Uses of Interface
org.graffiti.graph.Graph

Packages that use Graph

Package	Description
de.ipk_gatersleben.ag_nw.graffiti
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance	Provides the HammingDistancePlugin, a plugin for computing the hamming distances between graphs.
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder	Provides the NaivePatternFinderPlugin, a plugin for finding given patterns within a given graph.
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som
de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes
de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.pathway_kegg_operation
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.kegg_reaction
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.url_attribute_context_commands
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.plugin_settings
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.biopax
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.metatool
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.pajek
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sif
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.xwg_wilma
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kegg_xml
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kgml
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.pajek
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.petri_ina_pnt
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.text_list
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fish_eye
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.printer
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter
de.ipk_gatersleben.ag_nw.graffiti.services
org
org.graffiti.editor	Contains classes for the famous graffiti editor.
org.graffiti.editor.actions	Contains the editor's action classes.
org.graffiti.event	Contains event classes and listener interfaces that are used to react to events fired by the graph model.
org.graffiti.graph	Contains graph interfaces and classes.
org.graffiti.managers
org.graffiti.plugin.actions
org.graffiti.plugin.algorithm
org.graffiti.plugin.io	Contains interfaces and classes for reading and writing a graph object in diverse file formats.
org.graffiti.plugin.mode
org.graffiti.plugin.parameter
org.graffiti.plugin.tool
org.graffiti.plugin.view
org.graffiti.plugins.inspectors.defaults
org.graffiti.plugins.ios.exporters.gml
org.graffiti.plugins.ios.exporters.gmlxml
org.graffiti.plugins.ios.exporters.graphml	This package provides a plugin for writing Graphs to files using the graphML format.
org.graffiti.plugins.ios.exporters.graphviz
org.graffiti.plugins.ios.importers
org.graffiti.plugins.ios.importers.gml
org.graffiti.plugins.ios.importers.graphml	This package provides the interface to a plugin for reading Graphs from files using the graphML format.
org.graffiti.plugins.ios.importers.graphml.parser	This package provides the parsing facilities for reading in files in the graphML format.
org.graffiti.plugins.views.defaults
org.graffiti.plugins.views.matrix
org.graffiti.selection	Contains classes for the selection model.
org.graffiti.session	Contains classes, which are needed for the session handling.
org.graffiti.undo
org.vanted.animation
org.vanted.plugins.layout.multilevelframework	A layout algorithm to Vanted that implements the multi-level graph layout framework.
org.vanted.plugins.layout.stressminimization	A layout algorithm to Vanted that implements stress minimization.

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti

Methods in de.ipk_gatersleben.ag_nw.graffiti that return Graph

Modifier and Type	Method	Description
static Graph	GraphHelper.createClusterReferenceGraph(Graph graph, HashMap<String,Integer> clusterNodeIDandNumberOfContainingNodes)
static Graph	GraphHelper.getClusterSubGraph(Graph mainGraph, String validClusterID)

Methods in de.ipk_gatersleben.ag_nw.graffiti that return types with arguments of type Graph

Modifier and Type	Method	Description
static Collection<Graph>	GraphHelper.getConnectedComponentsAsCopy(List<Node> nodes)
static Collection<Graph>	GraphHelper.getConnectedComponentsAsCopy(Graph graph)	builds for all connected components a separate graph and returns them as a collection of graphs

Methods in de.ipk_gatersleben.ag_nw.graffiti with parameters of type Graph

Modifier and Type	Method	Description
static Edge	GraphHelperBio.addEdgeIfNotExistant(Graph graph, Node nodeA, Node nodeB, boolean directed, CollectionAttribute graphicsAttributeForEdge)
static Node	GraphHelperBio.addMapNode(Graph superGraph, KeggPathwayEntry kpe)
static Node	GraphHelper.addNodeToGraph(Graph graph, double posx, double posy, double frameThickness_3, double width_25, double height_25, Color frameColor_0_0_0_255, Color fillColor_0_100_250_100)	Adds a new node to a graph.
static void	GraphHelper.applyUndoableClusterIdAssignment(Graph graph, HashMap<GraphElement,String> ge2newClusterID, String description, boolean enableUndo)
static void	GraphHelper.applyUndoableEdgeReversal(Graph graph, Collection<Edge> edges, String description)
static int	GraphHelper.countOverlapps(Graph g, Vector2d pos, Vector2d size)
static byte[][]	GraphHelper.createAdjacencyMatrix(Graph g, boolean directed)	Creates the adjacency matrix for a given graph.
static Graph	GraphHelper.createClusterReferenceGraph(Graph graph, HashMap<String,Integer> clusterNodeIDandNumberOfContainingNodes)
static void	GraphHelper.displayGraph(Graph g)	displays a graph in the mainframe
static void	GraphHelper.enumerateNodePositions(Graph graphInstance, HashMap<CoordinateAttribute,Vector2d> oldPositions)
static void	GraphHelper.enumerateNodePositions3d(Graph graphInstance, HashMap<CoordinateAttribute,Vector3d> oldPositions)
static Color	NodeTools.getAxisColor(Graph g, Color defaultColor)
static Color	NodeTools.getCategoryBackgroundColorA(Graph g, Color defaultColor)
static Color	NodeTools.getCategoryBackgroundColorB(Graph g, Color defaultColor)
static Color	NodeTools.getCategoryBackgroundColorC(Graph g, Color defaultColor)
static Graph	GraphHelper.getClusterSubGraph(Graph mainGraph, String validClusterID)
static Color	NodeTools.getColorAttributeValue(Graph g, String attName, Color defaultColor)
static Collection<Graph>	GraphHelper.getConnectedComponentsAsCopy(Graph graph)	builds for all connected components a separate graph and returns them as a collection of graphs
static ArrayList<Node>	GraphHelperBio.getEnzymeNodes(Graph g)
static Color	NodeTools.getGridColor(Graph g, Color defaultColor)
static List<NodeHelper>	GraphHelper.getHelperNodes(Graph graph)
static Set<Node>	GraphHelper.getLeafNodes(Graph graph)
static ArrayList<Edge>	GraphHelperBio.getMapLinkEdges(Graph g)
static ArrayList<Node>	GraphHelperBio.getMapLinkNodes(Graph g)
static Collection<Edge>	GraphHelper.getSelectedOrAllEdges(Selection selection, Graph graph)
static Collection<GraphElement>	GraphHelper.getSelectedOrAllGraphElements(Graph graph)
static Collection<GraphElement>	GraphHelper.getSelectedOrAllGraphElements(Selection selection, Graph graph)
static List<Node>	GraphHelper.getSelectedOrAllNodes(Selection selection, Graph graph)	Returns a list of the currently selected nodes.
static void	GraphHelper.introduceNewBends(Graph graph, HashSet<Edge> edges, int percent, String shape, int bends, boolean massCenterFromSelection, String description, boolean enableUndo)	Add new bends to a graph
static void	GraphHelper.introduceNewBends(Graph graph, HashSet<Edge> workEdges, int minPercent, String edgeShape, int i, String description, boolean enableUndo)
static void	GraphHelper.issueCompleteRedrawForGraph(Graph g)
static void	GraphHelper.issueCompleteRedrawForView(View activeView, Graph g)
static void	GraphHelper.moveGraph(Graph graph, double offX, double offY)
static void	GraphHelper.postUndoableChanges(Graph myGraph, HashMap<CoordinateAttribute,Vector2d> coordinates2oldPositions, HashMap<CoordinateAttribute,Vector2d> coordinates2newPositions, String description)
static void	GraphHelper.postUndoableChanges3d(Graph myGraph, HashMap<CoordinateAttribute,Vector3d> coordinates2oldPositions, HashMap<CoordinateAttribute,Vector3d> coordinates2newPositions, String description)
static void	GraphHelper.postUndoableNodeAndEdgeAdditions(Graph graph, HashSet<Node> newNodes, HashSet<Edge> newEdges, String description)
static void	GraphHelper.printNodeLayout(Graph graph)
static void	GraphHelper.removeAllBends(Graph g, boolean enableUndo)	Deprecated.
static void	GraphHelper.removeBends(Graph graph, Collection<Edge> edges, boolean enableUndo)
static void	GraphHelper.setClusterGraphNodeSizeAndPositionFromReferenceGraph(Graph mainGraph, Graph clusterBackgroundGraph, BackgroundTaskStatusProviderSupportingExternalCall statusProvider)
static boolean	KeggSoapAndPathwayService.writeGML(Graph g, String fileName)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms with parameters of type Graph

Constructor	Description
ColorHelper(Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest with parameters of type Graph

Modifier and Type	Method	Description
static List<Node>	GrubbsTestAlgorithm.doGrubbsTest(List<Node> nodes, Graph g, double alpha, boolean removeOutliers)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation that return Graph

Modifier and Type	Method	Description
static Graph	ErdosRenyiGraphGenerator.createGraph(int numberOfNodes, boolean label, double p, boolean directed, boolean selfLoops)
static Graph	WattsStrogatzGraphGenerator.createGraph(int numberOfNodes, boolean label, int initDegree, double p)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance

Fields in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance declared as Graph

Modifier and Type	Field	Description
Graph	WorkTask.graph1

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance with parameters of type Graph

Modifier and Type	Method	Description
static int	HammingCalculator.compareTwoGraphs(Graph graph1, Graph graph2, HashSet<String> nodesGraph1, HashSet<String> nodesGraph2, WorkSettings t)	Computes the hamming distance between two given graphs

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance with parameters of type Graph

Constructor	Description
WorkTask(HashSet<String> nodesIn1, File graph2fn, int i, int j, String message2, int[][] hammingDistances, Graph graph1, WorkSettings ws, ArrayList<WorkTask> runningThreads)

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance with type arguments of type Graph

Constructor	Description
HammingCalculator(Collection<Graph> listOfGraphs, ArrayList<File> listOfGraphFileNames, boolean consNodes, boolean consEdges, boolean consEdgeLabels, int nodesDistance, int edgesDistance, boolean computeOrder, int validGraphIndex, String outputDir)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder that return Graph

Modifier and Type	Method	Description
Graph	UllmannSubraphIsomAdjMatrixState.getPatternGraph()
Graph	UllmannSubraphIsomAdjMatrixState.getTargetGraph()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder with parameters of type Graph

Modifier and Type	Method	Description
static void	PatternAttributeUtils.addAGNWContainer(Graph g)	Adds the top level container attribute "AGNW" to the given graph.
static void	PatternAttributeUtils.addPatternContainer(Graph g)	Adds the pattern container attribute "AGNW.PATTERN" to the given graph.
static void	PatternAttributeUtils.checkAndAddAGNWContainer(Graph g)	Adds the top level container attribute "AGNW" to the given graph, if it is not already there.
static void	PatternAttributeUtils.checkAndAddPatternContainer(Graph g)	Adds the pattern container attribute "AGNW.PATTERN" to the given graph, if it is not already there.
static boolean	PatternAttributeUtils.checkExistenceAGNWContainer(Graph g)	Checks, if the top level container attribute "AGNW" exists at the given graph.
static boolean	PatternAttributeUtils.checkExistencePatternContainer(Graph g)	Checks, if the pattern container attribute "AGNW.PATTERN" exists at the given graph.
static void	NaivePatternFinderAlgorithm.searchPatterns(Graph graph, List<Graph> patterns, Algorithm optLayoutAlgorithm, boolean ignoreEdgeDirection, boolean startWithLargestCircle, boolean allowOverlap, BackgroundTaskStatusProviderSupportingExternalCall status)	Search a number of pattern graphs in the target graph, beginning with the largest pattern (determined by number of nodes)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder with type arguments of type Graph

