NOT - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

Notification - Class in org.ginsim.core.notification

A notification message

Notification(Object, String, NotificationType) - Constructor for class org.ginsim.core.notification.Notification

notificationAction(int) - Method in class org.ginsim.gui.notifications.NotificationPanel

NotificationDetailFrame - Class in org.ginsim.gui.notifications

NotificationDetailFrame(String) - Constructor for class org.ginsim.gui.notifications.NotificationDetailFrame

NotificationListener - Interface in org.ginsim.core.notification

NotificationManager - Class in org.ginsim.core.notification

This class is the central class of the register/publish design pattern applied to Notifications This manager receive registration from object that have to receive Notification on specific topics It receive also all the Notification and distribute them to listening objects according to the Notification Topic

NotificationManager() - Constructor for class org.ginsim.core.notification.NotificationManager

Default constructor

NotificationPanel - Class in org.ginsim.gui.notifications

A panel to show interactive notification messages.

NotificationPanel(NotificationSource) - Constructor for class org.ginsim.gui.notifications.NotificationPanel

NotificationResolution - Class in org.ginsim.core.notification.resolvable

NotificationResolution() - Constructor for class org.ginsim.core.notification.resolvable.NotificationResolution

NotificationResolution(String[]) - Constructor for class org.ginsim.core.notification.resolvable.NotificationResolution

NotificationSource - Interface in org.ginsim.gui.notifications

NotificationType - Enum in org.ginsim.core.notification

notifyFailure(Exception) - Method in class org.ginsim.gui.shell.actions.ExportAction

notifySuccess() - Method in class org.ginsim.gui.shell.actions.ExportAction

notifyWarning(String) - Method in class org.ginsim.gui.shell.actions.ExportAction

nReader - Variable in class org.ginsim.core.io.parser.GINMLWriter

nstates - Variable in class org.ginsim.service.tool.avatar.params.AvatarStateStore

list of named states associated with non-input components

NULL_BORDER - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

NULL_CURVE - Static variable in class org.ginsim.core.graph.view.css.CSSEdgeStyle

NuSMVConfig - Class in org.ginsim.service.export.nusmv

NuSMVConfig(LogicalModel) - Constructor for class org.ginsim.service.export.nusmv.NuSMVConfig

NuSMVEncoder - Class in org.ginsim.service.export.nusmv

Exports a GINsim Regulatory graph into a NuSMV model description.

NuSMVEncoder() - Constructor for class org.ginsim.service.export.nusmv.NuSMVEncoder

NuSMVExportConfigPanel - Class in org.ginsim.servicegui.export.nusmv

NuSMVExportConfigPanel(RegulatoryGraph, NuSMVConfig, NuSMVExportAction) - Constructor for class org.ginsim.servicegui.export.nusmv.NuSMVExportConfigPanel

NuSMVExportService - Class in org.ginsim.service.export.nusmv

GINsim export service capable of encoding the working model into a NuSMV specification.

NuSMVExportService() - Constructor for class org.ginsim.service.export.nusmv.NuSMVExportService

NuSMVExportServiceGUI - Class in org.ginsim.servicegui.export.nusmv

GUI Action to export a NuSMV model description

NuSMVExportServiceGUI() - Constructor for class org.ginsim.servicegui.export.nusmv.NuSMVExportServiceGUI

O

o - Variable in class org.ginsim.gui.utils.data.ObjectEditor

ObjectAssociationManager - Class in org.ginsim.core.graph.objectassociation

The association manager can be used as proxy to retrieve or create associated objects.

ObjectEditor<T> - Class in org.ginsim.gui.utils.data

An ObjectEditor acts as proxy between an object and the UI to edit its properties.

ObjectEditor() - Constructor for class org.ginsim.gui.utils.data.ObjectEditor

ObjectPropertyEditorUI - Interface in org.ginsim.gui.utils.data

ObjectStore - Class in org.ginsim.core.utils.data

ObjectStore() - Constructor for class org.ginsim.core.utils.data.ObjectStore

ObjectStore(int) - Constructor for class org.ginsim.core.utils.data.ObjectStore

OmddVizFrame - Class in org.ginsim.servicegui.tool.omddViz

OmddVizFrame(RegulatoryGraph) - Constructor for class org.ginsim.servicegui.tool.omddViz.OmddVizFrame

OmddVizServiceGUI - Class in org.ginsim.servicegui.tool.omddViz

OmddVizServiceGUI() - Constructor for class org.ginsim.servicegui.tool.omddViz.OmddVizServiceGUI

OOoDocumentFormat - Static variable in class org.ginsim.common.document.GenericDocumentFormat

OOoDocumentWriter - Class in org.ginsim.common.document

OOoDocumentWriter is a backend to write OpenDocument text files.

OOoDocumentWriter() - Constructor for class org.ginsim.common.document.OOoDocumentWriter

open(String, String) - Method in interface org.ginsim.common.utils.OpenHelper

Open a link.

open(Object, Object) - Static method in class org.ginsim.common.utils.OpenUtils

Open a link.

open() - Method in class org.ginsim.core.annotation.AnnotationLink

open(String, String) - Method in class org.ginsim.core.annotation.BiblioList

open() - Method in class org.ginsim.core.annotation.DatabaseInfo

open(String, String) - Method in class org.ginsim.core.annotation.DatabaseInfo

open(String, String) - Method in class org.ginsim.core.annotation.HttpHelper

open(String) - Method in class org.ginsim.core.graph.GSGraphManager

Retrieve the Graph stored in the file at the given file path

open(File) - Method in class org.ginsim.core.graph.GSGraphManager

open(Set, File) - Method in class org.ginsim.core.graph.GSGraphManager

open(String) - Method in class org.ginsim.ScriptLauncher

Deprecated.

see ScriptLauncher.load(String)

openConfirmationDialog(String, String) - Static method in class org.ginsim.commongui.dialog.GUIMessageUtils

Open a confirmation Dialog box (OK/Cancel) with the given message and the given title

openErrorDialog(Exception, Component) - Static method in class org.ginsim.commongui.dialog.GUIMessageUtils

Open a Message Dialog box to indicate users an exception occurred and give some feedback.

openErrorDialog(String) - Static method in class org.ginsim.commongui.dialog.GUIMessageUtils

Open a Message Dialog box to indicate users an error occurred and give some feedback.

openErrorDialog(String, Component) - Static method in class org.ginsim.commongui.dialog.GUIMessageUtils

Open a Message Dialog box to indicate users an error occurred and give some feedback.

openFile(String) - Static method in class org.ginsim.common.utils.OpenUtils

Open a file at the given path

openHeader(int, String, String) - Method in class org.ginsim.common.document.DocumentWriter

Open a new header.

OpenHelper - Interface in org.ginsim.common.utils

Define methods required to handle open actions associated to a given "protocol"

openLink(int) - Method in class org.ginsim.core.annotation.Annotation

openList(String) - Method in class org.ginsim.common.document.DocumentWriter

Open a list element with a specific style A list is made of ListItems

openList(String, boolean) - Method in class org.ginsim.common.document.DocumentWriter

openListItem(String) - Method in class org.ginsim.common.document.DocumentWriter

Open a new list item and write the content in.

openParagraph(String) - Method in class org.ginsim.common.document.DocumentWriter

Open a paragraph with a style

openTable(String, String, String[]) - Method in class org.ginsim.common.document.DocumentWriter

Open a new table.

openTableCell(int, int, String) - Method in class org.ginsim.common.document.DocumentWriter

Open a new cell in the current table row

openTableCell(int, int, String, boolean) - Method in class org.ginsim.common.document.DocumentWriter

Open a new cell in the current table row

openTableCell(int, int, String, String, boolean) - Method in class org.ginsim.common.document.DocumentWriter

openTableCell(String) - Method in class org.ginsim.common.document.DocumentWriter

Open a new cell in the current table row with 1 colspan and rowspan

openTableCell(String, boolean) - Method in class org.ginsim.common.document.DocumentWriter

openTableRow() - Method in class org.ginsim.common.document.DocumentWriter

Open a new row in the current table.

openTableRow(String) - Method in class org.ginsim.common.document.DocumentWriter

Open a new row in the current table.

openTag(String) - Method in class org.ginsim.common.xml.XMLWriter

open a tag in the XML output file

openTag(String, String[]) - Method in class org.ginsim.common.xml.XMLWriter

open a tag and add it the specified attributes.

openURI(String) - Static method in class org.ginsim.common.utils.OpenUtils

Open an URI.

OpenUtils - Class in org.ginsim.common.utils

Open files and links (providing extensible "protocols" for specialised links handlers)

OpenUtils() - Constructor for class org.ginsim.common.utils.OpenUtils

openWarningDialog(String) - Static method in class org.ginsim.commongui.dialog.GUIMessageUtils

Open a Message Dialog box to indicate users a warning message.

OptionStore - Class in org.ginsim.common.application

Handle options: remember them during the session, restore them when first called and save them when exiting.

OptionStore() - Constructor for class org.ginsim.common.application.OptionStore

OR - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

OR - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

oracle - Variable in class org.ginsim.service.tool.avatar.simulation.Simulation

oracles - Variable in class org.colomoto.biolqm.StatefulLogicalModelImpl

oracles - Variable in class org.ginsim.service.tool.avatar.params.AvatarStateStore

list of named states associated with oracles

oraclesPanel - Variable in class org.ginsim.gui.graph.regulatorygraph.initialstate.CompleteStatePanel

org.colomoto.biolqm - package org.colomoto.biolqm

org.colomoto.biolqm.io.avatar - package org.colomoto.biolqm.io.avatar

org.ginsim - package org.ginsim

The base package for GINsim, with launcher classes.

org.ginsim.common.application - package org.ginsim.common.application

Some system or application level helpers: detect OS, manage options, translate messages...

org.ginsim.common.callable - package org.ginsim.common.callable

API for processes which can run in background, based on callable and threads.

org.ginsim.common.document - package org.ginsim.common.document

API to write reports and other simple documents in HTML, OpenDocument, or LaTeX.

org.ginsim.common.utils - package org.ginsim.common.utils

This package hosts a collection of miscellaneous utilities.

org.ginsim.common.xml - package org.ginsim.common.xml

This package contains helpers to write and parse XML files.

org.ginsim.commongui - package org.ginsim.commongui

org.ginsim.commongui.dialog - package org.ginsim.commongui.dialog

Help to create GUI dialogs, for data and messages.

org.ginsim.commongui.utils - package org.ginsim.commongui.utils

Collection of GUI helpers and widgets.

org.ginsim.core.annotation - package org.ginsim.core.annotation

Manage annotations: bibliography, Database entries and links.

org.ginsim.core.graph - package org.ginsim.core.graph

Define the main Graph interfaces, and a GraphManager to handle graph types

org.ginsim.core.graph.backend - package org.ginsim.core.graph.backend

Implementation of the graph backend.

org.ginsim.core.graph.dynamicgraph - package org.ginsim.core.graph.dynamicgraph

State Transition Graphs, representing dynamical behaviours.

org.ginsim.core.graph.hierarchicaltransitiongraph - package org.ginsim.core.graph.hierarchicaltransitiongraph

org.ginsim.core.graph.objectassociation - package org.ginsim.core.graph.objectassociation

Handling objects associated to Graphs.

org.ginsim.core.graph.reducedgraph - package org.ginsim.core.graph.reducedgraph

Loop-free graphs where each node represents a strongly connected component of the original graph.

org.ginsim.core.graph.regulatorygraph - package org.ginsim.core.graph.regulatorygraph

The regulatory graph is the main graph, it represents the model.

org.ginsim.core.graph.regulatorygraph.logicalfunction - package org.ginsim.core.graph.regulatorygraph.logicalfunction

Logical functions associated to nodes of the regulatory graph define their dynamical behaviour.

org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree - package org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree

org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function - package org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function

org.ginsim.core.graph.regulatorygraph.logicalfunction.parser - package org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

org.ginsim.core.graph.regulatorygraph.namedstates - package org.ginsim.core.graph.regulatorygraph.namedstates

Define states of a regulatory graph, which can be named and used as starting point for simulations.

org.ginsim.core.graph.regulatorygraph.perturbation - package org.ginsim.core.graph.regulatorygraph.perturbation

Perturbations to modify some parts of a model before analysis.

org.ginsim.core.graph.trapspacetree - package org.ginsim.core.graph.trapspacetree

org.ginsim.core.graph.tree - package org.ginsim.core.graph.tree

The Tree graph is a representation of a logical functions, allowing a graphical representation.

org.ginsim.core.graph.view - package org.ginsim.core.graph.view

Define the layout and appearance of graph elements.

org.ginsim.core.graph.view.css - package org.ginsim.core.graph.view.css

Customise Graph views through CSS-like commands.

org.ginsim.core.graph.view.shapes - package org.ginsim.core.graph.view.shapes

org.ginsim.core.graph.view.style - package org.ginsim.core.graph.view.style

Styles define visual properties for graph elements.

org.ginsim.core.io.parser - package org.ginsim.core.io.parser

Some tools to build parsers and writers for xml and text formats

org.ginsim.core.notification - package org.ginsim.core.notification

API for notifications: notifications, listener and a global manager to connect them

org.ginsim.core.notification.detailed - package org.ginsim.core.notification.detailed

org.ginsim.core.notification.resolvable - package org.ginsim.core.notification.resolvable

org.ginsim.core.service - package org.ginsim.core.service

Manage Services to extend the core features.

org.ginsim.core.utils.data - package org.ginsim.core.utils.data

Some simple data structures and collections

org.ginsim.gui - package org.ginsim.gui

Definition of the GUIManager: provide access to all opened windows

org.ginsim.gui.annotation - package org.ginsim.gui.annotation

Shared GUI to edit annotations

org.ginsim.gui.graph - package org.ginsim.gui.graph

Common GUI for all graphs, and definition of hooks for specialised parts.

org.ginsim.gui.graph.canvas - package org.ginsim.gui.graph.canvas

Custom implementation of the interactive view

org.ginsim.gui.graph.canvas.events - package org.ginsim.gui.graph.canvas.events

org.ginsim.gui.graph.dynamicgraph - package org.ginsim.gui.graph.dynamicgraph

Specialised GUI for the State Transition Graphs

org.ginsim.gui.graph.hierarchicaltransitiongraph - package org.ginsim.gui.graph.hierarchicaltransitiongraph

Specialised GUI for the Hierarchical Transition Graphs

org.ginsim.gui.graph.reducedgraph - package org.ginsim.gui.graph.reducedgraph

Specialised GUI for the Reduced Graphs (Graph of the SCC)

org.ginsim.gui.graph.regulatorygraph - package org.ginsim.gui.graph.regulatorygraph

Specialised GUI for the Regulatory graphs

org.ginsim.gui.graph.regulatorygraph.initialstate - package org.ginsim.gui.graph.regulatorygraph.initialstate

GUI for the definition and selection of states.

org.ginsim.gui.graph.regulatorygraph.logicalfunction - package org.ginsim.gui.graph.regulatorygraph.logicalfunction

GUI to view and edit logical functions associated to Regulatory Nodes

org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree - package org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd - package org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd

org.ginsim.gui.graph.regulatorygraph.perturbation - package org.ginsim.gui.graph.regulatorygraph.perturbation

GUI for the definition and selection of perturbations applied to a Regulatory Graph

org.ginsim.gui.graph.trapspacetree - package org.ginsim.gui.graph.trapspacetree

org.ginsim.gui.graph.tree - package org.ginsim.gui.graph.tree

Specialised GUI for the graphs representing logical functions.

org.ginsim.gui.graph.view.style - package org.ginsim.gui.graph.view.style

GUI for the definition of styles associated to graph elements.

org.ginsim.gui.guihelpers - package org.ginsim.gui.guihelpers

API for GUI helpers: they provide specialised GUI to show/edit specific data types.

org.ginsim.gui.notifications - package org.ginsim.gui.notifications

GUI to present notifications, and propose related actions when needed.

org.ginsim.gui.service - package org.ginsim.gui.service

API for GUI services, and a manager to load them and integrate them in the shell.

org.ginsim.gui.shell - package org.ginsim.gui.shell

Define the main shell: graph windows and common dialogs

org.ginsim.gui.shell.actions - package org.ginsim.gui.shell.actions

Define types of actions, which will be integrated in different parts of the shell.

org.ginsim.gui.shell.callbacks - package org.ginsim.gui.shell.callbacks

Define the Actions behind the menu entries

org.ginsim.gui.shell.editpanel - package org.ginsim.gui.shell.editpanel

Define edit panels: panels which follow graph selection events.

org.ginsim.gui.utils.data - package org.ginsim.gui.utils.data

Widgets and panels to handle datasets: mostly list edition/selection panels.

org.ginsim.gui.utils.data.models - package org.ginsim.gui.utils.data.models

org.ginsim.gui.utils.dialog.stackdialog - package org.ginsim.gui.utils.dialog.stackdialog

Definition of StackDialog: a run dialog where the main panel can be changed.

org.ginsim.gui.utils.widgets - package org.ginsim.gui.utils.widgets

Some common widgets

org.ginsim.gui.utils.widgets.treetable - package org.ginsim.gui.utils.widgets.treetable

org.ginsim.johnsonCycles - package org.ginsim.johnsonCycles

org.ginsim.service.export.cadp - package org.ginsim.service.export.cadp

org.ginsim.service.export.documentation - package org.ginsim.service.export.documentation

org.ginsim.service.export.image - package org.ginsim.service.export.image

org.ginsim.service.export.nusmv - package org.ginsim.service.export.nusmv

org.ginsim.service.export.prism - package org.ginsim.service.export.prism

org.ginsim.service.export.reggraph - package org.ginsim.service.export.reggraph

org.ginsim.service.export.sat - package org.ginsim.service.export.sat

org.ginsim.service.export.struct - package org.ginsim.service.export.struct

org.ginsim.service.format - package org.ginsim.service.format

org.ginsim.service.format.ginml - package org.ginsim.service.format.ginml

org.ginsim.service.format.sbml - package org.ginsim.service.format.sbml

org.ginsim.service.layout - package org.ginsim.service.layout

org.ginsim.service.tool.avatar.domain - package org.ginsim.service.tool.avatar.domain

org.ginsim.service.tool.avatar.params - package org.ginsim.service.tool.avatar.params

org.ginsim.service.tool.avatar.service - package org.ginsim.service.tool.avatar.service

org.ginsim.service.tool.avatar.simulation - package org.ginsim.service.tool.avatar.simulation

org.ginsim.service.tool.avatar.simulation.others - package org.ginsim.service.tool.avatar.simulation.others

org.ginsim.service.tool.avatar.utils - package org.ginsim.service.tool.avatar.utils

org.ginsim.service.tool.circuit - package org.ginsim.service.tool.circuit

org.ginsim.service.tool.composition - package org.ginsim.service.tool.composition

org.ginsim.service.tool.graphcomparator - package org.ginsim.service.tool.graphcomparator

org.ginsim.service.tool.interactionanalysis - package org.ginsim.service.tool.interactionanalysis

org.ginsim.service.tool.localgraph - package org.ginsim.service.tool.localgraph

org.ginsim.service.tool.modelbooleanizer - package org.ginsim.service.tool.modelbooleanizer

org.ginsim.service.tool.modelreduction - package org.ginsim.service.tool.modelreduction

org.ginsim.service.tool.modelreversion - package org.ginsim.service.tool.modelreversion

org.ginsim.service.tool.polytopesViz - package org.ginsim.service.tool.polytopesViz

org.ginsim.service.tool.reg2dyn - package org.ginsim.service.tool.reg2dyn

org.ginsim.service.tool.reg2dyn.helpers - package org.ginsim.service.tool.reg2dyn.helpers

org.ginsim.service.tool.reg2dyn.htg - package org.ginsim.service.tool.reg2dyn.htg

org.ginsim.service.tool.reg2dyn.limitedsimulation - package org.ginsim.service.tool.reg2dyn.limitedsimulation

org.ginsim.service.tool.reg2dyn.priorityclass - package org.ginsim.service.tool.reg2dyn.priorityclass

org.ginsim.service.tool.reg2dyn.updater - package org.ginsim.service.tool.reg2dyn.updater

org.ginsim.service.tool.scc - package org.ginsim.service.tool.scc

org.ginsim.service.tool.simulation - package org.ginsim.service.tool.simulation

org.ginsim.service.tool.stableregions - package org.ginsim.service.tool.stableregions

org.ginsim.service.tool.stablestates - package org.ginsim.service.tool.stablestates

org.ginsim.service.tool.trapspace - package org.ginsim.service.tool.trapspace

org.ginsim.servicegui.export.cadp - package org.ginsim.servicegui.export.cadp

org.ginsim.servicegui.export.documentation - package org.ginsim.servicegui.export.documentation

org.ginsim.servicegui.export.image - package org.ginsim.servicegui.export.image

org.ginsim.servicegui.export.maboss - package org.ginsim.servicegui.export.maboss

org.ginsim.servicegui.export.nusmv - package org.ginsim.servicegui.export.nusmv

org.ginsim.servicegui.export.petrinet - package org.ginsim.servicegui.export.petrinet

org.ginsim.servicegui.export.prism - package org.ginsim.servicegui.export.prism

org.ginsim.servicegui.export.reggraph - package org.ginsim.servicegui.export.reggraph

org.ginsim.servicegui.export.sat - package org.ginsim.servicegui.export.sat

org.ginsim.servicegui.export.struct - package org.ginsim.servicegui.export.struct

org.ginsim.servicegui.format - package org.ginsim.servicegui.format

org.ginsim.servicegui.format.ginml - package org.ginsim.servicegui.format.ginml

org.ginsim.servicegui.format.sbml - package org.ginsim.servicegui.format.sbml

org.ginsim.servicegui.layout - package org.ginsim.servicegui.layout

org.ginsim.servicegui.tool.avatar - package org.ginsim.servicegui.tool.avatar

org.ginsim.servicegui.tool.avatar.algopanels - package org.ginsim.servicegui.tool.avatar.algopanels

org.ginsim.servicegui.tool.avatar.others - package org.ginsim.servicegui.tool.avatar.others

org.ginsim.servicegui.tool.avatar.parameters - package org.ginsim.servicegui.tool.avatar.parameters

org.ginsim.servicegui.tool.circuit - package org.ginsim.servicegui.tool.circuit

search circuits in the regulatory graph.

org.ginsim.servicegui.tool.composition - package org.ginsim.servicegui.tool.composition

org.ginsim.servicegui.tool.composition.integrationgrammar - package org.ginsim.servicegui.tool.composition.integrationgrammar

org.ginsim.servicegui.tool.dataviewer - package org.ginsim.servicegui.tool.dataviewer

org.ginsim.servicegui.tool.decisionanalysis - package org.ginsim.servicegui.tool.decisionanalysis

org.ginsim.servicegui.tool.dynamicanalyser - package org.ginsim.servicegui.tool.dynamicanalyser

the state transition graph

org.ginsim.servicegui.tool.graphcomparator - package org.ginsim.servicegui.tool.graphcomparator

org.ginsim.servicegui.tool.interactionanalysis - package org.ginsim.servicegui.tool.interactionanalysis

org.ginsim.servicegui.tool.localgraph - package org.ginsim.servicegui.tool.localgraph

org.ginsim.servicegui.tool.lrgcolorizer - package org.ginsim.servicegui.tool.lrgcolorizer

org.ginsim.servicegui.tool.modelbooleanizer - package org.ginsim.servicegui.tool.modelbooleanizer

org.ginsim.servicegui.tool.modelreduction - package org.ginsim.servicegui.tool.modelreduction

org.ginsim.servicegui.tool.modelreversion - package org.ginsim.servicegui.tool.modelreversion

org.ginsim.servicegui.tool.omddViz - package org.ginsim.servicegui.tool.omddViz

org.ginsim.servicegui.tool.pathfinding - package org.ginsim.servicegui.tool.pathfinding

org.ginsim.servicegui.tool.polytopesViz - package org.ginsim.servicegui.tool.polytopesViz

org.ginsim.servicegui.tool.reg2dyn - package org.ginsim.servicegui.tool.reg2dyn

find the state transition graph from the regulatory one

org.ginsim.servicegui.tool.reg2dyn.limitedSimulation - package org.ginsim.servicegui.tool.reg2dyn.limitedSimulation

org.ginsim.servicegui.tool.reg2dyn.priorityclass - package org.ginsim.servicegui.tool.reg2dyn.priorityclass

org.ginsim.servicegui.tool.regulatorygraphanimation - package org.ginsim.servicegui.tool.regulatorygraphanimation

animate the regulatory graph (by simply changing nodes and edge's colors) according to a path/state in the state transition graph.

org.ginsim.servicegui.tool.regulatorytreefunction - package org.ginsim.servicegui.tool.regulatorytreefunction

org.ginsim.servicegui.tool.scc - package org.ginsim.servicegui.tool.scc

colorize the strongly connected components in a graph

org.ginsim.servicegui.tool.stableregions - package org.ginsim.servicegui.tool.stableregions

org.ginsim.servicegui.tool.stablestates - package org.ginsim.servicegui.tool.stablestates

org.ginsim.servicegui.tool.stateinregulatorygraph - package org.ginsim.servicegui.tool.stateinregulatorygraph

org.ginsim.servicegui.tool.trapspace - package org.ginsim.servicegui.tool.trapspace

OSXAdapter - Class in org.ginsim.common.application

Apple-provided adapter to help with OSX integration.

