Uses of Interface
org.graffiti.graph.GraphElement

Packages that use GraphElement

Package	Description
de.ipk_gatersleben.ag_nw.graffiti
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.xml_attribute
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms
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.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.layout_control.helper_classes
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter
org
org.graffiti.graph	Contains graph interfaces and classes.
org.graffiti.plugin.actions
org.graffiti.plugin.editcomponent
org.graffiti.plugin.inspector
org.graffiti.plugin.tool
org.graffiti.plugin.view
org.graffiti.plugins.modes.defaults
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.graffiti.util	Contains utility classes for frequently needed functionality.
org.vanted.animation.animations
org.vanted.plugins.layout.multilevelframework	A layout algorithm to Vanted that implements the multi-level graph layout framework.

Uses of GraphElement in de.ipk_gatersleben.ag_nw.graffiti

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

Modifier and Type	Method	Description
static Collection<GraphElement>	GraphHelper.getSelectedOrAllGraphElements()
static Collection<GraphElement>	GraphHelper.getSelectedOrAllGraphElements(Graph graph)
static Collection<GraphElement>	GraphHelper.getSelectedOrAllGraphElements(Selection selection, Graph graph)
static Collection<GraphElement>	GraphHelper.getSelectedOrAllGraphElements(EditorSession workSession)
static Collection<GraphElement>	GraphHelper.getVisibleElements(Collection<GraphElement> elements)

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

Modifier and Type	Method	Description
static Color	NodeTools.getChartBackgroundColor(GraphElement ge)
static Color	NodeTools.getChartBackgroundColor(GraphElement ge, int idx)
static Paint	NodeTools.getChartTitleColor(GraphElement ge)
static Font	NodeTools.getChartTitleFont(GraphElement ge)
static String	NodeTools.getClusterID(GraphElement node, String idIfNoCluster)
static List<MyComparableDataPoint>	NodeTools.getDataTimePoints(GraphElement n, boolean useSampleAverage)
static String	GraphHelperBio.getKeggName(GraphElement ge, String resultIfNotAvailable)
static String	GraphHelperBio.getKeggType(GraphElement ge, String resultIfNotAvailable)
static List<SubstanceInterface>	NodeTools.getMappedDataListFromNode(GraphElement graphElement)
static void	NodeTools.setClusterID(GraphElement node, String clusterId)
static void	GraphHelperBio.setKeggType(GraphElement ge, String keggType)
static void	NodeTools.setNodeComponentType(GraphElement ge, String nodeType)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti with type arguments of type GraphElement

Modifier and Type	Method	Description
static void	GraphHelper.applyUndoableClusterIdAssignment(Graph graph, HashMap<GraphElement,String> ge2newClusterID, String description, boolean enableUndo)
static Collection<String>	GraphHelper.getClusters(Collection<? extends GraphElement> elements)
static Collection<GraphElement>	GraphHelper.getVisibleElements(Collection<GraphElement> elements)
static void	GraphHelper.selectGraphElements(boolean clearBefore, Collection<? extends GraphElement> elements)
static void	GraphHelper.selectGraphElements(Collection<? extends GraphElement> elements)
static void	GraphHelper.unselectGraphElements(Collection<? extends GraphElement> elements)

Uses of GraphElement in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths that return GraphElement

Modifier and Type	Method	Description
GraphElement	WeightedDistanceInfo.getGraphElement()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths that return types with arguments of type GraphElement

Modifier and Type	Method	Description
Collection<GraphElement>	WeightedDistanceInfo.getConnectedGraphElements(boolean directed)
static Collection<GraphElement>	AllPathsSelectionAlgorithm.getPathElements(Collection<Node> validNodes, Node sourceNode, Collection<Node> targetNodes, boolean includeInnerEdges, boolean directed, boolean includeEdges, int maxDistance)
static Collection<GraphElement>	WeightedShortestPathSelectionAlgorithm.getShortestPathElements(Collection<GraphElement> validGraphElements, GraphElement startGraphElement, org.apache.commons.collections.set.ListOrderedSet targetGraphElements, boolean directed, boolean considerNodeWeight, boolean considerEdgeWeight, double maxDistance, AttributePathNameSearchType weightattribute, boolean putWeightOnEdges, boolean setAttribute, boolean setLabel)
Collection<GraphElement>	WeightedDistanceInfo.getSourceGraphElementsWithMinimalDistance()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths with parameters of type GraphElement