Modifier and Type	Method	Description
static void	NaivePatternFinderAlgorithm.searchPatterns(Graph graph, List<Graph> patterns, Algorithm optLayoutAlgorithm, boolean ignoreEdgeDirection, boolean startWithLargestCircle, boolean allowOverlap, BackgroundTaskStatusProviderSupportingExternalCall status)	Search a number of pattern graphs in the target graph, beginning with the largest pattern (determined by number of nodes)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder with parameters of type Graph

Constructor	Description
UllmannSubraphIsomAdjMatrixState(Graph patternGraph, Graph targetGraph, boolean ignoreEdgeDirection)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview that return Graph

Modifier and Type	Method	Description
Graph	RatioViewAlgorithm.executeAndReturnGraph(BackgroundTaskStatusProviderSupportingExternalCall status, boolean sortConsiderClusters, boolean showRangeAxisForNode1, boolean calcLog, NodeSortCommand sortCommand, String selSeriesName1, String selSeriesName2, int selTimePoint)
Graph	SubstanceRatioCalculationAlgorithm.executeAndReturnGraph(BackgroundTaskStatusProviderSupportingExternalCall status)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som that return Graph

Modifier and Type	Method	Description
static Graph	SOMguiHelper.createCentroidNodesGraph(Map som, String[] columns)

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som with parameters of type Graph

Modifier and Type	Method	Description
static void	SOMguiHelper.showSOMcentroidsAndClusterAssignmentSettings(Map som, String[] columns, Graph optSrcGraph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes with parameters of type Graph

Modifier and Type	Method	Description
static int	EnzymeService.getNumberOfEnzymeNodes(Graph graph)	Get the number of nodes in this graph which could possible be valid EC numbers.

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath with parameters of type Graph

Modifier and Type	Method	Description
void	TranspathPathway.addElementsToGraph(Graph g, String clusterID, HashMap<String,Node> graphElementId2graphNode)
void	TranspathReaction.addElementsToGraph(Graph g, String clusterID, HashMap<String,Node> graphElementId2graphNode)
static void	TranspathMolecule.connectMoleculeNodes(Graph g, Node moleculeNode1, Node moleculeNode2)
Node	TranspathMolecule.getGraphNode(Graph g, String clusterID, HashMap<String,Node> graphElementId2graphNode)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors with parameters of type Graph

Modifier and Type	Method	Description
static ChartColorAttribute	ChartColorAttribute.getAttribute(Graph graph)
static boolean	ChartColorAttribute.hasAttribute(Graph graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type with parameters of type Graph

Modifier and Type	Method	Description
static void	KeggReactionIdAttributeEditor.editReactions(Reaction r, Pathway p, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, HashMap<Entry,Node> entry2graphNode, Graph graph)
static void	KeggReactionIdAttributeEditor.editReactions(GraphElement ge, String currentReactionId, Graph graph, Selection selection)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.pathway_kegg_operation

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.pathway_kegg_operation with parameters of type Graph

Modifier and Type	Method	Description
static void	PathwayKeggLoading.collapsePathway(Graph graph, String curVal, Node sourceNode)
static Pathway	PathwayKeggLoading.processInternalMapLinks(Graph baseGraph, Pathway optAddPathway, Vector2d optCenterOfAddGraph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute with parameters of type Graph

Modifier and Type	Method	Description
ActionListener	LoadGraphFileAttributeAction.getActionListener(Attribute displayable, Graph graph, GraphElement ge, boolean performAltCommand)
ActionListener	LoadURLattributeAction.getActionListener(Attribute displayable, Graph graph, GraphElement ge, boolean performAltCommand)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe with parameters of type Graph

Modifier and Type	Method	Description
static Node	MergeNodes.mergeNode(Graph graph, Collection<Node> toBeMerged, Vector2d center, boolean retainClusterIDs)
static void	MergeNodes.mergeNodesIntoSingleNode(Graph graph, Collection<Node> workNodes)
static SplitResult	SplitNodeForSingleMappingData.splitNodes(Node graphNode, int mMinimumDegree, Graph graph, boolean mProcessSelfLoops, boolean mRepositionOfNodes)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go with parameters of type Graph

Modifier and Type	Method	Description
static Node	InterpreteGOtermsAlgorithm.processGoHierarchy(PositionGridGenerator pgg, HashMap<String,Node> goTerm2goNode, GoProcessing gp, String goTerm, Graph g)
static Node	InterpreteParentGOtermsAlgorithm.processGoHierarchy(PositionGridGenerator pgg, HashMap<String,Node> goTerm2goNode, GoProcessing gp, String goTerm, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.kegg_reaction

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.kegg_reaction that return Graph

Modifier and Type	Method	Description
static Graph	CreateKeggReactionNetworkAlgorithm.getReactionNetwork()

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools with parameters of type Graph

Modifier and Type	Method	Description
static void	EvaluateKGML.evaluateAndUpdateGraph(Graph graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper that return Graph

Modifier and Type	Method	Description
Graph	NodeHelper.getGraph()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper with parameters of type Graph

Modifier and Type	Method	Description
void	NodeHelper.setGraph(Graph graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.url_attribute_context_commands

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.url_attribute_context_commands with parameters of type Graph

Modifier and Type	Method	Description
JMenuItem[]	URLattributeContextMenuCommandPlugin.getContextCommand(MouseEvent lastMouseE, Component lastMouseSrc, Graph graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view that return Graph

Modifier and Type	Method	Description
Graph	FastView.getGraph()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view with parameters of type Graph

Modifier and Type	Method	Description
void	FastView.setGraph(Graph graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview that return Graph

Modifier and Type	Method	Description
Graph	NullView.getGraph()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview with parameters of type Graph

Modifier and Type	Method	Description
void	ClusterBackgroundDraw.init(Graph graph)
void	IPKGraffitiView.setGraph(Graph g)	This methods sets the graph and adds the background color attribute, since this View supports background coloring
void	NullView.setGraph(Graph graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent

Fields in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent declared as Graph

Modifier and Type	Field	Description
Graph	ChartOptions.graph

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent with parameters of type Graph

Modifier and Type	Method	Description
void	ChartOptions.setFurtherOptions(Graph graph, String chartTitle)
void	ChartOptions.setFurtherOptions(Graph graph, BioStatisticalCategoryDataset dataset, String chartTitle)
static void	XmlDataChartComponent.setSeriesColorsAndStroke(CategoryItemRenderer renderer, float outlineBorderWidth, Graph graph)
void	HeatMapOptions.writeToGraph(Graph g)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent with parameters of type Graph

Constructor	Description
ChartOptions(GraphElement ge, Graph graph, BioStatisticalCategoryDataset dataset, String chartTitle, PlotOrientation orientation, boolean showLegend, String domainAxis, String rangeAxis, boolean showRangeAxis, boolean showCategoryAxis, float outlineBorderWidth, int axisRotation, double lowerBound, double upperBound, boolean showGridRange, boolean showGridCategory, double gridWidth, double axisWidth, Color gridColor, Color axisColor, int axisFontSize, boolean showStdDevAsT, double stdDevTopWidth, boolean showStdDevAsFillRange, float shapeSize, float stdDevLineWidth, boolean showOnlyHalfErrorBar, boolean showShapes, boolean showLines, boolean usePieScaling, boolean connectPriorItems, int plotAxisSteps, boolean useLogYscale, int cpIdxA, int cpIdxC, Color cpColA, Color cpColBackground, Color cpColC, boolean useCustomRangeSteps, double customRangeSteps, boolean removeEmptyConditions)
HeatMapOptions(Graph graph)
XmlDataChartComponent(String preferredChartType, Graph graph, GraphElement ge)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar with parameters of type Graph

Constructor	Description
AllSuperGraphsCreator(Graph graph, String targetFolder, OrganismEntry[] orgs, boolean checkOrthologs, boolean checkEnzymes, boolean checkGlycans, boolean checkCompounds, boolean convertKOsToGenes)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control that return Graph

Modifier and Type	Method	Description
static Graph	TabPatternLayout.getCurrentPatternGraph()	For getting the current Pattern Graph.

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control with parameters of type Graph

Modifier and Type	Method	Description
static void	TabPatternLayout.showPattern(Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes with parameters of type Graph

Modifier and Type	Method	Description
MapResult	Experiment2GraphHelper.mapDataToGraphElements(boolean mapAlsoInCaseOfEmptyDataset, ExperimentInterface md, Collection<GraphElement> targetGraphElements, Graph addNewGraphElementsToThisGraph, boolean doUserMapping, String diagramStyle, int minimumLines, boolean considerEnzymeDb, boolean considerMappingToKEGGmapNodes, boolean selectResult)
MapResult	Experiment2GraphHelper.mapDataToGraphElements(boolean mapAlsoInCaseOfEmptyDataset, ExperimentInterface mappingData, Collection<GraphElement> targetGraphElements, Graph addNewGraphElementsToThisGraph, boolean doUserMapping, String diagramStyle, int minimumLines, int diagramsPerRow, boolean considerEnzymeDb, boolean considerMappingToKEGGmapNodes, boolean selectResult)	Maps the data from the XML document to the list of nodes

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg that return Graph

Modifier and Type	Method	Description
static Graph	KeggService.getKeggPathwayGravistoGraph(KeggPathwayEntry myEntry, boolean showErrorMessages, Color enzymeColors)
static Graph	KeggService.getKeggPathwayGravistoGraph(KeggPathwayEntry myEntry, boolean showErrorMessages, Color enzymeColors, boolean includeMapNodes)

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg with parameters of type Graph

Modifier and Type	Method	Description
static void	KeggService.colorizeEnzymesGlycansCompounds(Graph graph, String mapName, Color enzymeColor, boolean markNotPresent, boolean orthologs, boolean enzymes, boolean glycans, boolean compounds, boolean convertTypeToGeneWhenProcessingOrthologs)
static boolean	KeggService.loadKeggPathwayIntoEditor(KeggPathwayEntry myEntry, Graph loadBlockingIntoThisGraph, Color enzymeColor, boolean separateClusters)	If loadBlockingIntoThisGraph is != null, this method adds the loaded graph to the given graph instance.
static void	KeggService.loadKeggPathwayIntoGraph(InputStream in, Graph g, Color enzymeColor)
static void	KeggService.loadPathway(KeggPathwayEntry myEntry, Graph targetGraph, boolean processLabels)
static void	KeggService.loadPathway(KeggPathwayEntry myEntry, Graph targetGraph, Node initialMapNode, boolean processLabels)
static void	KeggService.loadPathway(KeggPathwayEntry myEntry, Graph targetGraph, Node initialMapNode, boolean askForNewWindow, boolean separateClusters)
static void	KeggService.mergeKeggGraphs(Graph mergeIntoThisGraph, Graph newGraph, Vector2d centerOfNewGraph, boolean linkToExistingMaps, boolean clusterSeparation)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg with parameters of type Graph

Constructor	Description
ReactionLabel(Reaction r, HashMap<Entry,Node> entry2graphNode, Pathway p, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, Graph graph)
RelationLabel(Relation r, HashMap<Entry,Node> entry2graphNode, Pathway pathway, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, Graph graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop with parameters of type Graph