OSXAdapter(String, Object, Method) - Constructor for class org.ginsim.common.application.OSXAdapter

out - Variable in class org.ginsim.service.tool.avatar.domain.ExhaustiveFinalPaths

outDegreeOf(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

outgoingEdgesOf(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

OutgoingNodesHandlingStrategy - Enum in org.ginsim.service.tool.reg2dyn.limitedsimulation

Indicates if the states in the immediates neighborhood should be added the the resulting dynamic graph of the simualtion.

output - Variable in class org.ginsim.common.document.DocumentWriter

output(String) - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

outputDir - Variable in class org.ginsim.common.document.DocumentWriter

outputDir - Variable in class org.ginsim.service.tool.avatar.simulation.Simulation

output directory to save the outputs

outputs - Variable in class org.ginsim.service.tool.modelreduction.ReductionConfig

overlay(Graphics2D, Rectangle) - Method in interface org.ginsim.gui.graph.canvas.CanvasEventManager

overlay(Graphics2D, Rectangle) - Method in interface org.ginsim.gui.graph.canvas.CanvasRenderer

Draw temporary information on top of the canvas.

overlay(Graphics2D, Rectangle) - Method in class org.ginsim.gui.graph.canvas.events.AddEdgeInGraphCanvasEventManager

overlay(Graphics2D, Rectangle) - Method in class org.ginsim.gui.graph.canvas.events.AddNodeInGraphCanvasEventManager

overlay(Graphics2D, Rectangle) - Method in class org.ginsim.gui.graph.canvas.events.GraphSelectionCanvasEventManager

overlay(Graphics2D, Rectangle) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

P

p_right - Variable in class org.ginsim.gui.utils.data.ListPanel

PADDING_HORIZONTAL - Static variable in class org.ginsim.core.graph.tree.TreeNode

PADDING_VERTICAL - Static variable in class org.ginsim.core.graph.tree.TreeNode

paint(Graphics, JComponent) - Method in class org.ginsim.commongui.utils.VerticalLabelUI

Transforms the Graphics for vertical rendering and invokes the super method.

paint(Graphics) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

paint(Graphics) - Method in class org.ginsim.gui.utils.widgets.treetable.JTreeTable.TreeTableCellRenderer

paintComponent(Graphics) - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

paintComponent(Graphics) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GlassPane

paintComponent(Graphics) - Method in class org.ginsim.gui.graph.view.style.AnchorSelector

panelAvatar - Variable in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

pointer to the panel with the parameters for an avatar simulation

PanelFactory - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

PanelFactory(LogicalFunctionPanel) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.PanelFactory

panelFF - Variable in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

pointer to the panel with the parameters for a firefront simulation

panelMC - Variable in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

pointer to the panel with the parameters for a Monte Carlo simulation

PARAM_ALLCONTEXTS - Static variable in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

PARAM_FLAVOR - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

PARAM_INITIALCIRCUITDESC - Static variable in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

PARAM_INITIALVERTEXINDEX - Static variable in class org.ginsim.core.graph.tree.TreeBuilderFromRegulatoryGraph

param_list - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

PARAM_MANAGER - Static variable in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

PARAM_MANUALOMDD - Static variable in class org.ginsim.core.graph.tree.TreeBuilderFromManualOmdd

PARAM_NODEORDER - Static variable in class org.ginsim.core.graph.tree.TreeBuilder

PARAM_OPENCIRCUITDESC - Static variable in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

PARAM_REGGRAPH - Static variable in class org.ginsim.core.graph.tree.TreeBuilderFromRegulatoryGraph

parameters - Variable in class org.ginsim.service.tool.avatar.domain.Result

Parameters description

parametersToString() - Method in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

parametersToString() - Method in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

parametersToString() - Method in class org.ginsim.service.tool.avatar.simulation.MonteCarloSimulation

parametersToString() - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

Prints the current parameters

paramList - Variable in class org.ginsim.servicegui.tool.avatar.parameters.AvaParameterEditionPanel

list of simulation contexts

ParamPanel - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

ParamPanel(TreeElement, JTree, boolean, int) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ParamPanel

ParamTree - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function

ParamTree(ArrayList, int) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTree

ParamTreeLeaf - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function

ParamTreeLeaf(ParamTreeNode, int) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

ParamTreeLeafPattern - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function

ParamTreeLeafPattern() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

ParamTreeLeafValue - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function

ParamTreeLeafValue(ParamTreeNode, int) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafValue

ParamTreeNode - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function

ParamTreeNode(RegulatoryNode, RegulatoryMultiEdge, ParamTreeNode, int) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

parent - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

parent - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

parent - Variable in class org.ginsim.core.graph.view.style.BaseStyle

parentIndex - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

parse(File, Set<String>, Graph) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicParser

create a new dynamical graph from a file.

parse(String) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

parse(String) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

parse(File, Set<String>, Graph) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphParser

create a new ReducedGraph from a file.

parse(File, Set, Graph<?, ?>) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryParser

create a new regulatory graph from a file.

parse(String) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheet

Return a new CSS object from a text.

parse(InputStream, Set) - Method in class org.ginsim.core.io.parser.GinmlParser

parse(String) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionSpecification

parseFunctions() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

parseOmdd() - Method in class org.ginsim.core.graph.tree.TreeBuilder

parseOmdd() - Method in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

parseOmdd() - Method in class org.ginsim.core.graph.tree.TreeBuilderFromMDD

parser - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperand

parser - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperator

parseStyle(String, Attributes) - Method in class org.ginsim.core.graph.view.style.StyleManager

ParsingWarning - Class in org.ginsim.common.xml

Describe a warning found while parsing an XML file.

ParsingWarning(SAXParseException) - Constructor for class org.ginsim.common.xml.ParsingWarning

ParsingWarningReport - Class in org.ginsim.common.xml

Store all warnings found while parsing an XML document.

ParsingWarningReport() - Constructor for class org.ginsim.common.xml.ParsingWarningReport

PASTE - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.TreeMenu

pasteExpressionsInExpression(TreeElement[], boolean, TreeExpression) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

pasteFunctionsInValue(TreeElement[], boolean, TreeValue) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

pasteParamsInValue(TreeElement[], boolean, TreeValue) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

pasteValuesInRoot(TreeElement[], TreeString) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

PathFinding - Class in org.ginsim.servicegui.tool.pathfinding

A class to find a path in any graph

PathFinding(ResultHandler, Graph, List<Object>) - Constructor for class org.ginsim.servicegui.tool.pathfinding.PathFinding

Create a new thread that will search a path between start and end The graphManager is used to find the outgoingEdges from a node.

PathFindingFrame - Class in org.ginsim.servicegui.tool.pathfinding

PathFindingFrame(Graph) - Constructor for class org.ginsim.servicegui.tool.pathfinding.PathFindingFrame

PathFindingServiceGUI - Class in org.ginsim.servicegui.tool.pathfinding

PathFindingServiceGUI() - Constructor for class org.ginsim.servicegui.tool.pathfinding.PathFindingServiceGUI

PathFindingTableModel<N> - Interface in org.ginsim.servicegui.tool.pathfinding

PathStyleProvider - Class in org.ginsim.servicegui.tool.pathfinding

PathStyleProvider(StyleManager) - Constructor for class org.ginsim.servicegui.tool.pathfinding.PathStyleProvider

pathToString() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSet

PATTERN - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

PatternHolder - Interface in org.ginsim.core.graph.regulatorygraph.namedstates

PatternSelectionPanel - Class in org.ginsim.gui.graph.regulatorygraph.initialstate

PatternSelectionPanel(RegulatoryGraph, boolean, PatternHolder) - Constructor for class org.ginsim.gui.graph.regulatorygraph.initialstate.PatternSelectionPanel

pcmanager - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

percievedBrightness(int, int, int) - Static method in class org.ginsim.common.utils.ColorPalette

Return the perceived brightness of the given color

perform(Graph, Object[], int) - Method in class org.ginsim.core.notification.resolvable.InvalidFunctionResolution

perform(Graph, Object[], int) - Method in class org.ginsim.core.notification.resolvable.NotificationResolution

performAction(int) - Method in class org.ginsim.gui.utils.data.ObjectEditor

performed(EditActionManager) - Method in class org.ginsim.gui.graph.DeleteAction

performed(EditActionManager) - Method in class org.ginsim.gui.graph.EditAction

Warn the edit action manager that this action was performed.

performed - Variable in class org.ginsim.service.tool.avatar.domain.Result

Number of performed iterations

performResolution(int) - Method in class org.ginsim.core.notification.resolvable.ResolvableErrorNotification

performResolution(int) - Method in interface org.ginsim.core.notification.resolvable.ResolvableNotification

Execute the resolution

performResolution(int) - Method in class org.ginsim.core.notification.resolvable.ResolvableWarningNotification

Execute the chosen option of the resolution associated to the Notification

performTask() - Method in class org.ginsim.service.export.documentation.JSONDocumentationWriter

performTask() - Method in class org.ginsim.service.export.image.SVGEncoder

performTask() - Method in class org.ginsim.service.tool.circuit.CircuitAnalyser

performTask() - Method in class org.ginsim.service.tool.circuit.CircuitSearcher

performTask() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparator

Build the basic topology for the diff graph (node+edges) by calling others functions 1) addNodesFromGraph on both graphs 2) setNodesColor 3) addEdgesFromGraph on each node on both graphs

performTask() - Method in class org.ginsim.service.tool.modelreduction.ReconstructionTask

performTask() - Method in class org.ginsim.service.tool.modelreduction.ReductionTask

performTask() - Method in class org.ginsim.service.tool.scc.SCCGraphAlgo

performTask() - Method in class org.ginsim.service.tool.scc.StronglyConnectedComponentTask

Perturbation - Interface in org.ginsim.core.graph.regulatorygraph.perturbation

A perturbation is a (series of) change that can be applied to a regulatory graph.

perturbation - Variable in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

perturbation - Variable in class org.ginsim.service.tool.avatar.domain.Result

Applied perturbations

perturbation - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

PerturbationCreatePanel - Class in org.ginsim.gui.graph.regulatorygraph.perturbation

PerturbationCreatePanel(PerturbationPanelCompanion, ListOfPerturbations) - Constructor for class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationCreatePanel

PerturbationFixed - Class in org.ginsim.core.graph.regulatorygraph.perturbation

PerturbationFixed(NodeInfo, int) - Constructor for class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationFixed

PerturbationGUIHelper - Class in org.ginsim.gui.graph.regulatorygraph.perturbation

PerturbationGUIHelper() - Constructor for class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationGUIHelper

PerturbationHolder - Interface in org.ginsim.core.graph.regulatorygraph.perturbation

An interface for configuration objects who store a selected perturbation.

PerturbationListener - Interface in org.ginsim.core.graph.regulatorygraph.perturbation

be warned when a mutant is added or removed.

PerturbationManager - Class in org.ginsim.core.graph.regulatorygraph.perturbation

Save/open perturbation definitions along with the model.

PerturbationManager() - Constructor for class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationManager

PerturbationMultiple - Class in org.ginsim.core.graph.regulatorygraph.perturbation

PerturbationMultiple(List<Perturbation>) - Constructor for class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationMultiple

Create a multiple perturbation

PerturbationPanel - Class in org.ginsim.gui.graph.regulatorygraph.perturbation

A panel to view, create and edit perturbations.

PerturbationPanel(ListOfPerturbations) - Constructor for class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationPanel

perturbationPanel - Variable in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

PerturbationPanelListHelper - Class in org.ginsim.gui.graph.regulatorygraph.perturbation

PerturbationParser - Class in org.ginsim.core.graph.regulatorygraph.perturbation

parser for perturbation definition file

PerturbationParser(RegulatoryGraph) - Constructor for class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationParser

PerturbationRange - Class in org.ginsim.core.graph.regulatorygraph.perturbation

PerturbationRange(NodeInfo, int, int) - Constructor for class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationRange

PerturbationRegulator - Class in org.ginsim.core.graph.regulatorygraph.perturbation

PerturbationRegulator(NodeInfo, NodeInfo, int) - Constructor for class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationRegulator

perturbations - Variable in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

perturbations - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

PerturbationSelectionPanel - Class in org.ginsim.gui.graph.regulatorygraph.perturbation

PerturbationSelectionPanel(StackDialog, RegulatoryGraph, PerturbationHolder) - Constructor for class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationSelectionPanel

PerturbationStore - Class in org.ginsim.core.graph.regulatorygraph.perturbation

Simple store for perturbation.

PerturbationStore() - Constructor for class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationStore

PerturbationType - Enum in org.ginsim.gui.graph.regulatorygraph.perturbation

PerturbationUser - Class in org.ginsim.core.graph.regulatorygraph.perturbation

Simple standalone perturbation user.

PerturbationUser(RegulatoryGraph, String) - Constructor for class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationUser

PerturbationUser(ListOfPerturbations, String) - Constructor for class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationUser

PetriNetAPNNFormatService - Class in org.ginsim.service.format

GINsim export service for the APNN Petri net format.

PetriNetAPNNFormatService() - Constructor for class org.ginsim.service.format.PetriNetAPNNFormatService

PetriNetExportAction - Class in org.ginsim.servicegui.export.petrinet

PetriNetExportAction(RegulatoryGraph, PetriNetFormat) - Constructor for class org.ginsim.servicegui.export.petrinet.PetriNetExportAction

PetriNetExportServiceGUI - Class in org.ginsim.servicegui.export.petrinet

GUI Action to export a LRG into Petri net

PetriNetExportServiceGUI() - Constructor for class org.ginsim.servicegui.export.petrinet.PetriNetExportServiceGUI

PetriNetINAFormatService - Class in org.ginsim.service.format

GINsim export service for the INA Petri net format.

PetriNetINAFormatService() - Constructor for class org.ginsim.service.format.PetriNetINAFormatService

PetriNetPNMLFormatService - Class in org.ginsim.service.format

GINsim export service for the PNML Petri net format.

PetriNetPNMLFormatService() - Constructor for class org.ginsim.service.format.PetriNetPNMLFormatService

placeNextClassic() - Method in interface org.ginsim.service.layout.LayoutAlgo

place the next classic node

placeNextClassic() - Method in class org.ginsim.service.layout.LevelLayout

placeNextClassic() - Method in class org.ginsim.service.layout.RingLayout

placeNextRoot() - Method in interface org.ginsim.service.layout.LayoutAlgo

place the next root node.

placeNextRoot() - Method in class org.ginsim.service.layout.LevelLayout

placeNextRoot() - Method in class org.ginsim.service.layout.RingLayout

placeNextStable() - Method in interface org.ginsim.service.layout.LayoutAlgo

place the next stable node

placeNextStable() - Method in class org.ginsim.service.layout.LevelLayout

placeNextStable() - Method in class org.ginsim.service.layout.RingLayout

PLAIN_TEXT_FLAVOR - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

plainData - Variable in class org.ginsim.gui.utils.data.MyBasicTransferable

play() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AnimatorUI

playerEnded() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

playPath(int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

PLUS - Variable in class org.ginsim.core.graph.dynamicgraph.DynamicNode

pattern constants

PNGraph - Class in org.ginsim.service.tool.stableregions

PNGraph() - Constructor for class org.ginsim.service.tool.stableregions.PNGraph

PNtoGraph - Class in org.ginsim.service.tool.stableregions

PNtoGraph(LogicalModel) - Constructor for class org.ginsim.service.tool.stableregions.PNtoGraph

pointAttractors - Variable in class org.ginsim.service.tool.avatar.domain.Result

Stable states

PolytopesSelector - Class in org.ginsim.service.tool.polytopesViz

PolytopesSelector() - Constructor for class org.ginsim.service.tool.polytopesViz.PolytopesSelector

PolytopesService - Class in org.ginsim.service.tool.polytopesViz

PolytopesService() - Constructor for class org.ginsim.service.tool.polytopesViz.PolytopesService

PolytopesVizFrame - Class in org.ginsim.servicegui.tool.polytopesViz

PolytopesVizFrame(DynamicGraph) - Constructor for class org.ginsim.servicegui.tool.polytopesViz.PolytopesVizFrame

PolytopesVizServiceGUI - Class in org.ginsim.servicegui.tool.polytopesViz

PolytopesVizServiceGUI() - Constructor for class org.ginsim.servicegui.tool.polytopesViz.PolytopesVizServiceGUI

pos - Variable in class org.ginsim.common.document.DocumentWriter

pos - Variable in class org.ginsim.service.tool.modelreduction.RemovedInfo

POS_HEADER - Static variable in class org.ginsim.common.document.DocumentWriter

POS_LIST - Static variable in class org.ginsim.common.document.DocumentWriter

POS_LIST_ITEM - Static variable in class org.ginsim.common.document.DocumentWriter

POS_OUT - Static variable in class org.ginsim.common.document.DocumentWriter

POS_PARAGRAPH - Static variable in class org.ginsim.common.document.DocumentWriter

POS_TABLE - Static variable in class org.ginsim.common.document.DocumentWriter

POS_TABLE_CELL - Static variable in class org.ginsim.common.document.DocumentWriter

POS_TABLE_ROW - Static variable in class org.ginsim.common.document.DocumentWriter

POSITIVE - Static variable in class org.ginsim.service.tool.circuit.CircuitDescr

pressed(Point, boolean) - Method in interface org.ginsim.gui.graph.canvas.CanvasEventManager

pressed(Point, boolean) - Method in class org.ginsim.gui.graph.canvas.events.AddEdgeInGraphCanvasEventManager

pressed(Point, boolean) - Method in class org.ginsim.gui.graph.canvas.events.AddNodeInGraphCanvasEventManager

pressed(Point, boolean) - Method in class org.ginsim.gui.graph.canvas.events.GraphSelectionCanvasEventManager

pressed(Point, boolean) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

previous - Variable in class org.ginsim.service.tool.reg2dyn.SimulationQueuedState

print() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTree

print(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

print(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

print(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafValue

print(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

printAttractors(Set<Set<String>>) - Method in class org.ginsim.service.tool.stableregions.PNGraph

printMe(List) - Method in class org.ginsim.service.tool.circuit.CircuitDescr

print the circuit in a nice order.

printPnGraph() - Method in class org.ginsim.service.tool.stableregions.PNGraph

printStackTrace() - Static method in class org.ginsim.common.application.LogManager

print the last "levels" stack trace lines

printStackTrace(int) - Static method in class org.ginsim.common.application.LogManager

priority - Static variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TAndOperator

priority - Static variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TNotOperator

priority - Static variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TOrOperator

PriorityClass - Class in org.ginsim.service.tool.reg2dyn.priorityclass

a priority class for the simulation.

PriorityClass() - Constructor for class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

PriorityClass(int, String) - Constructor for class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

PriorityClassContentEditor - Class in org.ginsim.servicegui.tool.reg2dyn.priorityclass

A panel to edit the content of a PriorityClass

PriorityClassContentEditor(PriorityDefinitionPanel) - Constructor for class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityClassContentEditor

PriorityDefinitionHelper - Class in org.ginsim.servicegui.tool.reg2dyn.priorityclass

GUI helper for the list of priority classes in a PriorityDefinition

PriorityDefinitionHelper() - Constructor for class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionHelper

PriorityDefinitionPanel - Class in org.ginsim.servicegui.tool.reg2dyn.priorityclass

configure priority classes.

PriorityDefinitionPanel(List<RegulatoryNode>, PrioritySetDefinition) - Constructor for class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionPanel

PriorityManagerHelper - Class in org.ginsim.servicegui.tool.reg2dyn.priorityclass

GUI helper for the list of priority class definitions

PriorityManagerHelper() - Constructor for class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityManagerHelper

PrioritySelectionPanel - Class in org.ginsim.servicegui.tool.reg2dyn

PrioritySelectionPanel(StackDialog, PrioritySetList) - Constructor for class org.ginsim.servicegui.tool.reg2dyn.PrioritySelectionPanel

PrioritySetAddMode - Enum in org.ginsim.service.tool.reg2dyn.priorityclass

Default modes to add a new priority set

PrioritySetDefinition - Class in org.ginsim.service.tool.reg2dyn.priorityclass

Definition of a set of priority classes: store a list of classes and assign all nodes to one of them.

PrioritySetDefinition(List<RegulatoryNode>, String) - Constructor for class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

PrioritySetList - Class in org.ginsim.service.tool.reg2dyn.priorityclass

The list of all available priority set definitions.

PrioritySetList(RegulatoryGraph) - Constructor for class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetList

PRISMConfig - Class in org.ginsim.service.export.prism

PRISMConfig(RegulatoryGraph) - Constructor for class org.ginsim.service.export.prism.PRISMConfig

PRISMEncoder - Class in org.ginsim.service.export.prism

Exports a Regulatory graph into a PRISM model description.

PRISMEncoder() - Constructor for class org.ginsim.service.export.prism.PRISMEncoder

PRISMExportConfigPanel - Class in org.ginsim.servicegui.export.prism

PRISMExportConfigPanel(PRISMConfig, PRISMExportAction) - Constructor for class org.ginsim.servicegui.export.prism.PRISMExportConfigPanel

PRISMExportService - Class in org.ginsim.service.export.prism

PRISMExportService() - Constructor for class org.ginsim.service.export.prism.PRISMExportService

PRISMExportServiceGUI - Class in org.ginsim.servicegui.export.prism

GUI Action to export a PRISM model description

PRISMExportServiceGUI() - Constructor for class org.ginsim.servicegui.export.prism.PRISMExportServiceGUI

probability - Variable in class org.ginsim.service.tool.avatar.domain.State

process() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTree

processKeyBinding(KeyStroke, KeyEvent, int, boolean) - Method in class org.ginsim.gui.utils.widgets.EnhancedJTable

ProgressListener<R> - Interface in org.ginsim.common.callable

Define methods to listen for background task: Implementors must handle progress messages and the end of the task.

progressListener() - Method in class org.ginsim.ScriptLauncher

PROP_ANNOTATION - Static variable in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

PROP_ANNOTATION - Static variable in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

PROP_ID - Static variable in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

PROP_ID - Static variable in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

PROP_INPUT - Static variable in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

PROP_MAX - Static variable in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

PROP_NAME - Static variable in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

PROP_NAME - Static variable in class org.ginsim.gui.graph.view.style.StyleEditor

PROP_NODEORDER - Static variable in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

PROP_RAW - Static variable in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

PROP_RAW - Static variable in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

PROP_SUBDOCUMENT - Static variable in class org.ginsim.common.document.DocumentWriter

propagate - Variable in class org.ginsim.service.tool.modelreduction.ReductionConfig

property - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

PropertyActionButton - Class in org.ginsim.gui.utils.data

PropertyActionButton() - Constructor for class org.ginsim.gui.utils.data.PropertyActionButton

propertyChange(PropertyChangeEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

propertyChange(PropertyChangeEvent) - Method in class org.ginsim.gui.utils.widgets.SplitPane

PropertySwitch - Class in org.ginsim.gui.utils.data

PropertySwitch() - Constructor for class org.ginsim.gui.utils.data.PropertySwitch

proxySignature - Variable in class org.ginsim.common.application.OSXAdapter

publish(String) - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

publishDeletion(Notification) - Method in class org.ginsim.core.notification.NotificationManager

Publish a notification so NotificationListerner that were registered and have subscribe to the type of the given notification will remove it from their notification list (deletion is due to notification timeout)

publishDetailedError(Object, String, String) - Static method in class org.ginsim.core.notification.NotificationManager

Publish an error message with details

publishDetailedInformation(Object, String, String) - Static method in class org.ginsim.core.notification.NotificationManager

Publish an information message with details

publishDetailedWarning(Object, String, String) - Static method in class org.ginsim.core.notification.NotificationManager

Publish an warning message with details

publishError(Object, String) - Static method in class org.ginsim.core.notification.NotificationManager

Publish an error message

publishException(Object, String, Exception) - Static method in class org.ginsim.core.notification.NotificationManager

Publish a Java exception

publishInformation(Object, String) - Static method in class org.ginsim.core.notification.NotificationManager

Publish an information message

publishResolvableError(Object, String, Graph, Object[], NotificationResolution) - Static method in class org.ginsim.core.notification.NotificationManager

Publish an error message with its resolution options

publishResolvableWarning(Object, String, Graph, Object[], NotificationResolution) - Static method in class org.ginsim.core.notification.NotificationManager

Publish a warning message with its resolution options

publishWarning(Object, String) - Static method in class org.ginsim.core.notification.NotificationManager

Publish a warning message

push(String) - Static method in class org.ginsim.common.application.Txt

Add a bundle to the text retriever.

pushSearchPath(String) - Static method in class org.ginsim.commongui.utils.ImageLoader

Q

queue - Variable in class org.ginsim.service.tool.reg2dyn.htg.TarjanSimulation

queue - Variable in class org.ginsim.service.tool.reg2dyn.limitedsimulation.LimitedSimulation

queue - Variable in class org.ginsim.service.tool.reg2dyn.Simulation

queueSearchCount - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

quiet - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

quiet - Variable in class org.ginsim.service.tool.avatar.simulation.Simulation

whether detailed logs of the behavior of the simulation are to be printed (true is suggested to not hamper efficiency)

quiet - Variable in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

whether detailed logs should be printed (not advisable for complex models)

quit() - Method in class org.ginsim.gui.GUIManager

try to close all frames

R

RAINBOW - Static variable in class org.ginsim.common.utils.ColorPalette

RANGE - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

RANGE - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

RangeSlider - Class in org.ginsim.gui.utils.widgets

An extension of JSlider to select a range of values using two thumb controls.

RangeSlider() - Constructor for class org.ginsim.gui.utils.widgets.RangeSlider

Constructs a RangeSlider with default minimum and maximum values of 0 and 100.

RangeSlider(int, int) - Constructor for class org.ginsim.gui.utils.widgets.RangeSlider

Constructs a RangeSlider with the specified default minimum and maximum values.

rank - Variable in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

rank of this class

rawPNG(Graph<N, E>) - Method in class org.ginsim.service.export.image.ImageExportService

rawPNG(Graph, StyleProvider) - Method in class org.ginsim.service.export.image.ImageExportService

Reachable - Class in org.ginsim.service.tool.avatar.simulation

Facilities to compute the set of reachable states from a portion of the state space of a given discrete system

Reachable() - Constructor for class org.ginsim.service.tool.avatar.simulation.Reachable

read(Reader, StringBuffer) - Static method in class org.ginsim.common.utils.IOUtils

readContent - Variable in enum org.ginsim.common.xml.CallMode

readFile(Reader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheet

Return a new CSS object from a Reader.

readFromFile(String) - Static method in class org.ginsim.common.utils.IOUtils

Produces a StringBuffer initialized with the given path

readFromFile(String, StringBuffer) - Static method in class org.ginsim.common.utils.IOUtils

Fill the given StringBuffer with the content of the file located at the given path

readFromResource(InputStream) - Static method in class org.ginsim.common.utils.IOUtils

ready - Variable in class org.ginsim.service.tool.reg2dyn.Simulation

ready2play() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AnimatorUI

inform the user that the animator is ready to play.

realDetph - Variable in class org.ginsim.core.graph.tree.TreeBuilder

As the omdd diagram could not contain all the levels (some could be skipped...), we try to reduce the tree width, by assigning a depth to each __used__ level.

reBuild() - Method in class org.ginsim.servicegui.export.cadp.VisibleComponentsWidget

reBuild() - Method in class org.ginsim.servicegui.tool.composition.AdjacencyMatrixWidget

receiveNotification(Notification) - Method in interface org.ginsim.core.notification.NotificationListener

Receive a notification from the NotificationManager and add it from the notification list

receiveNotification(Notification) - Method in class org.ginsim.gui.shell.MainFrame

Receive a notification and add it to the notification queue

ReconstructionTask - Class in org.ginsim.service.tool.modelreduction

Reconstruct a Regulatory Graph from a Logical model and restore layout, comments and metadata from an original graph.

ReconstructionTask(LogicalModel, RegulatoryGraph) - Constructor for class org.ginsim.service.tool.modelreduction.ReconstructionTask

ReconstructionTask(LogicalModel, RegulatoryGraph, ReductionConfig) - Constructor for class org.ginsim.service.tool.modelreduction.ReconstructionTask

ReducedGINMLWriter - Class in org.ginsim.core.graph.reducedgraph

Save the SCC graph in GINML

ReducedGINMLWriter(ReducedGraph) - Constructor for class org.ginsim.core.graph.reducedgraph.ReducedGINMLWriter

ReducedGraph<AG extends Graph<AV,AE>,AV,AE extends Edge<AV>> - Interface in org.ginsim.core.graph.reducedgraph

Graph of the strongly connected components.

ReducedGraphFactory<G extends Graph<V,E>,V,E extends Edge<V>> - Class in org.ginsim.core.graph.reducedgraph

Factory for the SCC graph.

ReducedGraphFactory() - Constructor for class org.ginsim.core.graph.reducedgraph.ReducedGraphFactory

ReducedGraphGUIHelper - Class in org.ginsim.gui.graph.reducedgraph

ReducedGraphGUIHelper() - Constructor for class org.ginsim.gui.graph.reducedgraph.ReducedGraphGUIHelper

ReducedGraphImpl<G extends Graph<V,E>,V,E extends Edge<V>> - Class in org.ginsim.core.graph.reducedgraph

Implementation of the Reduced Graph.

