Uses of Class
org.ginsim.core.graph.Edge

Packages that use Edge

Package	Description
org.ginsim.core.graph	Define the main Graph interfaces, and a GraphManager to handle graph types
org.ginsim.core.graph.backend	Implementation of the graph backend.
org.ginsim.core.graph.dynamicgraph	State Transition Graphs, representing dynamical behaviours.
org.ginsim.core.graph.hierarchicaltransitiongraph
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.trapspacetree
org.ginsim.core.graph.tree	The Tree graph is a representation of a logical functions, allowing a graphical representation.
org.ginsim.core.graph.view	Define the layout and appearance of graph elements.
org.ginsim.core.graph.view.style	Styles define visual properties for graph elements.
org.ginsim.core.io.parser	Some tools to build parsers and writers for xml and text formats
org.ginsim.gui.graph	Common GUI for all graphs, and definition of hooks for specialised parts.
org.ginsim.gui.graph.canvas	Custom implementation of the interactive view
org.ginsim.gui.graph.reducedgraph	Specialised GUI for the Reduced Graphs (Graph of the SCC)
org.ginsim.gui.graph.view.style	GUI for the definition of styles associated to graph elements.
org.ginsim.service.export.image
org.ginsim.service.export.struct
org.ginsim.service.tool.graphcomparator
org.ginsim.service.tool.interactionanalysis
org.ginsim.service.tool.scc
org.ginsim.servicegui.tool.pathfinding

Uses of Edge in org.ginsim.core.graph

Classes in org.ginsim.core.graph with type parameters of type Edge

Modifier and Type	Class and Description
class	AbstractDerivedGraph<V,E extends Edge<V>,AG extends Graph<AV,AE>,AV,AE extends Edge<AV>> Base class for graphs which need an associated graph.
class	AbstractDerivedGraph<V,E extends Edge<V>,AG extends Graph<AV,AE>,AV,AE extends Edge<AV>> Base class for graphs which need an associated graph.
class	AbstractGraph<V,E extends Edge<V>> Base class for graphs using a storage backend: it provides generic methods and storage abstraction.
interface	Graph<V,E extends Edge<V>> The main graph object in GINsim.
interface	GraphAssociation<AG extends Graph<AV,AE>,AV,AE extends Edge<AV>> Defines a graph associated with the implementor of this interface.
interface	GraphBackend<V,E extends Edge<V>> Abstract definition of a graph backend to avoid leaking implementation details in the main classes.
interface	GraphModel<V,E extends Edge<V>> Handle the basic structure of a graph.

Uses of Edge in org.ginsim.core.graph.backend

Classes in org.ginsim.core.graph.backend with type parameters of type Edge

Modifier and Type	Class and Description
class	EdgeAttributeReaderImpl<V,E extends Edge<V>> a generic edgeAttributeReader storing data into a dedicated hashmap
class	EdgeViewInfoImpl<V,E extends Edge<V>>
class	GsJGraphtBaseGraph<V,E extends Edge<V>> a "simple" jgrapht implementation using hashmap.
class	JgraphtBackendImpl<V,E extends Edge<V>>
class	NodeAttributeReaderImpl<V,E extends Edge<V>> A generic nodeAttributeReader showing a unified view of default and node-specific styles (from the graph backend).

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

Classes in org.ginsim.core.graph.dynamicgraph with type parameters of type Edge

Modifier and Type	Interface and Description
interface	TransitionGraph<V,E extends Edge<V>>
class	TransitionGraphImpl<V,E extends Edge<V>>

Subclasses of Edge in org.ginsim.core.graph.dynamicgraph

Modifier and Type	Class and Description
class	DynamicEdge Edges in a state transition graph.

Methods in org.ginsim.core.graph.dynamicgraph that return types with arguments of type Edge

Modifier and Type	Method and Description
List<Edge>	DynamicGraph.shortestPath(byte[] source, byte[] target) look for the shortest path between two states.

Method parameters in org.ginsim.core.graph.dynamicgraph with type arguments of type Edge

Modifier and Type	Method and Description
int[]	DynamicNode.getPattern(Graph<DynamicNode,Edge<DynamicNode>> graph)
String	DynamicNode.getPatternString(Graph<DynamicNode,Edge<DynamicNode>> graph)

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

Subclasses of Edge in org.ginsim.core.graph.hierarchicaltransitiongraph

Modifier and Type	Class and Description
class	DecisionOnEdge Store a label that represent the genes that are updated between two states source, and target.

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

Classes in org.ginsim.core.graph.reducedgraph with type parameters of type Edge

Modifier and Type	Interface and Description
interface	ReducedGraph<AG extends Graph<AV,AE>,AV,AE extends Edge<AV>> Graph of the strongly connected components.
class	ReducedGraphFactory<G extends Graph<V,E>,V,E extends Edge<V>> Factory for the SCC graph.
class	ReducedGraphImpl<G extends Graph<V,E>,V,E extends Edge<V>> Implementation of the Reduced Graph.