Modifier and Type	Method	Description
void	TabMetaCrop.addAnnotationsToGraphElements(Graph graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics with parameters of type Graph

Modifier and Type	Method	Description
JComponent	TabStatistics.createScatterPlotBlock(boolean plotAverage, boolean tickMarksVisible, boolean showRangeAxis, boolean showLegend, double minimumR, float outlineBorderWidth, boolean mergeDataset, double prob, boolean rankOrder, double currGammaValue, Color colR_1, Color colR0, Color colR1, Collection<GraphElement> gEe, Graph graph, boolean returnResult, Component lastScatterPlot, JComponent placeForScatter)
static List<Node>	TabStatistics.doDavidSchnellTest(List<Node> nodes, Graph g, int probab_123)	Returns all nodes which contain samples which are not normaly distributed.
JComponent	TabStatistics.getScatterPlot(Graph graph)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics with parameters of type Graph

Constructor

Description

MyCorrlationFinder(Collection<Node> nodes, Graph graph, EditorSession session, boolean considerTimeShifts, boolean mergeDataset, boolean colorCodeEdgesWithCorrelationValue, double minimumR, int currGammaValue, Color colR_1, Color colR0, Color colR1, Collection<Edge> correlationEdges, double prob, boolean plotAverage, boolean rankOrder, boolean showStatusResult, boolean dontAddNewEdgesOnlyUpdateExisting)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.plugin_settings

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.plugin_settings with parameters of type Graph

Modifier and Type	Method	Description
void	PreferencesDialog.initAlgorithmPreferencesPanel(JDialog thisDialog, Algorithm alg, Graph graph, Selection sele, HandlesAlgorithmData setAlgorithmDataObject, boolean executeMoveToTopAfterwards)
void	PreferencesDialog.initializeGUIforGivenContainer(Container cp, JDialog thisDialog, boolean vertical, boolean showCloseButton, boolean showAlgorithms, boolean showSettings, boolean showInteractiveAlgorithms, boolean showScripts, boolean showOnlyLayoutAlgorithms, Graph graph, Selection selection, HandlesAlgorithmData setAlgorithmDataObject, boolean executeMoveToTopAfterwards)
void	PreferencesDialog.updateSettingsPanel(JDialog thisDialog, Graph graph, Selection selection, HandlesAlgorithmData setAlgorithmDataObject, boolean executeMoveToTopAfterwards)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate with parameters of type Graph

Modifier and Type	Method	Description
void	RotateAlgorithm.attach(Graph g, Selection selection)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax with parameters of type Graph

Modifier and Type	Method	Description
static void	HelperClass.returnAttributeByPath(Graph elem, Pattern pattern, ArrayList<Attribute> set)	written by Hendrik Mehlhorn it is looking for all attributes that match a specific pattern and putting the result into the set passed into the function

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions that return Graph

Modifier and Type	Method	Description
Graph	LVL3ModelConverter.getGraph()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions with parameters of type Graph

Modifier and Type	Method	Description
void	LVL3ModelConverter.convertLVL3Model(org.biopax.paxtools.model.Model model, Graph g, boolean all)
void	LVL3ModelConverter.readGraph(org.biopax.paxtools.model.Model model, Graph g)	reads all nodes and edges of the graph first all physical entities will be read so pointing in interactions to them is possible afterwards the interactions will be read

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions with parameters of type Graph

Constructor	Description
BPBiochemicalReaction(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPCatalysis(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPComplexAssembly(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPControl(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPConversion(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPDegradation(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPGeneticInteraction(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPInteraction(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPModulation(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPMolecularInteraction(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPTemplateReaction(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPTemplateReactionRegulation(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPTransport(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
BPTransportWithBiochemicalReaction(Graph Graph, Hashtable<org.biopax.paxtools.model.level3.Entity,Node> Nodes)
PathWayHandler(org.biopax.paxtools.model.Model model, Graph graph)	constructor for import

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility with parameters of type Graph

Modifier and Type	Method	Description
static void	UtilityClassSelectorFromGraph.chooseClassToPutAttributesToModell(GraphElement elem, Graph g, org.biopax.paxtools.model.Model model)
static Map<String[],Attribute>	TreeAttributSearcher.getMapPathToAttributable(HashSet<SearchType> validSearchTypes, Graph attr)
static void	UBioChemicalReaction.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)
static void	UCatalysis.readAttributesFromNode(GraphElement edge, Graph g, org.biopax.paxtools.model.Model model)
static void	UComplex.readAttributesFromNode(GraphElement elem, Graph g, org.biopax.paxtools.model.Model model)
static void	UComplexAssembly.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)
static void	UControl.readAttributesFromNode(GraphElement edge, Graph g, org.biopax.paxtools.model.Model model)
static void	UConversion.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)
static void	UDegradation.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)
static void	UDna.readAttributesFromNode(GraphElement elem, Graph g, org.biopax.paxtools.model.Model model)
static void	UDnaRegion.readAttributesFromNode(GraphElement elem, Graph g, org.biopax.paxtools.model.Model model)
static void	UGene.readAttributesFromNode(GraphElement elem, Graph g, org.biopax.paxtools.model.Model model)
static void	UGeneticInteraction.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)
static void	UModulation.readAttributesFromNode(GraphElement edge, Graph g, org.biopax.paxtools.model.Model model)
static void	UMolecularInteraction.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)
static void	UPathway.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)
static void	UPhysicalEntity.readAttributesFromNode(GraphElement elem, Graph g, org.biopax.paxtools.model.Model model)
static void	UProtein.readAttributesFromNode(GraphElement elem, Graph g, org.biopax.paxtools.model.Model model)
static void	URna.readAttributesFromNode(GraphElement elem, Graph g, org.biopax.paxtools.model.Model model)
static void	URnaRegion.readAttributesFromNode(GraphElement elem, Graph g, org.biopax.paxtools.model.Model model)
static void	USmallMolecule.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)
static void	UTemplateReaction.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)
static void	UTemplateReactionRegulation.readAttributesFromNode(GraphElement edge, Graph g, org.biopax.paxtools.model.Model model)
static void	UTransport.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)
static void	UTransportWithBiochemicalReaction.readAttributesFromNode(GraphElement node, Graph g, org.biopax.paxtools.model.Model model)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.biopax

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.biopax with parameters of type Graph

Modifier and Type	Method	Description
boolean	BioPAX_OWL_Writer.validFor(Graph g)
void	BioPAX_OWL_Writer.write(OutputStream stream, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.metatool

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.metatool with parameters of type Graph

Modifier and Type	Method	Description
void	MetaToolReader.read(InputStream in, Graph g)
void	MetaToolReader.read(Reader reader, Graph newGraph)
boolean	MetatoolWriter.validFor(Graph g)
void	MetatoolWriter.write(OutputStream stream, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.pajek

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.pajek with parameters of type Graph

Modifier and Type	Method	Description
boolean	PajekWriter.validFor(Graph g)
boolean	PovrayWriter.validFor(Graph g)
void	PajekWriter.write(OutputStream out, Graph g)
void	PovrayWriter.write(OutputStream out, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml with parameters of type Graph

Modifier and Type	Method	Description
void	SBML_Compartment_Writer.addCompartment(org.sbml.jsbml.Model model, Graph g, String internHeadline, SBMLCompartmentHelper compartmentHelperObject)	Adds a compartment and its attributes to the model.
void	SBML_Constraint_Writer.addConstraint(Graph g, org.sbml.jsbml.Model model, String internHeadline, SBMLConstraintHelper constraintHelperObject)	Adds a constraint and its variables to the model
void	SBML_Event_Writer.addEvent(Graph g, org.sbml.jsbml.Model model, String internHeadline)	Adds an event to the model
void	SBML_FunctionDefinition_Writer.addFunctionDefinition(org.sbml.jsbml.Model model, Graph g, String internHeadline, SBMLFunctionDefinitionHelper functionDefinitionHelperObject)	Adds a function definition and its variables to the model
void	SBML_InitialAssignment_Writer.addInitialAssignment(Graph g, org.sbml.jsbml.Model model, String internHeadline, SBMLInitialAssignmentHelper iaHelperObject)	Adds an initial assignment and its variables to the model
void	SBML_Model_Writer.addModel(org.sbml.jsbml.Model model, Graph g)	Add attributes to the model.
void	SBML_Parameter_Writer.addParameter(Graph g, org.sbml.jsbml.Model model, String interHeadline, SBMLParameterHelper parameterHelperObject)	Adds a parameter and its variables to the model
void	SBML_Reaction_Writer.addReactions(Graph g, org.sbml.jsbml.Model model)	This method adds the reactions to a model
void	SBML_Rule_Writer.addRules(Graph g, org.sbml.jsbml.Model model)	Controls the processing of rules
void	SBML_SBase_Writer.addSBaseAttributes(org.sbml.jsbml.AbstractSBase sbase, Graph g)
void	SBML_SBase_Writer.addSBaseAttributes(org.sbml.jsbml.AbstractSBase sbase, Graph g, String niceID)	This Method helps processing the attributes with a variable headline inherited by SBase
void	SBML_SBML_Writer.addSBML(OutputStream stream, Graph g)	Processes the reading in an model
void	SBML_Species_Writer.addSpecies(org.sbml.jsbml.Model model, Graph g)	Adds a species and its variables to the model
void	SBML_Species_Writer.addSpeciesGlyph(org.sbml.jsbml.Model model, Graph g)
void	SBML_UnitDefinition_Writer.addUnitDefinition(org.sbml.jsbml.Model model, Graph g, String niceID)	Adds an unit definition and its variables to the model
Object	SBML_SBase_Writer.getAttribute(Graph g, String headline, String attributeName)	Shortens the statement for getting the value of an attribute
ArrayList<String>	SBML_SBase_Writer.headlineHelper(Graph g, String pattern)	Method returns all headlines in the graph tab which begin with a certain pattern
boolean	SBML_XML_Writer.validFor(Graph g)
void	SBML_XML_Writer.write(OutputStream stream, Graph g)	starts the reading in of the model
void	SBML_XML_Writer.write(Writer writer, Graph g)	Implemented method of interface InputSerializer.java

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sif

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sif with parameters of type Graph

Modifier and Type	Method	Description
boolean	SIFWriter.validFor(Graph g)
void	SIFWriter.write(OutputStream out, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.xwg_wilma

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.xwg_wilma with parameters of type Graph

Modifier and Type	Method	Description
boolean	XWGSerializer.validFor(Graph g)
void	XWGSerializer.write(OutputStream out, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax with parameters of type Graph

Modifier and Type	Method	Description
void	BioPAX_OWL_Reader.read(InputStream in, Graph g)	main read method
void	BioPAX_OWL_Reader.read(Reader reader, Graph newGraph)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax with parameters of type Graph

Constructor	Description
PathWayLoaderLvL2(org.biopax.paxtools.model.Model model, Graph g)
PathWayLoaderLvL3(org.biopax.paxtools.model.Model model, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions that return Graph

Modifier and Type	Method	Description
Graph	LVL2ModelConverter.getGraph()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions with parameters of type Graph

Modifier and Type	Method	Description
void	LVL2ModelConverter.convertLVL2Model(org.biopax.paxtools.model.Model model, Graph g, boolean all)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions with parameters of type Graph