ReducedGraphImpl(G) - Constructor for class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

ReducedGraphImpl(Set, File) - Constructor for class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

ReducedGraphImpl() - Constructor for class org.ginsim.core.graph.reducedgraph.ReducedGraphImpl

ReducedGraphParser - Class in org.ginsim.core.graph.reducedgraph

Load a SCC graph from GINML.

ReducedGraphParser(Set<String>, Attributes, String, String) - Constructor for class org.ginsim.core.graph.reducedgraph.ReducedGraphParser

ReducedGraphParser(Set<String>, Attributes, String) - Constructor for class org.ginsim.core.graph.reducedgraph.ReducedGraphParser

ReducedGraphParser() - Constructor for class org.ginsim.core.graph.reducedgraph.ReducedGraphParser

ReducedGraphTableModel - Class in org.ginsim.gui.graph.reducedgraph

this model is used to list the content of a strong components.

ReducedGraphTableModel() - Constructor for class org.ginsim.gui.graph.reducedgraph.ReducedGraphTableModel

ReducedParameterPanel - Class in org.ginsim.gui.graph.reducedgraph

this panel display some info about a strong component node: it'll mainly display the list of "real nodes" present in this node

ReducedParameterPanel(ReducedGraph) - Constructor for class org.ginsim.gui.graph.reducedgraph.ReducedParameterPanel

reduction - Variable in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

reduction - Variable in class org.ginsim.service.tool.avatar.domain.Result

Applied reductions

reduction - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

ReductionConfig - Class in org.ginsim.service.tool.modelreduction

ReductionConfig() - Constructor for class org.ginsim.service.tool.modelreduction.ReductionConfig

ReductionConfigDialog - Class in org.ginsim.servicegui.tool.modelreduction

ReductionConfigManager - Class in org.ginsim.service.tool.modelreduction

Save/open simulation parameters along with the model.

ReductionConfigManager() - Constructor for class org.ginsim.service.tool.modelreduction.ReductionConfigManager

ReductionConfigSelectionPanel - Class in org.ginsim.servicegui.tool.modelreduction

ReductionConfigSelectionPanel(StackDialog, RegulatoryGraph, ReductionHolder) - Constructor for class org.ginsim.servicegui.tool.modelreduction.ReductionConfigSelectionPanel

ReductionConfigurationPanel - Class in org.ginsim.servicegui.tool.modelreduction

The panel to configure reduction definitions.

ReductionConfigurationPanel(RegulatoryGraph) - Constructor for class org.ginsim.servicegui.tool.modelreduction.ReductionConfigurationPanel

ReductionConfigurationPanel(ListOfReductionConfigs) - Constructor for class org.ginsim.servicegui.tool.modelreduction.ReductionConfigurationPanel

ReductionGUIHelper - Class in org.ginsim.servicegui.tool.modelreduction

ReductionGUIHelper() - Constructor for class org.ginsim.servicegui.tool.modelreduction.ReductionGUIHelper

ReductionHolder - Interface in org.ginsim.service.tool.modelreduction

An interface for configuration objects which store a selected reduction.

ReductionLauncher - Interface in org.ginsim.service.tool.modelreduction

reductionPanel - Variable in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

reductions - Variable in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

reductions - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

ReductionSelectionPanel - Class in org.ginsim.servicegui.tool.modelreduction

ReductionSelectionPanel(StackDialog, RegulatoryGraph, ReductionHolder) - Constructor for class org.ginsim.servicegui.tool.modelreduction.ReductionSelectionPanel

ReductionServiceGUI - Class in org.ginsim.servicegui.tool.modelreduction

main method for the model simplification plugin

ReductionServiceGUI() - Constructor for class org.ginsim.servicegui.tool.modelreduction.ReductionServiceGUI

ReductionStub - Class in org.ginsim.service.tool.composition

Implements a ReductionLauncher interface to recover the results of invoking ModuleSimplifier

ReductionStub(RegulatoryGraph) - Constructor for class org.ginsim.service.tool.composition.ReductionStub

ReductionTask - Class in org.ginsim.service.tool.modelreduction

Build a simplified model, based on a complete one, by removing some nodes.

ReductionTask(RegulatoryGraph, ReductionConfig) - Constructor for class org.ginsim.service.tool.modelreduction.ReductionTask

ReductionTask(LogicalModel, ReductionConfig) - Constructor for class org.ginsim.service.tool.modelreduction.ReductionTask

ReductionTask(RegulatoryGraph, ReductionConfig, ReductionLauncher) - Constructor for class org.ginsim.service.tool.modelreduction.ReductionTask

ReductionTask(LogicalModel, ReductionConfig, ReductionLauncher) - Constructor for class org.ginsim.service.tool.modelreduction.ReductionTask

refresh(Object) - Method in class org.ginsim.core.graph.AbstractGraph

Declare an object visual setting change

refresh() - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

refresh() - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

refresh(Object) - Method in interface org.ginsim.core.graph.GraphViewListener

A single item was changed.

refresh() - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.LogicalFunctionView

refresh() - Method in interface org.ginsim.core.graph.view.AttributesReader

Let listeners know that the item has been updated

refresh(boolean) - Method in class org.ginsim.gui.annotation.AnnotationPanel

refresh(Object) - Method in class org.ginsim.gui.graph.canvas.CanvasGraphGUIImpl

refresh() - Method in class org.ginsim.gui.graph.dynamicgraph.StateTransitionGraphEditor

refresh() - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalGraphEditor

refresh(boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

refresh() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

refresh(boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

refresh() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

refresh() - Method in class org.ginsim.gui.graph.view.style.StyleColorizerCheckbox

refresh(boolean) - Method in class org.ginsim.gui.utils.data.HelpedListEditorUI

refresh() - Method in class org.ginsim.gui.utils.data.ListEditionPanel

refresh() - Method in class org.ginsim.gui.utils.data.ListPanel

force a refresh of the list

refresh() - Method in class org.ginsim.gui.utils.data.ListSelectionPanel

refresh(boolean) - Method in class org.ginsim.gui.utils.data.MinMaxEditor

refresh(boolean) - Method in class org.ginsim.gui.utils.data.ObjectEditor

refresh(boolean) - Method in interface org.ginsim.gui.utils.data.ObjectPropertyEditorUI

refresh(boolean) - Method in class org.ginsim.gui.utils.data.PropertyActionButton

refresh(boolean) - Method in class org.ginsim.gui.utils.data.PropertySwitch

refresh(boolean) - Method in class org.ginsim.gui.utils.data.SpinEditor

refresh(boolean) - Method in class org.ginsim.gui.utils.widgets.BooleanEditor

refresh() - Method in class org.ginsim.gui.utils.widgets.ButtonPopup

refresh(boolean) - Method in class org.ginsim.gui.utils.widgets.StatusTextField

refresh(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

Updates the parameters of the simulation panel given the new context

refresh() - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionSelectionPanel

refreshMain() - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

called when the main panel takes the focus back

refreshNode() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

refreshNode(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

refreshRoot() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

refreshView() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

Reg2DynService - Class in org.ginsim.service.tool.reg2dyn

Reg2DynService() - Constructor for class org.ginsim.service.tool.reg2dyn.Reg2DynService

Reg2DynServiceGUI - Class in org.ginsim.servicegui.tool.reg2dyn

main method for the reg2dyn plugin

Reg2DynServiceGUI() - Constructor for class org.ginsim.servicegui.tool.reg2dyn.Reg2DynServiceGUI

regGraph - Variable in class org.ginsim.core.graph.tree.TreeBuilderFromRegulatoryGraph

RegGraphEncoder - Class in org.ginsim.service.export.reggraph

Exports a logical model into the Regulatory Graph format.

RegGraphEncoder(RegulatoryGraph) - Constructor for class org.ginsim.service.export.reggraph.RegGraphEncoder

RegGraphExportService - Class in org.ginsim.service.export.reggraph

GINsim export service for the Regulatory Graph format.

RegGraphExportService() - Constructor for class org.ginsim.service.export.reggraph.RegGraphExportService

RegGraphExportServiceGUI - Class in org.ginsim.servicegui.export.reggraph

GUI Action to export the regulatory graph interactions and corresponding signs.

RegGraphExportServiceGUI() - Constructor for class org.ginsim.servicegui.export.reggraph.RegGraphExportServiceGUI

registerForDocumentExtra(String) - Method in class org.ginsim.common.document.DocumentWriter

Register the current document for extra (initialize the StringBuffer)

registerGraph(Graph) - Method in class org.ginsim.core.graph.GSGraphManager

register a graph without associated file path

registerGraph(G, String) - Method in class org.ginsim.core.graph.GSGraphManager

Memorize the link between the graph and the path of the file the graph has been loaded from or saved to

registerGUI(GraphGUI, MainFrame) - Method in class org.ginsim.gui.GUIManager

registerListener(NotificationListener, Object) - Method in class org.ginsim.core.notification.NotificationManager

Register a listener and subscribe it to the given topic

registerSelector(String, Class) - Static method in class org.ginsim.core.graph.view.css.Selector

Register your selector to enable parsing it.

RegulatoryAnimator - Class in org.ginsim.servicegui.tool.regulatorygraphanimation

Main class of the animator plugin.

RegulatoryEdge - Class in org.ginsim.core.graph.regulatorygraph

An interactions between the nodes of a regulatory graph..

RegulatoryEdge(RegulatoryMultiEdge) - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

RegulatoryEdgeEditor - Class in org.ginsim.gui.graph.regulatorygraph

RegulatoryEdgeEditor(RegulatoryGraph) - Constructor for class org.ginsim.gui.graph.regulatorygraph.RegulatoryEdgeEditor

RegulatoryEdgeSign - Enum in org.ginsim.core.graph.regulatorygraph

Possible signs for interactions.

RegulatoryFunctionTreeServiceGUI - Class in org.ginsim.servicegui.tool.regulatorytreefunction

RegulatoryFunctionTreeServiceGUI() - Constructor for class org.ginsim.servicegui.tool.regulatorytreefunction.RegulatoryFunctionTreeServiceGUI

RegulatoryGINMLWriter - Class in org.ginsim.core.graph.regulatorygraph

Save a Regulatory Graphs in GINML.

RegulatoryGINMLWriter(RegulatoryGraph) - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryGINMLWriter

RegulatoryGraph - Interface in org.ginsim.core.graph.regulatorygraph

The regulatory graph

RegulatoryGraphAnimationServiceGUI - Class in org.ginsim.servicegui.tool.regulatorygraphanimation

register the aRegGraph plugin: animate the regulatory graph according to a path in the associated state transition graph.

RegulatoryGraphAnimationServiceGUI() - Constructor for class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryGraphAnimationServiceGUI

RegulatoryGraphComparator - Class in org.ginsim.service.tool.graphcomparator

Compare 2 RegulatoryGraph

RegulatoryGraphComparator(RegulatoryGraph, RegulatoryGraph) - Constructor for class org.ginsim.service.tool.graphcomparator.RegulatoryGraphComparator

RegulatoryGraphEditor - Class in org.ginsim.gui.graph.regulatorygraph

RegulatoryGraphEditor(RegulatoryGraph) - Constructor for class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

RegulatoryGraphFactory - Class in org.ginsim.core.graph.regulatorygraph

Factory for regulatory graphs.

RegulatoryGraphFactory() - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphFactory

RegulatoryGraphGUIHelper - Class in org.ginsim.gui.graph.regulatorygraph

GUI helper for the regulatory graph.

RegulatoryGraphGUIHelper() - Constructor for class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphGUIHelper

RegulatoryGraphImpl - Class in org.ginsim.core.graph.regulatorygraph

Implementation of the RegulatoryGraph interface.

RegulatoryGraphImpl() - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

Create a new Regulatory graph

RegulatoryGraphOptionPanel - Class in org.ginsim.gui.graph.regulatorygraph

offer save option for regulatory graphs

RegulatoryGraphOptionPanel(Object[], int) - Constructor for class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphOptionPanel

create the save option panel for ginml based graphs

RegulatoryIntegration - Class in org.ginsim.service.tool.composition

The integration function and proper components associated to an input components

RegulatoryIntegration(IntegrationFunction, List<RegulatoryNode>) - Constructor for class org.ginsim.service.tool.composition.RegulatoryIntegration

RegulatoryMultiEdge - Class in org.ginsim.core.graph.regulatorygraph

Edges of the regulatory graph: provide a list of interactions.

RegulatoryMultiEdge(RegulatoryGraph, RegulatoryNode, RegulatoryNode, RegulatoryEdgeSign) - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

RegulatoryMultiEdge(RegulatoryGraph, RegulatoryNode, RegulatoryNode, RegulatoryEdgeSign, byte) - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

RegulatoryMultiEdge(RegulatoryGraph, RegulatoryNode, RegulatoryNode) - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

RegulatoryNode - Class in org.ginsim.core.graph.regulatorygraph

A node in the Regulatory graph, representing a regulatory component.

RegulatoryNode(String, RegulatoryGraph) - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

Constructs an empty vector and set the baseValue (0) and the maxValue (1)

RegulatoryNode(int, RegulatoryGraph) - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

RegulatoryNodeEditor - Class in org.ginsim.gui.graph.regulatorygraph

RegulatoryNodeEditor(RegulatoryGraph) - Constructor for class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

RegulatoryParser - Class in org.ginsim.core.graph.regulatorygraph

Load a regulatory graph from GINML.

RegulatoryParser() - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryParser

RegulatoryParser(Set, Attributes, String) - Constructor for class org.ginsim.core.graph.regulatorygraph.RegulatoryParser

release() - Method in class org.ginsim.gui.annotation.AnnotationPanel

release() - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

release() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

release() - Method in class org.ginsim.gui.utils.data.HelpedListEditorUI

release() - Method in class org.ginsim.gui.utils.data.MinMaxEditor

release() - Method in class org.ginsim.gui.utils.data.ObjectEditor

release() - Method in interface org.ginsim.gui.utils.data.ObjectPropertyEditorUI

release() - Method in class org.ginsim.gui.utils.data.PropertyActionButton

release() - Method in class org.ginsim.gui.utils.data.PropertySwitch

release() - Method in class org.ginsim.gui.utils.data.SpinEditor

release() - Method in class org.ginsim.gui.utils.widgets.BooleanEditor

release() - Method in class org.ginsim.gui.utils.widgets.StatusTextField

released(Point) - Method in interface org.ginsim.gui.graph.canvas.CanvasEventManager

released(Point) - Method in class org.ginsim.gui.graph.canvas.events.AddEdgeInGraphCanvasEventManager

released(Point) - Method in class org.ginsim.gui.graph.canvas.events.AddNodeInGraphCanvasEventManager

released(Point) - Method in class org.ginsim.gui.graph.canvas.events.GraphSelectionCanvasEventManager

released(Point) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

releaseEdges() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

remove(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

remove(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

remove(RegulatoryMultiEdge, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

remove() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeValue

remove(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

remove() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesIterator

remove(int) - Method in class org.ginsim.core.utils.data.ListenableNamedList

remove(L, int[]) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

remove(State) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Removes a given state from the state-set

remove(State) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Removes a given state from the state-set

remove(RegulatoryNode) - Method in class org.ginsim.service.tool.modelreduction.ReductionConfig

remove(int) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

remove(Object) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

remove(int[]) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

Remove a group of items

remove() - Method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

remove() - Method in class org.ginsim.service.tool.reg2dyn.updater.DeterministicSimulationUpdater

remove() - Method in class org.ginsim.service.tool.reg2dyn.updater.GenericSimulationUpdater

remove() - Method in class org.ginsim.servicegui.tool.modelreduction.TargetEdgesIterator

remove() - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityClassContentEditor

Remove genes from the selected class: they will go to the next class (cycling from last to first).

removeActionListener(TableActionListener) - Method in class org.ginsim.gui.utils.widgets.EnhancedJTable

removeAllObjects(Graph) - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

Remove all references from associated objects

removeBlockClose(Graph, Object) - Method in class org.ginsim.gui.GUIManager

Remove a block on closing

removeBlockEdit(Graph, Object) - Method in class org.ginsim.gui.GUIManager

Remove a block on Edition

removeChild(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

RemovedInfo - Class in org.ginsim.service.tool.modelreduction

RemovedInfo(RegulatoryNode, int, Collection<RegulatoryMultiEdge>) - Constructor for class org.ginsim.service.tool.modelreduction.RemovedInfo

removeEdge(E) - Method in class org.ginsim.core.graph.AbstractGraph

Remove an edge from the graph.

removeEdge(V, V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

removeEdge(E) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

removeEdge(DynamicEdge) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

removeEdge(E) - Method in interface org.ginsim.core.graph.GraphBackend

remove an edge from the graph.

removeEdge(E) - Method in interface org.ginsim.core.graph.GraphModel

Remove an edge from the graph.

removeEdge(RegulatoryMultiEdge, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

removeEdge(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

removeEdge(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

removeEdge(int, RegulatoryGraph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

remove an edge from this multiEdge

removeEdgeFromInteraction(RegulatoryMultiEdge, int) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

when an incoming edge is deleted, we don't want to see it appear in interactions anymore.

removeEdgeFromInteraction(RegulatoryMultiEdge) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

when an incoming edge is deleted, we don't want to see it appear in interactions anymore.

removeFile(String) - Method in class org.ginsim.core.annotation.BiblioList

removeGraphGUIListener(GraphGUIListener<G, V, E>) - Method in class org.ginsim.gui.graph.BaseGraphGUI

removeGraphGUIListener(GraphGUIListener<G, V, E>) - Method in interface org.ginsim.gui.graph.GraphGUI

Remove a listener.

removeGraphListener(G, GraphListener<G>) - Method in class org.ginsim.core.graph.GSGraphManager

removeInteraction(LogicalParameter) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

Removes the specified interaction to the interactions of the node

removeInteractions(int) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

remove Interactions at index row

removeInteractions(int[]) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

remove a selection of rows

removeItems(L, int[]) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

removeListener(ObjectPropertyEditorUI) - Method in class org.ginsim.gui.utils.data.ObjectEditor

removeListListener(GenericListListener) - Method in class org.ginsim.core.utils.data.ListenableNamedList

removeMask(int, int) - Static method in class org.ginsim.common.utils.MaskUtils

Remove a mask from a value.

removeNeighbour(int, int) - Method in class org.ginsim.service.tool.composition.GenericTopology

removeNeighbour(int, int) - Method in interface org.ginsim.service.tool.composition.Topology

removeNeighbour(int, int) - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

removeNeighbour(int, int) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

removeNeighbour(int, int) - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

removeNode(V) - Method in class org.ginsim.core.graph.AbstractGraph

Remove a node from the graph.

removeNode(V) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

remove a node from the JgraphT graph

removeNode(V) - Method in interface org.ginsim.core.graph.GraphBackend

remove a node from the graph.

removeNode(V) - Method in interface org.ginsim.core.graph.GraphModel

Remove a node from the graph.

removeNode(RegulatoryNode) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

removeNode(RegulatoryNode) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

removeNullFunction(byte) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

removeObject(Graph, String) - Method in class org.ginsim.core.graph.objectassociation.ObjectAssociationManager

remove an object previously associated to a graph with addObject(Object, Object).

removeOption(String) - Static method in class org.ginsim.common.application.OptionStore

remove a saved option.

removePerturbations(Collection<Perturbation>) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

removeRegulation(int) - Method in class org.ginsim.gui.graph.regulatorygraph.MultiEdgeEditPanel

removeSelection(int[]) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetList

removeTab(String) - Method in class org.ginsim.gui.shell.editpanel.EditPanel

Remove an editing tab.

removeTabToEditPanel(String) - Method in class org.ginsim.gui.shell.MainFrame

Remove a given EditTab from the edit panel

removeTransition(String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

removeTreeModelListener(TreeModelListener) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

removeTreeModelListener(TreeModelListener) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

removeVertex(V) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

rename(int, String) - Method in class org.ginsim.core.utils.data.NamedList

Change the name of one element.

renameStyle(Style, String) - Method in class org.ginsim.core.graph.view.style.StyleManager

render(Graphics2D) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

render(Graphics2D) - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

render(Graphics2D) - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

Render an edge on a given graphics.

render(Graphics2D) - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

Render the current node on a given graphics.

render(Graphics2D, Rectangle) - Method in interface org.ginsim.gui.graph.canvas.CanvasRenderer

Draw on the canvas.

render(Graphics2D, Rectangle) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

renderer - Variable in class org.ginsim.gui.graph.canvas.events.AbstractHelpCanvasEventManager

renderMoving(Graphics2D, MovingEdgeType, int, int) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

renderMoving(Graphics2D, int, int) - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

renderMoving(Graphics2D, MovingEdgeType, int, int) - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

Render an edge while the edge or at least one of its connected node is moved.

renderMoving(Graphics2D, int, int) - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

Render the current node while moving it.

renderMovingPoint(Graphics2D, int, int, int) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

renderMovingPoint(Graphics2D, int, int, int) - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

reordered(int[]) - Method in interface org.ginsim.common.utils.ListReorderListener

reordered(int[]) - Method in class org.ginsim.core.annotation.Annotation

repaint() - Method in class org.ginsim.core.graph.AbstractGraph

repaint() - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

repaint() - Method in interface org.ginsim.core.graph.GraphBackend

Trigger a repaint of the damaged areas

repaint() - Method in interface org.ginsim.core.graph.GraphViewListener

The full view was changed.

repaint() - Method in class org.ginsim.gui.graph.canvas.CanvasGraphGUIImpl

repaint() - Method in interface org.ginsim.gui.graph.GraphGUI

Force a repaint (should be used only by layout actions)

repaintCanvas() - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

reportFor(RegulatoryNode, RegulatoryNode) - Method in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisReport

Get the report for target from the map or creates i if it doesn't exists.

rescanSign(Graph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

reset() - Method in class org.ginsim.common.utils.Timer

Reset timestamps: as if this object was just created.

reset(List<T>, int, String) - Method in class org.ginsim.core.utils.data.ValueList

reset() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

empty the table of init states.

reset() - Method in class org.ginsim.servicegui.tool.circuit.CircuitConfigureSearch

resetDefaultStyle() - Method in class org.ginsim.core.graph.view.css.AllSelector

resetDefaultStyle() - Method in class org.ginsim.core.graph.view.css.Selector

Reset the categories to their default values.

resetDefaultStyle() - Method in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

reshape(int, int, int, int) - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

residual - Variable in class org.ginsim.service.tool.avatar.domain.Result

FireFront residual probability

ResolvableErrorNotification - Class in org.ginsim.core.notification.resolvable

ResolvableErrorNotification(Object, String, Graph, Object[], NotificationResolution) - Constructor for class org.ginsim.core.notification.resolvable.ResolvableErrorNotification

ResolvableNotification - Interface in org.ginsim.core.notification.resolvable

ResolvableWarningNotification - Class in org.ginsim.core.notification.resolvable

ResolvableWarningNotification(Object, String, Graph, Object[], NotificationResolution) - Constructor for class org.ginsim.core.notification.resolvable.ResolvableWarningNotification

resolveEntity(String, String) - Method in class org.ginsim.common.xml.XMLHelper

do the "entity resolver" job, a bit lazy, this needs some cleanups to become more generalist, but it does the job for GINsim...

respondToEdges() - Method in class org.ginsim.core.graph.view.css.Selector

Indicates if the Selector contains edges styles.

respondToEdges() - Method in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

respondToNodes() - Method in class org.ginsim.core.graph.view.css.Selector

Indicates if the Selector contains nodes styles.

restore(Object) - Method in class org.ginsim.core.graph.view.GraphicalAttributesStore

Deprecated.

restore(String) - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewer

restoreAll() - Method in class org.ginsim.core.graph.view.GraphicalAttributesStore

Deprecated.

restoreAllEdges(EdgeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Restore all the edges previously saved.

restoreAllEdges(Collection, EdgeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Restore all the edges from the collection edges.

restoreAllNodes(NodeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Restore all the nodes previously saved.

restoreAllNodes(Collection, NodeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Restore all the nodes from the collection nodes.

restoreEdge(Object, EdgeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Restore an edge if it has been previously saved.

restoreNode(Object, NodeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

Restore a node if it has been previously saved.

result - Variable in class org.ginsim.common.callable.BasicProgressListener

Result - Class in org.ginsim.service.tool.avatar.domain

Result() - Constructor for class org.ginsim.service.tool.avatar.domain.Result

result - Variable in class org.ginsim.service.tool.graphcomparator.GraphComparator

ResultHandler - Interface in org.ginsim.servicegui.tool.pathfinding

A simple interface to retrieve the results in the PathFinding thread.

resultLog - Variable in class org.ginsim.service.tool.avatar.simulation.Simulation

ResultsDialog - Class in org.ginsim.commongui.dialog

A small dialog to display a textarea with a close button.