Modifier and Type	Method	Description
void	WeightedDistanceInfo.checkDistanceAndMemorizePossibleSourceElement(GraphElement workGraphElement, double distanceUntilNeighbourElement)
static Collection<GraphElement>	WeightedShortestPathSelectionAlgorithm.getShortestPathElements(Collection<GraphElement> validGraphElements, GraphElement startGraphElement, org.apache.commons.collections.set.ListOrderedSet targetGraphElements, boolean directed, boolean considerNodeWeight, boolean considerEdgeWeight, double maxDistance, AttributePathNameSearchType weightattribute, boolean putWeightOnEdges, boolean setAttribute, boolean setLabel)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths with type arguments of type GraphElement

Modifier and Type	Method	Description
static Collection<GraphElement>	WeightedShortestPathSelectionAlgorithm.getShortestPathElements(Collection<GraphElement> validGraphElements, GraphElement startGraphElement, org.apache.commons.collections.set.ListOrderedSet targetGraphElements, boolean directed, boolean considerNodeWeight, boolean considerEdgeWeight, double maxDistance, AttributePathNameSearchType weightattribute, boolean putWeightOnEdges, boolean setAttribute, boolean setLabel)

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

Constructor	Description
WeightedDistanceInfo(double initDistance, GraphElement sourceNode, GraphElement thisNode, boolean considerNodeWeight, boolean considerEdgeWeight, AttributePathNameSearchType weightattribute, boolean putWeightOnEdges, boolean addAttribute)

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

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

Modifier and Type	Method	Description
static SOMdataEntry	IAPnodeTools.getSOMdataSet(GraphElement n, int columnCount, String[] columnDesc, boolean returnNaN, boolean useSampleAverageValues)

Uses of GraphElement in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings with parameters of type GraphElement

Modifier and Type	Method	Description
JComponent	ChartComponent.getChart(GraphElement ge)
JComponent	GraffitiCharts.getChart(GraphElement ge)
JComponent	ChartComponentManager.getChartComponent(String ct, GraphElement ge)

Uses of GraphElement 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 GraphElement

Modifier and Type	Method	Description
static void	KeggReactionIdAttributeEditor.editReactions(GraphElement ge, String currentReactionId, Graph graph, Selection selection)

Uses of GraphElement 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 GraphElement

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 GraphElement in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.xml_attribute

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.xml_attribute with type arguments of type GraphElement

Modifier and Type	Method	Description
static void	XMLAttributeEditor.showMappedDataForSelection(Collection<GraphElement> graphElements, String attributeName)

Uses of GraphElement in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms

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

Modifier and Type	Method	Description
static void	RemoveMappingDataAlgorithm.removeMappingDataFrom(GraphElement n)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms with type arguments of type GraphElement

Modifier and Type	Method	Description
static Collection<ExperimentInterface>	ExtractMappingDataAlgorithm.getExperiments(Collection<GraphElement> workNodes, boolean onlyOne, BackgroundTaskStatusProviderSupportingExternalCall status)

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

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools that return types with arguments of type GraphElement

Modifier and Type	Method	Description
static Collection<GraphElement>	ContextMenuHelper.getActiveSelection()

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

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper that implement GraphElement

Modifier and Type	Class	Description
class	NodeHelper

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

Modifier and Type	Method	Description
int	NodeHelper.compareTo(GraphElement o)
static boolean	GraphElementHelper.hasDataMapping(GraphElement ge)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper with parameters of type GraphElement

Constructor	Description
GraphElementHelper(GraphElement ge)

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

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

Modifier and Type	Method	Description
Set<AttributeComponent>	FastView.getAttributeComponentsForElement(GraphElement ge)
GraphElementComponent	FastView.getComponentForElement(GraphElement ge)
boolean	FastView.isHidden(GraphElement ge)
void	FastView.repaint(GraphElement ge)

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

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

Modifier and Type	Method	Description
Set<AttributeComponent>	NullView.getAttributeComponentsForElement(GraphElement ge)
GraphElementComponent	NullView.getComponentForElement(GraphElement ge)
void	NullView.repaint(GraphElement ge)