Constructor	Description
BPbiochemicalReaction(Graph Graph, Hashtable<String,Node> Nodes)
BPcatalysis(Graph Graph, Hashtable<String,Node> Nodes)
BPcomplexAssembly(Graph Graph, Hashtable<String,Node> Nodes)
BPcontrol(Graph Graph, Hashtable<String,Node> Nodes)
BPconversion(Graph Graph, Hashtable<String,Node> Nodes)
BPinteraction(Graph Graph, Hashtable<String,Node> Nodes)
BPmodulation(Graph Graph, Hashtable<String,Node> Nodes)
BPphysicalInteraction(Graph Graph, Hashtable<String,Node> Nodes)
BPtransport(Graph Graph, Hashtable<String,Node> Nodes)
BPtransportWithBiochemicalReaction(Graph Graph, Hashtable<String,Node> Nodes)
PathWayHandler(org.biopax.paxtools.model.Model model, Graph graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kegg_xml

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kegg_xml with parameters of type Graph

Modifier and Type	Method	Description
void	KEGG_XML_Reader.read(InputStream in, Graph g)
void	KEGG_XML_Reader.read(Reader reader, Graph g)
void	KEGG_XML_Reader.read(String filename, Graph g)
void	KEGG2_XML_Reader.read(InputStream in, Graph g)
void	KEGG2_XML_Reader.read(Reader reader, Graph g)
void	KEGG2_XML_Reader.read(String filename, Graph g)
boolean	KEGG2_XML_Writer.validFor(Graph g)
void	KEGG2_XML_Writer.write(OutputStream stream, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kgml

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kgml with parameters of type Graph

Modifier and Type	Method	Description
void	KEGG_XML_Reader_g.read(InputStream in, Graph g)
void	KEGG_XML_Reader_g.read(Reader in, Graph g)
void	KEGG_XML_Reader_g.read(String filename, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.pajek

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.pajek with parameters of type Graph

Modifier and Type	Method	Description
void	PajekReader.read(InputStream in, Graph g)
void	PajekReader.read(Reader reader, Graph g)
void	PajekReader.read(String filename, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.petri_ina_pnt

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.petri_ina_pnt with parameters of type Graph

Modifier and Type	Method	Description
void	PNTReader.read(InputStream in, Graph g)
void	PNTReader.read(Reader in, Graph g)
boolean	PNTSerializer.validFor(Graph g)
void	PNTSerializer.write(OutputStream out, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml with parameters of type Graph

Modifier and Type	Method	Description
void	SBML_Compartment_Reader.addCompartment(org.sbml.jsbml.ListOf<org.sbml.jsbml.Compartment> compartmentList, Graph g)	Method reads in compartments and is called from class SBML_XML_Reader.java
void	SBML_Constraint_Reader.addConstraint(org.sbml.jsbml.ListOf<org.sbml.jsbml.Constraint> listOfConstraints, Graph g)	Method reads in constraints and is called from class SBML_XML_Reader.java
void	SBML_Event_Reader.addEvents(List<org.sbml.jsbml.Event> eventList, Graph g)	Adds an events to the graph tab
void	SBML_FunctionDefinition_Reader.addFunktionDefinition(org.sbml.jsbml.ListOf<org.sbml.jsbml.FunctionDefinition> functionDefinitionList, Graph g)	Method reads in function definitions and is called from class SBML_XML_Reader.java
void	SBML_InitialAssignment_Reader.addInitialAssignments(org.sbml.jsbml.ListOf<org.sbml.jsbml.InitialAssignment> initialAssignmentList, Graph g)	Method reads in initial assignments and is called from class SBML_XML_Reader.java
void	SBML_SBase_Reader.addNamespaces(Map<String,String> namespaces, Graph g, String path, String attribute)	Adds a map of namespaces (namespace, URL) to the graph tab.
static void	SBML_SBase_Reader.addNamespaces(org.sbml.jsbml.xml.XMLNode node, Graph g, String path, String attribute)	Adds the namespaces of an XMLNode to the graph tab
void	SBML_SBase_Reader.addNotes(org.sbml.jsbml.xml.XMLNode notesObject, String notesString, Graph g, String path, String notesName)	This method adds notes to the current object in the graph tab
void	SBML_Parameter_Reader.addParameter(org.sbml.jsbml.ListOf<org.sbml.jsbml.Parameter> parameterList, Graph g)	Method reads in parameter and is called from class SBML_XML_Reader.java
void	SBML_Reaction_Reader.addReactions(Graph g, org.sbml.jsbml.ListOf<org.sbml.jsbml.Reaction> reactionList, String modelID, PositionGridGenerator pgg, SBMLReactionHelper reactionhelper)	Method reads in function definitions and is called from class SBML_XML_Reader.java.
void	SBML_Rule_Reader.addRule(org.sbml.jsbml.ListOf<org.sbml.jsbml.Rule> listOfRules, Graph g)	Method reads in rules and is called from class SBML_XML_Reader.java
void	SBML_SBML_Reader.addSBML(org.sbml.jsbml.SBMLDocument document, Graph g)	Method reads in the model tag information and is called from class SBML_XML_Reader.java
void	SBML_Species_Reader.addSpecies(Graph g, org.sbml.jsbml.ListOf<org.sbml.jsbml.Species> speciesList, PositionGridGenerator pgg, SBMLSpeciesHelper specieshelper)	reads in species and is called from class SBML_XML_Reader.java.
void	SBML_UnitDefinition_Reader.addUnitDefinitions(org.sbml.jsbml.ListOf<org.sbml.jsbml.UnitDefinition> unitDefinitionList, Graph g)	Method reads in unit definitions and is called from class SBML_XML_Reader.java
void	SBML_Model_Reader.controlImport(org.sbml.jsbml.SBMLDocument document, Graph g, BackgroundTaskStatusProviderSupportingExternalCallImpl status)	Passes the import on to other classes
void	SBML_XML_Reader.read(InputStream in, Graph g)
void	SBML_XML_Reader.read(Reader reader, Graph g)
void	SBML_XML_Reader.read(org.sbml.jsbml.SBMLDocument document, Graph g, BackgroundTaskStatusProviderSupportingExternalCallImpl status)	Method controls the import of the SBML document.

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.text_list

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.text_list with parameters of type Graph

Modifier and Type	Method	Description
void	SIFreader.read(InputStream in, Graph g)
void	SIFreader.read(Reader reader, Graph g)
void	SIFreader.read(String filename, Graph g)
void	TextListReader.read(InputStream in, Graph g)
void	TextListReader.read(Reader reader, Graph g)
void	TextListReader.read(String filename, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml that return Graph

Modifier and Type	Method	Description
Graph	XGMMLHandler.getGraph()
Graph	XGMMLReader.read(InputStream in_Stream)	Reads a graph from the given input stream.

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml with parameters of type Graph

Modifier and Type	Method	Description
void	XGMMLReader.read(InputStream in_Stream, Graph out_Graph)	Reads a graph from the given input stream.
void	XGMMLReader.read(Reader in, Graph out_Graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml that return Graph

Modifier and Type	Method	Description
Graph	Pathway.getGraph()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml with parameters of type Graph

Modifier and Type	Method	Description
Node	Entry.addGraphNode(Graph graph)
void	Pathway.getGraph(Graph graph)
static String	KeggGmlHelper.getKeggId(Graph graph)
static String	KeggGmlHelper.getKeggImageUrl(Graph graph)
static String	KeggGmlHelper.getKeggLinkUrl(Graph graph)
static String	KeggGmlHelper.getKeggMapNumber(Graph graph)
static String	KeggGmlHelper.getKeggOrg(Graph graph)
static String	KeggGmlHelper.getKeggTitle(Graph graph)
static Pathway	Pathway.getPathwayFromGraph(Graph graph, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, HashMap<Entry,Node> entry2graphNode)
static Collection<Relation>	Relation.getRelationElementsFromGraph(Collection<Entry> entries, Graph graph, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors)
static void	KeggGmlHelper.setKeggId(Graph graph, String id)
static void	KeggGmlHelper.setKeggImageUrl(Graph graph, String imageURL)
static void	KeggGmlHelper.setKeggLinkUrl(Graph graph, String linkURL)
static void	KeggGmlHelper.setKeggMapNumber(Graph graph, String number)
static void	KeggGmlHelper.setKeggOrg(Graph graph, String org)
static void	KeggGmlHelper.setKeggTitle(Graph graph, String title)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml with parameters of type Graph