ResultsDialog(Frame, String) - Constructor for class org.ginsim.commongui.dialog.ResultsDialog

ResultsDialog(Frame) - Constructor for class org.ginsim.commongui.dialog.ResultsDialog

retrieveAssociated() - Method in class org.ginsim.gui.utils.data.ListEditionPanel

returnClass - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperand

returnClassName - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperator

revertPath(int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

rewind the path.

rewind() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AnimatorUI

RewiringAction - Enum in org.ginsim.service.tool.modelreduction

rewriteGraph(StateSet, StateSet, FinalPaths) - Method in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

Method for rewiring a cycle

rewriteGraph(MDDStateSet, MDDStateSet, FinalPaths) - Method in class org.ginsim.service.tool.avatar.simulation.others.AvatarMDDSimulation

Method for rewiring a cycle

rightArg - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBinaryOperator

RING - Static variable in class org.ginsim.service.layout.LayoutService

RING_INV - Static variable in class org.ginsim.service.layout.LayoutService

RingLayout - Class in org.ginsim.service.layout

level placement of nodes

RingLayout() - Constructor for class org.ginsim.service.layout.RingLayout

root - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanParser

root - Variable in class org.ginsim.core.graph.tree.TreeBuilderFromMDD

root - Variable in class org.ginsim.core.graph.tree.TreeImpl

root - Variable in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

RootPanel - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

RootPanel(TreeElement, JTree, boolean, int) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.RootPanel

round(double, int) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

round(double) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

RuleWriter(List<RegulatoryNode>, CADPWriter.StateVarWriter) - Constructor for class org.ginsim.service.export.cadp.CADPModuleWriter.RuleWriter

run(int) - Method in class org.ginsim.core.graph.tree.TreeBuilder

Run the parser on the OMDDNode root, and fill the tree.

run() - Method in class org.ginsim.gui.utils.data.GenericPropertyInfo

run() - Method in class org.ginsim.gui.utils.dialog.stackdialog.HandledStackDialog

run() - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

run(LogicalModel) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

run() - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

run() - Method in interface org.ginsim.gui.utils.dialog.stackdialog.StackDialogHandler

run(String, String[]) - Method in class org.ginsim.ScriptLauncher

Run a script: the method is called by the main launcher to launch a GINsim script

run(CADPExportConfig, String) - Method in class org.ginsim.service.export.cadp.CADPExportService

run(RegulatoryGraph, GenericDocumentFormat, String) - Method in class org.ginsim.service.export.documentation.LRGDocumentationService

run(LogicalModel, String) - Method in class org.ginsim.service.export.nusmv.NuSMVExportService

run(NuSMVConfig, String) - Method in class org.ginsim.service.export.nusmv.NuSMVExportService

run(PRISMConfig, String) - Method in class org.ginsim.service.export.prism.PRISMExportService

run(SATConfig, String) - Method in class org.ginsim.service.export.sat.SATExportService

run(GINMLFormatConfig, String) - Method in class org.ginsim.service.format.ginml.GINMLFormatService

run(String[], EnumAlgorithm) - Static method in class org.ginsim.service.tool.avatar.service.AvatarService

Runs a simulation from an input set of arguments

run(AvatarSimulation) - Static method in class org.ginsim.service.tool.avatar.service.AvatarServiceFacade

Runs an avatar simulation

run(String[]) - Static method in class org.ginsim.service.tool.avatar.service.AvatarServiceFacade

Runs an avatar simulation from a given set of arguments

run(FirefrontSimulation) - Static method in class org.ginsim.service.tool.avatar.service.FirefrontServiceFacade

Runs a firefront simulation

run(String[]) - Static method in class org.ginsim.service.tool.avatar.service.FirefrontServiceFacade

Runs a firefront simulation from a given set of arguments

run(String[]) - Static method in class org.ginsim.service.tool.avatar.service.MonteCarloServiceFacade

Runs a Monte Carlo simulation from a given set of arguments

run(MonteCarloSimulation) - Static method in class org.ginsim.service.tool.avatar.service.MonteCarloServiceFacade

run() - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

run(RegulatoryGraph, CompositionConfig) - Method in class org.ginsim.service.tool.composition.CompositionService

Run the Composition by replicating a Regulatory graph, according to a Topology and an IntegrationFunctionMapping and return the composed graph after invoking the necessary reduction operations

run(Graph, Graph, Graph) - Method in class org.ginsim.service.tool.graphcomparator.GraphComparatorService

Compare graph_1 and graph_2 and return a GraphComparatorResult object.

run(RegulatoryGraph, Perturbation, List<RegulatoryNode>) - Method in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisAlgo

Search all the non functional interactions in the graph 'g' and do some actions on them depending on the options (opt_*).

run(RegulatoryGraph, Perturbation, List<RegulatoryNode>) - Method in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisService

Run the Interaction analysis by instantiating and calling a InteractionAnalysisAlgo and return an InteractionAnalysisAlgoResult containing the report and the colorizer.

run() - Method in class org.ginsim.service.tool.localgraph.LocalGraph

run(RegulatoryGraph, List<byte[]>) - Method in class org.ginsim.service.tool.localgraph.LocalGraphService

run(RegulatoryGraph, List<byte[]>, Perturbation) - Method in class org.ginsim.service.tool.localgraph.LocalGraphService

run(DynamicGraph, String) - Method in class org.ginsim.service.tool.polytopesViz.PolytopesService

run(DynamicGraph, StatesSet) - Method in class org.ginsim.service.tool.polytopesViz.PolytopesService

run() - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.LimitedSimulation

run the simulation in a new thread.

run(HierarchicalTransitionGraph, SimulationConstraint, LogicalModel, SimulationParameters) - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.LimitedSimulationService

Construct the dynamic graph correponding the contraint on the HTG.

run() - Method in class org.ginsim.service.tool.reg2dyn.Simulation

run the simulation in a new thread.

run() - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

run(LogicalModel) - Method in class org.ginsim.servicegui.export.nusmv.NuSMVExportConfigPanel

run(LogicalModel) - Method in class org.ginsim.servicegui.export.prism.PRISMExportConfigPanel

run(LogicalModel) - Method in class org.ginsim.servicegui.export.sat.SATExportConfigPanel

run(LogicalModel) - Method in class org.ginsim.servicegui.format.ginml.GINMLFormatConfigPanel

run() - Method in class org.ginsim.servicegui.format.sbml.SBMLQualExportConfigPanel

run() - Method in class org.ginsim.servicegui.layout.MultidimensionLayoutGUI

run(LogicalModel) - Method in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

run() - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

run() - Method in class org.ginsim.servicegui.tool.composition.CompositionConfigDialog

run() - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewer

run(Collection<HierarchicalNode>) - Method in class org.ginsim.servicegui.tool.decisionanalysis.DecisionAnalysis

run(LogicalModel) - Method in class org.ginsim.servicegui.tool.decisionanalysis.DecisionAnalysisFrame

run() - Method in class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorFrame

run() - Method in class org.ginsim.servicegui.tool.interactionanalysis.InteractionAnalysisFrame

run() - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphFrame

run() - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionConfigDialog

run() - Method in class org.ginsim.servicegui.tool.omddViz.OmddVizFrame

run() - Method in class org.ginsim.servicegui.tool.pathfinding.PathFinding

run() - Method in class org.ginsim.servicegui.tool.pathfinding.PathFindingFrame

run() - Method in class org.ginsim.servicegui.tool.polytopesViz.PolytopesVizFrame

run(LogicalModel) - Method in class org.ginsim.servicegui.tool.reg2dyn.limitedSimulation.LimitedSimulationFrame

run(LogicalModel) - Method in class org.ginsim.servicegui.tool.reg2dyn.SingleSimulationFrame

run(LogicalModel) - Method in class org.ginsim.servicegui.tool.stablestates.StableStateSwingUI

run() - Method in class org.ginsim.servicegui.tool.stateinregulatorygraph.StateInRegGraphFrame

run(LogicalModel) - Method in class org.ginsim.servicegui.tool.trapspace.TrapSpaceSwingUI

runAction(L, int, int) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

runAnalyse() - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

runAvatarResults() - Method in class org.ginsim.servicegui.tool.avatar.AvatarResults

Executes the instantiated simulation and displays its results

runIsFinished() - Method in class org.ginsim.gui.graph.view.style.ColorizerPanel

Enable the colorizeButton.

runLayout(DynamicGraph) - Static method in class org.ginsim.service.layout.DynamicLayout3D

runLayout() - Method in class org.ginsim.service.layout.DynamicLayoutMultidimention

runLayout(int, Graph) - Static method in class org.ginsim.service.layout.LayoutService

runs - Variable in class org.ginsim.service.tool.avatar.domain.Result

Maximum number of iterations

runs - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

number of iterations

runs - Variable in class org.ginsim.service.tool.avatar.simulation.MonteCarloSimulation

number of iterations

runSim() - Method in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

runSim() - Method in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

runSim() - Method in class org.ginsim.service.tool.avatar.simulation.MonteCarloSimulation

runSim() - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

Performs the simulation

runSimulation() - Method in class org.ginsim.service.tool.avatar.simulation.others.AvatarMDDSimulation

runSimulation() - Method in class org.ginsim.service.tool.avatar.simulation.others.FirefrontMDDSimulation

runSimulation() - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

Performs the simulation

runSimulationOnInitialStates() - Method in class org.ginsim.service.tool.reg2dyn.htg.TarjanSimulation

The main entrance for the algorithm.

S

s_dtd - Variable in class org.ginsim.common.xml.XMLHelper

s_filename - Variable in class org.ginsim.common.xml.XMLHelper

SATConfig - Class in org.ginsim.service.export.sat

SATConfig(RegulatoryGraph) - Constructor for class org.ginsim.service.export.sat.SATConfig

SATEncoder - Class in org.ginsim.service.export.sat

Exports a Regulatory graph into a SAT model description.

SATEncoder() - Constructor for class org.ginsim.service.export.sat.SATEncoder

SATExportConfigPanel - Class in org.ginsim.servicegui.export.sat

SATExportConfigPanel(SATConfig, SATExportAction) - Constructor for class org.ginsim.servicegui.export.sat.SATExportConfigPanel

SATExportService - Class in org.ginsim.service.export.sat

GINsim export service capable of encoding the model properties into a SAT specification in CNF.

SATExportService() - Constructor for class org.ginsim.service.export.sat.SATExportService

SATExportServiceGUI - Class in org.ginsim.servicegui.export.sat

GINsim export service capable of encoding the model properties into a SAT specification in CNF.

SATExportServiceGUI() - Constructor for class org.ginsim.servicegui.export.sat.SATExportServiceGUI

SATExportType - Enum in org.ginsim.service.export.sat

save() - Method in interface org.ginsim.commongui.SavingGUI

save(String) - Method in class org.ginsim.core.graph.AbstractGraph

save(String, Collection<V>, Collection<E>) - Method in class org.ginsim.core.graph.AbstractGraph

save(String) - Method in interface org.ginsim.core.graph.Graph

Save this graph.

save(String, Collection<V>, Collection<E>) - Method in interface org.ginsim.core.graph.Graph

Save some components of this graph.

save() - Method in class org.ginsim.gui.graph.BaseGraphGUI

saveAs() - Method in class org.ginsim.gui.graph.BaseGraphGUI

saveAs() - Method in interface org.ginsim.gui.graph.GraphGUI

Pick a destination and save the graph.

saveEdges(XMLWriter, Collection<E>) - Method in class org.ginsim.core.io.parser.GINMLWriter

saveEvent() - Method in class org.ginsim.commongui.dialog.SimpleDialog

saveGnuPlotPath() - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

export the selected path to be drawn with gnuplot

saveInteractionsModel(XMLWriter) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

saveNodes(XMLWriter, Collection<V>) - Method in class org.ginsim.core.io.parser.GINMLWriter

saveOptions() - Static method in class org.ginsim.common.application.OptionStore

save all options in a file, to restore them at next run.

saveOutput() - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

saveReport(DocumentWriter, RegulatoryGraph) - Method in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisReport

Write the report using the specified DocumentWriter.

SavingGUI - Interface in org.ginsim.commongui

A GUI with an associated save action

SBMLQualConfig - Class in org.ginsim.service.format.sbml

SBMLQualConfig(RegulatoryGraph) - Constructor for class org.ginsim.service.format.sbml.SBMLQualConfig

SBMLQualExportConfigPanel - Class in org.ginsim.servicegui.format.sbml

SBMLQualExportConfigPanel(SBMLQualConfig, ExportAction<RegulatoryGraph>) - Constructor for class org.ginsim.servicegui.format.sbml.SBMLQualExportConfigPanel

SBMLqualService - Class in org.ginsim.service.format.sbml

SBMLqualService() - Constructor for class org.ginsim.service.format.sbml.SBMLqualService

SBMLqualServiceGUI - Class in org.ginsim.servicegui.format.sbml

SBMLqualServiceGUI() - Constructor for class org.ginsim.servicegui.format.sbml.SBMLqualServiceGUI

SCC_TYPE_COMPLEX_COMPONENT - Static variable in class org.ginsim.core.graph.reducedgraph.NodeReducedData

SCC_TYPE_SIMPLE_CYCLE - Static variable in class org.ginsim.core.graph.reducedgraph.NodeReducedData

SCC_TYPE_UNIQUE_NODE - Static variable in class org.ginsim.core.graph.reducedgraph.NodeReducedData

SCCGraphAlgo - Class in org.ginsim.service.tool.scc

Search for strongly connected components, and build the SCC graph.

SCCGraphAlgo(Graph) - Constructor for class org.ginsim.service.tool.scc.SCCGraphAlgo

get ready to run.

SCCGraphService - Class in org.ginsim.service.tool.scc

SCCGraphService() - Constructor for class org.ginsim.service.tool.scc.SCCGraphService

SCCResult - Class in org.ginsim.johnsonCycles

SCCResult(List[], int) - Constructor for class org.ginsim.johnsonCycles.SCCResult

score(int) - Method in class org.ginsim.service.tool.circuit.CircuitAlgo

compute a score for the context.

score - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

ScriptLauncher - Class in org.ginsim

A helper when running GINsim in script mode.

ScriptLauncher() - Constructor for class org.ginsim.ScriptLauncher

scroll(int, boolean) - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

search() - Method in class org.ginsim.gui.shell.SearchFrame

search() - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicSearchPathConfig

SearchFrame - Class in org.ginsim.gui.shell

This class provide a frame to search the nodes of a graph correponding to a certain pattern.

SearchFrame(GraphGUI<?, ?, ?>) - Constructor for class org.ginsim.gui.shell.SearchFrame

searchNodes(String) - Method in class org.ginsim.core.graph.AbstractGraph

Search the vertices with ID matching the given regular expression.

searchNodes(String) - Method in interface org.ginsim.core.graph.GraphModel

Search the vertices with ID matching the given regular expression.

searchNodes(String) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

searchNodes(String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

second - Variable in class org.ginsim.service.tool.graphcomparator.ComparedItemInfo

SEL_EMPTY - Static variable in class org.ginsim.gui.utils.data.ListPanelHelper

SEL_MULTIPLE - Static variable in class org.ginsim.gui.utils.data.ListPanelHelper

SEL_SINGLE - Static variable in class org.ginsim.gui.utils.data.ListPanelHelper

select(Point) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

select(Point) - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

select(Point) - Method in interface org.ginsim.core.graph.view.AttributesReader

Test if a point can be used to select the current item.

select(Shape) - Method in interface org.ginsim.gui.graph.canvas.CanvasRenderer

Select all objects inside the provided shape (usually a simple selection rectangle).

select(Shape) - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

select(Object) - Method in class org.ginsim.gui.graph.EditActionManager

SELECT - Static variable in class org.ginsim.gui.utils.data.ColumnDefinition

selectAll() - Method in class org.ginsim.gui.graph.GraphSelection

Select all the edges and

selectAll() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

selectAllEdges() - Method in class org.ginsim.gui.graph.GraphSelection

Select all the edges

selectAllNodes() - Method in class org.ginsim.gui.graph.GraphSelection

Select all the nodes

selected - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

selected - Variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

selectEdge(E) - Method in class org.ginsim.gui.graph.GraphSelection

Select a single edge

selectedItemChanged() - Method in class org.ginsim.gui.utils.data.PropertySwitch

selectFile() - Method in class org.ginsim.gui.shell.actions.ExportAction

The action was launched, show a GUI if needed, select a file and if all went fine, call the backend

selectFile() - Method in class org.ginsim.gui.shell.actions.ImportAction

The action was launched, select a file and if all went fine, call the import service gui

selectFile(LogicalModel) - Method in class org.ginsim.servicegui.export.petrinet.PetriNetExportAction

selection - Variable in class org.ginsim.gui.graph.BaseGraphGUI

selectionCache - Variable in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

Cache all selected items for faster access and memory: allows to detect items needing to be redrawn

SelectionCallBack - Class in org.ginsim.gui.shell.callbacks

SelectionCallBack() - Constructor for class org.ginsim.gui.shell.callbacks.SelectionCallBack

selectionChange() - Method in class org.ginsim.gui.graph.tree.TreeActionPanel

selectionChanged() - Method in class org.ginsim.gui.graph.canvas.CanvasGraphGUIImpl

selectionChanged() - Method in interface org.ginsim.gui.graph.GraphGUI

Update selection to reflect the internal selection object

SelectionType - Enum in org.ginsim.gui.shell.editpanel

Define the possible types of selection.

selectionUpdated(int[]) - Method in interface org.ginsim.gui.utils.data.ListPanelCompanion

selectionUpdated(int[]) - Method in class org.ginsim.servicegui.tool.avatar.parameters.AvaParameterEditionPanel

selectionUpdated(int[]) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityClassContentEditor

selectionUpdated(int[]) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.UpdatingPanel

selectionUpdated(int[]) - Method in class org.ginsim.servicegui.tool.reg2dyn.SimulationParameterEditionPanel

selectItem(int) - Method in class org.ginsim.gui.utils.data.ListPanel

selectLeft2Right() - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

Get the selection in the left table (jTable), and select the corresponding rows in the right list (jList)

selectNode(V) - Method in class org.ginsim.gui.graph.GraphSelection

Select a single node.

selectNodes() - Method in class org.ginsim.gui.shell.SearchFrame

selectOpenFilename(Frame) - Static method in class org.ginsim.gui.shell.FileSelectionHelper

selectOpenFilename(Frame, String[], String) - Static method in class org.ginsim.gui.shell.FileSelectionHelper

selectOpenFilename(Frame, FileFilter) - Static method in class org.ginsim.gui.shell.FileSelectionHelper

selector - Variable in class org.ginsim.core.graph.view.css.Colorizer

Selector - Class in org.ginsim.core.graph.view.css

A Selector implementation for GINsim.

Selector(String) - Constructor for class org.ginsim.core.graph.view.css.Selector

selectors - Static variable in class org.ginsim.core.graph.view.css.Selector

selectSaveFilename(Frame) - Static method in class org.ginsim.gui.shell.FileSelectionHelper

selectSaveFilename(Frame, String[], String) - Static method in class org.ginsim.gui.shell.FileSelectionHelper

selectSaveFilename(Frame, FileFilter) - Static method in class org.ginsim.gui.shell.FileSelectionHelper

selectText(Point) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

SeparatorComboBox - Class in org.ginsim.gui.utils.widgets

From http://www.camick.com/java/source/SeparatorComboBox.java Class that allows you to add a JSeparator to the ComboBoxModel.

SeparatorComboBox() - Constructor for class org.ginsim.gui.utils.widgets.SeparatorComboBox

Standard constructor.

SeparatorComboBox(ComboBoxModel) - Constructor for class org.ginsim.gui.utils.widgets.SeparatorComboBox

Standard constructor.

SeparatorComboBox(Object[]) - Constructor for class org.ginsim.gui.utils.widgets.SeparatorComboBox

Standard constructor.

SeparatorComboBox(List<?>) - Constructor for class org.ginsim.gui.utils.widgets.SeparatorComboBox

Standard constructor.

separators - Static variable in interface org.ginsim.gui.service.ServiceGUI

An array of the separator The desired seprators must be ordered by weight

Service - Interface in org.ginsim.core.service

This interface is the central interface for GINsim services.

service(Class<Service>) - Method in class org.ginsim.ScriptLauncher

Get a service instance

service(String) - Method in class org.ginsim.ScriptLauncher

Get a service instance by name

ServiceClassInfo - Class in org.ginsim.core.service

ServiceClassInfo(Class) - Constructor for class org.ginsim.core.service.ServiceClassInfo

ServiceGUI - Interface in org.ginsim.gui.service

This interface is the central interface for GUIs for GINsim services.

ServiceStatus - Annotation Type in org.ginsim.core.service

set_initialStates(List, Map, Map) - Method in class org.ginsim.service.tool.reg2dyn.Simulation

setAboutHandler(Object, Method) - Static method in class org.ginsim.common.application.OSXAdapter

setActivesEdges(List, int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

setActivesEdges(int, List) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

Set the active Edge of an interaction

setActivesEdges(int, List, int) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

Set the active Edge of an interaction

setAliases(String, Perturbation) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

Deprecated.

setAllData(Collection<RegulatoryMultiEdge>) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

setAnchor(EdgeAnchor) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

setAnchor(EdgeAnchor) - Method in class org.ginsim.core.graph.backend.EdgeViewInfoImpl

setAnchor(EdgeAnchor) - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

setAnchor(EdgeAnchor) - Method in interface org.ginsim.core.graph.view.EdgeViewInfo

setAnchor(EdgeAnchor) - Method in class org.ginsim.gui.graph.view.style.AnchorSelector

setAnnotation(Annotation) - Method in class org.ginsim.gui.annotation.AnnotationPanel

setApplicationEventHandled(Object, boolean) - Method in class org.ginsim.common.application.OSXAdapter

setArg(TBooleanTreeNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TUnaryOperator

setArgs(TBooleanTreeNode, TBooleanTreeNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBinaryOperator

setAsMapped(RegulatoryNode) - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

setAsMapped(RegulatoryNode) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

setAsMapped(RegulatoryNode) - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

setAssociatedGraph(AG) - Method in class org.ginsim.core.graph.AbstractDerivedGraph

Associate the given graph to the current one

setAssociatedGraph(AG) - Method in interface org.ginsim.core.graph.GraphAssociation

Associate the given graph to the current one

setAssociatedGraphID(String) - Method in class org.ginsim.core.graph.AbstractDerivedGraph

set the path to the associated graph.

setAssociatedGraphID(String) - Method in interface org.ginsim.core.graph.GraphAssociation

setAssociatedGUI(SavingGUI) - Method in class org.ginsim.commongui.dialog.SimpleDialog

setAttribute(String, String) - Method in class org.ginsim.core.graph.AbstractGraph

setAttribute(String, String) - Method in interface org.ginsim.core.graph.Graph

setAttribute(String, String) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

setAutoHide(int) - Method in class org.ginsim.gui.utils.data.ListPanel

set when to autohide most of this widget.

setBaseStyle(S) - Method in class org.ginsim.core.graph.view.style.BaseStyleOverride

setBounds(int, int, int, int) - Method in class org.ginsim.gui.utils.widgets.treetable.JTreeTable.TreeTableCellRenderer

setBounds(String, double, double) - Method in class org.ginsim.service.tool.avatar.domain.Result

Bounds the probability of a given attractor

setCache(StatesSet) - Method in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

setChildsCount(byte[]) - Method in interface org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraph

Set the array indicating for each node in the nodeOrder their count of childs.

setChildsCount(byte[]) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

setCircuit(CircuitDescr) - Method in class org.ginsim.service.tool.circuit.CircuitDescrInTree

setColorizer(Colorizer) - Method in class org.ginsim.service.tool.polytopesViz.PolytopesService

setComment(String) - Method in class org.ginsim.core.annotation.Annotation

Set the string containing the comments.

setCompatibleStableStates(List<List<byte[]>>) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

setCompatMode(boolean) - Method in class org.ginsim.core.graph.view.style.StyleManager

Enable or disable styles.

setComponents(JTextArea) - Method in class org.ginsim.service.tool.avatar.simulation.Simulation

setContent(Object) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemModel

setContent(HierarchicalNode) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalTableModel

setContent(List) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedGraphTableModel

set the content of the table model

setContext(int[]) - Method in class org.ginsim.service.tool.circuit.CircuitDescr

setCopyHeaders() - Method in class org.ginsim.gui.utils.widgets.EnhancedJTable

setCurrent(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

setCurrent(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.parameters.AvaParameterEditionPanel

setCurve(boolean) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

setCurve(boolean) - Method in class org.ginsim.core.graph.backend.EdgeViewInfoImpl

setCurve(boolean) - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

Set the edge as curve property.

setCurve(boolean) - Method in interface org.ginsim.core.graph.view.EdgeViewInfo

setCustomProperty(StyleProperty, Object) - Method in class org.ginsim.core.graph.dynamicgraph.DefaultDynamicEdgeStyle

setCustomProperty(StyleProperty, Object) - Method in class org.ginsim.core.graph.regulatorygraph.DefaultRegulatoryEdgeStyle

setCustomProperty(StyleProperty, Object) - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

setCustomProperty(StyleProperty, Object) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

setDashPattern(EdgePattern) - Method in class org.ginsim.core.graph.view.SimpleStroke

setData(List) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionList

setData(List) - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanData

setData(String[], List<RegulatoryNode>) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

setData(ValueList) - Method in class org.ginsim.gui.utils.data.models.ValueListComboModel

setDebug(int) - Static method in class org.ginsim.common.application.LogManager

Give the mask of the log you want to display

setDefaultEdgeStyle(EdgeStyle<V, E>) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

setDefaultEdgeStyle(EdgeStyle<V, E>) - Method in interface org.ginsim.core.graph.GraphBackend

setDepth(int) - Method in class org.ginsim.core.graph.tree.TreeNode

setDisabling(boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

setDisabling(boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

setDOAPFile(String) - Static method in class org.ginsim.gui.shell.AboutDialog

setDocumentProperties(Map) - Method in class org.ginsim.common.document.DocumentWriter

Add a map of properties to the document.

setDocumentProperties(Object[]) - Method in class org.ginsim.common.document.DocumentWriter

Add an array of properties to the document

setDocumentProperty(Object, Object) - Method in class org.ginsim.common.document.DocumentWriter

Set a property for the document.

setDropable(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

setEdge(E) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

setEdge(E, boolean) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

setEdge(E) - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

set the edge on which we work

setEdge(E, boolean) - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

Set the edge on which we work, knowing that it is selected.

setEdge(Collection<RegulatoryMultiEdge>) - Method in class org.ginsim.gui.graph.regulatorygraph.IncomingEdgeListModel

set the list of incoming edge

setEdge(RegulatoryMultiEdge) - Method in class org.ginsim.gui.graph.regulatorygraph.MultiEdgeEditPanel

setEdgeAnchor(E, EdgeAnchor) - Method in class org.ginsim.core.graph.view.style.StyleManager

setEdgeAutomatingRouting() - Method in class org.ginsim.service.tool.graphcomparator.GraphComparatorResult

Try to fix the edges routing

setEdgeCurved(E, boolean) - Method in class org.ginsim.core.graph.view.style.StyleManager

setEdgeIndexes(List) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

setEdges(List) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

Set the vector of GsEdgeIndex

setEdgeWeight(E, double) - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

setEditable(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

setEdited(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

setEditedItem(Object) - Method in class org.ginsim.gui.graph.dynamicgraph.DynamicItemAttributePanel

setEditedItem(DynamicGraph) - Method in class org.ginsim.gui.graph.dynamicgraph.StateTransitionGraphEditor

setEditedItem(T) - Method in interface org.ginsim.gui.graph.GUIEditor

setEditedItem(DecisionOnEdge) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalEdgeParameterPanel

setEditedItem(HierarchicalTransitionGraph) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalGraphEditor

setEditedItem(HierarchicalNode) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalNodeParameterPanel

setEditedItem(NodeReducedData) - Method in class org.ginsim.gui.graph.reducedgraph.ReducedParameterPanel

setEditedItem(Object) - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

setEditedItem(Object) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

setEditedItem(Object) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

setEditedItem(RegulatoryMultiEdge) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryEdgeEditor

setEditedItem(TrapSpaceNode) - Method in class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeMainPanel

setEditedItem(Tree) - Method in class org.ginsim.gui.graph.tree.TreeActionPanel

setEditedItem(T) - Method in class org.ginsim.gui.utils.data.ObjectEditor

setEditedItem(DynamicNode) - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalEditTab

setEditedObject(Object) - Method in class org.ginsim.gui.annotation.AnnotationPanel

setEditedObject(Object) - Method in class org.ginsim.gui.graph.regulatorygraph.NodeMaxValueSpinModel

setEditedObject(Object) - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

setEditedObject(Object) - Method in class org.ginsim.gui.utils.data.models.SpinModel

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in class org.ginsim.gui.annotation.AnnotationPanel

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in class org.ginsim.gui.graph.regulatorygraph.InteractionPanel

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionPanel

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in class org.ginsim.gui.utils.data.HelpedListEditorUI

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in class org.ginsim.gui.utils.data.MinMaxEditor

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in interface org.ginsim.gui.utils.data.ObjectPropertyEditorUI

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in class org.ginsim.gui.utils.data.PropertyActionButton

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in class org.ginsim.gui.utils.data.PropertySwitch

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in class org.ginsim.gui.utils.data.SpinEditor

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in class org.ginsim.gui.utils.widgets.BooleanEditor

setEditedProperty(GenericPropertyInfo, GenericPropertyHolder) - Method in class org.ginsim.gui.utils.widgets.StatusTextField

setEdition(boolean[]) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

setEditorModel(FunctionEditorModel) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

setEnabled(String, boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.TreeMenu

setEnabled(boolean) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionPanel

setError(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

setExitStates(MDDStateSet) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Stores the set of reachable states from the current state-set

setExitStates(StateSet) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Stores the set of reachable states from the current state-set

setExportType(SATExportType) - Method in class org.ginsim.service.export.sat.SATConfig

setExtensionList(String[], String) - Method in class org.ginsim.gui.shell.GsFileFilter

setExtra(boolean) - Method in class org.ginsim.gui.graph.dynamicgraph.StableTableModel

setFileHandler(Object, Method) - Static method in class org.ginsim.common.application.OSXAdapter

setFixedInputs(boolean) - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

setForeground(Color) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

setFrameTitle(Graph, boolean) - Method in class org.ginsim.gui.utils.widgets.Frame