Methods in org.ginsim.core.graph.reducedgraph that return Edge

Modifier and Type	Method and Description
Edge<NodeReducedData>	ReducedGraphImpl.addEdge(NodeReducedData source, NodeReducedData target) add an edge to this graph.
Edge<NodeReducedData>	ReducedGraph.addEdge(NodeReducedData source, NodeReducedData target) add an edge to this graph.

Methods in org.ginsim.core.graph.reducedgraph with parameters of type Edge

Modifier and Type	Method and Description
void	ReducedGINMLWriter.hook_edgeAttribute(XMLWriter out, Edge<NodeReducedData> edge)

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

Subclasses of Edge in org.ginsim.core.graph.regulatorygraph

Modifier and Type	Class and Description
class	RegulatoryMultiEdge Edges of the regulatory graph: provide a list of interactions.

Uses of Edge in org.ginsim.core.graph.trapspacetree

Subclasses of Edge in org.ginsim.core.graph.trapspacetree

Modifier and Type	Class and Description
class	TrapSpaceInclusion

Uses of Edge in org.ginsim.core.graph.tree

Subclasses of Edge in org.ginsim.core.graph.tree

Modifier and Type	Class and Description
class	TreeEdge

Methods in org.ginsim.core.graph.tree that return Edge

Modifier and Type	Method and Description
Edge<TreeNode>	Tree.addEdge(TreeNode source, TreeNode target, int value) add an edge between source and target

Uses of Edge in org.ginsim.core.graph.view

Classes in org.ginsim.core.graph.view with type parameters of type Edge

Modifier and Type	Interface and Description
interface	EdgeAttributesReader<V,E extends Edge<V>> graphic info on an edge.
interface	EdgeViewInfo<V,E extends Edge<V>> Store basic view information on an edge: intermediate points and optional style.
interface	ViewCopyHelper<G extends Graph<V,E>,V,E extends Edge<V>> Provide a mapping between the elements of two graphs, used to transfer visual properties.

Methods in org.ginsim.core.graph.view with parameters of type Edge

Modifier and Type	Method and Description
void	GraphicalAttributesStore.ensureStoreEdge(Edge edge) Deprecated.
static org.ginsim.core.graph.view.PointList	ViewHelper.getModifiedPoints(NodeAttributesReader nodeReader, EdgeAttributesReader edgeReader, Edge<?> edge, List<Point> modifiedPoints)
static List<Point>	ViewHelper.getMovingPoints(MovingEdgeType type, int movex, int movey, NodeAttributesReader nreader, EdgeAttributesReader ereader, Edge<?> edge) Get the routing points for an edge which is affected by a move preview.
static List<Point>	ViewHelper.getPoints(NodeAttributesReader nodeReader, EdgeAttributesReader edgeReader, Edge<?> edge) Route an edge: add automated intermediate points if needed, compute the points on the nodes bounding boxes.
static void	ViewHelper.trimPoints(Edge edge, List<Point> points, NodeAttributesReader nreader, EdgeAttributesReader ereader) Remove the first and last points if they are inside the source and target bounding box

Uses of Edge in org.ginsim.core.graph.view.style

Classes in org.ginsim.core.graph.view.style with type parameters of type Edge

Modifier and Type	Interface and Description
interface	EdgeStyle<V,E extends Edge<V>> Define the visual parameters of an edge.
class	EdgeStyleImpl<V,E extends Edge<V>> Simple implementation for EdgeStyle.
class	EdgeStyleOverride<V,E extends Edge<V>>
class	StyleManager<V,E extends Edge<V>> Store and handle styles for a Graph.
interface	StyleProvider<V,E extends Edge<V>> Define a style provider: it provides styles for nodes and edges and can be applied to a StyleManager to temporarily override the graph styles.

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

Classes in org.ginsim.core.io.parser with type parameters of type Edge

Modifier and Type	Class and Description
class	GINMLWriter<G extends Graph<V,E>,V,E extends Edge<V>> Base GINMLWriter class: it provides the common parts of a GINML file and hooks for specialised writers to add their graph-specific data.

Methods in org.ginsim.core.io.parser with parameters of type Edge

Modifier and Type	Method and Description
static void	GinmlHelper.applyEdgeVisualSettings(Edge<?> edge, StyleManager styleManager, EdgeAttributesReader ereader, NodeAttributesReader nreader, String qName, Attributes attributes) we are reading edge visual settings from a ginml file, apply them on the current edge.