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

Constructor	Description
IPKnodeComponent(GraphElement ge)

Uses of GraphElement 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 GraphElement

Modifier and Type	Field	Description
GraphElement	ChartOptions.ge

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

Modifier and Type	Method	Description
static String	XmlDataChartComponent.getChartTitle(GraphElement ge, int idx)
static JPanel	XmlDataChartComponent.prettifyChart(GraphElement ge, ChartOptions co, String chartType, JFreeChart jfChart)
void	ChartOptions.readAttributes(GraphElement ge)
int	ChartOptions.setLayoutOfChartComponent(GraphElement ge, JComponent chartcomponent, Integer mappedDataListSize)

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

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)
XmlDataChartComponent(String preferredChartType, Graph graph, GraphElement ge)

Uses of GraphElement 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 GraphElement

Modifier and Type	Method	Description
static void	Experiment2GraphHelper.addMappingData2Node(SubstanceInterface xmlSubstanceNode, GraphElement graphNode, String diagramStyle)
static ExperimentInterface	Experiment2GraphHelper.getMappedDataListFromGraphElement(GraphElement graphElement)	Get a list of mapped xml data that has been assigned to a node (or other GraphElement).
static ExperimentInterface	Experiment2GraphHelper.getMappedDataListFromGraphElement(GraphElement graphElement, String mapVarName)
static Integer	Experiment2GraphHelper.getMappedDataListSizeFromGraphElement(GraphElement graphElement)
static XMLAttribute	Experiment2GraphHelper.getXMLdataAttribute(GraphElement graphElement)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes with type arguments of type GraphElement

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 GraphElement in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics with type arguments of type GraphElement

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)

Uses of GraphElement in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit with type arguments of type GraphElement

Modifier and Type	Method	Description
static void	ZoomFitChangeComponent.zoomRegion(boolean smooth, Zoomable view, Collection<GraphElement> elements)
static void	ZoomFitChangeComponent.zoomRegion(boolean smooth, Zoomable view, Collection<GraphElement> elements, int zoomIntoValue)

Uses of GraphElement 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 GraphElement

Modifier and Type	Method	Description
static void	HelperClass.returnAttributeByPath(GraphElement elem, Pattern pattern, ArrayList<Attribute> set)	finds Attributes in GraphElements

Uses of GraphElement 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 GraphElement

Modifier and Type	Method	Description
static void	UBioChemicalReaction.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.BiochemicalReaction i)	adds all information within the biopax class to the attribute set of the node
static void	UCatalysis.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Catalysis i)	adds all information within the biopax class to the attribute set of the node
static void	UComplex.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Complex i)	adds all information within the biopax class to the attribute set of the node
static void	UComplexAssembly.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.ComplexAssembly i)	adds all information within the biopax class to the attribute set of the node
static void	UControl.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Control i)	adds all information within the biopax class to the attribute set of the node
static void	UConversion.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Conversion i)	adds all information within the biopax class to the attribute set of the node
static void	UDegradation.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Degradation i)	adds all information within the biopax class to the attribute set of the node
static void	UDna.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Dna i)	adds all information within the biopax class to the attribute set of the node
static void	UDnaRegion.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.DnaRegion i)	adds all information within the biopax class to the attribute set of the node
static void	UGene.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Gene i)	adds all information within the biopax class to the attribute set of the node
static void	UGeneticInteraction.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.GeneticInteraction i)	adds all information within the biopax class to the attribute set of the node
static void	UModulation.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Modulation i)	adds all information within the biopax class to the attribute set of the node
static void	UMolecularInteraction.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.MolecularInteraction i)	adds all information within the biopax class to the attribute set of the node
static void	UPathway.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Pathway i)	adds all information within the biopax class to the attribute set of the node
static void	UPhysicalEntity.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.PhysicalEntity i)	adds all information within the biopax class to the attribute set of the node
static void	UProtein.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Protein i)	adds all information within the biopax class to the attribute set of the node
static void	URna.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Rna i)	adds all information within the biopax class to the attribute set of the node
static void	URnaRegion.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.RnaRegion i)	adds all information within the biopax class to the attribute set of the node
static void	USmallMolecule.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.SmallMolecule i)	adds all information within the biopax class to the attribute set of the node
static void	UTemplateReaction.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.TemplateReaction i)	adds all information within the biopax class to the attribute set of the node
static void	UTemplateReactionRegulation.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.TemplateReactionRegulation i)	adds all information within the biopax class to the attribute set of the node
static void	UTransport.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.Transport i)	adds all information within the biopax class to the attribute set of the node
static void	UTransportWithBiochemicalReaction.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction i)	adds all information within the biopax class to the attribute set of the node
static void	UtilityClassSelectorFromGraph.chooseClassToPutAttributesToModell(GraphElement elem, Graph g, org.biopax.paxtools.model.Model model)
static void	UtilityClassSelectorToGraph.chooseClassToPutAttributesToNodes(GraphElement elem, Object i)
static Map<String[],Attribute>	TreeAttributSearcher.getMapPathToAttributable(HashSet<SearchType> validSearchTypes, GraphElement 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 GraphElement 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 GraphElement