Modifier and Type	Method	Description
static void	SBMLHelper.addAlgebraicRule(Graph g, String function)
SBMLAlgebraicRule	SBMLRuleHelper.addAlgebraicRule(Graph g, String internHeadline)
SBMLAlgebraicRule	SBMLRuleHelper.addAlgebraicRule(Graph g, String internHeadline, String presentedHeadline)
List<SBMLAlgebraicRule>	SBMLRuleHelper.addAlgebraicRules(Graph g, List<String> internHeadlines)
SBMLAssignmentRule	SBMLRuleHelper.addAssignmentRule(Graph g, String internHeadline)
SBMLAssignmentRule	SBMLRuleHelper.addAssignmentRule(Graph g, String internHeadline, String presentedHeadline)
static void	SBMLHelper.addAssignmentRuleFunction(Graph g, String variable, String function)
List<SBMLAssignmentRule>	SBMLRuleHelper.addAssignmentRules(Graph g, List<String> internHeadlines)
static void	SBMLHelper.addAssignmentRuleVariable(Graph g, String variable)
SBMLCompartment	SBMLCompartmentHelper.addCompartment(Graph g, String internHeadline)
SBMLCompartment	SBMLCompartmentHelper.addCompartment(Graph g, String internHeadline, String presentedHeadline)
static void	SBMLHelper.addCompartmentConstant(Graph g, String id, boolean constant)
static void	SBMLHelper.addCompartmentName(Graph g, String id, String name)
List<SBMLCompartment>	SBMLCompartmentHelper.addCompartments(Graph g, List<String> internHeadlines)
static void	SBMLHelper.addCompartmentSize(Graph g, String id, Double value)
static void	SBMLHelper.addCompartmentSpatialDimensions(Graph g, String id, Double value)
static void	SBMLHelper.addCompartmentUnits(Graph g, String id, String units)
SBMLConstraint	SBMLConstraintHelper.addConstraint(Graph g, String internHeadline)
SBMLConstraint	SBMLConstraintHelper.addConstraint(Graph g, String internHeadline, String presentedHeadline)
static void	SBMLHelper.addConstraintConstraint(Graph g, String formula)
static void	SBMLHelper.addConstraintMessage(Graph g, String formula, String message)
List<SBMLConstraint>	SBMLConstraintHelper.addConstraints(Graph g, List<String> internHeadlines)
static void	SBMLHelper.addDelayToEvent(Graph g, String id, String function)
static void	SBMLHelper.addDelayToEvent(Graph g, String id, org.sbml.jsbml.Delay delay)
SBMLEventAssignmentHelper	SBMLEventHelper.addEventAssignment(Graph g, String internHeadline, int eaCount)
SBMLEventAssignmentHelper	SBMLEventHelper.addEventAssignment(Graph g, String internHeadline, String presentedHeadline, int eventAssignmentCount)
static void	SBMLHelper.addEventAssignmentToEvent(Graph g, String id, String variable, String function)
static void	SBMLHelper.addEventAssignmentToEvent(Graph g, String id, org.sbml.jsbml.EventAssignment eventAssignment)
static void	SBMLHelper.addEventName(Graph g, String id, String name)
static void	SBMLHelper.addEventUseValuesFromTriggerTime(Graph g, String id, boolean useValuesFromTriggerTime)
SBMLFunctionDefinition	SBMLFunctionDefinitionHelper.addFunctionDefinition(Graph g, String internHeadline)
SBMLFunctionDefinition	SBMLFunctionDefinitionHelper.addFunctionDefinition(Graph g, String internHeadline, String presentedHeadline)
static void	SBMLHelper.addFunctionDefinitionFunction(Graph g, String id, String function)
static void	SBMLHelper.addFunctionDefinitionName(Graph g, String id, String name)
List<SBMLFunctionDefinition>	SBMLFunctionDefinitionHelper.addFunctionDefinitions(Graph g, List<String> internHeadlines)
SBMLInitialAssignment	SBMLInitialAssignmentHelper.addInitialAssignment(Graph g, String internHeadline)
SBMLInitialAssignment	SBMLInitialAssignmentHelper.addInitialAssignment(Graph g, String internHeadline, String presentedHeadline)
static void	SBMLHelper.addInitialAssignmentFunction(Graph g, String symbol, String function)
List<SBMLInitialAssignment>	SBMLInitialAssignmentHelper.addInitialAssignments(Graph g, List<String> internHeadlines)
SBMLLocalParameter	KineticLawHelper.addLocalParameter(Graph g, int localParameterCount)
SBMLLocalParameter	KineticLawHelper.addLocalParemeter(Graph g, String presentedAttributeName, String internAttributeName)
SBMLParameter	SBMLParameterHelper.addParameter(Graph g, String internHeadline)
SBMLParameter	SBMLParameterHelper.addParameter(Graph g, String internHeadline, String presentedHeadline)
static void	SBMLHelper.addParameterConstant(Graph g, String id, boolean constant)
static void	SBMLHelper.addParameterName(Graph g, String id, String name)
List<SBMLParameter>	SBMLParameterHelper.addParameters(Graph g, List<String> internHeadlines)
static void	SBMLHelper.addParameterUnits(Graph g, String id, String units)
static void	SBMLHelper.addParameterValue(Graph g, String id, Double value)
static void	SBMLHelper.addPriorityToEvent(Graph g, String id, String function)
static void	SBMLHelper.addPriorityToEvent(Graph g, String id, org.sbml.jsbml.Priority priority)
SBMLRateRule	SBMLRuleHelper.addRateRule(Graph g, String internHeadline)
SBMLRateRule	SBMLRuleHelper.addRateRule(Graph g, String internHeadline, String presentedHeadline)
static void	SBMLHelper.addRateRuleFunction(Graph g, String variable, String function)
List<SBMLRateRule>	SBMLRuleHelper.addRateRules(Graph g, List<String> internHeadlines)
static void	SBMLHelper.addRateRuleVariable(Graph g, String variable)
static void	SBMLHelper.addTriggerFunction(Graph g, String eventID, String function)
static void	SBMLHelper.addTriggerInitialValue(Graph g, String eventID, boolean initialValue)
static void	SBMLHelper.addTriggerPersistent(Graph g, String eventID, boolean persistent)
static void	SBMLHelper.addTriggerToEvent(Graph g, String id, boolean initialValue, boolean persistent, String formula)
static void	SBMLHelper.addTriggerToEvent(Graph g, String id, org.sbml.jsbml.Trigger trigger)
SBMLUnitDefinition	SBMLUnitDefinitionHelper.addUnitDefinition(Graph g, String internHeadline)
SBMLUnitDefinition	SBMLUnitDefinitionHelper.addUnitDefinition(Graph g, String internHeadline, String presentedHeadline)
static void	SBMLHelper.addUnitDefinitionID(Graph g, String oldID, String newID)
static void	SBMLHelper.addUnitDefinitionName(Graph g, String id, String name)
List<SBMLUnitDefinition>	SBMLUnitDefinitionHelper.addUnitDefinitions(Graph g, List<String> internHeadlines)
static void	SBMLHelper.addUnitToUnitDefinition(Graph g, String id, org.sbml.jsbml.Unit unit)
static void	SBMLHelper.addUnitToUnitDefinition(Graph g, String id, org.sbml.jsbml.Unit.Kind kind, double exponent, double multiplier, int scale)
static int	SBMLHelper.countFunctionDefinitions(Graph g)	Returns the number of function definitions in the graph
static org.sbml.jsbml.AlgebraicRule	SBMLHelper.createAlgebraicRule(Graph g, String formula)
static void	SBMLHelper.createAlgebraicRule(Graph g, org.sbml.jsbml.AlgebraicRule ar)
static org.sbml.jsbml.AssignmentRule	SBMLHelper.createAssignmentRule(Graph g, String variable)
static org.sbml.jsbml.AssignmentRule	SBMLHelper.createAssignmentRule(Graph g, String variable, String formula)
static void	SBMLHelper.createAssignmentRule(Graph g, org.sbml.jsbml.AssignmentRule ar)
static org.sbml.jsbml.Compartment	SBMLHelper.createCompartment(Graph g, String id)	Creates an compartment in the graph tab with an specific id
static void	SBMLHelper.createCompartment(Graph g, org.sbml.jsbml.Compartment compartment)
static org.sbml.jsbml.Constraint	SBMLHelper.createConstraint(Graph g, String math)
static void	SBMLHelper.createConstraint(Graph g, org.sbml.jsbml.Constraint constraint)
static org.sbml.jsbml.Event	SBMLHelper.createEvent(Graph g, String id)
static void	SBMLHelper.createEvent(Graph g, org.sbml.jsbml.Event event)
static org.sbml.jsbml.FunctionDefinition	SBMLHelper.createFunctionDefinition(Graph g, String id)
static void	SBMLHelper.createFunctionDefinition(Graph g, org.sbml.jsbml.FunctionDefinition fd)
static org.sbml.jsbml.InitialAssignment	SBMLHelper.createInitialAssignment(Graph g, String symbol)
static void	SBMLHelper.createInitialAssignment(Graph g, org.sbml.jsbml.InitialAssignment ia)
static org.sbml.jsbml.Parameter	SBMLHelper.createParameter(Graph g, String id)
static void	SBMLHelper.createParameter(Graph g, org.sbml.jsbml.Parameter parameter)
static org.sbml.jsbml.RateRule	SBMLHelper.createRateRule(Graph g, String variable)
static org.sbml.jsbml.RateRule	SBMLHelper.createRateRule(Graph g, String variable, String formula)
static void	SBMLHelper.createRateRule(Graph g, org.sbml.jsbml.RateRule rr)
static Node	SBMLHelper.createReaction(Graph g, String id, String name)
static Node	SBMLHelper.createReaction(Graph g, org.sbml.jsbml.Reaction reaction)
static Node	SBMLHelper.createSpecies(Graph g, String id, String name)	Creates a new species node and sets its id
static Node	SBMLHelper.createSpecies(Graph g, org.sbml.jsbml.Species species)
static org.sbml.jsbml.UnitDefinition	SBMLHelper.createUnitDefinition(Graph g, String id)
static void	SBMLHelper.createUnitDefinition(Graph g, org.sbml.jsbml.UnitDefinition ud)
static void	SBMLHelper.deleteAlgebraicRule(Graph g, String formula)
static void	SBMLHelper.deleteAlgebraicRuleFunction(Graph g, String function)
static void	SBMLHelper.deleteAssignmentRule(Graph g, String variable)
static void	SBMLHelper.deleteAssignmentRuleFunction(Graph g, String variable)
static void	SBMLHelper.deleteAssignmentRuleVariable(Graph g, String variable)
static void	SBMLHelper.deleteCompartment(Graph g, String id)
static void	SBMLHelper.deleteCompartmentConstant(Graph g, String id)
static void	SBMLHelper.deleteCompartmentID(Graph g, String id)
static void	SBMLHelper.deleteCompartmentName(Graph g, String id)
static void	SBMLHelper.deleteCompartmentSize(Graph g, String id)
static void	SBMLHelper.deleteCompartmentSpatialDimensions(Graph g, String id)
static void	SBMLHelper.deleteCompartmentUnits(Graph g, String id)
static void	SBMLHelper.deleteConstraint(Graph g, String formula)
static void	SBMLHelper.deleteConstraintMessage(Graph g, String constraint)
static void	SBMLHelper.deleteDelayFunction(Graph g, String id)
static void	SBMLHelper.deleteEvent(Graph g, String id)
static void	SBMLHelper.deleteEventAssignment(Graph g, String id, String variable)
static void	SBMLHelper.deleteEventID(Graph g, String id)
static void	SBMLHelper.deleteEventName(Graph g, String id)
static void	SBMLHelper.deleteEventUseValuesFromTriggerTime(Graph g, String id)
static void	SBMLHelper.deleteFunctionDefinition(Graph g, String id)
static void	SBMLHelper.deleteFunctionDefinitionFunction(Graph g, String id)
static void	SBMLHelper.deleteFunctionDefinitionID(Graph g, String id)
static void	SBMLHelper.deleteFunctionDefinitionName(Graph g, String id)
static void	SBMLHelper.deleteInitialAssignment(Graph g, String symbol)
static void	SBMLHelper.deleteInitialAssignmentFunction(Graph g, String symbol)
static void	SBMLHelper.deleteInitialAssignmentSymbol(Graph g, String symbol)
static void	SBMLHelper.deleteParameter(Graph g, String id)
static void	SBMLHelper.deleteParameterConstant(Graph g, String id)
static void	SBMLHelper.deleteParameterID(Graph g, String id)
static void	SBMLHelper.deleteParameterName(Graph g, String id)
static void	SBMLHelper.deleteParameterUnits(Graph g, String id)
static void	SBMLHelper.deleteParameterValue(Graph g, String id)
static void	SBMLHelper.deletePriority(Graph g, String id)
static void	SBMLHelper.deletePriorityFunction(Graph g, String id)
static void	SBMLHelper.deleteRateRule(Graph g, String variable)
static void	SBMLHelper.deleteRateRuleFunction(Graph g, String variable)
static void	SBMLHelper.deleteRateRuleVariable(Graph g, String variable)
static void	SBMLHelper.deleteTriggeInitialValue(Graph g, String id)
static void	SBMLHelper.deleteTrigger(Graph g, String id)
static void	SBMLHelper.deleteTriggerFunction(Graph g, String id)
static void	SBMLHelper.deleteTriggerPersistent(Graph g, String id)
static void	SBMLHelper.deleteUnitDefinitionID(Graph g, String id)
static void	SBMLHelper.deleteUnitDefinitionName(Graph g, String id)
List<String>	SBMLRuleHelper.getAlgebraicRuleHeadlines(Graph g)
static List<org.sbml.jsbml.AssignmentRule>	SBMLHelper.getAllAssignmentRules(Graph g)	Returns a list of assignment rules with distinct headlines
static List<org.sbml.jsbml.Compartment>	SBMLHelper.getAllCompartments(Graph g)	Returns a list of compartments with distinct headlines
static List<org.sbml.jsbml.Constraint>	SBMLHelper.getAllConstraints(Graph g)	Returns a list of constraint with distinct headlines
static List<org.sbml.jsbml.Event>	SBMLHelper.getAllEvent(Graph g)	Returns a list of event with distinct headlines
static List<org.sbml.jsbml.FunctionDefinition>	SBMLHelper.getAllFunctionDefinitions(Graph g)	Returns a list of filled JSBML FunctionDefinition objects
static List<org.sbml.jsbml.InitialAssignment>	SBMLHelper.getAllInitialAssignment(Graph g)	Returns a list of initial assignment with distinct headlines
static List<org.sbml.jsbml.Parameter>	SBMLHelper.getAllParameters(Graph g)	Returns a list of parameter with distinct headlines
static List<org.sbml.jsbml.UnitDefinition>	SBMLHelper.getAllUnitDefinitions(Graph g)	Returns a filled list of UnitDefinition objects
static ArrayList<String>	SBMLHelper.getAssignmentRuleHeadlines(Graph g)	Returns a list of all assignment rule headlines in the graph
List<String>	SBMLRuleHelper.getAssignmentRuleHeadlines(Graph g)
List<String>	SBMLCompartmentHelper.getCompartmentHeadlines(Graph g)
List<String>	SBMLConstraintHelper.getConstraintHeadlines(Graph g)
List<String>	SBMLFunctionDefinitionHelper.getFunctionDefinitionHeadlines(Graph g)
List<String>	SBMLInitialAssignmentHelper.getInitialAssignmentHeadlines(Graph g)
List<String>	SBMLParameterHelper.getParameterHeadlines(Graph g)
List<String>	SBMLRuleHelper.getRateRuleHeadlines(Graph g)
static Node	SBMLHelper.getReactionNode(Graph g, String id)	Returns the reaction node with a distinct id
static List<Node>	SBMLHelper.getReactionNodes(Graph g)	Returns all reaction nodes of the graph
static Node	SBMLHelper.getSpeciesNode(Graph g, String id)	Returns the species node with a distinct id
static List<Node>	SBMLHelper.getSpeciesNodes(Graph g)	Returns all species nodes of the graph
List<String>	SBMLUnitDefinitionHelper.getUnitDefinitionHeadlines(Graph g)
static boolean	SBMLHelper.isSetAssignmentRuleFunction(Graph g, String variable)
static boolean	SBMLHelper.isSetAssignmentRuleVariable(Graph g, String variable)
static boolean	SBMLHelper.isSetCompartmentConstants(Graph g, String id)
static boolean	SBMLHelper.isSetCompartmentID(Graph g, String id)
static boolean	SBMLHelper.isSetCompartmentName(Graph g, String id)
static boolean	SBMLHelper.isSetCompartmentSize(Graph g, String id)
static boolean	SBMLHelper.isSetCompartmentSpatialDimensions(Graph g, String id)
static boolean	SBMLHelper.isSetCompartmentUnits(Graph g, String id)
static boolean	SBMLHelper.isSetConstraintMessage(Graph g, String constraint)
static boolean	SBMLHelper.isSetDelay(Graph g, String id)
static boolean	SBMLHelper.isSetDelayFunction(Graph g, String id)
static boolean	SBMLHelper.isSetEventName(Graph g, String id)
static boolean	SBMLHelper.isSetEventUseValuesFromTriggerTime(Graph g, String id)
static boolean	SBMLHelper.isSetFunctionDefinitionFunction(Graph g, String id)
static boolean	SBMLHelper.isSetFunctionDefinitionID(Graph g, String id)
static boolean	SBMLHelper.isSetFunctionDefinitionName(Graph g, String id)
static boolean	SBMLHelper.isSetInitialAssignmentFunction(Graph g, String symbol)
static boolean	SBMLHelper.isSetInitialAssignmentSymbol(Graph g, String symbol)
static boolean	SBMLHelper.isSetLayoutID(Graph g, Node node)
static boolean	SBMLHelper.isSetParameterConstant(Graph g, String id)
static boolean	SBMLHelper.isSetParameterName(Graph g, String id)
static boolean	SBMLHelper.isSetParameterUnits(Graph g, String id)
static boolean	SBMLHelper.isSetParameterValue(Graph g, String id)
static boolean	SBMLHelper.isSetPriority(Graph g, String id)
static boolean	SBMLHelper.isSetRateRuleFunction(Graph g, String variable)
static boolean	SBMLHelper.isSetRateRuleVariable(Graph g, String variable)
static boolean	SBMLHelper.isSetTriggerFunction(Graph g, String id)
static boolean	SBMLHelper.isSetTriggerInitialValue(Graph g, String id)
static boolean	SBMLHelper.isSetTriggerPersistent(Graph g, String id)
static boolean	SBMLHelper.isSetUnitDefinitionID(Graph g, String id)
static boolean	SBMLHelper.isSetUnitDefinitionName(Graph g, String id)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml with parameters of type Graph