Uses of Edge in org.ginsim.gui.graph

Classes in org.ginsim.gui.graph with type parameters of type Edge

Modifier and Type	Class and Description
class	AddEdgeAction<V,E extends Edge<V>>
class	BaseGraphGUI<G extends Graph<V,E>,V,E extends Edge<V>> Abstract class providing generic parts of a Graph GUI.
interface	GraphGUI<G extends Graph<V,E>,V,E extends Edge<V>> Deal with the GUI view of a graph: get a component, provide access to selected items and view options.
interface	GraphGUIHelper<G extends Graph<V,E>,V,E extends Edge<V>> GUI-side helper for a graph type.
interface	GraphGUIListener<G extends Graph<V,E>,V,E extends Edge<V>> Interface for objects which listen for Graph GUI events.
class	GraphSelection<V,E extends Edge<V>> Manage the selection for a GraphGUI

Uses of Edge in org.ginsim.gui.graph.canvas

Classes in org.ginsim.gui.graph.canvas with type parameters of type Edge

Modifier and Type	Class and Description
class	CanvasGraphGUIImpl<G extends Graph<V,E>,V,E extends Edge<V>>

Uses of Edge in org.ginsim.gui.graph.reducedgraph

Methods in org.ginsim.gui.graph.reducedgraph that return types with arguments of type Edge

Modifier and Type	Method and Description
GUIEditor<Edge<NodeReducedData>>	ReducedGraphGUIHelper.getEdgeEditionPanel(ReducedGraph graph)

Uses of Edge in org.ginsim.gui.graph.view.style

Methods in org.ginsim.gui.graph.view.style with parameters of type Edge

Modifier and Type	Method and Description
void	EdgeRoutingPanel.setSelected(Edge selected)

Method parameters in org.ginsim.gui.graph.view.style with type arguments of type Edge

Modifier and Type	Method and Description
void	StyleTab.edit(Collection nodes, Collection<Edge> edges)

Uses of Edge in org.ginsim.service.export.image

Methods in org.ginsim.service.export.image with type parameters of type Edge

Modifier and Type	Method and Description
<N,E extends Edge<N>> byte[]	ImageExportService.rawPNG(Graph<N,E> graph)

Method parameters in org.ginsim.service.export.image with type arguments of type Edge

Modifier and Type	Method and Description
void	ImageExportService.exportPNG(Graph<?,Edge<?>> graph, String fileName) Export a model view as PNG image.
void	ImageExportService.exportPNG(Graph<?,Edge<?>> graph, String fileName, int f) Export a model view as PNG image.
void	ImageExportService.exportSVG(Graph graph, Collection nodes, Collection<Edge> edges, String fileName) Export the graph to a SVG file

Constructor parameters in org.ginsim.service.export.image with type arguments of type Edge

Constructor and Description
SVGEncoder(Graph graph, Collection nodes, Collection<Edge> edges, String fileName)

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

Method parameters in org.ginsim.service.export.struct with type arguments of type Edge

Modifier and Type	Method and Description
void	GraphStructureExportService.biolayoutExport(Graph graph, Collection<Edge<?>> edges, String filename) Encode the graph to struct output
void	BiolayoutEncoder.encode(Graph graph, Collection<Edge<?>> edges, String filename) Encode the graph to struct output
void	GraphvizEncoder.encode(Graph graph, Collection<Object> nodes, Collection<Edge<?>> edges, String filename) Encode the graph to graphviz output
void	GraphStructureExportService.graphvizExport(Graph graph, Collection<Object> nodes, Collection<Edge<?>> edges, String filename)

Uses of Edge in org.ginsim.service.tool.graphcomparator

Classes in org.ginsim.service.tool.graphcomparator with type parameters of type Edge

Modifier and Type	Class and Description
class	GraphComparator<V,E extends Edge<V>,G extends Graph<V,E>> Compare two Graphs.
class	GraphComparatorResult<V,E extends Edge<V>,G extends Graph<V,E>> 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

Methods in org.ginsim.service.tool.graphcomparator with parameters of type Edge

Modifier and Type	Method and Description
EdgeStyle	GraphComparatorStyleProvider.getEdgeStyle(Edge edge, EdgeStyle baseStyle)

Uses of Edge in org.ginsim.service.tool.interactionanalysis

Methods in org.ginsim.service.tool.interactionanalysis with parameters of type Edge

Modifier and Type	Method and Description
EdgeStyle	InteractionAnalysisStyleProvider.getEdgeStyle(Edge edge, EdgeStyle baseStyle)

Uses of Edge in org.ginsim.service.tool.scc

Methods in org.ginsim.service.tool.scc with parameters of type Edge

Modifier and Type	Method and Description
EdgeStyle	ConnectivityStyleProvider.getEdgeStyle(Edge edge, EdgeStyle baseStyle)

Uses of Edge in org.ginsim.servicegui.tool.pathfinding

Methods in org.ginsim.servicegui.tool.pathfinding with parameters of type Edge

Modifier and Type	Method and Description
EdgeStyle	PathStyleProvider.getEdgeStyle(Edge edge, EdgeStyle baseStyle)