Modifier and Type	Method	Description
Object	SBML_SBase_Writer.getAttribute(GraphElement n, String headline, String attributeName)

Uses of GraphElement in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility with parameters of type GraphElement

Modifier and Type	Method	Description
static void	UbioChemicalReaction.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.biochemicalReaction i)
static void	Ucatalysis.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.catalysis i)
static void	Ucomplex.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.complex i)
static void	UcomplexAssembly.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.complexAssembly i)
static void	Ucontrol.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.control i)
static void	Uconversion.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.conversion i)
static void	Udna.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.dna i)
static void	Umodulation.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.modulation i)
static void	Upathway.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.pathway i)
static void	UphysicalEntity.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.physicalEntity i)
static void	UphysicalInteraction.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.physicalInteraction i)
static void	Uprotein.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.protein i)
static void	Urna.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.rna i)
static void	UsmallMolecule.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.smallMolecule i)
static void	Utransport.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.transport i)
static void	UtransportWithBiochemicalReaction.addAttributesToNode(GraphElement elem, org.biopax.paxtools.model.level2.transportWithBiochemicalReaction i)
static void	UtilityClassSelectorToGraph.chooseClassToPutAttributesToNodes(GraphElement elem, Object i)

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

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection that return GraphElement

Modifier and Type	Method	Description
GraphElement	ValueAndGraphElement.getGraphElement()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection that return types with arguments of type GraphElement

Modifier and Type	Method	Description
HashMap<GraphElement,Integer>	SearchOption.getPositionsOfGraphElementsForThisSearchOption(Collection<GraphElement> searchScope)

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

Modifier and Type	Method	Description
double	AttributePathNameSearchType.getAttributeValue(GraphElement ge, double returnIfNotAvail)
void	AttributePathNameSearchType.setAttributeValue(GraphElement ge, double value)
void	AttributePathNameSearchType.setAttributeValue(GraphElement ge, Color color)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection with type arguments of type GraphElement

Modifier and Type	Method	Description
boolean	SearchOption.doesMatch(Attributable attr, Collection<GraphElement> searchScope, int idxOfAttr)
HashMap<GraphElement,Integer>	SearchOption.getPositionsOfGraphElementsForThisSearchOption(Collection<GraphElement> searchScope)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection with parameters of type GraphElement

Constructor	Description
ValueAndGraphElement(Comparable<?> value, GraphElement ge)

Uses of GraphElement in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids with type arguments of type GraphElement

Modifier and Type	Method	Description
static int	ReplaceLabelFromAlternativeSubstanceNames.enumerateExistingAlternativeSubstanceIDsAndTheirExamples(Collection<? extends GraphElement> graphElements, int maxID, HashMap<Integer,String> exampleValues)

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

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter with type arguments of type GraphElement

Modifier and Type	Method	Description
static Rectangle	PngJpegAlgorithm.getViewRectFromSelection(View view, Collection<GraphElement> graphElements)
static Rectangle	PngJpegAlgorithm.getViewRectFromSelection(View view, Collection<GraphElement> graphElements, boolean print)