Constructor	Description
KineticLawHelper(Graph g, Map<String,List<Node>> reactionClones)	Constructor.
SBMLAlgebraicRule(Graph g, String internHeadline)
SBMLAlgebraicRule(Graph g, String internHeadline, String presentedHeadline)
SBMLAssignmentRule(Graph g, String internHeadline)
SBMLAssignmentRule(Graph g, String internHeadline, String presentedHeadline)
SBMLCompartment(Graph g, String internHeadline)	Constructor.
SBMLCompartment(Graph g, String internHeadline, String presentedHeadline)	Constructor.
SBMLConstraint(Graph g, String internHeadline)
SBMLConstraint(Graph g, String internHeadline, String presentedHeadline)
SBMLEventAssignmentHelper(Graph g, String internHeadline, int eventAssignmentCount)
SBMLEventAssignmentHelper(Graph g, String internHeadline, String presentedHeadline, int eventAssignmentCount)
SBMLEventHelper(Graph g, String internHeadline)
SBMLEventHelper(Graph g, String internHeadline, String presentedHeadline)
SBMLFunctionDefinition(Graph g, String internHeadline)	Constructor.
SBMLFunctionDefinition(Graph g, String internHeadline, String presentedHeadline)	Constructor.
SBMLInitialAssignment(Graph g, String internHeadline)
SBMLInitialAssignment(Graph g, String internHeadline, String presentedHeadline)
SBMLLocalParameter(Graph g, int localParameterCount)
SBMLLocalParameter(Graph g, String presentedAttributeName, String internAttributeName)	Constructor.
SBMLParameter(Graph g, String internHeadline)
SBMLParameter(Graph g, String internHeadline, String presentedHeadline)
SBMLRateRule(Graph g, String internHeadline)
SBMLRateRule(Graph g, String internHeadline, String presentedHeadline)
SBMLReactionHelper(Graph g)	Constructor.
SBMLSpeciesHelper(Graph g)	Constructor.
SBMLUnit(Graph g, String internHeadline, int subUnitCount)
SBMLUnit(Graph g, String internHeadline, String presentedHeadline, int subUnitCount)
SBMLUnitDefinition(Graph g, String internHeadline)
SBMLUnitDefinition(Graph g, String internHeadline, String presentedHeadline)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph with parameters of type Graph

Modifier and Type	Method	Description
static ArrayList<Node>	ApplyGraphLayout.applyLayoutFromGraphToGraph(Selection s, Graph g, Graph layoutedGraph, String commandName, boolean considerEdgeLayout)
void	ApplyGraphLayout.attach(Graph g, Selection selection)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle with parameters of type Graph

Modifier and Type	Method	Description
void	CircleLayouterWithMinimumCrossingsAlgorithm.attach(Graph graph, Selection selection)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components with parameters of type Graph

Modifier and Type	Method	Description
static void	ConnectedComponentLayout.layoutConnectedComponents(Graph graph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout that return Graph

Modifier and Type	Method	Description
Graph	CopyPatternLayoutAlgorithm.getGraph()

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fish_eye

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fish_eye with parameters of type Graph

Modifier and Type	Method	Description
void	FishEyeLayout.attach(Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover with parameters of type Graph

Modifier and Type	Method	Description
static void	CenterLayouterAlgorithm.moveGraph(Graph graph, String nameOfOperation, boolean moveToTop, double offX, double offY)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder with parameters of type Graph

Modifier and Type	Method	Description
void	PatternSpringembedder.attach(Graph g, Selection s)
void	PatternSpringembedder3d.attach(Graph g, Selection s)
static void	MyTools.initNodeCache(ArrayList<NodeCacheEntry> nodeArray, HashMap<Node,NodeCacheEntry> nodeSearch, Graph graph, Selection selection, ArrayList<Graph> patternGraphs)	As the attribute access is very slow, this method initializes the NodeCacheEntry structures.
static void	MyTools.initNodeCache3d(ArrayList<NodeCacheEntry3d> nodeArray, HashMap<Node,NodeCacheEntry3d> nodeSearch, Graph graph, Selection selection)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder with parameters of type Graph

Constructor	Description
MyNonInteractiveSpringEmb(Graph gi, Selection s, ThreadSafeOptions tso)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache with parameters of type Graph

Modifier and Type	Method	Description
void	PatternSpringembedder.attach(Graph g)
void	PatternSpringembedder.attach(Graph g, Selection selection)
static void	MyTools.initNodeCache(ArrayList<NodeCacheEntry> nodeArray, HashMap<Node,NodeCacheEntry> nodeSearch, Graph graph)	As the attribute access is very slow, this method initializes the NodeCacheEntry structures.

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands with parameters of type Graph

Modifier and Type	Method	Description
void	RemoveBendsAlgorithm.attach(Graph graph, Selection selection, boolean attachUndo)	See AbstractAlgorithm.attach(Graph, Selection).
static void	PajekClusterColor.executeClusterColoringOnGraph(Graph g)	Colour clusters based on the stored ClusterColorAttribute for the graph.
static void	PajekClusterColor.executeClusterColoringOnGraph(Graph g, ClusterColorAttribute cca)
static void	PajekClusterColor.executeClusterColoringOnGraph(Graph g, Collection<String> clusters, ClusterColorAttribute cca)
static void	PajekClusterColor.removeClusterColoringOnGraph(Graph g)	Re-colours graph elements to their default fill and outline colours.

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands with parameters of type Graph

Constructor	Description
AreaManager(Graph g)
MyClusterGraphBasedReLayoutService(boolean waitForLayout, Graph g)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup with parameters of type Graph

Modifier and Type	Method	Description
void	NumberNodesAndEdgesAlgorithm.attach(Graph g, Selection s)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection with parameters of type Graph

Modifier and Type	Method	Description
void	ExportDataTableAlgorithm.attach(Graph graph, Selection selection)
static void	SearchAndSelecAlgorithm.enumerateAllAttributes(ArrayList<AttributePathNameSearchType> possibleAttributes, Graph graph, HashSet<SearchType> validSearchTypes)
static int	RemoveSelectedNodesPreserveEdgesAlgorithm.removeNodesPreserveEdges(ArrayList<Node> workNodes, Graph graph, boolean ignoreDirection, boolean layoutParallelEdges, BackgroundTaskStatusProviderSupportingExternalCall optStatus)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references that return Graph

Modifier and Type	Method	Description
Graph	SessionLinkInfo.getGraph()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references with parameters of type Graph

Modifier and Type	Method	Description
static Node	PathwayReferenceAutoCreationAlgorithm.addMapLinkNode(String fileName, Graph graph, Node initNode, ActionEvent ae, boolean searchExistingMapLinkNode, boolean searchAndLinkSimilarNodes, boolean searchAndLinkSameTarget)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references with type arguments of type Graph

Modifier and Type	Method	Description
void	PathwayReferenceAutoCreationAlgorithm.connectGraphToGraphs(Collection<Graph> graphs, String workSessionFilePath, boolean linkviz)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references with parameters of type Graph

Constructor	Description
SessionLinkInfo(Graph otherGraph)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.printer

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.printer with parameters of type Graph

Modifier and Type	Method	Description
void	PrintAlgorithm.attach(Graph g, Selection s)	Unused for this plugin.