Set the title of the frame

setFunctionParameters(List) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

setGraphicPanel(FunctionPanel) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

setGraphName(String) - Method in class org.ginsim.core.graph.AbstractGraph

changes (if success) the name associated with this graph.

setGraphName(String) - Method in interface org.ginsim.core.graph.GraphModel

changes (if success) the name associated with this graph.

setGsa(Annotation) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

setHandler(OSXAdapter) - Static method in class org.ginsim.common.application.OSXAdapter

setId(String, RegulatoryGraph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

change the id of this node.

setImage(BufferedImage) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GlassPane

setImageReady(boolean) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GlassPane

setImpossible() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

setIn(Set<HierarchicalNode>) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

setInCycle(HTGSimulationQueueSCC) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

Set the SCC that contains the state.

setIndex(int) - Method in interface org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueItem

setIndex(int) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueSCC

setIndex(int) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

setInitialStates(List<byte[]>) - Method in interface org.colomoto.biolqm.StatefulLogicalModel

Changes the set of initial states

setInitialStates(List<byte[]>) - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

setInitialStates(List<byte[]>) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

setInitStatesIterator(Iterator<byte[]>) - Method in class org.ginsim.service.tool.reg2dyn.Simulation

setInput(boolean, Graph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

setInputStates(NamedStateList) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesHandler

setInsets(int, int, int, int) - Method in class org.ginsim.gui.utils.widgets.GsButton

setInteractionName(BooleanParser, String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanGene

setInteractionsModel(TreeInteractionsModel) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

setKey(String) - Method in class org.ginsim.core.annotation.BiblioList

setKey(String) - Method in class org.ginsim.service.tool.avatar.domain.AbstractStateSet

setLabel(String) - Method in class org.ginsim.core.graph.tree.TreeNode

setLabelCount(short) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

setLink(String, int, Graph) - Method in class org.ginsim.core.annotation.Annotation

setList(L) - Method in class org.ginsim.gui.utils.data.ListEditionPanel

setList(L) - Method in class org.ginsim.gui.utils.data.ListPanel

set the list to show.

setList(PrioritySetDefinition) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionPanel

setListVisible(List<RegulatoryNode>) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

setLogicalFunctionList(LogicalFunctionList) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanGene

setLogicalModel(LogicalModel) - Method in interface org.ginsim.core.graph.dynamicgraph.TransitionGraph

Associate a logicalModel with this STG, notably to retrieve extra values.

setLogicalModel(LogicalModel) - Method in class org.ginsim.core.graph.dynamicgraph.TransitionGraphImpl

setLow_index(int) - Method in interface org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueItem

setLow_index(int) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueSCC

setLow_index(int) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

setMainPanel(Component) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

Intercept the setMainPanel method to integrate with this frame's panel

setMainPanel(Component) - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

setMainPanel(Component, GridBagConstraints) - Method in class org.ginsim.servicegui.tool.avatar.AvatarLogicalModelActionDialog

Adds a component to the main panel satisfying the inputted gridbag layout constraint

setManualParameters(List) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

setMapping(IntegrationFunctionMapping) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

setMapping(IntegrationFunctionMapping) - Method in class org.ginsim.service.tool.composition.CompositionConfig

setMapping(Map<RegulatoryMultiEdge, LocalGraphCategory>, Map<RegulatoryNode, ActivityLevel>) - Method in class org.ginsim.service.tool.localgraph.LocalGraphStyleProvider

setMaxCols(int[]) - Method in class org.ginsim.gui.utils.widgets.EnhancedJTable

setMaxDepth(int) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

setMaxValue(byte, RegulatoryGraph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

Sets the max value to the node

setMaxValue(Object) - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

setMaxValueTable(Map<NodeInfo, List<Integer>>) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

setMessage(String) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

setMessage(String) - Method in class org.ginsim.gui.shell.StartupDialog

setMessage(String) - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

set the progress level, to give the user some feedback

setMessage(String, int) - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

setMessage(String) - Method in class org.ginsim.servicegui.export.cadp.InitialStatesWidget

setMin(int, byte, RegulatoryGraph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

change a sub edge's min value.

setMinValue(Object) - Method in interface org.ginsim.gui.utils.data.models.MinMaxSpinModel

set the min value.

setMode(boolean) - Method in interface org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraph

Set the mode

setMode(boolean) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

setMode(int) - Method in interface org.ginsim.core.graph.tree.Tree

setMode(int) - Method in class org.ginsim.core.graph.tree.TreeImpl

setMode(int) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

change the simulation mode for this class

setModelName(String) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

setMouseListener(MouseListener) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

setMouseMotionListener(MouseMotionListener) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

setName(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

setName(String) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

setName(String, RegulatoryGraph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

set the name of the gene.

setName(String) - Method in class org.ginsim.core.graph.view.style.BaseStyle

setName(String) - Method in class org.ginsim.core.graph.view.style.BaseStyleOverride

setName(String) - Method in interface org.ginsim.core.graph.view.style.Style

setName(String) - Method in interface org.ginsim.core.utils.data.NamedObject

change the name of this object

setName(String) - Method in class org.ginsim.gui.utils.widgets.SplitPane

setName(String) - Method in class org.ginsim.service.tool.avatar.params.AvatarParameters

setName(String) - Method in class org.ginsim.service.tool.modelreduction.ReductionConfig

setName(String) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

change this class' name.

setName(String) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

setName(String) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

setName(String) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionAsynchronous

setName(String) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionComplete

setName(String) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSequential

setName(String) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSynchronous

setNode(V) - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

setNode(V, boolean) - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

setNode(RegulatoryNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

setNode(V) - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

change the edited node.

setNode(V, boolean) - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

change the edited node, knowing that it is selected

setNode(RegulatoryNode) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

set the current node

setNode(Object) - Method in class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

setNode(Object) - Method in interface org.ginsim.service.tool.reg2dyn.helpers.SimulationHelper

setNode(Object) - Method in class org.ginsim.service.tool.reg2dyn.helpers.STGSimulationHelper

setNode(DynamicNode, int[]) - Method in class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

setNode(N, int[]) - Method in interface org.ginsim.servicegui.tool.pathfinding.PathFindingTableModel

setNodeOrder(List<NodeInfo>) - Method in interface org.ginsim.core.graph.dynamicgraph.DynamicGraph

Set a list of String representing the order of node as defined by the model

setNodeOrder(List<NodeInfo>) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

Set a list of String representing the order of node as defined by the model

setNodeOrder(List<NodeInfo>) - Method in interface org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraph

Set a list of NodeInfo representing the order of node as defined by the model

setNodeOrder(List<NodeInfo>) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

Set a list of NodeInfo representing the order of node as defined by the model

setNodeOrder(List<RegulatoryNode>) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Set a list of class dependent objects representing the order of node as defined by the model

setNodeOrder(List<RegulatoryNode>) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

setNormalStates(NamedStateList) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStatesHandler

setNotSourceNode(String) - Method in class org.ginsim.service.tool.stableregions.PNGraph

setObject(int, Object) - Method in class org.ginsim.core.utils.data.ObjectStore

setOffsets(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GlassPane

setOption(String, Object) - Static method in class org.ginsim.common.application.OptionStore

save the value of an option.

setOptions(List) - Method in class org.ginsim.gui.utils.widgets.ButtonPopup

setOracles(List<List<byte[]>>) - Method in interface org.colomoto.biolqm.StatefulLogicalModel

Stores a set of oracles within the model

setOracles(List<List<byte[]>>) - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

setOracles(List<List<byte[]>>) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Associates a set of oracles to the graph

setOracles(List<List<byte[]>>) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

setOut(PrintStream) - Static method in class org.ginsim.common.application.LogManager

Define the outputStream.

setOut(Set<HierarchicalNode>) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

setOutgoingList(Collection<RegulatoryMultiEdge>) - Method in class org.ginsim.servicegui.tool.modelreduction.TargetEdgesIterator

setOutput(OutputStream) - Method in class org.ginsim.common.document.DocumentWriter

setOutput(File) - Method in class org.ginsim.common.document.DocumentWriter

setOutput(boolean, Graph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

setParam(NamedStateStore) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.CompleteStatePanel

setParam(NamedStateStore) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

setParam(Map) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

reverse job of the "getContent" method

setParam(Map, List<String>) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

Updates the current table given a map of the state patterns

setParam(Map) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

Updates the current table given a map of the state patterns

setParameter(String, Object) - Method in class org.ginsim.core.graph.tree.TreeBuilder

setParameterValue(int, int, RegulatoryGraph) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

setParent(TreeElement) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

setParent(ParamTreeNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

setParent(ParamTreeNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

setParentIndex(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

setParentIndex(int) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

setParentList(L) - Method in interface org.ginsim.gui.utils.data.ListPanelCompanion

setParentList(AvatarParameterList) - Method in class org.ginsim.servicegui.tool.avatar.parameters.AvaParameterEditionPanel

setParentList(List) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityClassContentEditor

setParentList(PrioritySetList) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.UpdatingPanel

setParentList(SimulationParameterList) - Method in class org.ginsim.servicegui.tool.reg2dyn.SimulationParameterEditionPanel

setParser(TBooleanParser) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionList

setParser(TBooleanParser) - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanData

setParser(TBooleanParser) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperand

setParser(TBooleanParser) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperator

setParser(TBooleanParser) - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNode

setPath(List<Object>) - Method in class org.ginsim.servicegui.tool.pathfinding.PathFindingFrame

setPath(List) - Method in class org.ginsim.servicegui.tool.pathfinding.PathStyleProvider

setPath(List<Object>) - Method in interface org.ginsim.servicegui.tool.pathfinding.ResultHandler

setPattern(NamedState) - Method in interface org.ginsim.core.graph.regulatorygraph.namedstates.PatternHolder

setPattern(NamedState) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

setPattern(byte[], boolean[]) - Method in class org.ginsim.servicegui.tool.lrgcolorizer.LRGPatternStyleProvider

setPerturbation(Perturbation) - Method in interface org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationHolder

Select a perturbation.

setPerturbation(Perturbation) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationStore

setPerturbation(Perturbation) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationUser

setPerturbation(Perturbation) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

setPerturbation(Perturbation) - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphFrame

setPoint(Point) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GlassPane

setPoints(List<Point>) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

setPoints(List<Point>) - Method in class org.ginsim.core.graph.backend.EdgeViewInfoImpl

setPoints(List<Point>) - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

set points used by this edge

setPoints(List<Point>) - Method in interface org.ginsim.core.graph.view.EdgeViewInfo

setPopupVisible(boolean) - Method in class org.ginsim.gui.utils.widgets.SeparatorComboBox

Prevent closing of the popup when attempting to select the separator with the mouse.

setPos(int, int) - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

setPos(int, int) - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

change the node's position.

setPosition(int, int) - Method in interface org.ginsim.core.graph.view.NodeViewInfo

Set the position of this node.

setPreferencesHandler(Object, Method) - Static method in class org.ginsim.common.application.OSXAdapter

setProbPaths(FinalPaths) - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Stores the set of outgoing transitions from the current state-set

setProbPaths(FinalPaths) - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Stores the set of outgoing transitions from the current state-set

setProgress(String) - Method in class org.ginsim.common.callable.BasicProgressListener

setProgress(int) - Method in class org.ginsim.common.callable.BasicProgressListener

setProgress(String) - Method in interface org.ginsim.common.callable.ProgressListener

Show task status/progress.

setProgress(int) - Method in interface org.ginsim.common.callable.ProgressListener

Set a numeric progress counter

setProgress(int) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

setProgress(String) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

setProgress(int) - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

setProgress(String) - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

setProgress(int) - Method in class org.ginsim.servicegui.tool.reg2dyn.BaseSimulationFrame

setProgress(String) - Method in class org.ginsim.servicegui.tool.reg2dyn.BaseSimulationFrame

setProgressionText(String) - Method in class org.ginsim.servicegui.tool.pathfinding.PathFindingFrame

setPropagateFixed(String, boolean) - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

setProperty(Object, Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

setProperty(String, String, int) - Method in class org.ginsim.core.graph.view.css.CSSEdgeStyle

setProperty(String, String, int) - Method in class org.ginsim.core.graph.view.css.CSSNodeStyle

setProperty(String, String, int) - Method in interface org.ginsim.core.graph.view.css.CSSStyle

Define the value of a property of a style

setProperty(StyleProperty, Object) - Method in class org.ginsim.core.graph.view.style.BaseStyleOverride

setProperty(StyleProperty, Object) - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

setProperty(StyleProperty, Object) - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

setProperty(StyleProperty, Object) - Method in interface org.ginsim.core.graph.view.style.Style

Assign a value to a property.

setProperty(TextProperty) - Method in class org.ginsim.gui.utils.widgets.StatusTextField

setQueueSearchCount(long) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

setQuitHandler(Object, Method) - Static method in class org.ginsim.common.application.OSXAdapter

setReady() - Method in class org.ginsim.service.tool.circuit.CircuitSearchStoreConfig

setReduce(boolean) - Method in class org.ginsim.service.tool.composition.CompositionConfig

setReducedCompatibleStableStates(List<List<byte[]>>) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

setReduction(ReductionConfig) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

setReduction(ReductionConfig) - Method in interface org.ginsim.service.tool.modelreduction.ReductionHolder

Select a reduction.

setRenderer(CanvasRenderer) - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

setResult(T) - Method in class org.ginsim.common.callable.BasicProgressListener

setResult(R) - Method in interface org.ginsim.common.callable.ProgressListener

The task finished and returns its result.

setResult(StateList) - Method in class org.ginsim.gui.graph.dynamicgraph.StableTableModel

setResult(Object) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

setResult(List) - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

setResult(Object) - Method in class org.ginsim.servicegui.tool.reg2dyn.SingleSimulationFrame

setResults(String) - Method in class org.ginsim.commongui.dialog.ResultsDialog

Define the results and put it in the textarea

setResults(String) - Method in class org.ginsim.servicegui.tool.graphcomparator.GraphComparatorCaptionFrame

setReturnClass(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperand

setReturnClass(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperator

setReturnClass(String) - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNode

setRoot(TBooleanTreeNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

setRoot(TBooleanTreeNode) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

setRoot(TreeNode) - Method in interface org.ginsim.core.graph.tree.Tree

Define the root (a TreeNode) of the tree

setRoot(TreeNode) - Method in class org.ginsim.core.graph.tree.TreeImpl

setRootInfos() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

setRunning(boolean) - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

setRunText(String, String) - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

setSaved(boolean) - Method in class org.ginsim.gui.graph.BaseGraphGUI

setSaved(boolean) - Method in interface org.ginsim.gui.graph.GraphGUI

Set the graph has been saved or has not been modified since opened

setSCC(HierarchicalNode) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueSCC

setScrollPane(VirtualScrollPane) - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

setScrollPane(VirtualScrollPane) - Method in interface org.ginsim.gui.graph.canvas.VirtualScrollable

Associate the view with a scrollPane.

setScrollPosition(int, int) - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

setScrollPosition(int, int) - Method in interface org.ginsim.gui.graph.canvas.VirtualScrollable

Scroll this view to a specified position.

setSelected(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

setSelected(Perturbation) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationSelectionPanel

setSelected(Edge) - Method in class org.ginsim.gui.graph.view.style.EdgeRoutingPanel

setSelected(T) - Method in class org.ginsim.gui.utils.data.ListSelectionPanel

setSelected(NodeInfo, boolean) - Method in class org.ginsim.service.tool.modelreduction.ReductionConfig

setSelected(int, int) - Method in class org.ginsim.servicegui.tool.composition.AdjacencyMatrixWidget

setSelected(ReductionConfig) - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionConfigSelectionPanel

setSelected(UpdaterDefinition) - Method in class org.ginsim.servicegui.tool.reg2dyn.PrioritySelectionPanel

setSelected(int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AnimatorUI

choose the selected item in the path list.

setSelectedAction(EditAction) - Method in class org.ginsim.gui.graph.EditActionManager

Change the selected edit action.

setSelectedEdges(Collection<E>) - Method in class org.ginsim.gui.graph.GraphSelection

Set the list of selected edges to the edges in the list l

setSelectedIndex(int) - Method in class org.ginsim.core.utils.data.ValueList

setSelectedIndex(int) - Method in class org.ginsim.gui.utils.widgets.SeparatorComboBox

Prevent selection of the separator by keyboard or mouse

setSelectedItem(Object) - Method in class org.ginsim.gui.utils.data.models.ValueListComboModel

setSelectedNodes(Collection<V>) - Method in class org.ginsim.gui.graph.GraphSelection

Set the list of selected nodes to the nodes in the list l

setSelectedNodes(List<RegulatoryNode>) - Method in class org.ginsim.servicegui.export.cadp.VisibleComponentsWidget

setSelection(Point, boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

setSelection(Collection<V>, Collection<E>) - Method in class org.ginsim.gui.graph.GraphSelection

Set the selection

setSelection(boolean[], boolean[]) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

setSelection(boolean[]) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

Sets the selected states based on a boolean array

setSelectionPath(TreePath) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.GsJTree

setSigma(HierarchicalSigmaSet) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

return the set sigma

setSign(RegulatoryEdgeSign) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

setSign(int, RegulatoryEdgeSign, Graph) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

change the sign of a sub edge.

setSon(int, ParamTreeElement) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

setStable(boolean, NodeAttributesReader) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicNode

set if this state is stable.

setStable() - Method in class org.ginsim.service.tool.reg2dyn.helpers.HTGSimulationHelper

setStable() - Method in interface org.ginsim.service.tool.reg2dyn.helpers.SimulationHelper

setStable() - Method in class org.ginsim.service.tool.reg2dyn.helpers.STGSimulationHelper

setStackDialog(HandledStackDialog) - Method in class org.ginsim.gui.utils.dialog.stackdialog.AbstractStackDialogHandler

setStackDialog(HandledStackDialog) - Method in interface org.ginsim.gui.utils.dialog.stackdialog.StackDialogHandler

setStackDialog(HandledStackDialog) - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewer

setStartPosition(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GlassPane

setState(int[], List<RegulatoryNode>) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

setState(int[], List<RegulatoryNode>, boolean) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

setState(byte[]) - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

setState(byte[], int, Object) - Method in class org.ginsim.service.tool.reg2dyn.updater.BaseSimulationUpdater

set the state which should be used as basis.

setState(byte[], int, Object) - Method in class org.ginsim.service.tool.reg2dyn.updater.DeterministicSimulationUpdater

setState(byte[], int, Object) - Method in class org.ginsim.service.tool.reg2dyn.updater.GenericSimulationUpdater

setState(byte[], int, Object) - Method in interface org.ginsim.service.tool.reg2dyn.updater.SimulationUpdater

setState(byte[]) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGCustomStyleProvider

setState(byte[]) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.LRGStateStyleProvider

setStateAll(int[], List<RegulatoryNode>) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

setStates(List<byte[]>) - Method in interface org.ginsim.core.graph.regulatorygraph.RegulatoryGraph

Associates a set of initial states to the graph

setStates(List<byte[]>) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

setStates(List<byte[]>) - Method in class org.ginsim.service.tool.localgraph.LocalGraph

setStockIcon(String) - Method in class org.ginsim.gui.utils.widgets.StockButton

setStore(UpdaterDefinitionStore) - Method in class org.ginsim.servicegui.tool.reg2dyn.PrioritySelectionPanel

setString(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeString

setStrippingOutput(String, boolean) - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

setStyle(EdgeStyle) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

setStyle(EdgeStyle<V, E>) - Method in class org.ginsim.core.graph.backend.EdgeViewInfoImpl

setStyle(NodeStyle<V>) - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

setStyle(String, CSSStyle) - Method in class org.ginsim.core.graph.view.css.Selector

Set the style for a category id.

setStyle(EdgeStyle) - Method in interface org.ginsim.core.graph.view.EdgeAttributesReader

setStyle(EdgeStyle<V, E>) - Method in interface org.ginsim.core.graph.view.EdgeViewInfo

setStyle(NodeStyle<V>) - Method in interface org.ginsim.core.graph.view.NodeAttributesReader

setStyle(NodeStyle) - Method in interface org.ginsim.core.graph.view.NodeViewInfo

Set the style to use for this node.

setStyle(StyleProvider) - Method in class org.ginsim.gui.graph.view.style.ColorizerPanel

Set the style and enable the colorizeButton.

setStyle(Style) - Method in class org.ginsim.gui.graph.view.style.StyleEditionPanel

setStyle(Style) - Method in class org.ginsim.gui.graph.view.style.StyleEditor

setStyleProvider(StyleProvider<V, E>) - Method in class org.ginsim.core.graph.view.style.StyleManager

Define the style provider, it will override graph's style until it is removed.

setStyles(DocumentStyle) - Method in class org.ginsim.common.document.DocumentWriter

Define a new DocumentStyle for the document

setSymmetry(boolean) - Method in class org.ginsim.servicegui.tool.composition.AdjacencyMatrixWidget

setTable(EnhancedJTable) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

setTable(EnhancedJTable) - Method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

setTautological() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

setText(String, Graph) - Method in class org.ginsim.core.annotation.AnnotationLink

setText(String, int) - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanel

setText(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

setText(String, int) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

setText(String) - Method in class org.ginsim.gui.utils.widgets.StatusTextField

setThreshold(RegulatoryEdge, int) - Method in class org.ginsim.gui.graph.regulatorygraph.MultiEdgeEditPanel

setTitle(String) - Method in class org.ginsim.gui.utils.data.ListPanel

setTopology(Topology) - Method in class org.ginsim.service.export.cadp.CADPExportConfig

setTopology(Topology) - Method in class org.ginsim.service.tool.composition.CompositionConfig

setTransferable(GsTransferable) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.DropListener

setTransferable(GsTransferable) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsDragSourceListener

setTree(Tree) - Method in class org.ginsim.core.graph.tree.TreeBuilder

setTreeEditable() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

setType(byte) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

setTypeFromString(String) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Set the type from a string

setUnrecoverable(HierarchicalNode, Collection<HierarchicalNode>, HierarchicalSigmaSetFactory, HierarchicalTransitionGraph) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSet

setup() - Static method in class org.ginsim.core.annotation.HttpHelper

setup() - Static method in class org.ginsim.core.annotation.MiriamURNHelper

setUpdateDup(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

setUpdatePolicy() - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

setUpdatePolicy(int) - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

setUpdatingMode(UpdaterDefinition) - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

setUpdatingMode(UpdaterDefinition) - Method in interface org.ginsim.service.tool.reg2dyn.priorityclass.UpdaterDefinitionStore

Store a priority definition

setUpdatingMode(UpdaterDefinition) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

setUpperValue(int) - Method in class org.ginsim.gui.utils.widgets.RangeSlider

Sets the upper value in the range.

setUserID(String) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

Change the ID used to remember the selected perturbation (and other settings)

setVal(int, Object) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

setValue(byte) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeValue

setValue(int, Graph) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

set value of the interaction

setValue(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

setValue(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

setValue(Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafValue

setValue(String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperand

setValue(String) - Method in class org.ginsim.gui.graph.dynamicgraph.StateTransitionGraphEditor

setValue(String) - Method in class org.ginsim.gui.graph.hierarchicaltransitiongraph.HierarchicalGraphEditor

setValue(Object) - Method in class org.ginsim.gui.graph.regulatorygraph.NodeMaxValueSpinModel

setValue(int, String) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

setValue(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryGraphEditor

setValue(int, String) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

setValue(int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.RegulatoryNodeEditor

setValue(int, String) - Method in class org.ginsim.gui.graph.view.style.StyleEditor

setValue(int, int) - Method in class org.ginsim.gui.graph.view.style.StyleEditor

setValue(int) - Method in class org.ginsim.gui.utils.data.GenericPropertyInfo

setValue(String) - Method in class org.ginsim.gui.utils.data.GenericPropertyInfo

setValue(L, int, int, Object) - Method in class org.ginsim.gui.utils.data.ListPanelHelper

setValue(Object) - Method in class org.ginsim.gui.utils.data.models.MaxSpinModel

setValue(Object) - Method in class org.ginsim.gui.utils.data.models.MinSpinModel

setValue(int, String) - Method in class org.ginsim.gui.utils.data.ObjectEditor

setValue(int, int) - Method in class org.ginsim.gui.utils.data.ObjectEditor

setValue(String) - Method in interface org.ginsim.gui.utils.data.TextProperty

setValue(int) - Method in class org.ginsim.gui.utils.widgets.RangeSlider

Sets the lower value in the range.

setValue(AvatarParameterList, int, int, Object) - Method in class org.ginsim.servicegui.tool.avatar.parameters.AvatarParametersHelper

setValue(PrioritySetDefinition, int, int, Object) - Method in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityDefinitionHelper

setValueAt(Object, int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

setValueAt(Object, int, int) - Method in class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

setValueAt(Object, int, int) - Method in class org.ginsim.gui.utils.data.SimpleStateListTableModel

setValueAt(Object, Object, int) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

setValueAt(Object, Object, int) - Method in interface org.ginsim.gui.utils.widgets.treetable.TreeTableModel

Sets the value for node node, at column number column.

setValueAt(Object, int, int) - Method in class org.ginsim.gui.utils.widgets.treetable.TreeTableModelAdapter

setValueAt(Object, int, int) - Method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

setValueAt(Object, int, int) - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicAnalyserPathModel

setValueAt(Object, int, int) - Method in class org.ginsim.servicegui.tool.pathfinding.DynamicAnalyserPathModel

setValueAt(Object, int, int) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.AReg2GPModel

setVerbose(int) - Static method in class org.ginsim.common.application.LogManager

Set the verbose level of the logs 0 = log; 1= info; 2 = trace

setView(LogicalFunctionView) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

setViewListener(GraphViewListener) - Method in class org.ginsim.core.graph.backend.JgraphtBackendImpl

setViewListener(GraphViewListener) - Method in interface org.ginsim.core.graph.GraphBackend

setVisiblePanel(String) - Method in class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

setWarning(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

setWeight(int) - Method in class org.ginsim.gui.service.AbstractServiceGUI

setWeight(int) - Method in interface org.ginsim.gui.service.ServiceGUI

define the new weight of the service

setWeight(int) - Method in class org.ginsim.gui.shell.actions.BaseAction

setWidth(int) - Method in class org.ginsim.core.graph.tree.TreeNode

setWidth(float) - Method in class org.ginsim.core.graph.view.SimpleStroke

setZoomLevel(ZoomEffect) - Method in class org.ginsim.gui.graph.BaseGraphGUI

setZoomLevel(ZoomEffect) - Method in class org.ginsim.gui.graph.canvas.CanvasGraphGUIImpl

shape - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

shape - Variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

SHAPE - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

shCol - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

shortestPath(byte[], byte[]) - Method in interface org.ginsim.core.graph.dynamicgraph.DynamicGraph

look for the shortest path between two states.

shortestPath(byte[], byte[]) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

look for the shortest path between two states.

shortStamp() - Method in class org.ginsim.common.utils.Timer

Get the time elapsed since the last timestamp.

shouldAdd(byte[], byte[]) - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.SimulationConstraint

Return a positive value if the state should be added to the graph.

shouldColorizeInitially() - Method in class org.ginsim.gui.graph.view.style.ColorizerPanel

Indicates if the initialColorizationCheckbox is checked or not

shouldStoreOldStyle - Variable in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

showInfo() - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

showInHTGButton() - Method in class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalEditTab

ShowNonEditableStringCellRenderer - Class in org.ginsim.servicegui.export.cadp

Class changing the TableCellRenderer in order to place visually identify non-editable cells

ShowNonEditableStringCellRenderer(TableCellRenderer) - Constructor for class org.ginsim.servicegui.export.cadp.ShowNonEditableStringCellRenderer

showOutputFrame(Result) - Method in class org.ginsim.servicegui.tool.avatar.AvatarResults

Creates the graphical display of the results from an executed simulation (called after finishing 'runAvatarResults')

showPanel(String) - Method in class org.ginsim.gui.utils.data.ListEditionPanel

showPartialReduction(List<NodeInfo>) - Method in class org.ginsim.service.tool.composition.ReductionStub

Stub method ignoring GUI options (non-Javadoc)

showPartialReduction(List<NodeInfo>) - Method in interface org.ginsim.service.tool.modelreduction.ReductionLauncher

showPartialReduction(List<NodeInfo>) - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionConfigDialog

showValue(List, int) - Static method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

showValue(Integer, int) - Static method in class org.ginsim.servicegui.export.cadp.LRMInitialStateModel

sigmaFactory - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

The simulation parameters

sign - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

SIGN_NAME - Static variable in class org.ginsim.service.tool.circuit.CircuitDescr

SimpleCanvas - Class in org.ginsim.gui.graph.canvas

A simple canvas component.