Uses of GraphElement in org

Methods in org with parameters of type GraphElement

Modifier and Type	Method	Description
static double	AttributeHelper.getFrameThickNess(GraphElement ge)
static ArrayList<String>	AttributeHelper.getLabels(GraphElement graphElement)
static ArrayList<String>	AttributeHelper.getLabels(GraphElement graphElement, boolean includeMainLabel)
static String	AttributeHelper.getNiceEdgeOrNodeLabel(GraphElement ge, String nodeLabelIfMissing)
static double	AttributeHelper.getOpacity(GraphElement ge)	Gets the opacity of a given graph element
static String	AttributeHelper.getSBMLid(GraphElement ge)
static String	AttributeHelper.getSBMLrole(GraphElement ge)
static boolean	AttributeHelper.isHiddenGraphElement(GraphElement ge)
static boolean	AttributeHelper.isSBMLreaction(GraphElement ge)
static boolean	AttributeHelper.isSBMLreversibleReaction(GraphElement ge)
static void	AttributeHelper.setBorderWidth(GraphElement graphElement, double frameThickness)
static void	AttributeHelper.setDashInfo(GraphElement edgeOrNode, float[] values)
static void	AttributeHelper.setDashInfo(GraphElement edgeOrNode, float a, float b)
static void	AttributeHelper.setFrameThickNess(GraphElement ge, double frameThinkness)
static void	AttributeHelper.setHidden(boolean doHide, GraphElement ge)
static void	AttributeHelper.setLabel(int idx, GraphElement ge, String label, String fontName, String alignment)
static void	AttributeHelper.setLabel(GraphElement ge, String label)
static void	AttributeHelper.setLabelColor(int index, GraphElement ge, Color color)
static void	AttributeHelper.setOpacity(GraphElement ge, double opacity)	Sets the opacity of a given graph element This value will also influence the opacity of dependent Graph Attribute Components (Labels, Charts, etc)
static void	AttributeHelper.setPathwayReference(GraphElement ge, String url)
static void	AttributeHelper.setSBMLid(GraphElement ge, String id)
static void	AttributeHelper.setSBMLmodelID(GraphElement ge, String modelID)
static void	AttributeHelper.setSBMLreversibleReaction(GraphElement ge, String reactionReversible)
static void	AttributeHelper.setSBMLrole(GraphElement ge, String role)

Method parameters in org with type arguments of type GraphElement

Modifier and Type	Method	Description
static void	AttributeHelper.setHidden(Collection<GraphElement> graphElements, boolean doHide)
static void	AttributeHelper.setHidden(Set<GraphElement> graphElements, boolean doHide)

Uses of GraphElement in org.graffiti.graph

Subinterfaces of GraphElement in org.graffiti.graph

Modifier and Type	Interface	Description
interface	Edge	Provides an interfaces for a GraphEdge.
interface	Node	Provides an interfaces for a graph node.

Classes in org.graffiti.graph that implement GraphElement

Modifier and Type	Class	Description
class	AbstractEdge	Provides default implementations of methods on edges.
class	AbstractGraphElement	GraphElements are Attributables which know the graph they belong to.
class	AbstractNode	Abstract class AbstractNode common functionality for Node implementations.
class	AdjListEdge	Implementation of the Edge interface for a Graph with adjacency list representation.
class	AdjListNode	Implements a graph node with adjacency list representation.

Methods in org.graffiti.graph that return types with arguments of type GraphElement

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.
Collection<GraphElement>	AbstractGraph.getGraphElements()	Returns all nodes and all edges contained in this graph.
Collection<GraphElement>	Graph.getGraphElements()	Returns all nodes and all edges contained in this graph.

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

Modifier and Type	Method	Description
int	AdjListEdge.compareTo(GraphElement arg0)
int	AdjListNode.compareTo(GraphElement arg0)

Method parameters in org.graffiti.graph with type arguments of type GraphElement

Modifier and Type	Method	Description
void	AdjListGraph.deleteAll(Collection<? extends GraphElement> graphelements)
void	Graph.deleteAll(Collection<? extends GraphElement> graphelements)

Uses of GraphElement in org.graffiti.plugin.actions

Methods in org.graffiti.plugin.actions that return types with arguments of type GraphElement

Modifier and Type	Method	Description
List<GraphElement>	SelectionAction.getSelectedItems()	Returns the current list of selected items of this action.