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter with parameters of type Graph

Modifier and Type	Method	Description
static void	PngJpegAlgorithm.createPNGimageFromGraph(Graph g)
static void	PngJpegAlgorithm.createPNGimageFromGraph(Graph g, String fullPathAndFileName, PngJpegAlgorithmParams settings)
void	PngJpegAlgorithm.execute(Graph targetGraph, String filenameMain, String imageType, int imageTypeVal, ObjectRef resultView, ImageFileResultProcessor imageFileResultProcessor)
static BufferedImage	PngJpegAlgorithm.getActiveGraphViewImage(Graph targetGraph, int imageType, String fileExtension, PngJpegAlgorithmParams params, BackgroundTaskStatusProviderSupportingExternalCall optStatus)
static BufferedImage	PngJpegAlgorithm.getActiveGraphViewImage(Graph targetGraph, int imageType, String fileExtension, PngJpegAlgorithmParams params, BackgroundTaskStatusProviderSupportingExternalCall optStatus, boolean allowBackgroundThread)
Collection<BufferedImageResult>	PngJpegAlgorithm.getActiveGraphViewImage(Graph targetGraph, int imageType, String fileExtension, BackgroundTaskStatusProviderSupportingExternalCall optStatus)
Collection<BufferedImageResult>	PngJpegAlgorithm.getActiveGraphViewImage(Graph targetGraph, int imageType, String fileExtension, BackgroundTaskStatusProviderSupportingExternalCall optStatus, boolean allowBackgroundThread)
static String	PngJpegAlgorithm.getCachedFileName(String extension, Graph graph, Algorithm algorithm, ObjectRef lastEvent, ObjectRef lastFolder)

Uses of Graph in de.ipk_gatersleben.ag_nw.graffiti.services

Methods in de.ipk_gatersleben.ag_nw.graffiti.services with parameters of type Graph

Modifier and Type	Method	Description
static void	AlgorithmServices.selectAndRunLayoutAlgorithm(Graph clusterReferenceGraph, Selection selection, String commandTitle, boolean executeMoveToTopAfterwards)	This method calls a user defined layout algorithm for the given graph.

Constructors in de.ipk_gatersleben.ag_nw.graffiti.services with parameters of type Graph

Constructor	Description
RunAlgorithmDialog(String title, Graph graph, Selection selection, boolean returnAlgorithmInsteadOfRun, boolean executeMoveToTopAfterwards)

Uses of Graph in org

Methods in org with parameters of type Graph

Modifier and Type	Method	Description
static double	AttributeHelper.getHeatMapGamma(Graph graph)
static double	AttributeHelper.getHeatMapLowerBound(Graph graph)
static double	AttributeHelper.getHeatMapMiddleBound(Graph graph)
static double	AttributeHelper.getHeatMapUpperBound(Graph graph)
static void	AttributeHelper.moveGraph(Graph graph, int x, int y)

Uses of Graph in org.graffiti.editor

Methods in org.graffiti.editor that return Graph

Modifier and Type	Method	Description
Graph	MainFrame.getGraph(File file)
Graph	MainFrame.getGraph(String fileName, URL url)
Graph	MainFrame.getGraph(IOurl url)
Graph	MainFrame.getGraph(IOurl url, String fileName)	Will not be able to read cluster information (in separate file) for ".net" files and .gz-files
Graph	MainFrame.loadGraph(String fileName, URL url)	Loads a graph from a file;

Methods in org.graffiti.editor that return types with arguments of type Graph

Modifier and Type	Method	Description
Vector<Graph>	GravistoService.getMainGraphs()	Returns a Vector which contains a list of graphs from the main view.
ArrayList<Graph>	GravistoService.getPatternGraphs()	Returns a Vector which contains a list of pattern graphs.

Methods in org.graffiti.editor with parameters of type Graph

Modifier and Type	Method	Description
EditorSession	MainFrame.createNewSession(Graph g)
Session	MainFrame.getEditorSessionForGraph(Graph graph)
EditorSession	GravistoService.getSessionFromGraph(Graph graph)
EditorSession	MainFrame.lookUpSession(Graph g, boolean createIfNotFound)
void	GravistoService.runAlgorithm(Algorithm algorithm, Graph graph, Selection selection, boolean enableMultipleSessionProcessing, ActionEvent event)
void	GravistoService.runAlgorithm(Algorithm algorithm, Graph graph, Selection selection, ActionEvent event)
void	GravistoService.runPlugin(String pluginNameOrClassName, Graph g, ActionEvent event)	Starts a plugin and returns, as soon as the plugin execution has finished.
void	MainFrame.saveGraphAs(Graph graph, String fileName, String fileTypeDescription)
void	MainFrame.showGraph(Graph g, ActionEvent e)
void	MainFrame.showGraph(Graph g, ActionEvent e, LoadSetting interaction)

Uses of Graph in org.graffiti.editor.actions

Methods in org.graffiti.editor.actions that return Graph

Modifier and Type	Method	Description
static Graph	CopyAction.doCopyGraphMethodImproved(Graph sourceGraph, Selection selection, boolean returnGraphInsteadPastingInClipboard)
static Graph	CopyAction.doCopyGraphMethodImproved(Graph sourceGraph, Selection selection, boolean returnGraphInsteadPastingInClipboard, OutputSerializer os)

Methods in org.graffiti.editor.actions with parameters of type Graph

Modifier and Type	Method	Description
static void	CopyAction.doCopyGraph(Graph sourceGraph, Selection selection)
static void	CopyAction.doCopyGraphMethodImproved(Graph sourceGraph, Selection selection)
static Graph	CopyAction.doCopyGraphMethodImproved(Graph sourceGraph, Selection selection, boolean returnGraphInsteadPastingInClipboard)
static Graph	CopyAction.doCopyGraphMethodImproved(Graph sourceGraph, Selection selection, boolean returnGraphInsteadPastingInClipboard, OutputSerializer os)
void	FileHandlingListeners.fileSaved(File file, String ext, Graph graph)
static boolean	FileSaveAsAction.safeFile(File file, String ext, String fileTypeDescription, Graph graph)
void	FileHandlingManager.throwFileSaved(File file, String ext, Graph graph)

Uses of Graph in org.graffiti.event

Methods in org.graffiti.event that return Graph

Modifier and Type	Method	Description
Graph	GraphEvent.getGraph()	Returns the graph that has been changed.

Constructors in org.graffiti.event with parameters of type Graph

Constructor	Description
GraphEvent(Graph graph)	Constructs a graph event object with the specified source component.

Uses of Graph in org.graffiti.graph

Classes in org.graffiti.graph that implement Graph

Modifier and Type	Class	Description
class	AbstractGraph	Provides further functionality for graphs.
class	AdjListGraph	Implements the Graph -interface using an adjacency list representation of the graph.
class	OptAdjListGraph	Implements the Graph-interface using an adjacency list representation of the graph.

Methods in org.graffiti.graph that return Graph

Modifier and Type	Method	Description
Graph	AbstractGraphElement.getGraph()	Returns the Graph the AbstractGraphElement belongs to.
Graph	GraphElement.getGraph()	Returns the Graph the GraphElement belongs to.

Methods in org.graffiti.graph with parameters of type Graph

Modifier and Type	Method	Description
Collection<GraphElement>	AbstractGraph.addGraph(Graph g)	Adds a Graph g to the current graph.
Collection<GraphElement>	Graph.addGraph(Graph g)	Adds a Graph g to the current Graph.
void	AdjListEdge.setGraph(Graph graph)
void	AdjListNode.setGraph(Graph graph)
void	Edge.setGraph(Graph graph)
void	Node.setGraph(Graph graph)

Constructors in org.graffiti.graph with parameters of type Graph

Constructor	Description
AbstractEdge(Graph graph)	Constructs a new AbstractEdge.
AbstractEdge(Graph graph, CollectionAttribute coll)	Constructs a new AbstractEdge.
AbstractGraphElement(Graph graph)	Constructs a new AbstrctGraphElement.
AbstractGraphElement(Graph graph, CollectionAttribute coll)	Constructs a new AbstrctGraphElement.
AbstractNode(Graph graph)	Constructs a new AbstractNode.
AbstractNode(Graph graph, CollectionAttribute coll)	Constructs a new AbstractNode.
AdjListGraph(Graph g, ListenerManager listenerManager)	Constructs a new instance of an AdjListGraph from an instance of any Graph implementation.
AdjListGraph(Graph g, ListenerManager listenerManager, CollectionAttribute coll)	Constructs a new instance of an AdjListGraph from an instance of any Graph implementation.
OptAdjListGraph(Graph g, ListenerManager listenerManager)	Constructs a new instance of an OptAdjListGraph from an instance of any Graph implementation.
OptAdjListGraph(Graph g, ListenerManager listenerManager, CollectionAttribute coll)	Constructs a new instance of an OptAdjListGraph from an instance of any Graph implementation.

Uses of Graph in org.graffiti.managers

Methods in org.graffiti.managers with parameters of type Graph

Modifier and Type	Method	Description
JFileChooser	DefaultIOManager.createSaveFileChooser(Graph g)
JFileChooser	IOManager.createSaveFileChooser(Graph g)	Creates and returns a file open chooser dialog with the registered file extensions from the output serializers and checking, if output serializer is capable of writing the graph.

Uses of Graph in org.graffiti.plugin.actions

Methods in org.graffiti.plugin.actions with parameters of type Graph

Modifier and Type	Method	Description
ActionListener	URLattributeAction.getActionListener(Attribute displayable, Graph graph, GraphElement ge, boolean performAltCommand)

Uses of Graph in org.graffiti.plugin.algorithm

Methods in org.graffiti.plugin.algorithm that return Graph

Modifier and Type	Method	Description
Graph	ThreadSafeOptions.getGraphInstance()	DOCUMENT ME!

Methods in org.graffiti.plugin.algorithm with parameters of type Graph

Modifier and Type	Method	Description
void	AnimatedAlgorithm.animate(Graph g)	Starts the animation of the algorithm.
void	AbstractAlgorithm.attach(Graph graph, Selection selection)
void	Algorithm.attach(Graph g, Selection selection)	Attaches the given graph to this algorithm.
void	AnimatedAlgorithm.execute(Graph g)	Executes the whole algorithm as one big step.
JMenuItem[]	ProvidesDirectMouseClickContextMenu.getContextCommand(MouseEvent lastMouseE, Component lastMouseSrc, Graph graph)
void	ThreadSafeOptions.setGraphInstance(Graph newG)	DOCUMENT ME!

Uses of Graph in org.graffiti.plugin.io

Methods in org.graffiti.plugin.io that return Graph

Modifier and Type	Method	Description
Graph	AbstractInputSerializer.read(InputStream in)	Reads in a graph from the given input stream.
Graph	AbstractIOSerializer.read(InputStream in)	Reads in a graph from the given input stream.
Graph	InputSerializer.read(InputStream in)	Reads in a graph from the given input stream.

