Uses of Class
org.ginsim.common.application.GsException

Packages that use GsException

Package	Description
org.ginsim	The base package for GINsim, with launcher classes.
org.ginsim.common.utils	This package hosts a collection of miscellaneous utilities.
org.ginsim.common.xml	This package contains helpers to write and parse XML files.
org.ginsim.core.annotation	Manage annotations: bibliography, Database entries and links.
org.ginsim.core.graph	Define the main Graph interfaces, and a GraphManager to handle graph types
org.ginsim.core.graph.dynamicgraph	State Transition Graphs, representing dynamical behaviours.
org.ginsim.core.graph.hierarchicaltransitiongraph
org.ginsim.core.graph.objectassociation	Handling objects associated to Graphs.
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	The regulatory graph is the main graph, it represents the model.
org.ginsim.core.graph.regulatorygraph.logicalfunction	Logical functions associated to nodes of the regulatory graph define their dynamical behaviour.
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	Perturbations to modify some parts of a model before analysis.
org.ginsim.core.io.parser	Some tools to build parsers and writers for xml and text formats
org.ginsim.gui.shell.actions	Define types of actions, which will be integrated in different parts of the shell.
org.ginsim.gui.utils.dialog.stackdialog	Definition of StackDialog: a run dialog where the main panel can be changed.
org.ginsim.service.export.cadp
org.ginsim.service.export.nusmv
org.ginsim.service.export.prism
org.ginsim.service.export.struct
org.ginsim.service.layout
org.ginsim.service.tool.avatar.params
org.ginsim.service.tool.composition
org.ginsim.service.tool.localgraph
org.ginsim.service.tool.modelreduction
org.ginsim.service.tool.reg2dyn
org.ginsim.service.tool.reg2dyn.htg
org.ginsim.service.tool.reg2dyn.limitedsimulation
org.ginsim.servicegui.layout
org.ginsim.servicegui.tool.composition
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.

Uses of GsException in org.ginsim

Methods in org.ginsim that throw GsException

Modifier and Type	Method and Description
RegulatoryGraph	ScriptLauncher.load(org.colomoto.biolqm.LogicalModel model)
Graph<?,?>	ScriptLauncher.load(String filename) Open a graph from a file.
Graph<?,?>	ScriptLauncher.open(String filename) Deprecated. see ScriptLauncher.load(String)

Uses of GsException in org.ginsim.common.utils

Methods in org.ginsim.common.utils that throw GsException

Modifier and Type	Method and Description
static boolean	IOUtils.isFileWritable(String path) Verify if the file at the given path can be opened in write mode

Uses of GsException in org.ginsim.common.xml

Methods in org.ginsim.common.xml that throw GsException

Modifier and Type	Method and Description
void	XMLHelper.startParsing(File file) start parsing a file.
void	XMLHelper.startParsing(File file, boolean b) start parsing a file.
void	XMLHelper.startParsing(InputStream is)
void	XMLHelper.startParsing(InputStream is, boolean validating)

Uses of GsException in org.ginsim.core.annotation

Methods in org.ginsim.core.annotation that throw GsException

Modifier and Type	Method and Description
BiblioList	BiblioManager.doOpen(InputStream is, Graph graph)

Uses of GsException in org.ginsim.core.graph

Methods in org.ginsim.core.graph that throw GsException

Modifier and Type	Method and Description
protected void	AbstractGraph.doSave(OutputStreamWriter osw, Collection<V> nodes, Collection<E> edges) save implementation for a specific graph type.
AG	AbstractDerivedGraph.getAssociatedGraph()
AG	GraphAssociation.getAssociatedGraph() Given access to the graph that has been associated to the current graph
String	AbstractDerivedGraph.getAssociatedGraphID()
String	GraphAssociation.getAssociatedGraphID()
Graph	GSGraphManager.open(File file)
Graph	GSGraphManager.open(Set set, File file)
Graph	GSGraphManager.open(String file_path) Retrieve the Graph stored in the file at the given file path
void	AbstractGraph.save(String save_path)
void	Graph.save(String path) Save this graph.
void	AbstractGraph.save(String save_path, Collection<V> vertices, Collection<E> edges)
void	Graph.save(String path, Collection<V> nodes, Collection<E> edges) Save some components of this graph.
void	GraphModel.setGraphName(String graphName) changes (if success) the name associated with this graph.
void	AbstractGraph.setGraphName(String graph_name) changes (if success) the name associated with this graph.