SimpleCanvas() - Constructor for class org.ginsim.gui.graph.canvas.SimpleCanvas

simpleDecoratedList(String) - Method in class org.ginsim.service.export.cadp.CADPWriter.GateWriter

SimpleDialog - Class in org.ginsim.commongui.dialog

Base dialog which can remember its default size.

SimpleDialog(Frame, String, int, int) - Constructor for class org.ginsim.commongui.dialog.SimpleDialog

SimpleDimension - Class in org.ginsim.gui.graph.canvas

SimpleDimension() - Constructor for class org.ginsim.gui.graph.canvas.SimpleDimension

simpleList() - Method in class org.ginsim.service.export.cadp.CADPWriter.GateWriter

simpleList() - Method in class org.ginsim.service.export.cadp.CADPWriter.StateVarWriter

simpleListWithModuleId(int) - Method in class org.ginsim.service.export.cadp.CADPWriter.GateWriter

SimpleServiceGUI<S extends Service> - Class in org.ginsim.gui.service

SimpleServiceGUI(Class<? extends Action>, int) - Constructor for class org.ginsim.gui.service.SimpleServiceGUI

SimpleStateListTableModel - Class in org.ginsim.gui.utils.data

A simple Table model to display a list of state.

SimpleStateListTableModel(RegulatoryGraph) - Constructor for class org.ginsim.gui.utils.data.SimpleStateListTableModel

SimpleStateListTableModel(RegulatoryGraph, List) - Constructor for class org.ginsim.gui.utils.data.SimpleStateListTableModel

SimpleStateListTableModel(RegulatoryGraph, boolean) - Constructor for class org.ginsim.gui.utils.data.SimpleStateListTableModel

SimpleStateListTableModel(RegulatoryGraph, boolean, List) - Constructor for class org.ginsim.gui.utils.data.SimpleStateListTableModel

SimpleStroke - Class in org.ginsim.core.graph.view

Simple stroke implementation, inspired by BasicStroke but for which we can change the width and dash pattern.

SimpleStroke() - Constructor for class org.ginsim.core.graph.view.SimpleStroke

Simulation - Class in org.ginsim.service.tool.avatar.simulation

Class defining an abstract simulation and providing facilities for their management.
Specialized simulations (e.g.

Simulation() - Constructor for class org.ginsim.service.tool.avatar.simulation.Simulation

Simulation - Class in org.ginsim.service.tool.reg2dyn

This is the main part of the simulation.

Simulation(LogicalModel, ProgressListener<Graph>, SimulationParameters) - Constructor for class org.ginsim.service.tool.reg2dyn.Simulation

Constructs an empty dynamic graph

SimulationConstraint - Class in org.ginsim.service.tool.reg2dyn.limitedsimulation

Indicates from a set of states and a strategy if a given sate should be added to the simulation.

SimulationConstraint(StatesSet, OutgoingNodesHandlingStrategy) - Constructor for class org.ginsim.service.tool.reg2dyn.limitedsimulation.SimulationConstraint

Create a new simulation constraint

SimulationHelper - Interface in org.ginsim.service.tool.reg2dyn.helpers

SimulationPanel - Class in org.ginsim.servicegui.tool.avatar.algopanels

Class for managing the panel with the parameters of a simulation (e.g.

SimulationPanel() - Constructor for class org.ginsim.servicegui.tool.avatar.algopanels.SimulationPanel

SimulationParameter - Class in org.ginsim.service.tool.simulation

SimulationParameter() - Constructor for class org.ginsim.service.tool.simulation.SimulationParameter

SimulationParameterEditionPanel - Class in org.ginsim.servicegui.tool.reg2dyn

The panel to edit a simulation parameter.

SimulationParameterEditionPanel(ListEditionPanel<SimulationParameters, SimulationParameterList>, StackDialog) - Constructor for class org.ginsim.servicegui.tool.reg2dyn.SimulationParameterEditionPanel

SimulationParameterList - Class in org.ginsim.service.tool.reg2dyn

store all simulation parameters and offer a mean to access them.

SimulationParameterList(Graph) - Constructor for class org.ginsim.service.tool.reg2dyn.SimulationParameterList

SimulationParameterList(Graph<RegulatoryNode, RegulatoryMultiEdge>, SimulationParameters) - Constructor for class org.ginsim.service.tool.reg2dyn.SimulationParameterList

SimulationParameters - Class in org.ginsim.service.tool.reg2dyn

remember, save and restore a simulation parameter.

SimulationParameters(SimulationParameterList) - Constructor for class org.ginsim.service.tool.reg2dyn.SimulationParameters

empty constructor for everyday use.

SimulationParameters(RegulatoryGraph) - Constructor for class org.ginsim.service.tool.reg2dyn.SimulationParameters

empty constructor without parameter list.

SimulationParametersGUIHelper - Class in org.ginsim.servicegui.tool.reg2dyn

GUI helper for the simulation parameters: provide edition and selection panels

SimulationParametersGUIHelper() - Constructor for class org.ginsim.servicegui.tool.reg2dyn.SimulationParametersGUIHelper

SimulationParametersManager - Class in org.ginsim.service.tool.reg2dyn

Save/open simulation parameters along with the model.

SimulationParametersManager() - Constructor for class org.ginsim.service.tool.reg2dyn.SimulationParametersManager

SimulationParametersParser - Class in org.ginsim.service.tool.reg2dyn

parser for simulation parameters file

SimulationParametersParser(RegulatoryGraph) - Constructor for class org.ginsim.service.tool.reg2dyn.SimulationParametersParser

SimulationQueuedState - Class in org.ginsim.service.tool.reg2dyn

SimulationQueuedState(byte[], int, Object, boolean) - Constructor for class org.ginsim.service.tool.reg2dyn.SimulationQueuedState

SimulationService - Class in org.ginsim.service.tool.simulation

Simple simulation service

SimulationService() - Constructor for class org.ginsim.service.tool.simulation.SimulationService

simulationStrategy - Variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

SimulationUpdater - Interface in org.ginsim.service.tool.reg2dyn.updater

This is the part of the simulation in charge for generating the following states.

SimulationUtils - Class in org.ginsim.service.tool.avatar.simulation

Facilities associated with simulation services.

SimulationUtils() - Constructor for class org.ginsim.service.tool.avatar.simulation.SimulationUtils

SINGLE - Static variable in class org.ginsim.gui.utils.data.ColumnDefinition

SingleSimulationFrame - Class in org.ginsim.servicegui.tool.reg2dyn

The frame displayed to the user when he want to run a simulation

SingleSimulationFrame(Frame, SimulationParameterList) - Constructor for class org.ginsim.servicegui.tool.reg2dyn.SingleSimulationFrame

size() - Method in class org.ginsim.core.utils.data.ValueList

size() - Method in class org.ginsim.service.tool.avatar.domain.AbstractStateSet

size() - Method in class org.ginsim.service.tool.avatar.domain.CompactStateSet

size() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Returns the number of states in the state-set

size() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Returns the number of states in the state-set

SKIPPED - Static variable in class org.ginsim.core.graph.tree.TreeNode

The value should be -42 if the node is skipped and added in the tree.

smallStateSpace - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

size of small state spaces for the inflationary mode

source - Variable in class org.ginsim.core.graph.Edge

source - Variable in enum org.ginsim.core.graph.view.MovingEdgeType

SOUTHEAST - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

SOUTHWEST - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

SPEC_FIRST - Static variable in class org.ginsim.service.tool.graphcomparator.GraphComparatorStyleProvider

SPEC_SECOND - Static variable in class org.ginsim.service.tool.graphcomparator.GraphComparatorStyleProvider

SpinEditor - Class in org.ginsim.gui.utils.data

SpinEditor() - Constructor for class org.ginsim.gui.utils.data.SpinEditor

SpinModel - Class in org.ginsim.gui.utils.data.models

model for a max spinbutton, depends on a GsMinMaxSpinModel

SpinModel() - Constructor for class org.ginsim.gui.utils.data.models.SpinModel

SplitPane - Class in org.ginsim.gui.utils.widgets

SplitPane() - Constructor for class org.ginsim.gui.utils.widgets.SplitPane

StableRegionsService - Class in org.ginsim.service.tool.stableregions

StableRegionsService() - Constructor for class org.ginsim.service.tool.stableregions.StableRegionsService

StableRegionsServiceGUI - Class in org.ginsim.servicegui.tool.stableregions

StableRegionsServiceGUI() - Constructor for class org.ginsim.servicegui.tool.stableregions.StableRegionsServiceGUI

StableStatesService - Class in org.ginsim.service.tool.stablestates

This service provides an analytic search for stable states, implemented in bioLQM.

StableStatesService() - Constructor for class org.ginsim.service.tool.stablestates.StableStatesService

This constructor should be called by the service manager, other users will have to get the first instance

StableStatesServiceGUI - Class in org.ginsim.servicegui.tool.stablestates

Define the action for stableStates service

StableStatesServiceGUI() - Constructor for class org.ginsim.servicegui.tool.stablestates.StableStatesServiceGUI

StableStateSwingUI - Class in org.ginsim.servicegui.tool.stablestates

A simple GUI to launch stable states search and view the result

StableStateSwingUI(JFrame, RegulatoryGraph) - Constructor for class org.ginsim.servicegui.tool.stablestates.StableStateSwingUI

StableTableModel - Class in org.ginsim.gui.graph.dynamicgraph

Simple table model to view stable state search results.

StableTableModel() - Constructor for class org.ginsim.gui.graph.dynamicgraph.StableTableModel

StableTableModel(RegulatoryGraph) - Constructor for class org.ginsim.gui.graph.dynamicgraph.StableTableModel

stack - Variable in class org.ginsim.gui.utils.dialog.stackdialog.AbstractStackDialogHandler

StackDialog - Class in org.ginsim.gui.utils.dialog.stackdialog

a generic stackable dialog.

StackDialog(Graph<?, ?>, String, int, int) - Constructor for class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

StackDialog(Frame, DefaultDialogSize) - Constructor for class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

StackDialog(Frame, String, int, int) - Constructor for class org.ginsim.gui.utils.dialog.stackdialog.StackDialog

stackDialog - Variable in class org.ginsim.servicegui.tool.avatar.parameters.AvaParameterEditionPanel

pointer to main/parent panel

StackDialogHandler - Interface in org.ginsim.gui.utils.dialog.stackdialog

stamp() - Method in class org.ginsim.common.utils.Timer

Get the time elapsed since the last reset.

StandaloneGUI - Annotation Type in org.ginsim.gui.service

STARLEVEL - Static variable in interface org.ginsim.core.graph.dynamicgraph.DynamicGraph

startDocument() - Method in class org.ginsim.common.document.DocumentWriter

startDocument() - Method in class org.ginsim.common.document.LaTeXDocumentWriter

startDocument() - Method in class org.ginsim.common.document.OOoDocumentWriter

startDocument() - Method in class org.ginsim.common.document.WikiDocumentWriter

startDocument() - Method in class org.ginsim.common.document.XHTMLDocumentWriter

startElement(String, String, String, Attributes) - Method in class org.ginsim.common.application.OptionStore

Handler to parse the saved file.

startElement(String, String, String, Attributes) - Method in class org.ginsim.common.xml.XMLHelper

startElement(int, Attributes) - Method in class org.ginsim.common.xml.XMLHelper

startElement(String, String, String, Attributes) - Method in class org.ginsim.core.graph.dynamicgraph.DynamicParser

startElement(String, String, String, Attributes) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphParser

startElement(String, String, String, Attributes) - Method in class org.ginsim.core.graph.reducedgraph.ReducedGraphParser

startElement(int, Attributes) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationParser

startElement(String, String, String, Attributes) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryParser

startElement(String, String, String, Attributes) - Method in class org.ginsim.core.io.parser.GinmlParser

startElement(String, String, String, Attributes) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParametersParser

STARTONLY - Static variable in class org.ginsim.common.xml.XMLHelper

startParsing(File, boolean) - Method in class org.ginsim.common.xml.XMLHelper

start parsing a file.

startParsing(File) - Method in class org.ginsim.common.xml.XMLHelper

start parsing a file.

startParsing(InputStream) - Method in class org.ginsim.common.xml.XMLHelper

startParsing(InputStream, boolean) - Method in class org.ginsim.common.xml.XMLHelper

startup(List<String>) - Method in class org.ginsim.gui.GUIManager

StartupDialog - Class in org.ginsim.gui.shell

StartupDialog(boolean) - Constructor for class org.ginsim.gui.shell.StartupDialog

state - Variable in class org.ginsim.core.graph.dynamicgraph.DynamicNode

each int is the state of the corresponding gene in the regulatory graph (according to nodeOrder).

State - Class in org.ginsim.service.tool.avatar.domain

State(byte[]) - Constructor for class org.ginsim.service.tool.avatar.domain.State

State(byte[], double) - Constructor for class org.ginsim.service.tool.avatar.domain.State

state - Variable in class org.ginsim.service.tool.avatar.domain.State

state - Variable in class org.ginsim.service.tool.reg2dyn.SimulationQueuedState

StateActionPanel - Class in org.ginsim.gui.graph.dynamicgraph

StateActionPanel(DynamicItemModel) - Constructor for class org.ginsim.gui.graph.dynamicgraph.StateActionPanel

stateChanged(ChangeEvent) - Method in class org.ginsim.gui.graph.canvas.VirtualScrollPane

stateChanged(ChangeEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

stateChanged(ChangeEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationCreatePanel

stateChanged(ChangeEvent) - Method in class org.ginsim.gui.utils.dialog.stackdialog.LogicalModelActionDialog

stateChanged(ChangeEvent) - Method in class org.ginsim.gui.utils.widgets.BooleanEditor

stateFromArray(byte[]) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Generate a new omdd corresponding to the state and with the status 1

stateFromArray(byte[], int) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Generate a new omdd corresponding to the state and with the status status

stateFromString(String) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Generate a new omdd corresponding to the state and with the status 1

stateFromString(String, int) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Generate a new omdd corresponding to the state and with the status 1>

StatefulLogicalModel - Interface in org.colomoto.biolqm

Extension of a logical model with the possibility to store initial states and oracles

StatefulLogicalModelImpl - Class in org.colomoto.biolqm

Extension of a logical model with the possibility to maintain a set of initial states and oracles.
Implements the StatefulLogicalModel interface.

StatefulLogicalModelImpl(MDDManager, List<NodeInfo>, int[], List<NodeInfo>, int[], List<byte[]>, String) - Constructor for class org.colomoto.biolqm.StatefulLogicalModelImpl

Creates a stateful logical model based on a MDD

StatefulLogicalModelImpl(List<NodeInfo>, MDDManager, int[], List<byte[]>, String) - Constructor for class org.colomoto.biolqm.StatefulLogicalModelImpl

Creates a stateful logical model based on a MDD

StatefulLogicalModelImpl(LogicalModel, List<byte[]>, String) - Constructor for class org.colomoto.biolqm.StatefulLogicalModelImpl

Creates a stateful logical model based on an existing logical model

StateInRegGraphFrame - Class in org.ginsim.servicegui.tool.stateinregulatorygraph

The main frame.

StateInRegGraphFrame(JFrame, Graph) - Constructor for class org.ginsim.servicegui.tool.stateinregulatorygraph.StateInRegGraphFrame

StateInRegulatoryGraphServiceGUI - Class in org.ginsim.servicegui.tool.stateinregulatorygraph

StateInRegulatoryGraphServiceGUI() - Constructor for class org.ginsim.servicegui.tool.stateinregulatorygraph.StateInRegulatoryGraphServiceGUI

StateListPanel - Class in org.ginsim.gui.graph.regulatorygraph.initialstate

Manager for the list of states in the initial state panel

StateListPanel(InitialStatePanel, NamedStateList, boolean, String) - Constructor for class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

Initializes the table of states

StateProbComparator - Class in org.ginsim.service.tool.avatar.utils

Comparator of states according to their probability

StateProbComparator(boolean) - Constructor for class org.ginsim.service.tool.avatar.utils.StateProbComparator

states - Variable in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

pointer to the panel with the initial states and oracles

StateSet - Class in org.ginsim.service.tool.avatar.domain

Default representation of a state-set recurring to a hash-map of states
States are efficiently stored and accessed using minimal keys

StateSet() - Constructor for class org.ginsim.service.tool.avatar.domain.StateSet

Creates an empty state-set

StateSet(State) - Constructor for class org.ginsim.service.tool.avatar.domain.StateSet

Creates a state-set with the given state

StateSet(List<byte[]>) - Constructor for class org.ginsim.service.tool.avatar.domain.StateSet

Creates a state-set with the given list of states

StateSet(List<byte[]>, double) - Constructor for class org.ginsim.service.tool.avatar.domain.StateSet

Creates a state-set with the given list of states and their probability of occurrence

StateSet(StateSet) - Constructor for class org.ginsim.service.tool.avatar.domain.StateSet

Clones a given state-set

StateSetComparator - Class in org.ginsim.service.tool.avatar.utils

StateSetComparator() - Constructor for class org.ginsim.service.tool.avatar.utils.StateSetComparator

statesSelected - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

statesSet - Variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

The set of states

StatesSet - Class in org.ginsim.core.graph.hierarchicaltransitiongraph

A wrapper of OMDDNode that adds the essentials methods to store states.

StatesSet(MDDManager, byte[]) - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Initialize a new set of states

StatesSet(MDDManager, int, byte[]) - Constructor for class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Initialize a new set of states

statesToFullList() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

statesToFullList(List<byte[]>) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Fill a list with all the states in the omdd Each item of the returned list is a string representation using wildcard * (-1).

StatesToHierarchicalEditTab - Class in org.ginsim.service.tool.reg2dyn.limitedsimulation

StatesToHierarchicalEditTab provides a ParameterPanel for the mainframe presenting information on the hierarchicalNode corresponding to the selected DynamicNode.

StatesToHierarchicalEditTab(DynamicGraph, HierarchicalTransitionGraph) - Constructor for class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalEditTab

StatesToHierarchicalMappingManager - Class in org.ginsim.service.tool.reg2dyn.limitedsimulation

An GraphAssociatedObjectManager providing an HashMap storing a mapping between states and their corresponding HierarchicalNode Usage : (HashMap) ObjectAssociationManager.getInstance().getObject(dynamicGraph, StatesToHierarchicalMappingManager.key, true);

StatesToHierarchicalMappingManager() - Constructor for class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalMappingManager

statesToList() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Initialize and fill a list with all the states in the omdd Each item of the returned list is a string representation using wildcard * (-1).

statestore - Variable in class org.ginsim.service.tool.avatar.params.AvatarParameters

statestore - Variable in class org.ginsim.servicegui.tool.avatar.AvatarConfigFrame

named store with the initial states and oracles

statesToSchemaList() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Initialize and fill a list with all the states in the omdd Each item of the returned list is a string representation using wildcard * (-1).

statesToSchemaList(List<byte[]>) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Fill a list with all the states in the omdd Each item of the returned list is a string representation using wildcard * (-1).

statesToString() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

statesToString(boolean) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

statesToString(boolean) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Return a String representation of the omdd

StateTableModel - Interface in org.ginsim.gui.graph.dynamicgraph

stateTransitionGraph - Variable in class org.ginsim.service.tool.reg2dyn.helpers.STGSimulationHelper

StateTransitionGraphEditor - Class in org.ginsim.gui.graph.dynamicgraph

StateTransitionGraphEditor(DynamicGraph) - Constructor for class org.ginsim.gui.graph.dynamicgraph.StateTransitionGraphEditor

StateVarWriter(List<RegulatoryNode>) - Constructor for class org.ginsim.service.export.cadp.CADPWriter.StateVarWriter

status - Variable in class org.ginsim.core.service.ServiceClassInfo

StatusTextField - Class in org.ginsim.gui.utils.widgets

StatusTextField() - Constructor for class org.ginsim.gui.utils.widgets.StatusTextField

StatusTextField(String, boolean) - Constructor for class org.ginsim.gui.utils.widgets.StatusTextField

std(List<Integer>) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMath

Returns the standard deviation of an integer list

step - Variable in class org.ginsim.core.graph.view.style.IntegerProperty

step - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

step - Variable in class org.ginsim.service.tool.reg2dyn.htg.TarjanSimulation

STGLimitedSimulationHelper - Class in org.ginsim.service.tool.reg2dyn.limitedsimulation

STGLimitedSimulationHelper(LogicalModel, HierarchicalTransitionGraph, SimulationParameters, SimulationConstraint) - Constructor for class org.ginsim.service.tool.reg2dyn.limitedsimulation.STGLimitedSimulationHelper

STGPathStyleProvider - Class in org.ginsim.servicegui.tool.regulatorygraphanimation

STGPathStyleProvider(DynamicGraph, RegulatoryAnimator) - Constructor for class org.ginsim.servicegui.tool.regulatorygraphanimation.STGPathStyleProvider

STGSimulation - Class in org.ginsim.service.tool.simulation

Simulation module to construct STG based on the updaters in LogicalModel

STGSimulation(LogicalModel, MultipleSuccessorsUpdater) - Constructor for class org.ginsim.service.tool.simulation.STGSimulation

STGSimulation(LogicalModel, MultipleSuccessorsUpdater, SimulationStrategy) - Constructor for class org.ginsim.service.tool.simulation.STGSimulation

STGSimulationHelper - Class in org.ginsim.service.tool.reg2dyn.helpers

This is the SimulationHelper used for the simulation of STG.

STGSimulationHelper(LogicalModel, SimulationParameters) - Constructor for class org.ginsim.service.tool.reg2dyn.helpers.STGSimulationHelper

StockButton - Class in org.ginsim.gui.utils.widgets

StockButton(String, Icon) - Constructor for class org.ginsim.gui.utils.widgets.StockButton

StockButton(String) - Constructor for class org.ginsim.gui.utils.widgets.StockButton

StockButton(String, boolean) - Constructor for class org.ginsim.gui.utils.widgets.StockButton

storeAll() - Method in class org.ginsim.core.graph.view.GraphicalAttributesStore

Deprecated.

storeAllEdges(Collection, EdgeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

store all the nodes from the collection nodes.

storeAllNodes(Collection, NodeAttributesReader) - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheetManager

store all the nodes from the collection nodes.

strategy - Variable in class org.ginsim.service.tool.avatar.domain.Result

Associated type of simulation (e.g.

strategy - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

Avatar rewiring strategy

STRATEGY_HTG - Static variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

STRATEGY_SCCG - Static variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

STRATEGY_STG - Static variable in class org.ginsim.service.tool.reg2dyn.SimulationParameters

strict - Variable in class org.ginsim.service.tool.modelreduction.ReductionConfig

stringNodeOrder(Collection) - Method in class org.ginsim.core.io.parser.GINMLWriter

StrongConnectedComponents - Class in org.ginsim.johnsonCycles

This is a helpclass for the search of all elementary cycles in a graph with the algorithm of Johnson.

StrongConnectedComponents(int[][]) - Constructor for class org.ginsim.johnsonCycles.StrongConnectedComponents

Constructor.

StronglyConnectedComponentTask - Class in org.ginsim.service.tool.scc

Search for strongly connected components.

StronglyConnectedComponentTask(Graph) - Constructor for class org.ginsim.service.tool.scc.StronglyConnectedComponentTask

get ready to run.

structureChanged() - Method in interface org.ginsim.core.utils.data.GenericListListener

structureChanged() - Method in class org.ginsim.service.tool.avatar.params.AvatarParameterList

structureChanged() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameterList

Style - Interface in org.ginsim.core.graph.view.style

Define common methods for styles.

style - Variable in class org.ginsim.gui.graph.view.style.ColorizerPanel

STYLE_EDGES - Static variable in class org.ginsim.core.graph.view.css.AllSelector

STYLE_IN - Static variable in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

STYLE_NODES - Static variable in class org.ginsim.core.graph.view.css.AllSelector

STYLE_OUT - Static variable in class org.ginsim.service.tool.polytopesViz.PolytopesSelector

StyleColorizerCheckbox - Class in org.ginsim.gui.graph.view.style

JPanel to control the colorization of a graph via a GUI.

StyleColorizerCheckbox(String, Graph<?, ?>, StyleProvider) - Constructor for class org.ginsim.gui.graph.view.style.StyleColorizerCheckbox

Create a ColorizerPanel containing the colorizeButton.

StyleEditionPanel - Class in org.ginsim.gui.graph.view.style

StyleEditionPanel(GraphGUI, StyleManager) - Constructor for class org.ginsim.gui.graph.view.style.StyleEditionPanel

StyleEditor - Class in org.ginsim.gui.graph.view.style

StyleEditor(StyleManager) - Constructor for class org.ginsim.gui.graph.view.style.StyleEditor

StyleManager<V,E extends Edge<V>> - Class in org.ginsim.core.graph.view.style

Store and handle styles for a Graph.

StyleManager(Graph<V, E>, GraphBackend<V, E>, GraphFactory) - Constructor for class org.ginsim.core.graph.view.style.StyleManager

Create a style manager, defining default styles.

styleManager - Variable in class org.ginsim.core.io.parser.GINMLWriter

styleManager - Variable in class org.ginsim.gui.graph.view.style.StyleColorizerCheckbox

StyleProperty - Class in org.ginsim.core.graph.view.style

StyleProperty(String, boolean) - Constructor for class org.ginsim.core.graph.view.style.StyleProperty

StyleProvider<V,E extends Edge<V>> - Interface in org.ginsim.core.graph.view.style

Define a style provider: it provides styles for nodes and edges and can be applied to a StyleManager to temporarily override the graph styles.

styleProvider - Variable in class org.ginsim.gui.graph.view.style.StyleColorizerCheckbox

styles2ginml(XMLWriter) - Method in class org.ginsim.core.graph.view.style.StyleManager

Save all styles to GINML

stylesUpdated() - Method in class org.ginsim.core.graph.view.style.StyleManager

Called when all styling has been modified, it will refresh the view.