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

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

Uses of GraphElement in org.graffiti.plugin.editcomponent

Methods in org.graffiti.plugin.editcomponent with parameters of type GraphElement

Modifier and Type	Method	Description
abstract void	GraphComponentEditComponent.setGraphElement(GraphElement graphElement)	Sets the graph component selectable by this edit component.
void	SingleGraphElementEditComponent.setGraphElement(GraphElement ge)	Sets the graph component selectable by this edit component.

Uses of GraphElement in org.graffiti.plugin.inspector

Method parameters in org.graffiti.plugin.inspector with type arguments of type GraphElement

Modifier and Type	Method	Description
void	InspectorTab.setEditPanelGraphElementMap(Map<GraphElement,GraphElement> map)
void	InspectorTab.setEditPanelGraphElementMap(Map<GraphElement,GraphElement> map)

Uses of GraphElement in org.graffiti.plugin.tool

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

Modifier and Type	Method	Description
void	ReceiveHighlightInfo.isHighlighted(GraphElement n)

Uses of GraphElement in org.graffiti.plugin.view

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

Modifier and Type	Method	Description
GraphElement	GraphElementComponentInterface.getGraphElement()	Returns the graphElement.

Methods in org.graffiti.plugin.view that return types with arguments of type GraphElement

Modifier and Type	Method	Description
Map<GraphElement,GraphElementComponent>	AbstractView.getComponentElementMap()
Map<GraphElement,GraphElementComponent>	AbstractView.getGraphElementComponentMap()

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

Modifier and Type	Method	Description
Set<AttributeComponent>	AbstractView.getAttributeComponentsForElement(GraphElement ge)
Set<AttributeComponent>	View.getAttributeComponentsForElement(GraphElement ge)
GraphElementComponent	AbstractView.getComponentForElement(GraphElement ge)	Returns the main GraphElementComponent associated with the given GraphELement.
GraphElementComponent	View.getComponentForElement(GraphElement ge)	Returns the main GraphElementComponent associated with the given GraphElement.
GraphElementComponent	AbstractView.getGraphElementComponent(GraphElement ge)
boolean	GraphView.isHidden(GraphElement ge)
void	AbstractView.removeGraphElementComponent(GraphElement ge)
void	View.repaint(GraphElement ge)	Repaints the given graph element

Uses of GraphElement in org.graffiti.plugins.modes.defaults

Methods in org.graffiti.plugins.modes.defaults that return GraphElement

Modifier and Type	Method	Description
static GraphElement	AdvancedLabelTool.getEditGraphElement()

Methods in org.graffiti.plugins.modes.defaults with parameters of type GraphElement

Modifier and Type	Method	Description
static void	AdvancedLabelTool.processLabelEdit(GraphElement ge)

Method parameters in org.graffiti.plugins.modes.defaults with type arguments of type GraphElement

Modifier and Type	Method	Description
void	DeleteAction.delete(List<GraphElement> elements)

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

Methods in org.graffiti.plugins.views.defaults that return GraphElement

Modifier and Type	Method	Description
GraphElement	AbstractGraphElementComponent.getGraphElement()	Returns the graphElement.

Methods in org.graffiti.plugins.views.defaults that return types with arguments of type GraphElement

Modifier and Type	Method	Description
ArrayList<GraphElement>	GraffitiView.getSortedGraphElements(boolean inverse)

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

Modifier and Type	Method	Description
boolean	GraffitiView.isHidden(GraphElement ge)
void	GraffitiView.repaint(GraphElement ge)
void	GraffitiView.sortGraphElements(GraphElement[] ges)

Constructors in org.graffiti.plugins.views.defaults with parameters of type GraphElement

Constructor	Description
EdgeComponent(GraphElement ge, NodeComponent source, NodeComponent target)	Constructor for EdgeComponent.
NodeComponent(GraphElement ge)	Constructor for NodeComponent.

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

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

Modifier and Type	Method	Description
void	MatrixView.repaint(GraphElement ge)

Uses of GraphElement in org.graffiti.selection

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

Modifier and Type	Method	Description
List<GraphElement>	Selection.getElements()	Returns a list containing all edges and nodes in this selection.
Map<GraphElement,GraphElement>	Selection.getNewMarked()	Returns the map holding graph elements that have been marked since the last selectionChanged event.
Map<GraphElement,GraphElement>	Selection.getNewMarked()	Returns the map holding graph elements that have been marked since the last selectionChanged event.
Map<GraphElement,GraphElement>	Selection.getNewUnmarked()	Returns the map holding graph elements that have been unmarked since the last selectionChanged event.
Map<GraphElement,GraphElement>	Selection.getNewUnmarked()	Returns the map holding graph elements that have been unmarked since the last selectionChanged event.