Uses of GsException in org.ginsim.core.graph.dynamicgraph

Methods in org.ginsim.core.graph.dynamicgraph that throw GsException

Modifier and Type	Method and Description
void	DynamicParser.parse(File file, Set<String> set, Graph graph) create a new dynamical graph from a file.

Constructors in org.ginsim.core.graph.dynamicgraph that throw GsException

Constructor and Description
DynamicParser(Set<String> set, Attributes attributes, String s_dtd)

Uses of GsException in org.ginsim.core.graph.hierarchicaltransitiongraph

Constructors in org.ginsim.core.graph.hierarchicaltransitiongraph that throw GsException

Constructor and Description
HierarchicalTransitionGraphParser(Set<String> nodeToParse, Attributes attributes, String s_dtd)

Uses of GsException in org.ginsim.core.graph.objectassociation

Methods in org.ginsim.core.graph.objectassociation that throw GsException

Modifier and Type	Method and Description
T	GraphAssociatedObjectManager.doOpen(InputStream is, Graph graph) open associated object.
void	BasicGraphAssociatedManager.doSave(OutputStreamWriter os, Graph graph)
void	GraphAssociatedObjectManager.doSave(OutputStreamWriter out, Graph graph) save the object associated with this graph.

Uses of GsException in org.ginsim.core.graph.reducedgraph

Methods in org.ginsim.core.graph.reducedgraph that throw GsException

Modifier and Type	Method and Description
void	ReducedGraphParser.parse(File file, Set<String> set, Graph graph) create a new ReducedGraph from a file.

Constructors in org.ginsim.core.graph.reducedgraph that throw GsException

Constructor and Description
ReducedGraphImpl(Set set, File file)
ReducedGraphParser(Set<String> set, Attributes attributes, String s_dtd)
ReducedGraphParser(Set<String> set, Attributes attributes, String s_dtd, String s_filename)

Uses of GsException in org.ginsim.core.graph.regulatorygraph

Methods in org.ginsim.core.graph.regulatorygraph that throw GsException

Modifier and Type	Method and Description
RegulatoryEdge	RegulatoryGraph.addNewEdge(String from, String to, byte minvalue, RegulatoryEdgeSign sign) add an edge from textual parameters (for the parser).
RegulatoryEdge	RegulatoryGraphImpl.addNewEdge(String from, String to, byte minvalue, RegulatoryEdgeSign sign)
RegulatoryEdge	RegulatoryGraph.addNewEdge(String from, String to, byte minvalue, String sign) add an edge from textual parameters (for the parser).
RegulatoryEdge	RegulatoryGraphImpl.addNewEdge(String from, String to, byte minvalue, String sign)
void	RegulatoryGraph.changeNodeId(Object node, String newId)
void	RegulatoryGraphImpl.changeNodeId(Object node, String newId)
void	RegulatoryParser.parse(File file, Set set, Graph<?,?> graph) create a new regulatory graph from a file.

Constructors in org.ginsim.core.graph.regulatorygraph that throw GsException

Constructor and Description
RegulatoryParser(Set set, Attributes attributes, String s_dtd)

Uses of GsException in org.ginsim.core.graph.regulatorygraph.logicalfunction

Methods in org.ginsim.core.graph.regulatorygraph.logicalfunction that throw GsException

Modifier and Type	Method and Description
Object	BooleanParser.getEdge(String value)
void	BooleanGene.setInteractionName(BooleanParser parser, String value)

Uses of GsException in org.ginsim.core.graph.regulatorygraph.namedstates

Methods in org.ginsim.core.graph.regulatorygraph.namedstates that throw GsException