StyleTab - Class in org.ginsim.gui.graph.view.style

The style tab: forward selection to the actual Style panel.

StyleTab(GraphGUI) - Constructor for class org.ginsim.gui.graph.view.style.StyleTab

styleUpdated(Style) - Method in class org.ginsim.core.graph.view.style.StyleManager

Called when a style has been modified, it will refresh the view.

subReport() - Constructor for class org.ginsim.service.tool.circuit.CircuitAlgo.subReport

sum(List<Integer>) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMath

Returns the sum of an integer list

sum(Collection<Double>) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMath

Returns the sum of a double collection

sum(double[]) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMath

Returns the sum of a double array

sumCollection(Collection<Integer>) - Static method in class org.ginsim.service.tool.avatar.utils.AvaMath

Returns the sum of an integer collection

summary - Variable in class org.ginsim.service.tool.circuit.CircuitDescrInTree

summary(List<NodeInfo>) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

summary(List<NodeInfo>) - Method in interface org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinition

summary(List<NodeInfo>) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionAsynchronous

summary(List<NodeInfo>) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionComplete

summary(List<NodeInfo>) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSequential

summary(List<NodeInfo>) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSynchronous

supports(Object) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatesGUIHelper

supports(Object) - Method in class org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationGUIHelper

supports(Object) - Method in interface org.ginsim.gui.guihelpers.GUIHelper

Test if this helper supports a given object

supports(Object) - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionGUIHelper

supports(Object) - Method in class org.ginsim.servicegui.tool.reg2dyn.SimulationParametersGUIHelper

SVGEllipse - Class in org.ginsim.core.graph.view.shapes

An ellipse shape which can be saved in SVG.

SVGEllipse(int, int, int, int) - Constructor for class org.ginsim.core.graph.view.shapes.SVGEllipse

SVGEncoder - Class in org.ginsim.service.export.image

Save a graph view as SVG.

SVGEncoder(Graph, Collection, Collection<Edge>, String) - Constructor for class org.ginsim.service.export.image.SVGEncoder

SVGPolygon - Class in org.ginsim.core.graph.view.shapes

A polygon shape which can be saved in SVG.

SVGPolygon(int[], int[]) - Constructor for class org.ginsim.core.graph.view.shapes.SVGPolygon

SVGRectangle - Class in org.ginsim.core.graph.view.shapes

SVGRectangle(int, int, int, int) - Constructor for class org.ginsim.core.graph.view.shapes.SVGRectangle

SVGShape - Interface in org.ginsim.core.graph.view

A Shape which can be exported as SVG

SVGWriter - Class in org.ginsim.common.xml

XMLWriter extension with some SVG-specific methods.

SVGWriter(String, Dimension) - Constructor for class org.ginsim.common.xml.SVGWriter

SVGWriter(OutputStreamWriter, Dimension) - Constructor for class org.ginsim.common.xml.SVGWriter

SW - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

switchStyles() - Method in class org.ginsim.gui.graph.view.style.StyleTab

SYMBOL - Static variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TAndOperator

SYMBOL - Static variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TNotOperator

SYMBOL - Static variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TOrOperator

SYNCHRONOUS - Static variable in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

this class is synchronous

SYNCHRONOUS - Static variable in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetList

SynchronousSimulationUpdater - Class in org.ginsim.service.tool.reg2dyn.updater

SynchronousSimulationUpdater(ModelHelper) - Constructor for class org.ginsim.service.tool.reg2dyn.updater.SynchronousSimulationUpdater

SynchronousSimulationUpdater(LogicalModel) - Constructor for class org.ginsim.service.tool.reg2dyn.updater.SynchronousSimulationUpdater

T

t(String) - Static method in class org.ginsim.common.application.Txt

The main method: retrieve the text for a given key

t(String, String...) - Static method in class org.ginsim.common.application.Txt

Retrieve the text for a given key, and replace marks by the provided parameters.

t1 - Variable in class org.ginsim.service.tool.avatar.simulation.Simulation

T__10 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

T__10 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

T__11 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

T__11 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

T__12 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarLexer

T__12 - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

t_context - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

t_mark - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

t_me - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

GsRegulatoryMultiEdges in this circuit

t_status - Variable in class org.ginsim.service.tool.circuit.CircuitSearchStoreConfig

t_sub - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

t_typeName - Static variable in class org.ginsim.servicegui.tool.reg2dyn.priorityclass.PriorityClassContentEditor

t_vertex - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

vertices in this circuit

tab(int) - Method in class org.ginsim.core.graph.tree.TreeBuilder

Little helper function to write a tree in stdout

TABLE_BORDER - Static variable in class org.ginsim.common.document.DocumentStyle

TableActionListener - Interface in org.ginsim.gui.utils.data

Be warned when your buttons in a EnhancedTable is clicked

tableChanged(TableModelEvent) - Method in class org.ginsim.gui.annotation.AnnotationPanel

tableChanged(TableModelEvent) - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphFrame

tableChanged(TableModelEvent) - Method in class org.ginsim.servicegui.tool.stablestates.StableStateSwingUI

TableHeaderTransferHandler - Class in org.ginsim.gui.utils.widgets

TableHeaderTransferHandler() - Constructor for class org.ginsim.gui.utils.widgets.TableHeaderTransferHandler

TableInteractionsModel - Class in org.ginsim.gui.graph.regulatorygraph

This is the model behind the interaction editor

TableInteractionsModel(RegulatoryGraph, List) - Constructor for class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

default constructor

TableInteractionsModel(RegulatoryNode) - Constructor for class org.ginsim.gui.graph.regulatorygraph.TableInteractionsModel

constructor with GsNodeRegulationData

TAndOperator - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TAndOperator() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TAndOperator

target - Variable in class org.ginsim.core.graph.Edge

target - Variable in enum org.ginsim.core.graph.view.MovingEdgeType

TargetEdgesIterator - Class in org.ginsim.servicegui.tool.modelreduction

TargetEdgesIterator(Map<RegulatoryNode, List<RegulatoryNode>>) - Constructor for class org.ginsim.servicegui.tool.modelreduction.TargetEdgesIterator

targetMethod - Variable in class org.ginsim.common.application.OSXAdapter

targetObject - Variable in class org.ginsim.common.application.OSXAdapter

targetpanel - Variable in class org.ginsim.gui.utils.data.ListPanel

targets - Variable in class org.ginsim.service.tool.modelreduction.RemovedInfo

TarjanSimulation - Class in org.ginsim.service.tool.reg2dyn.htg

Run a simulation to construct a HierarchicalTransitionGraph

TarjanSimulation(HTGSimulation, ProgressListener<Graph>) - Constructor for class org.ginsim.service.tool.reg2dyn.htg.TarjanSimulation

taskUpdated(Task) - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

taskUpdated(Task) - Method in class org.ginsim.servicegui.tool.modelreduction.ReductionConfigDialog

taskUpdated(Task) - Method in class org.ginsim.servicegui.tool.stablestates.StableStateSwingUI

taskUpdated(Task) - Method in class org.ginsim.servicegui.tool.trapspace.TrapSpaceSwingUI

tauInit - Variable in class org.ginsim.service.tool.avatar.simulation.AvatarSimulation

cycle expansion rate

TBinaryOperator - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TBinaryOperator() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBinaryOperator

TBooleanData - Interface in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TBooleanOperand - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TBooleanOperand() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperand

TBooleanOperator - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TBooleanOperator() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperator

TBooleanParser - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TBooleanParser(String, String) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanParser

TBooleanTreeNode - Interface in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TBooleanTreeNodeFactory - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TBooleanTreeNodeFactory(String, String, TBooleanParser) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNodeFactory

TempDir - Class in org.ginsim.common.utils

Handle the creation and destruction of temporary directory.

TempDir() - Constructor for class org.ginsim.common.utils.TempDir

TERMINAL_CYCLE - Static variable in class org.ginsim.service.tool.scc.ConnectivityStyleProvider

TERMINAL_NODE - Static variable in class org.ginsim.service.tool.scc.ConnectivityStyleProvider

TERMINAL_PALETTE - Static variable in class org.ginsim.service.tool.scc.ConnectivityStyleProvider

TestCycles - Class in org.ginsim.johnsonCycles

Testfile for elementary cycle search.

TestCycles() - Constructor for class org.ginsim.johnsonCycles.TestCycles

TEXT - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

text - Variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

textcolor - Variable in class org.ginsim.core.graph.view.css.CSSNodeStyle

TextProperty - Interface in org.ginsim.gui.utils.data

Created by aurelien on 1/23/14.

threshold - Variable in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

time(Callable<?>, int) - Static method in class org.ginsim.common.callable.Timing

Get the time taken for each run in a series of calls

time(Callable<?>) - Static method in class org.ginsim.common.callable.Timing

Get the time taken by a Callable's call method

time(Runnable) - Static method in class org.ginsim.common.callable.Timing

Get the time taken by a Callable's call method

time - Variable in class org.ginsim.service.tool.avatar.domain.Result

Simulation time (miliseconds)

Timeout - Class in org.ginsim.common.callable

Run timeouts counter and call back when elapsed.

Timeout() - Constructor for class org.ginsim.common.callable.Timeout

timeout() - Method in interface org.ginsim.common.callable.TimeoutObject

the timeout is elapsed

timeout() - Method in class org.ginsim.core.notification.Notification

timeout - Variable in enum org.ginsim.core.notification.NotificationType

TimeoutObject - Interface in org.ginsim.common.callable

Objects waiting for a timeout

Timer - Class in org.ginsim.common.utils

Simple spent-time collector: get current time and return time elapsed since the previous one.

Timer() - Constructor for class org.ginsim.common.utils.Timer

Create a timer, and initialize the base timestamp

timeSpent - Variable in class org.ginsim.service.tool.interactionanalysis.InteractionAnalysisReport

How much time the algo did run

Timing - Class in org.ginsim.common.callable

Estimate the time needed for a callable to run.

Timing() - Constructor for class org.ginsim.common.callable.Timing

title - Variable in class org.ginsim.gui.utils.data.ColumnDefinition

title - Static variable in class org.ginsim.service.tool.reg2dyn.limitedsimulation.StatesToHierarchicalEditTab

TitleToolTipPanel - Class in org.ginsim.servicegui.tool.avatar.others

Dedicated panel where tool tips are allowed to appear on the left superior area

TitleToolTipPanel() - Constructor for class org.ginsim.servicegui.tool.avatar.others.TitleToolTipPanel

TNotOperator - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TNotOperator() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TNotOperator

toArray(List<Integer>) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Converts a list of integers to an array

toBigKey(byte[]) - Static method in class org.ginsim.service.tool.avatar.domain.Dictionary

Computes the key of a long state based on the values of its components

toBuffer() - Method in class org.ginsim.common.xml.XMLWriter

ask to store the next calls into a string buffer.

toByteArray(int[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Converts an integer array to a byte array

toByteArray(CompositionContext) - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

toCSS() - Method in class org.ginsim.core.graph.view.css.Selector

toCSVString() - Method in class org.ginsim.service.tool.avatar.domain.Result

toDescrString() - Method in class org.ginsim.core.graph.tree.TreeNode

toDot() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

toDot(Object) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

toDot() - Method in class org.ginsim.core.graph.tree.TreeNode

toDot(Object) - Method in class org.ginsim.core.graph.tree.TreeNode

toDot() - Method in interface org.ginsim.core.io.parser.Dotify

Return a dot representation of the object as a String

toDot(Object) - Method in interface org.ginsim.core.io.parser.Dotify

Return a dot representation of the edge as a String The object is the source of the edge, the first parameter is the target.

toFullString() - Method in class org.ginsim.service.tool.avatar.params.AvatarParameters

Serializes the AvatarParameters into a string

toggleColorize(Graph<?, ?>) - Method in class org.ginsim.core.graph.view.css.Colorizer

Call doColorize() if the graph is not already colored, undoColorize() otherwise.

toggleSelectAll() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitStateTableModel

toHTMLString() - Method in class org.ginsim.service.tool.avatar.domain.Result

Serializes the results into HTML

tokenNames - Static variable in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationGrammarParser

toKey(byte[]) - Static method in class org.ginsim.service.tool.avatar.domain.Dictionary

Computes the key of a state based on the values of its components

toLongString() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

toLongString() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Detailed description of the states in the state-set as a String object

toLongString() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Detailed description of the states in the state-set as a String object

toNumericKey(byte[]) - Static method in class org.ginsim.service.tool.avatar.domain.Dictionary

Computes the key of a state based on the values of its components

ToolAction - Class in org.ginsim.gui.shell.actions

ToolAction(String, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.ToolAction

ToolAction(String, String, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.ToolAction

ToolAction(String, ImageIcon, String, KeyStroke, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.ToolAction

ToolkitAction - Class in org.ginsim.gui.shell.actions

ToolkitAction(String, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.ToolkitAction

ToolkitAction(String, String, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.ToolkitAction

ToolkitAction(String, ImageIcon, String, KeyStroke, ServiceGUI) - Constructor for class org.ginsim.gui.shell.actions.ToolkitAction

ToolTipsable - Interface in org.ginsim.common.utils

Interface for objects which provide a text to display in a tooltip.

toOpenString(byte[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

topic - Variable in class org.ginsim.core.notification.Notification

Topology - Interface in org.ginsim.service.tool.composition

Represents the interface of any Topology

TOrOperator - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TOrOperator() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TOrOperator

toShortString() - Method in class org.ginsim.service.tool.avatar.domain.State

toStateSet(List<byte[]>, List<NodeInfo>) - Static method in class org.ginsim.service.tool.avatar.simulation.MDDUtils

Maps an oracle (set of state patterns) into a set of specific states

toString() - Method in class org.colomoto.biolqm.io.avatar.AvatarClause

toString(List<byte[]>) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

List of states to string

toString(byte[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Byte array to string

toString(int[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Integer array to string

toString(long[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Long array to string

toString(BigInteger[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

BigInteger array to string

toString(double[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Double array to string

toString(String[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

String array to string

toString(boolean[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Boolean array to string

toString(int[][]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Integer matrix to string

toString(double[][]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Double matrix to string

toString() - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

toString() - Method in class org.ginsim.common.document.GenericDocumentFormat

toString() - Method in class org.ginsim.common.utils.FileFormatDescription

toString() - Method in class org.ginsim.core.annotation.AnnotationLink

toString() - Method in class org.ginsim.core.graph.dynamicgraph.DynamicNode

toString() - Method in class org.ginsim.core.graph.Edge

toString() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.DecisionOnEdge

Return a string representation of the label with the name of the genes.

toString() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

toString() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNodeSet

toString() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalSigmaSet

toString() - Method in class org.ginsim.core.graph.reducedgraph.NodeReducedData

toString(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanGene

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeString

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeValue

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalFunctionListElement

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeaf

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafPattern

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeLeafValue

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.param2function.ParamTreeNode

toString(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBinaryOperator

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperand

toString() - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperator

toString(boolean) - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanTreeNode

toString(boolean) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TUnaryOperator

toString() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedState

toString() - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

toString() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryEdge

toString() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

toString() - Method in class org.ginsim.core.graph.trapspacetree.TrapSpaceNode

toString() - Method in class org.ginsim.core.graph.tree.TreeNode

toString() - Method in class org.ginsim.core.graph.view.css.CascadingStyleSheet

toString() - Method in class org.ginsim.core.graph.view.css.CSSEdgeStyle

a css string representation of this style.

toString(int) - Method in class org.ginsim.core.graph.view.css.CSSEdgeStyle

a css string representation of this style.

toString() - Method in class org.ginsim.core.graph.view.css.CSSNodeStyle

a css string representation of this style.

toString(int) - Method in class org.ginsim.core.graph.view.css.CSSNodeStyle

a css string representation of this style.

toString() - Method in class org.ginsim.core.graph.view.css.Selector

toString(String) - Method in class org.ginsim.core.graph.view.css.Selector

toString() - Method in class org.ginsim.core.graph.view.style.EdgeStyleImpl

toString() - Method in class org.ginsim.core.graph.view.style.NodeStyleImpl

toString() - Method in class org.ginsim.core.notification.Notification

toString() - Method in class org.ginsim.core.service.ServiceClassInfo

toString() - Method in class org.ginsim.core.utils.data.ValueList

toString() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.InitialStatePanel

toString() - Method in class org.ginsim.service.export.cadp.CADPCommonWriter

toString() - Method in class org.ginsim.service.export.cadp.CADPExpWriter

toString() - Method in class org.ginsim.service.export.cadp.CADPIntegrationWriter

toString() - Method in class org.ginsim.service.export.cadp.CADPMclWriter

toString() - Method in class org.ginsim.service.export.cadp.CADPModuleWriter.FunctionWriter

toString() - Method in class org.ginsim.service.export.cadp.CADPModuleWriter.RuleWriter

toString() - Method in class org.ginsim.service.export.cadp.CADPModuleWriter

toString() - Method in class org.ginsim.service.export.cadp.CADPReadMeWriter

toString() - Method in class org.ginsim.service.export.cadp.CADPSvlWriter

toString() - Method in enum org.ginsim.service.export.sat.SATExportType

toString() - Method in class org.ginsim.service.tool.avatar.domain.CompactStateSet

toString() - Method in class org.ginsim.service.tool.avatar.domain.CycleGraph

toString() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

toString() - Method in class org.ginsim.service.tool.avatar.domain.Result

toString() - Method in class org.ginsim.service.tool.avatar.domain.State

toString() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

toString() - Method in class org.ginsim.service.tool.avatar.params.AvatarParameterList

toString() - Method in class org.ginsim.service.tool.avatar.params.AvatarParameters

toString() - Method in enum org.ginsim.service.tool.avatar.service.EnumAlgorithm

toString() - Method in class org.ginsim.service.tool.circuit.CircuitDescrInTree

toString() - Method in class org.ginsim.service.tool.circuit.FunctionalityContext

toString() - Method in class org.ginsim.service.tool.modelreduction.ReductionConfig

toString() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueSCC

toString() - Method in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulationQueueState

toString() - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PriorityClass

toString() - Method in enum org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetAddMode

toString() - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

toString() - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

toString() - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionAsynchronous

toString() - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionComplete

toString() - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSequential

toString() - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSynchronous

toString() - Method in class org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationFunctionClause

toSVG(SVGWriter) - Method in class org.ginsim.core.graph.view.shapes.SVGEllipse

toSVG(SVGWriter, String[]) - Method in class org.ginsim.core.graph.view.shapes.SVGEllipse

toSVG(SVGWriter) - Method in class org.ginsim.core.graph.view.shapes.SVGPolygon

toSVG(SVGWriter, String[]) - Method in class org.ginsim.core.graph.view.shapes.SVGPolygon

toSVG(SVGWriter) - Method in class org.ginsim.core.graph.view.shapes.SVGRectangle

toSVG(SVGWriter, String[]) - Method in class org.ginsim.core.graph.view.shapes.SVGRectangle

toSVG(SVGWriter) - Method in interface org.ginsim.core.graph.view.SVGShape

toSVG(SVGWriter, String[]) - Method in interface org.ginsim.core.graph.view.SVGShape

total_levels - Variable in class org.ginsim.core.graph.tree.TreeBuilder

The total number of levels that are not skipped

totalProbability() - Method in class org.ginsim.service.tool.avatar.domain.MDDStateSet

Sums the probability of all of the internal states

totalProbability() - Method in class org.ginsim.service.tool.avatar.domain.StateSet

Sums the probability of all of the internal states

toToolTip() - Method in interface org.ginsim.common.utils.ToolTipsable

retrieve the tooltip text

toToolTip() - Method in class org.ginsim.core.graph.Edge

toToolTip() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.DecisionOnEdge

toToolTip() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

toToolTip() - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

toUniqueString() - Method in class org.ginsim.core.graph.tree.TreeNode

toXML(XMLWriter) - Method in interface org.ginsim.common.xml.XMLize

write the XML representation of this object to a file

toXML(XMLWriter) - Method in class org.ginsim.core.annotation.Annotation

toXML(XMLWriter) - Method in class org.ginsim.core.annotation.BiblioList

toXML(XMLWriter) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

toXML(XMLWriter, String) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

toXML(XMLWriter) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

toXML(XMLWriter) - Method in interface org.ginsim.core.graph.regulatorygraph.perturbation.Perturbation

Save the perturbation definition to XML (to save in zginml)

toXML(XMLWriter) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationFixed

toXML(XMLWriter) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationMultiple

toXML(XMLWriter) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationRange

toXML(XMLWriter) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.PerturbationRegulator

toXML(XMLWriter) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

toXML(XMLWriter) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

toXML(XMLWriter) - Method in class org.ginsim.service.tool.avatar.params.AvatarParameters

toXML(XMLWriter) - Method in class org.ginsim.service.tool.modelreduction.ReductionConfig

toXML(XMLWriter) - Method in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

toXML(XMLWriter) - Method in class org.ginsim.service.tool.reg2dyn.SimulationParameters

toXML(XMLWriter) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionAsynchronous

toXML(XMLWriter) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionComplete

toXML(XMLWriter) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSequential

toXML(XMLWriter) - Method in class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSynchronous

trace(Object) - Static method in class org.ginsim.common.application.LogManager

Log a trace.

trace(Object, boolean) - Static method in class org.ginsim.common.application.LogManager

Log a trace.

TRANSIENT_CYCLE - Static variable in class org.ginsim.service.tool.scc.ConnectivityStyleProvider

TRANSIENT_NODE - Static variable in class org.ginsim.service.tool.scc.ConnectivityStyleProvider

TRANSIENT_PALETTE - Static variable in class org.ginsim.service.tool.scc.ConnectivityStyleProvider

transientMinSize - Variable in class org.ginsim.service.tool.avatar.domain.Result

Maximum number of iterations

TransitionGraph<V,E extends Edge<V>> - Interface in org.ginsim.core.graph.dynamicgraph

TransitionGraphImpl<V,E extends Edge<V>> - Class in org.ginsim.core.graph.dynamicgraph

TransitionGraphImpl(GraphFactory) - Constructor for class org.ginsim.core.graph.dynamicgraph.TransitionGraphImpl

trapspace - Variable in class org.ginsim.core.graph.trapspacetree.TrapSpaceNode

TrapSpaceInclusion - Class in org.ginsim.core.graph.trapspacetree

TrapSpaceInclusion(Graph<TrapSpaceNode, TrapSpaceInclusion>, TrapSpaceNode, TrapSpaceNode) - Constructor for class org.ginsim.core.graph.trapspacetree.TrapSpaceInclusion

TrapSpaceInclusionDiagram - Interface in org.ginsim.core.graph.trapspacetree

Trap-space inclusion diagram provide an over-approximation of the attractor reachability landscape.

TrapSpaceNode - Class in org.ginsim.core.graph.trapspacetree

Simple node containing a trap-space definition and further analysis results.

TrapSpaceNode(TrapSpace) - Constructor for class org.ginsim.core.graph.trapspacetree.TrapSpaceNode

TrapSpaceServiceGUI - Class in org.ginsim.servicegui.tool.trapspace

Define the action for stableStates service

TrapSpaceServiceGUI() - Constructor for class org.ginsim.servicegui.tool.trapspace.TrapSpaceServiceGUI

TrapSpaceServiceWrapper - Class in org.ginsim.service.tool.trapspace

Search for trap-spaces in Regulatory graphs.

TrapSpaceServiceWrapper() - Constructor for class org.ginsim.service.tool.trapspace.TrapSpaceServiceWrapper

This constructor should be called by the service manager, other users will have to get the first instance

TrapSpaceSwingUI - Class in org.ginsim.servicegui.tool.trapspace

A simple GUI to launch the identification of trap-spaces and view the result.

TrapSpaceSwingUI(JFrame, RegulatoryGraph) - Constructor for class org.ginsim.servicegui.tool.trapspace.TrapSpaceSwingUI

TrapSpaceTableModel - Class in org.ginsim.servicegui.tool.trapspace

TrapSpaceTableModel() - Constructor for class org.ginsim.servicegui.tool.trapspace.TrapSpaceTableModel

TrapSpaceTreeFactory - Class in org.ginsim.core.graph.trapspacetree

TrapSpaceTreeFactory() - Constructor for class org.ginsim.core.graph.trapspacetree.TrapSpaceTreeFactory

TrapSpaceTreeGUIHelper - Class in org.ginsim.gui.graph.trapspacetree

TrapSpaceTreeGUIHelper() - Constructor for class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeGUIHelper

TrapSpaceTreeImpl - Class in org.ginsim.core.graph.trapspacetree

TrapSpaceTreeImpl(GraphFactory) - Constructor for class org.ginsim.core.graph.trapspacetree.TrapSpaceTreeImpl

TrapSpaceTreeMainPanel - Class in org.ginsim.gui.graph.trapspacetree

TrapSpaceTreeMainPanel(TrapSpaceInclusionDiagram) - Constructor for class org.ginsim.gui.graph.trapspacetree.TrapSpaceTreeMainPanel

Tree - Interface in org.ginsim.core.graph.tree

tree - Variable in class org.ginsim.core.graph.tree.TreeBuilder

tree - Variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

tree - Variable in class org.ginsim.gui.utils.widgets.treetable.JTreeTable

tree - Variable in class org.ginsim.servicegui.tool.circuit.CircuitFrame

TreeActionPanel - Class in org.ginsim.gui.graph.tree

This action panel allow the user to select the * omdd representation method * the gene associated with the logical function to display (in the case of regulatoryGraph)

TreeActionPanel() - Constructor for class org.ginsim.gui.graph.tree.TreeActionPanel

TreeBuilder - Class in org.ginsim.core.graph.tree

TreeBuilder() - Constructor for class org.ginsim.core.graph.tree.TreeBuilder

TreeBuilderFromCircuit - Class in org.ginsim.core.graph.tree

A treeParser for the context of functionality

TreeBuilderFromCircuit() - Constructor for class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

TreeBuilderFromManualOmdd - Class in org.ginsim.core.graph.tree

TreeBuilderFromManualOmdd() - Constructor for class org.ginsim.core.graph.tree.TreeBuilderFromManualOmdd

TreeBuilderFromMDD - Class in org.ginsim.core.graph.tree

TreeBuilderFromMDD() - Constructor for class org.ginsim.core.graph.tree.TreeBuilderFromMDD

TreeBuilderFromRegulatoryGraph - Class in org.ginsim.core.graph.tree

TreeBuilderFromRegulatoryGraph() - Constructor for class org.ginsim.core.graph.tree.TreeBuilderFromRegulatoryGraph

TreeEdge - Class in org.ginsim.core.graph.tree

TreeEdge(Graph, TreeNode, TreeNode, int) - Constructor for class org.ginsim.core.graph.tree.TreeEdge

TreeElement - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree

TreeElement(TreeElement) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeElement

treeElement - Variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

TreeExpression - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree

TreeExpression(TreeElement, TBooleanTreeNode, FunctionsCreator) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

TreeExpression(TreeElement, String, FunctionsCreator) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeExpression

TreeFactory - Class in org.ginsim.core.graph.tree

TreeFactory() - Constructor for class org.ginsim.core.graph.tree.TreeFactory

TreeGUIHelper - Class in org.ginsim.gui.graph.tree

TreeGUIHelper() - Constructor for class org.ginsim.gui.graph.tree.TreeGUIHelper

TreeImpl - Class in org.ginsim.core.graph.tree

TreeImpl(TreeBuilder) - Constructor for class org.ginsim.core.graph.tree.TreeImpl

Create a new Tree and link it to the parser.