Methods in org.graffiti.selection with parameters of type GraphElement

Modifier and Type	Method	Description
void	Selection.add(GraphElement ge)	Adds the given node or edge to the selection.
boolean	Selection.contains(GraphElement ge)
void	Selection.remove(GraphElement ge)	Removes the given node or edge from the selection.

Method parameters in org.graffiti.selection with type arguments of type GraphElement

Modifier and Type	Method	Description
void	Selection.setNewMarked(Map<GraphElement,GraphElement> newMarked)	Sets the list of graph elements that have been marked but the selection listeners have not yet been notified.
void	Selection.setNewMarked(Map<GraphElement,GraphElement> newMarked)	Sets the list of graph elements that have been marked but the selection listeners have not yet been notified.
void	Selection.setNewUnmarked(Map<GraphElement,GraphElement> newUnmarked)	Sets the list of graph elements that have been unmarked but the selection listeners have not yet been notified.
void	Selection.setNewUnmarked(Map<GraphElement,GraphElement> newUnmarked)	Sets the list of graph elements that have been unmarked but the selection listeners have not yet been notified.

Uses of GraphElement in org.graffiti.session

Methods in org.graffiti.session that return types with arguments of type GraphElement

Modifier and Type	Method	Description
Map<GraphElement,GraphElement>	EditorSession.getGraphElementsMap()	Returns the graphElementMap.
Map<GraphElement,GraphElement>	EditorSession.getGraphElementsMap()	Returns the graphElementMap.

Uses of GraphElement in org.graffiti.undo

Constructor parameters in org.graffiti.undo with type arguments of type GraphElement

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

Uses of GraphElement in org.graffiti.util

Methods in org.graffiti.util with parameters of type GraphElement

Modifier and Type	Method	Description
static void	GeneralEditorUtils.setLabel(GraphElement ge, String val)	Searches if the given Attributable already contains a LabelAttribute.

Uses of GraphElement in org.vanted.animation.animations

Constructors in org.vanted.animation.animations with parameters of type GraphElement

Constructor	Description
FrameThicknessAnimation(GraphElement attributable, List<DoubleTimePoint> dataPoints, double loopDuration)
FrameThicknessAnimation(GraphElement attributable, List<DoubleTimePoint> dataPoints, double loopDuration, double startTime)
FrameThicknessAnimation(GraphElement attributable, List<DoubleTimePoint> dataPoints, double loopDuration, double startTime, int noLoops)
FrameThicknessAnimation(GraphElement attributable, List<DoubleTimePoint> dataPoints, double loopDuration, double startTime, int noLoops, Looper looper)
FrameThicknessAnimation(GraphElement attributable, List<DoubleTimePoint> dataPoints, double loopDuration, double startTime, int noLoops, Looper looper, Interpolator interpolator)
LabelColorAnimation(GraphElement attributable, List<ColorTimePoint> dataPoints, double loopDuration, double startTime, int labelIndex)
LabelColorAnimation(GraphElement attributable, List<ColorTimePoint> dataPoints, double loopDuration, double startTime, int noLoops, int labelIndex)
LabelColorAnimation(GraphElement attributable, List<ColorTimePoint> dataPoints, double loopDuration, double startTime, int noLoops, Looper looper, int labelIndex)
LabelColorAnimation(GraphElement attributable, List<ColorTimePoint> dataPoints, double loopDuration, double startTime, int noLoops, Looper looper, Interpolator interpolator, int labelIndex)
LabelColorAnimation(GraphElement attributable, List<ColorTimePoint> dataPoints, double loopDuration, double startTime, int noLoops, Looper looper, Interpolator interpolator, ColorMode colorMode, int labelIndex)
LabelColorAnimation(GraphElement attributable, List<ColorTimePoint> dataPoints, double loopDuration, int labelIndex)

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

Classes in org.vanted.plugins.layout.multilevelframework that implement GraphElement

Modifier and Type	Class	Description
class	MergedNode	A Node implementation that represents several nodes in a coarsening level within MultilevelGraph.