Modifier and Type	Method and Description
NamedStatesHandler	NamedStatesManager.doOpen(InputStream is, Graph graph)
void	NamedStatesManager.doSave(OutputStreamWriter os, Graph graph)

Uses of GsException in org.ginsim.core.graph.regulatorygraph.perturbation

Methods in org.ginsim.core.graph.regulatorygraph.perturbation that throw GsException

Modifier and Type	Method and Description
ListOfPerturbations	PerturbationManager.doOpen(InputStream is, Graph graph)
void	PerturbationManager.doSave(OutputStreamWriter os, Graph graph)

Uses of GsException in org.ginsim.core.io.parser

Methods in org.ginsim.core.io.parser that throw GsException

Modifier and Type	Method and Description
Graph	GinmlParser.parse(InputStream is, Set map)

Uses of GsException in org.ginsim.gui.shell.actions

Methods in org.ginsim.gui.shell.actions that throw GsException

Modifier and Type	Method and Description
protected abstract void	ImportAction.doImport(String filename) Main import function: will be called after the target file was selected

Uses of GsException in org.ginsim.gui.utils.dialog.stackdialog

Methods in org.ginsim.gui.utils.dialog.stackdialog that throw GsException

Modifier and Type	Method and Description
protected void	LogicalModelActionDialog.run()
protected void	HandledStackDialog.run()
protected abstract void	StackDialog.run()

Uses of GsException in org.ginsim.service.export.cadp

Methods in org.ginsim.service.export.cadp that throw GsException

Modifier and Type	Method and Description
void	CADPExportService.export(CADPExportConfig config, String fileheadname) Exports the necessary files for CADP
void	CADPIntegrationWriter.init()
void	CADPExportService.run(CADPExportConfig config, String fileheadname)

Constructors in org.ginsim.service.export.cadp that throw GsException

Constructor and Description
CADPIntegrationWriter(CADPExportConfig config)
IntegrationProcessWriter(Map.Entry<RegulatoryNode,Integer> inputFromModule, List<Map.Entry<RegulatoryNode,Integer>> listExternal, IntegrationFunction integrationFunction)

Uses of GsException in org.ginsim.service.export.nusmv

Methods in org.ginsim.service.export.nusmv that throw GsException

Modifier and Type	Method and Description
void	NuSMVExportService.export(NuSMVConfig config, File file)
void	NuSMVExportService.run(org.colomoto.biolqm.LogicalModel model, String filename)
void	NuSMVExportService.run(NuSMVConfig config, String filename)
void	NuSMVEncoder.write(NuSMVConfig config, Writer out) Export the graph to a NUSMV model description

Uses of GsException in org.ginsim.service.export.prism

Methods in org.ginsim.service.export.prism that throw GsException

Modifier and Type	Method and Description
void	PRISMExportService.export(PRISMConfig config, File file)
void	PRISMExportService.run(PRISMConfig config, String filename)
void	PRISMEncoder.write(PRISMConfig config, Writer out) Export the graph to a PRISM model description

Uses of GsException in org.ginsim.service.export.struct

Methods in org.ginsim.service.export.struct that throw GsException

Modifier and Type	Method and Description
void	GraphStructureExportService.cytoscapeExport(RegulatoryGraph graph, String filename) Run the Cytoscape export by instantiating and calling a CytoscapeEncoder
void	CytoscapeEncoder.encode(RegulatoryGraph graph, String filename) Encode the RegulatoryGraph graph into a file named filename

Uses of GsException in org.ginsim.service.layout

Methods in org.ginsim.service.layout that throw GsException

Modifier and Type	Method and Description
void	DynamicLayout3D.layout(DynamicGraph graph)
void	DynamicLayoutMultidimention.runLayout()
static void	DynamicLayout3D.runLayout(DynamicGraph graph)
static void	LayoutService.runLayout(int ref, Graph graph)