Methods in org.graffiti.plugin.io with parameters of type Graph

Modifier and Type	Method	Description
void	GraphPostProcessor.processNewGraph(Graph g)	Call back for processing newly created graphs and newly loaded graphs.
abstract void	AbstractInputSerializer.read(InputStream in, Graph g)	Reads in a graph from the given input stream.
void	AbstractInputSerializer.read(String filename, Graph g)	Reads in a graph from the given filename.
void	AbstractInputSerializer.read(URL url, Graph g)	Reads in the graph from the given url.
abstract void	AbstractIOSerializer.read(InputStream in, Graph g)	Reads in a graph from the given input stream.
void	AbstractIOSerializer.read(String filename, Graph g)	Reads in a graph from the given filename.
void	AbstractIOSerializer.read(URL url, Graph g)	Reads in the graph from the given url.
void	InputSerializer.read(InputStream in, Graph g)	Reads in a graph from the given input stream.
void	InputSerializer.read(Reader reader, Graph newGraph)
void	InputSerializer.read(String filename, Graph g)	Reads in a graph from the given filename.
void	InputSerializer.read(URL url, Graph g)	Reads in the graph from the given url.
boolean	AbstractOutputSerializer.validFor(Graph g)	As standard, an output serializer will be valid writer for any type of graph
boolean	OutputSerializer.validFor(Graph g)
void	AbstractIOSerializer.write(String filename, Graph g)	Writes the contents of the given graph to a file.
void	AbstractOutputSerializer.write(Graph g, String filename)	Writes the contents of the given graph to a file.
void	OutputSerializer.write(OutputStream stream, Graph g)	Writes the contents of the given graph to a stream.
void	SupportsWriterOutput.write(Writer output, Graph resultGraph)

Uses of Graph in org.graffiti.plugin.mode

Methods in org.graffiti.plugin.mode with parameters of type Graph

Modifier and Type	Method	Description
void	GraphConstraint.validate(Graph g)	Checks whether the specified graph satisfies the defined constraint.

Uses of Graph in org.graffiti.plugin.parameter

Constructors in org.graffiti.plugin.parameter with parameters of type Graph

Constructor	Description
NodeParameter(Graph graph, Node initalNode, String name, String description)	Constructs a new node parameter.

Uses of Graph in org.graffiti.plugin.tool

Methods in org.graffiti.plugin.tool with parameters of type Graph

Modifier and Type	Method	Description
void	AbstractTool.setGraph(Graph graph)	Sets the graph of this tool.
void	Tool.setGraph(Graph g)	Sets the graph this tool works on.

Uses of Graph in org.graffiti.plugin.view

Methods in org.graffiti.plugin.view that return Graph

Modifier and Type	Method	Description
Graph	AbstractView.getGraph()
Graph	View.getGraph()

Methods in org.graffiti.plugin.view with parameters of type Graph

Modifier and Type	Method	Description
abstract void	AbstractView.setGraph(Graph g)	Sets the graph this view displays.
void	View.setGraph(Graph graph)	Sets the graph of the view to the specified value.

Constructors in org.graffiti.plugin.view with parameters of type Graph

Constructor	Description
AbstractView(Graph currentGraph)	Constructs a new GraffitiView for the specified Graph.

Uses of Graph in org.graffiti.plugins.inspectors.defaults

Methods in org.graffiti.plugins.inspectors.defaults with parameters of type Graph

Modifier and Type	Method	Description
static void	DefaultEditPanel.issueCompleteRedrawForView(View activeView, Graph g)

Uses of Graph in org.graffiti.plugins.ios.exporters.gml

Methods in org.graffiti.plugins.ios.exporters.gml with parameters of type Graph

Modifier and Type	Method	Description
boolean	GMLWriter.validFor(Graph g)
void	GMLgzWriter.write(OutputStream stream, Graph g)
void	GMLWriter.write(OutputStream o, Graph g)
void	GMLWriter.write(Writer o, Graph g)

Uses of Graph in org.graffiti.plugins.ios.exporters.gmlxml

Methods in org.graffiti.plugins.ios.exporters.gmlxml with parameters of type Graph

Modifier and Type	Method	Description
boolean	GMLXMLWriter.validFor(Graph g)
void	GMLXMLWriter.write(OutputStream o, Graph g)

Uses of Graph in org.graffiti.plugins.ios.exporters.graphml

Methods in org.graffiti.plugins.ios.exporters.graphml with parameters of type Graph

Modifier and Type	Method	Description
boolean	GraphMLWriter.validFor(Graph g)
void	GraphMLgzWriter.write(OutputStream stream, Graph g)
void	GraphMLWriter.write(OutputStream stream, Graph g)

Uses of Graph in org.graffiti.plugins.ios.exporters.graphviz

Methods in org.graffiti.plugins.ios.exporters.graphviz with parameters of type Graph

Modifier and Type	Method	Description
void	DOTreader.read(InputStream in, Graph g)
void	DOTreader.read(Reader in, Graph g)
boolean	DOTSerializer.validFor(Graph g)
void	DOTSerializer.write(OutputStream out, Graph g)

Uses of Graph in org.graffiti.plugins.ios.importers

Methods in org.graffiti.plugins.ios.importers that return Graph

Modifier and Type	Method	Description
static Graph	TypedAttributeService.createTypedHashMapAttributes(Graph g)

Methods in org.graffiti.plugins.ios.importers with parameters of type Graph

Modifier and Type	Method	Description
static Graph	TypedAttributeService.createTypedHashMapAttributes(Graph g)

Uses of Graph in org.graffiti.plugins.ios.importers.gml

Methods in org.graffiti.plugins.ios.importers.gml that return Graph

Modifier and Type	Method	Description
Graph	parser.getGraph()	Returns the read in graph from the parser.
Graph	GMLReader.read(InputStream in)	Reads in a graph from the given input stream.

Methods in org.graffiti.plugins.ios.importers.gml with parameters of type Graph

Modifier and Type	Method	Description
void	GMLReader.read(InputStream in, Graph g)	Reads in a graph from the given input stream.
void	GMLReader.read(Reader reader, Graph newGraph)

Uses of Graph in org.graffiti.plugins.ios.importers.graphml

Methods in org.graffiti.plugins.ios.importers.graphml with parameters of type Graph

Modifier and Type	Method	Description
void	GraphMLReader.read(InputStream in, Graph g)
void	GraphMLReader.read(Reader reader, Graph newGraph)

Uses of Graph in org.graffiti.plugins.ios.importers.graphml.parser

Methods in org.graffiti.plugins.ios.importers.graphml.parser with parameters of type Graph

Modifier and Type	Method	Description
void	GraphMLParser.parse(InputStream in, Graph g)	Parses the given InputStream and adds the read in data to the given Graph.
void	GraphMLParser.parse(Reader reader, Graph g)

Constructors in org.graffiti.plugins.ios.importers.graphml.parser with parameters of type Graph

Constructor	Description
GraphMLFilter(XMLReader parent, Graph graph)	Constructs a new GraphMLFilter.

Uses of Graph in org.graffiti.plugins.views.defaults

Methods in org.graffiti.plugins.views.defaults with parameters of type Graph

Modifier and Type	Method	Description
void	GraffitiView.setGraph(Graph g)	Sets the graph this view displays.

Uses of Graph in org.graffiti.plugins.views.matrix

Methods in org.graffiti.plugins.views.matrix with parameters of type Graph

Modifier and Type	Method	Description
void	MatrixView.setGraph(Graph graph)

Constructors in org.graffiti.plugins.views.matrix with parameters of type Graph

Constructor	Description
MatrixModel(Graph graph)	Constructs a new matrix model.
MatrixView(Graph graph)	Constructs a new matrix view.

Uses of Graph in org.graffiti.selection

Methods in org.graffiti.selection that return types with arguments of type Graph

Modifier and Type	Method	Description
Collection<Graph>	Selection.getGraph()

Uses of Graph in org.graffiti.session

Methods in org.graffiti.session that return Graph

Modifier and Type	Method	Description
Graph	Session.getGraph()	Returns the graph of this session.

Constructors in org.graffiti.session with parameters of type Graph

Constructor	Description
EditorSession(Graph graph)	Constructs a new EditorSession.
GraphConstraintChecker(Graph g, ConstraintCheckerListener ccl)	Constructs a new GraphConstraintChecker checking constraints on the specified Graph.
Session(Graph graph)	Constructs a new session instance with the given graph.

Uses of Graph in org.graffiti.undo

Constructors in org.graffiti.undo with parameters of type Graph

Constructor	Description
AddEdgeEdit(Edge edge, Graph graph, Map<GraphElement,GraphElement> geMap)	Constructor for AddEdgeEdit.
AddNodeEdit(Node node, Graph graph, Map<GraphElement,GraphElement> geMap)	Constructor for AddNodeEdit.
ChangeAttributesEdit(Graph graph, Map attributeToOldValueMap, Map geMap)	Creates a new AttributeChangeEdit object.
ChangeAttributesEdit(Graph graph, Attribute attribute, Map geMap)	Creates a new AttributeChangeEdit object.
GraphElementsDeletionEdit(Collection<GraphElement> graphElemList, Graph graph, Map<GraphElement,GraphElement> geMap)
GraphElementsEdit(Graph graph, Map<GraphElement,GraphElement> geMap)	Create a nes GraphElementsEdit.

Uses of Graph in org.vanted.animation

Constructors in org.vanted.animation with parameters of type Graph

Constructor	Description
Animator(Graph graph)	Creates an animator will perform a single loop forever.
Animator(Graph graph, int noLoops)	Creates an animator that will automatically calculate the loop duration to be the same as the animation who's loop duration is largest
Animator(Graph graph, int noLoops, double loopDuration)	Creates an animator that needs to have its loop duration manually specified.
Animator(Graph graph, int noLoops, int loopDuration, TimeUnit timeUnit)	Creates an animator that needs to have its loop duration manually specified.
Animator(Graph graph, int noLoops, LoopDuration loopDuration)	Creates an animator that needs to have its loop duration manually specified.
Animator(Graph graph, NumberOfLoops noLoops)	Creates an animator that will automatically calculate the loop duration to be the same as the animation who's loop duration is largest

Uses of Graph in org.vanted.plugins.layout.multilevelframework

Subinterfaces of Graph in org.vanted.plugins.layout.multilevelframework

Modifier and Type	Interface	Description
interface	CoarsenedGraph	Adds a method to get the MergedNodes of a coarsening level to the Graph interface.

Methods in org.vanted.plugins.layout.multilevelframework that return Graph

Modifier and Type	Method	Description
Graph	MultilevelGraph.getTopLevel()	Get the topmost (i.e.

Methods in org.vanted.plugins.layout.multilevelframework with parameters of type Graph

Modifier and Type	Method	Description
void	ForceDirectedLayoutWrapper.attach(Graph g, Selection s)
void	MultilevelFrameworkLayout.attach(Graph g, Selection selection)
void	LayoutAlgorithmWrapper.execute(Graph graph)	Execute the algorithm, assuming an empty selection
void	LayoutAlgorithmWrapper.execute(Graph graph, Selection selection)	Execute the layout algorithm with the given Graph and Selection.

Constructors in org.vanted.plugins.layout.multilevelframework with parameters of type Graph

Constructor	Description
MergedNode(Graph g)	Deprecated.
MergedNode(Graph g, Set<Node> nodes)	Create a new MergedNode.
MergedNode(Graph g, CollectionAttribute col)	Deprecated.
MultilevelGraph(Graph level_0)	Create a MultilevelGraph.

Uses of Graph in org.vanted.plugins.layout.stressminimization

Methods in org.vanted.plugins.layout.stressminimization with parameters of type Graph

Modifier and Type	Method	Description
void	BackgroundExecutionAlgorithm.attach(Graph g, Selection selection)