Uses of Interface
org.graffiti.graph.GraphElement
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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()
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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)
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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)
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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)
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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)
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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)
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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)
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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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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 nodestatic 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)
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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)
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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)
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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)
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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)
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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)
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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 elementstatic 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)
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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 aGraph
Edge
.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 classAbstractNode
common functionality forNode
implementations.class
AdjListEdge
Implementation of theEdge
interface for aGraph
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 aGraph
g to the currentGraph
.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)
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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)
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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)
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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)
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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 mainGraphElementComponent
associated with the givenGraphELement
.GraphElementComponent
View. getComponentForElement(GraphElement ge)
Returns the mainGraphElementComponent
associated with the givenGraphElement
.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)
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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)
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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 newGraffitiAbstractUndoableEdit
object.GraffitiAbstractUndoableEdit(Map<GraphElement,GraphElement> geMap)
Creates a newGraffitiAbstractUndoableEdit
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 nesGraphElementsEdit
.GraphElementsEdit(Graph graph, Map<GraphElement,GraphElement> geMap)
Create a nesGraphElementsEdit
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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)
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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
ANode
implementation that represents several nodes in a coarsening level withinMultilevelGraph
.