Constructors in org.ginsim.service.layout that throw GsException

Constructor and Description
DynamicLayoutMultidimention(DynamicGraph graph, byte[] nodeOrder, boolean straightEdges, Color[] colorPalette)

Uses of GsException in org.ginsim.service.tool.avatar.params

Methods in org.ginsim.service.tool.avatar.params that throw GsException

Modifier and Type	Method and Description
AvatarParameterList	AvatarParametersManager.doOpen(InputStream is, Graph graph)
void	AvatarParametersManager.doSave(OutputStreamWriter os, Graph graph)

Uses of GsException in org.ginsim.service.tool.composition

Methods in org.ginsim.service.tool.composition that throw GsException

Modifier and Type	Method and Description
void	IntegrationFunctionMapping.addMapping(RegulatoryNode input, List<RegulatoryNode> properList, IntegrationFunction integrationFunction)

Uses of GsException in org.ginsim.service.tool.localgraph

Methods in org.ginsim.service.tool.localgraph that throw GsException

Modifier and Type	Method and Description
Map<RegulatoryMultiEdge,LocalGraphCategory>	LocalGraphService.run(RegulatoryGraph graph, List<byte[]> selStates)
Map<RegulatoryMultiEdge,LocalGraphCategory>	LocalGraphService.run(RegulatoryGraph graph, List<byte[]> selStates, Perturbation mutant)

Uses of GsException in org.ginsim.service.tool.modelreduction

Methods in org.ginsim.service.tool.modelreduction that throw GsException

Modifier and Type	Method and Description
ListOfReductionConfigs	ReductionConfigManager.doOpen(InputStream is, Graph graph)

Uses of GsException in org.ginsim.service.tool.reg2dyn

Methods in org.ginsim.service.tool.reg2dyn that throw GsException

Modifier and Type	Method and Description
Graph	Simulation.do_simulation()
SimulationParameterList	SimulationParametersManager.doOpen(InputStream is, Graph graph)
void	SimulationParametersManager.doSave(OutputStreamWriter os, Graph graph)

Uses of GsException in org.ginsim.service.tool.reg2dyn.htg

Methods in org.ginsim.service.tool.reg2dyn.htg that throw GsException

Modifier and Type	Method and Description
Graph	HTGSimulation.do_simulation() Run the simulation, handle exception and build the graph.

Uses of GsException in org.ginsim.service.tool.reg2dyn.limitedsimulation

Methods in org.ginsim.service.tool.reg2dyn.limitedsimulation that throw GsException

Modifier and Type	Method and Description
Graph	LimitedSimulation.do_simulation()
Object	StatesToHierarchicalMappingManager.doOpen(InputStream is, Graph graph)
void	StatesToHierarchicalMappingManager.doSave(OutputStreamWriter out, Graph graph)
DynamicGraph	LimitedSimulationService.run(HierarchicalTransitionGraph htg, SimulationConstraint constraint, org.colomoto.biolqm.LogicalModel model, SimulationParameters params) Construct the dynamic graph correponding the contraint on the HTG.

Uses of GsException in org.ginsim.servicegui.layout

Methods in org.ginsim.servicegui.layout that throw GsException

Modifier and Type	Method and Description
protected void	MultidimensionLayoutGUI.run()

Uses of GsException in org.ginsim.servicegui.tool.composition

Methods in org.ginsim.servicegui.tool.composition that throw GsException

Modifier and Type	Method and Description
protected void	CompositionConfigDialog.run()

Uses of GsException in org.ginsim.servicegui.tool.regulatorygraphanimation

Methods in org.ginsim.servicegui.tool.regulatorygraphanimation that throw GsException

Modifier and Type	Method and Description
static void	AReg2GPConfig.doSaveGnuPlotArrowPath(File scriptfile, File datafile, List path, List nodeOrder, boolean[] selected)
static void	AReg2GPConfig.doSaveGnuPlotMultiPath(File scriptfile, File datafile, List path, List nodeOrder, boolean[] selected)
protected void	AReg2GPConfig.export() do the export.