TreeInteractionsModel - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree

TreeInteractionsModel(RegulatoryGraph) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

TreeMenu - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

TreeMenu(ActionListener) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.TreeMenu

TreeNode - Class in org.ginsim.core.graph.tree

TreeNode(String, int, int, byte) - Constructor for class org.ginsim.core.graph.tree.TreeNode

Create a new TreeNode with a default value of -1

TreeNode(String, int, int, byte, byte) - Constructor for class org.ginsim.core.graph.tree.TreeNode

TreeNode(TreeNode) - Constructor for class org.ginsim.core.graph.tree.TreeNode

Create a new TreeNode by copying the values of the other TreeNode

TreeParam - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree

TreeParam(TreeElement, List) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

TreeParam(TreeElement) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeParam

TreeString - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree

TreeString(TreeElement, String) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeString

TreeTableCellEditor() - Constructor for class org.ginsim.gui.utils.widgets.treetable.JTreeTable.TreeTableCellEditor

TreeTableCellRenderer(TreeModel) - Constructor for class org.ginsim.gui.utils.widgets.treetable.JTreeTable.TreeTableCellRenderer

TreeTableModel - Interface in org.ginsim.gui.utils.widgets.treetable

TreeTableModel is the model used by a JTreeTable.

TreeTableModelAdapter - Class in org.ginsim.gui.utils.widgets.treetable

This is a wrapper class takes a TreeTableModel and implements the table model interface.

TreeTableModelAdapter(TreeTableModel, JTree) - Constructor for class org.ginsim.gui.utils.widgets.treetable.TreeTableModelAdapter

TreeValue - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree

TreeValue(TreeElement, byte) - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeValue

trimPoints(Edge, List<Point>, NodeAttributesReader, EdgeAttributesReader) - Static method in class org.ginsim.core.graph.view.ViewHelper

Remove the first and last points if they are inside the source and target bounding box

truncated - Variable in class org.ginsim.service.tool.avatar.domain.Result

Number of truncated iterations

TruthTableFormatService - Class in org.ginsim.service.format

GINsim import service for the TruthTable Format.

TruthTableFormatService() - Constructor for class org.ginsim.service.format.TruthTableFormatService

TruthTableFormatServiceGUI - Class in org.ginsim.servicegui.format

GUI Action to import create a model specified in the TruthTable format

TruthTableFormatServiceGUI() - Constructor for class org.ginsim.servicegui.format.TruthTableFormatServiceGUI

TUnaryOperator - Class in org.ginsim.core.graph.regulatorygraph.logicalfunction.parser

TUnaryOperator() - Constructor for class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TUnaryOperator

Txt - Class in org.ginsim.common.application

Retrieve text from resource bundles: define GUI text outside of the code.

Txt() - Constructor for class org.ginsim.common.application.Txt

TYPE - Static variable in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

type - Variable in class org.ginsim.gui.utils.data.ColumnDefinition

type - Variable in class org.ginsim.gui.utils.data.GenericPropertyInfo

TYPE_BRANCH - Static variable in class org.ginsim.core.graph.tree.TreeNode

TYPE_EDEN_TRANSIENT_COMPONENT_COLOR - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_LEAF - Static variable in class org.ginsim.core.graph.tree.TreeNode

TYPE_STABLE_STATE - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_STABLE_STATE_COLOR - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_STABLE_STATE_STRING - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_TERMINAL_CYCLE - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_TERMINAL_CYCLE_COLOR - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_TERMINAL_CYCLE_STRING - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_TRANSIENT_COMPONENT - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_TRANSIENT_COMPONENT_ALONE_COLOR - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_TRANSIENT_COMPONENT_COLOR - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_TRANSIENT_COMPONENT_STRING - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_TRANSIENT_CYCLE - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_TRANSIENT_CYCLE_COLOR - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

TYPE_TRANSIENT_CYCLE_STRING - Static variable in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

typedList() - Method in class org.ginsim.service.export.cadp.CADPWriter.GateWriter

typedList() - Method in class org.ginsim.service.export.cadp.CADPWriter.StateVarWriter

typedMixedList() - Method in class org.ginsim.service.export.cadp.CADPWriter.InitialStateWriter

typedSimpleList(int) - Method in class org.ginsim.service.export.cadp.CADPWriter.InitialStateWriter

typedStateConcat(int) - Method in class org.ginsim.service.export.cadp.CADPWriter.InitialStateWriter

typeFromString(String) - Static method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Return an int representation for a given string

typeToString() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Return a string representation for the type of this node.

typeToString(int) - Static method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Return a string representation for a given type.

U

undoColorize(Graph<?, ?>) - Method in class org.ginsim.core.graph.view.css.Colorizer

Supposing that the style have been saved, this function will restore the original style of all the edges/nodes if the selector respond to the the edges/nodes respectively.

undoColorize() - Method in class org.ginsim.gui.graph.view.style.ColorizerPanel

Cancel the colorization of the graph, update the button name accordingly

undoColorize() - Method in class org.ginsim.gui.graph.view.style.StyleColorizerCheckbox

Cancel the colorization of the graph, update the button name accordingly

undoColorize() - Method in class org.ginsim.service.tool.polytopesViz.PolytopesService

unload(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.AvatarPanel

unload(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.FirefrontPanel

unload(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.MonteCarloPanel

unload(AvatarParameters) - Method in class org.ginsim.servicegui.tool.avatar.algopanels.SimulationPanel

Saves the parameters within the fields of the panel

unload(AvatarParameters, AvatarConfigFrame) - Static method in class org.ginsim.servicegui.tool.avatar.parameters.AvatarParametersHelper

Populates the fields of the main panel from a given simulation context (parameters)

unselectAll() - Method in class org.ginsim.gui.graph.GraphSelection

Unselect all the edges and nodes

unselectAllEdges() - Method in class org.ginsim.gui.graph.GraphSelection

Unselect all the edges

unselectAllNodes() - Method in class org.ginsim.gui.graph.GraphSelection

Unselect all the nodes

unselectEdge(E) - Method in class org.ginsim.gui.graph.GraphSelection

unselectNode(V) - Method in class org.ginsim.gui.graph.GraphSelection

unsetAsMapped(RegulatoryNode) - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

unsetAsMapped(RegulatoryNode) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

unsetAsMapped(RegulatoryNode) - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

UP - Static variable in class org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetDefinition

update(int, int) - Method in enum org.ginsim.core.graph.dynamicgraph.ChangeType

update(String, String) - Method in interface org.ginsim.core.graph.objectassociation.UserSupporter

A user was updated, make sure to clean related data.

update(String, String) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

update() - Method in class org.ginsim.gui.utils.data.models.MaxSpinModel

update the display

update() - Method in class org.ginsim.gui.utils.data.models.MinSpinModel

update the display

update(String, String) - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

update() - Method in class org.ginsim.servicegui.tool.avatar.parameters.AvaParameterEditionPanel

Updates the panel based on the most recent changes to the context of a simulation

updateAnchor() - Method in class org.ginsim.gui.graph.view.style.EdgeRoutingPanel

updateExpression(byte, TreeExpression, String) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

updateGraphNotificationMessage(Graph) - Method in class org.ginsim.servicegui.tool.regulatorygraphanimation.RegulatoryAnimator

updateInteraction(int, List) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameterList

updateInteraction(int, List) - Method in class org.ginsim.core.graph.regulatorygraph.RegulatoryNode

change an interaction's list of edges: we have to check that the new list of edges is not in an existing interaction.

updateLayout(NodeAttributesReader, TreeNode) - Method in class org.ginsim.core.graph.tree.TreeBuilder

updateMaxDepth() - Method in class org.ginsim.servicegui.tool.reg2dyn.SimulationParameterEditionPanel

Update the currentParameter.maxdepth value when the corresponding widget is changed.

updateMaxNodes() - Method in class org.ginsim.servicegui.tool.reg2dyn.SimulationParameterEditionPanel

Update the currentParameter.maxnodes value when the corresponding widget is changed.

updateModel(LogicalModel) - Method in class org.ginsim.service.export.nusmv.NuSMVConfig

updateModel(LogicalModel) - Method in class org.ginsim.service.export.prism.PRISMConfig

updateModel(LogicalModel) - Method in class org.ginsim.service.export.sat.SATConfig

updateModel(LogicalModel) - Method in class org.ginsim.service.format.ginml.GINMLFormatConfig

updateNodeLayout() - Method in class org.ginsim.core.graph.tree.TreeBuilder

Compute the layout for each node in this tree

updateNotificationMessage() - Method in class org.ginsim.gui.notifications.NotificationPanel

updateNumberInstances(int) - Method in class org.ginsim.servicegui.export.cadp.CADPExportConfigPanel

updateNumberInstances(int) - Method in class org.ginsim.servicegui.tool.composition.CompositionPanel

updateNumberInstances(int) - Method in interface org.ginsim.servicegui.tool.composition.CompositionSpecificationDialog

updateParam(NamedStateStore) - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.CompleteStatePanel

Updates the information on the state panel

updater - Variable in class org.ginsim.service.tool.avatar.simulation.FirefrontSimulation

updater - Variable in class org.ginsim.service.tool.reg2dyn.Simulation

UpdaterDefinition - Interface in org.ginsim.service.tool.reg2dyn.updater

UpdaterDefinitionAsynchronous - Class in org.ginsim.service.tool.reg2dyn.updater

UpdaterDefinitionComplete - Class in org.ginsim.service.tool.reg2dyn.updater

UpdaterDefinitionSequential - Class in org.ginsim.service.tool.reg2dyn.updater

UpdaterDefinitionSequential() - Constructor for class org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinitionSequential

UpdaterDefinitionStore - Interface in org.ginsim.service.tool.reg2dyn.priorityclass

Simple interface to store and retrieve a priority class setup.

UpdaterDefinitionSynchronous - Class in org.ginsim.service.tool.reg2dyn.updater

updateSelection(List<V>, List<E>) - Method in class org.ginsim.gui.graph.BaseGraphGUI

updateSelectionCache() - Method in class org.ginsim.gui.graph.canvas.GraphCanvasRenderer

updateSimulationMethod() - Method in class org.ginsim.servicegui.tool.reg2dyn.SimulationParameterEditionPanel

updateSize() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

Compute the size.

updateSize() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Count the number of states in the Omdd and update the size accordingly

updateSize() - Method in class org.ginsim.gui.graph.regulatorygraph.IncomingEdgeListModel

recalculate the size of the list

updateSize() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

updateSize() - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

updateStatus(byte[], int) - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Change the status associated of state in the set to newStatus

updateStatus(CircuitGUIStatus) - Method in class org.ginsim.servicegui.tool.circuit.CircuitFrame

updateTable() - Method in class org.ginsim.gui.graph.regulatorygraph.initialstate.StateListPanel

The table's structure has changed, update it.

updateUI() - Method in class org.ginsim.gui.utils.widgets.RangeSlider

Overrides the superclass method to install the UI delegate to draw two thumbs.

updateValue(byte, byte) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

UpdatingPanel - Class in org.ginsim.servicegui.tool.reg2dyn.priorityclass

UpdatingPanel(ListEditionPanel<UpdaterDefinition, PrioritySetList>) - Constructor for class org.ginsim.servicegui.tool.reg2dyn.priorityclass.UpdatingPanel

USE_BIOLQM_UPDATERS - Static variable in interface org.ginsim.service.tool.reg2dyn.updater.UpdaterDefinition

usePerturbation(String, Perturbation) - Method in class org.ginsim.core.graph.regulatorygraph.perturbation.ListOfPerturbations

Announce the use of a perturbation.

useReduction(String, ReductionConfig) - Method in class org.ginsim.service.tool.modelreduction.ListOfReductionConfigs

UserSupporter - Interface in org.ginsim.core.graph.objectassociation

A User Supporter handles some simple data store for "users".

V

v_all - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

v_dual - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

v_functional - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

v_list - Variable in class org.ginsim.service.tool.circuit.CircuitSearchStoreConfig

v_listener - Variable in class org.ginsim.gui.utils.data.ObjectEditor

v_negative - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

v_positive - Variable in class org.ginsim.service.tool.circuit.CircuitDescr

v_prop - Variable in class org.ginsim.gui.utils.data.ObjectEditor

v_stables - Variable in class org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

validateText(String) - Method in interface org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanel

validateText(String) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.FunctionPanelImpl

value - Variable in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanOperand

VALUE_FLAVOR - Static variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.dnd.GsTransferable

valueChanged(TreeSelectionEvent) - Method in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.LogicalFunctionTreePanel

valueChanged(ListSelectionEvent) - Method in class org.ginsim.gui.graph.view.style.StyleTab

valueChanged(ListSelectionEvent) - Method in class org.ginsim.gui.shell.SearchFrame

valueChanged(ListSelectionEvent) - Method in class org.ginsim.gui.utils.data.ListPanel

valueChanged(ListSelectionEvent) - Method in class org.ginsim.servicegui.tool.localgraph.LocalGraphFrame

valueForPathChanged(TreePath, Object) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.graphictree.TreeInteractionsModel

valueForPathChanged(TreePath, Object) - Method in class org.ginsim.gui.utils.widgets.treetable.AbstractTreeTableModel

ValueList<T> - Class in org.ginsim.core.utils.data

Group a list of values and a selected item from this list.

ValueList(List<T>) - Constructor for class org.ginsim.core.utils.data.ValueList

ValueList(List<T>, int) - Constructor for class org.ginsim.core.utils.data.ValueList

ValueList(List<T>, String) - Constructor for class org.ginsim.core.utils.data.ValueList

ValueList(List<T>, int, String) - Constructor for class org.ginsim.core.utils.data.ValueList

ValueListComboModel - Class in org.ginsim.gui.utils.data.models

ValueListComboModel() - Constructor for class org.ginsim.gui.utils.data.models.ValueListComboModel

ValueListComboModel(ValueList) - Constructor for class org.ginsim.gui.utils.data.models.ValueListComboModel

valueOf(String) - Static method in enum org.ginsim.common.application.CurrentOS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.common.xml.CallMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.graph.dynamicgraph.ChangeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.graph.GraphChangeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.graph.regulatorygraph.ActivityLevel

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.graph.regulatorygraph.RegulatoryEdgeSign

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.graph.view.EdgeAnchor

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.graph.view.EdgeEnd

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.graph.view.EdgePattern

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.graph.view.MovingEdgeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.graph.view.NodeBorder

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.graph.view.NodeShape

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.notification.NotificationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.core.service.EStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.gui.graph.canvas.events.DragStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.gui.graph.EditMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.gui.graph.ZoomEffect

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.gui.shell.editpanel.SelectionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.service.export.sat.SATExportType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.service.tool.avatar.service.EnumAlgorithm

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.service.tool.avatar.simulation.AvatarSimulation.AvatarStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.service.tool.composition.IntegrationFunction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.service.tool.interactionanalysis.InteractionStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.service.tool.localgraph.LocalGraphCategory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.service.tool.modelreduction.RewiringAction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.service.tool.reg2dyn.limitedsimulation.OutgoingNodesHandlingStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetAddMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.servicegui.tool.circuit.CircuitGUIStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationLogicalOperator

Returns the enum constant of this type with the specified name.

ValuePanel - Class in org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree

ValuePanel(TreeElement, JTree, boolean, int, boolean) - Constructor for class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.ValuePanel

values() - Static method in enum org.ginsim.common.application.CurrentOS

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.common.xml.CallMode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.graph.dynamicgraph.ChangeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.graph.GraphChangeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.graph.regulatorygraph.ActivityLevel

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.graph.regulatorygraph.RegulatoryEdgeSign

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.graph.view.EdgeAnchor

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.graph.view.EdgeEnd

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.graph.view.EdgePattern

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.graph.view.MovingEdgeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.graph.view.NodeBorder

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.graph.view.NodeShape

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.notification.NotificationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.core.service.EStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.gui.graph.canvas.events.DragStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.gui.graph.EditMode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.gui.graph.regulatorygraph.perturbation.PerturbationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.gui.graph.ZoomEffect

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.gui.shell.editpanel.SelectionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.service.export.sat.SATExportType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.service.tool.avatar.service.EnumAlgorithm

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.service.tool.avatar.simulation.AvatarSimulation.AvatarStrategy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.service.tool.composition.IntegrationFunction

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.service.tool.interactionanalysis.InteractionStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.service.tool.localgraph.LocalGraphCategory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.service.tool.modelreduction.RewiringAction

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.service.tool.reg2dyn.limitedsimulation.OutgoingNodesHandlingStrategy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.service.tool.reg2dyn.priorityclass.PrioritySetAddMode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.servicegui.tool.circuit.CircuitGUIStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.ginsim.servicegui.tool.composition.integrationgrammar.IntegrationLogicalOperator

Returns an array containing the constants of this enum type, in the order they are declared.

verifOperandList(List) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.BooleanParser

verifOperandList(List) - Method in class org.ginsim.core.graph.regulatorygraph.logicalfunction.parser.TBooleanParser

vertex - Variable in class org.ginsim.service.tool.modelreduction.RemovedInfo

VERTEX_BG - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

VERTEX_BORDER - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

VERTEX_FG - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

VERTEX_HEIGHT - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

VERTEX_SHAPE - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

VERTEX_TEXT - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

VERTEX_WIDTH - Static variable in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

vertexRemoved(Object, List) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

vertexSet() - Method in class org.ginsim.core.graph.backend.GsJGraphtBaseGraph

vertexUpdated(Object, List) - Method in class org.ginsim.core.graph.regulatorygraph.namedstates.NamedStateList

VERTICAL - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

VerticalLabelUI - Class in org.ginsim.commongui.utils

A UI delegate for JLabel that rotates the label 90º

VerticalLabelUI() - Constructor for class org.ginsim.commongui.utils.VerticalLabelUI

Constructs a VerticalLabelUI with the default anticlockwise rotation

VerticalLabelUI(boolean) - Constructor for class org.ginsim.commongui.utils.VerticalLabelUI

Constructs a VerticalLabelUI with the desired rotation.

verticalLabelUI - Static variable in class org.ginsim.commongui.utils.VerticalLabelUI

VerticalTableHeaderCellRenderer - Class in org.ginsim.commongui.utils

A renderer for a JTableHeader with text rotated 90° counterclockwise.

VerticalTableHeaderCellRenderer() - Constructor for class org.ginsim.commongui.utils.VerticalTableHeaderCellRenderer

Constructs a VerticalTableHeaderCellRenderer.

view(String, GUIHelper) - Method in class org.ginsim.servicegui.tool.dataviewer.DataViewer

view() - Method in class org.ginsim.servicegui.tool.dynamicanalyser.DynamicSearchPathConfig

ViewCopyHelper<G extends Graph<V,E>,V,E extends Edge<V>> - Interface in org.ginsim.core.graph.view

Provide a mapping between the elements of two graphs, used to transfer visual properties.

ViewHelper - Class in org.ginsim.core.graph.view

Common logics to manage bounding boxes, anchor points and related tricks for edge routing.

ViewHelper() - Constructor for class org.ginsim.core.graph.view.ViewHelper

VirtualScrollable - Interface in org.ginsim.gui.graph.canvas

Define methods to integrate a view into a VirtualScrollPane.

VirtualScrollPane - Class in org.ginsim.gui.graph.canvas

ScrollPane-like panel to host a "smart" canvas.

VirtualScrollPane(VirtualScrollable) - Constructor for class org.ginsim.gui.graph.canvas.VirtualScrollPane

VisibleComponentsWidget - Class in org.ginsim.servicegui.export.cadp

Widget to specify the visible components

VisibleComponentsWidget(CompositionSpecificationDialog) - Constructor for class org.ginsim.servicegui.export.cadp.VisibleComponentsWidget

visibleRow - Variable in class org.ginsim.gui.utils.widgets.treetable.JTreeTable.TreeTableCellRenderer

vreader - Variable in class org.ginsim.core.graph.view.GraphicalAttributesStore

Deprecated.

vreader - Variable in class org.ginsim.service.tool.reg2dyn.helpers.STGSimulationHelper

vreader - Variable in class org.ginsim.service.tool.reg2dyn.htg.HTGSimulation

W

W_EXPORT_DOC - Static variable in interface org.ginsim.gui.service.ServiceGUI

Weight for menu export, images/doc

W_EXPORT_GENERIC - Static variable in interface org.ginsim.gui.service.ServiceGUI

Weight for menu export, generic graph viz

W_EXPORT_SPECIFIC - Static variable in interface org.ginsim.gui.service.ServiceGUI

Weight for menu export, specific file types

W_GRAPH_COLORIZE - Static variable in interface org.ginsim.gui.service.ServiceGUI

Weight for menu Graph, action affecting the graphicalAttributes

W_GRAPH_SELECTION - Static variable in interface org.ginsim.gui.service.ServiceGUI

Weight for menu Graph, action affecting the selection

W_TOOLKITS_MAIN - Static variable in interface org.ginsim.gui.service.ServiceGUI

Weight for menu Toolits, all

W_TOOLS_MAIN - Static variable in interface org.ginsim.gui.service.ServiceGUI

Weight for menu Tools, action like simulation, stablestates...

W_UNDER_DEVELOPMENT - Static variable in interface org.ginsim.gui.service.ServiceGUI

Extra weight for UNDER_DEVELOPMENT actions

warning(SAXParseException) - Method in class org.ginsim.common.xml.XMLHelper

WarningNotification - Class in org.ginsim.core.notification

WarningNotification(Object, String) - Constructor for class org.ginsim.core.notification.WarningNotification

WEST - Static variable in class org.ginsim.gui.utils.widgets.GsPanel

whatToDoWithGraph(Graph<?, ?>) - Method in class org.ginsim.gui.GUIManager

whatToDoWithGraph(Graph<?, ?>, Graph<?, ?>) - Method in class org.ginsim.gui.GUIManager

Manage the action to execute on the new graph (that was generated from the parent graph).

WhatToDoWithGraph - Class in org.ginsim.gui

This class define a frame that is opened when a graph is computed from an other one.

WhatToDoWithGraph(Graph) - Constructor for class org.ginsim.gui.WhatToDoWithGraph

Create the frame.

whichCanApply(RegulatoryNode, Collection<RegulatoryNode>) - Static method in enum org.ginsim.service.tool.composition.IntegrationFunction

whichCanApply(RegulatoryNode) - Static method in enum org.ginsim.service.tool.composition.IntegrationFunction

WIDTH - Static variable in class org.ginsim.common.document.DocumentStyle

width - Variable in class org.ginsim.commongui.dialog.DefaultDialogSize

WIDTH - Static variable in class org.ginsim.core.graph.view.style.StyleProperty

width - Variable in class org.ginsim.gui.graph.regulatorygraph.logicalfunction.graphictree.BooleanFunctionTreePanel

widthPerDepth - Variable in class org.ginsim.core.graph.tree.TreeBuilder

Indicates for each depth, the sub-total (width) of children or 0 if the depth is not skipped (realDepth == -1).

widthPerDepth_acc - Variable in class org.ginsim.core.graph.tree.TreeBuilder

Indicates for each depth, the total (width) of children or 0 if the depth is not skipped (realDepth == -1).

WikiDocumentWriter - Class in org.ginsim.common.document

Wiki-like backend for the document writer.

WikiDocumentWriter() - Constructor for class org.ginsim.common.document.WikiDocumentWriter

window2canvas(Point) - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

write(String) - Method in class org.ginsim.common.xml.XMLWriter

write(char) - Method in class org.ginsim.common.xml.XMLWriter

write() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalNode

write() - Method in class org.ginsim.core.graph.hierarchicaltransitiongraph.StatesSet

Return a parenthesis based representation of the MDD

write(OutputStreamWriter, Collection<V>, Collection<E>) - Method in class org.ginsim.core.io.parser.GINMLWriter

write(NuSMVConfig, Writer) - Method in class org.ginsim.service.export.nusmv.NuSMVEncoder

Export the graph to a NUSMV model description

write(PRISMConfig, Writer) - Method in class org.ginsim.service.export.prism.PRISMEncoder

Export the graph to a PRISM model description

write(Writer) - Method in class org.ginsim.service.export.reggraph.RegGraphEncoder

write(SATConfig, Writer) - Method in class org.ginsim.service.export.sat.SATEncoder

Export the graph to a SAT model description

writeEsc(String, boolean) - Method in class org.ginsim.common.xml.XMLWriter

writeEscaped(String) - Method in class org.ginsim.common.document.LaTeXDocumentWriter

writeGINML(XMLWriter) - Method in class org.ginsim.core.graph.backend.EdgeAttributeReaderImpl

writeGINML(XMLWriter) - Method in class org.ginsim.core.graph.backend.NodeAttributeReaderImpl

writeGINML(XMLWriter) - Method in interface org.ginsim.core.graph.view.AttributesReader

Save the visual settings in GINML.

writePNGFile(BufferedImage, File) - Static method in class org.ginsim.service.tool.avatar.utils.ChartGNUPlot

Saves a given image in a PNG file

writeText(String) - Method in class org.ginsim.common.document.DocumentWriter

Write the text into the current opened element.

writeTextln(String) - Method in class org.ginsim.common.document.DocumentWriter

Write the text into the current opened element and append a new line at the end.

X

XHTMLDocumentFormat - Static variable in class org.ginsim.common.document.GenericDocumentFormat

XHTMLDocumentWriter - Class in org.ginsim.common.document

XHTMLDocumentWriter is a backend to write xHTML files

XHTMLDocumentWriter() - Constructor for class org.ginsim.common.document.XHTMLDocumentWriter

XMLHelper - Class in org.ginsim.common.xml

Base class for XML parsers.

XMLHelper() - Constructor for class org.ginsim.common.xml.XMLHelper

XMLize - Interface in org.ginsim.common.xml

Interface for object that can save themselves to XML.

XMLWriter - Class in org.ginsim.common.xml

A helper to write well formed XML documents.

XMLWriter(String) - Constructor for class org.ginsim.common.xml.XMLWriter

Create a XMLWriter with the path to a file.

XMLWriter(String, String) - Constructor for class org.ginsim.common.xml.XMLWriter

Create a XMLWriter with the path to a file.

XMLWriter(OutputStreamWriter) - Constructor for class org.ginsim.common.xml.XMLWriter

Create a XMLWriter with an existing Writer.

XMLWriter(OutputStreamWriter, String) - Constructor for class org.ginsim.common.xml.XMLWriter

Create a XMLWriter with an existing Writer.

XMLWriter(OutputStream) - Constructor for class org.ginsim.common.xml.XMLWriter

Create a XMLWriter with an output stream.

xr - Variable in class org.ginsim.common.xml.XMLHelper

Y

yAdjustment - Variable in class org.ginsim.servicegui.tool.avatar.AvatarLogicalModelActionDialog

Z

ZIP_PREFIX - Static variable in class org.ginsim.core.graph.AbstractGraph

zoom(ZoomEffect) - Method in class org.ginsim.gui.graph.canvas.SimpleCanvas

ZoomEffect - Enum in org.ginsim.gui.graph

_

_initRealDepth(int) - Method in class org.ginsim.core.graph.tree.TreeBuilderFromCircuit

_initRealDepth(int) - Method in class org.ginsim.core.graph.tree.TreeBuilderFromMDD

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _