Uses of Interface
org.graffiti.graph.Node

Packages that use Node

Package	Description
de.ipk_gatersleben.ag_nw.graffiti
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest
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.shortest_paths
de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image
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.kegg.kegg_type.reaction_gui
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui
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.go_cluster_histogram
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.ipk_graffitiview
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.kegg.special
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics
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.metatool
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kgml
de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml
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.expand_reduce_space
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fish_eye
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid	Provides the GridLayouterPlugin, a plugin for placing nodes on a grid.
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.radial_tree
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout	Provides the GridLayouterPlugin, a plugin for placing nodes on a grid.
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.tree_simple
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy
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.services
org
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.plugin.algorithm
org.graffiti.plugin.parameter
org.graffiti.plugins.attributecomponents.simplelabel
org.graffiti.plugins.modes.defaults
org.graffiti.selection	Contains classes for the selection model.
org.graffiti.undo
org.graffiti.util	Contains utility classes for frequently needed functionality.
org.vanted.indexednodes	Provides graph data structures (and operations on them) that are more efficient for some purposes.
org.vanted.plugins.layout.adaptagrams.edgerouting
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 Node in de.ipk_gatersleben.ag_nw.graffiti

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

Modifier and Type	Method	Description
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.

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

Modifier and Type	Method	Description
static Set<Set<Node>>	GraphHelper.getConnectedComponents(Collection<Node> nodes)
static Set<Node>	GraphHelper.getConnectedNodes(Node startNode)	gets the nodes which can be reached by the the specified nodes
static ArrayList<Node>	GraphHelperBio.getEnzymeNodes(Graph g)
static Set<Node>	GraphHelper.getLeafNodes(Collection<Node> sourceNodes)
static Set<Node>	GraphHelper.getLeafNodes(Graph graph)
static ArrayList<Node>	GraphHelperBio.getMapLinkNodes(Graph g)
static List<Node>	GraphHelper.getSelectedNodes(EditorSession workSession)
static List<Node>	GraphHelper.getSelectedOrAllNodes()
static List<Node>	GraphHelper.getSelectedOrAllNodes(Selection selection, Graph graph)	Returns a list of the currently selected nodes.
static List<Node>	GraphHelper.getSelectedOrAllNodes(EditorSession workSession)
static Collection<Node>	GraphHelper.getVisibleNodes(Collection<Node> elements)

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

Modifier and Type	Method	Description
static Edge	GraphHelperBio.addEdgeCopyIfNotExistant(Edge refEdge, Node a, Node b)
static Edge	GraphHelperBio.addEdgeIfNotExistant(Graph graph, Node nodeA, Node nodeB, boolean directed, CollectionAttribute graphicsAttributeForEdge)
static Double	GraphHelper.getClusteringCoefficientDirected(Node n)
static Double	GraphHelper.getClusteringCoefficientUndirected(Node n)
static Set<Node>	GraphHelper.getConnectedNodes(Node startNode)	gets the nodes which can be reached by the the specified nodes
static void	GraphHelper.getConnectedNodes(Node startNode, boolean directed, Set<Node> result)
static Color	NodeTools.getLabelColor(Node node)
static Font	NodeTools.getLabelFont(Node node)
static String	NodeTools.getNodeComponentType(Node node)
static void	GraphHelper.selectGraphElement(Node n)

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

Modifier and Type	Method	Description
static void	GraphHelper.applyUndoableNodeAndBendPositionUpdate(HashMap<Node,Vector2d> nodes2newPositions, HashMap<CoordinateAttribute,Vector2d> bends2newPositions, String description)
static void	GraphHelper.applyUndoableNodePositionAndSizeUpdate(HashMap<Node,Vector2d> nodes2newPositions, HashMap<Node,Vector2d> nodes2newNodeSize, String description)
static void	GraphHelper.applyUndoableNodePositionUpdate(HashMap<Node,Vector2d> nodes2newPositions, String description)
static void	GraphHelper.applyUndoableNodeSizeUpdate(HashMap<Node,Vector2d> nodes2newNodeSize, String description)
static void	GraphHelperBio.connectNodesWithSameLabel(List<Node> nodes)
static void	GraphHelper.exchangePositions(List<Node> nodes, NodeSortCommand sortCommand, boolean sortConsiderCluster)
static Set<Set<Node>>	GraphHelper.getConnectedComponents(Collection<Node> nodes)
static Collection<Graph>	GraphHelper.getConnectedComponentsAsCopy(List<Node> nodes)
static void	GraphHelper.getConnectedNodes(Node startNode, boolean directed, Set<Node> result)
static Set<Node>	GraphHelper.getLeafNodes(Collection<Node> sourceNodes)
static Vector2d	NodeTools.getMaximumXY(Collection<Node> nodeList, double factorXY, double minx, double miny, boolean includeSizeInformation)
static Vector2d	NodeTools.getMaximumXY(Collection<Node> nodeList, double factorXY, double minx, double miny, boolean includeSizeInformation, boolean includeInvisibleNodes)
static Vector2d	NodeTools.getMinimumXY(Collection<Node> nodeList, double factorXY, double subx, double suby, boolean includeSizeInformation)
static Vector2d	NodeTools.getMinimumXY(Collection<Node> nodeList, double factorXY, double subx, double suby, boolean includeSizeInformation, boolean includeInvisibleNodes)
static void	GraphHelper.getShortestDistances(HashMap<Node,Integer> result, HashSet<Node> from, boolean directed, int currentDistance)
static void	GraphHelper.getShortestDistances(HashMap<Node,Integer> result, HashSet<Node> from, boolean directed, int currentDistance)
static Collection<NodeHelper>	GraphHelper.getSortedNodeHelpers(Collection<Node> nodes, NodeSortCommand sortCommand, boolean sortConsiderCluster)
static Collection<Node>	GraphHelper.getVisibleNodes(Collection<Node> elements)
static void	GraphHelperBio.mergeNodesWithSameLabel(List<Node> nodes, boolean selectOnlyTrueOrMergeIsFalse, boolean extendSelection, boolean considerCluster)
static void	GraphHelperBio.mergeNodesWithSameLabel(List<Node> nodes, boolean selectOnlyTrueOrMergeIsFalse, boolean extendSelection, boolean considerCluster, boolean considerPositionPlusMinus10, boolean retainClusterIDs)
static void	GraphHelper.moveNodes(Collection<Node> nodes, double deltaX, double deltaY)	Moves given nodes by the given delta coordinates
static void	GraphHelper.postUndoableNodeAndEdgeAdditions(Graph graph, HashSet<Node> newNodes, HashSet<Edge> newEdges, String description)
static void	GraphHelper.removeBendsBetweenSelectedNodes(Collection<Node> nodes, boolean enableUndo)	Deprecated.
static void	GraphHelper.selectNodes(boolean clearBefore, Collection<Node> nodes)
static void	GraphHelper.selectNodes(Collection<Node> nodes)
static void	NodeTools.setCenter(List<Node> nodeList, Vector2d center)

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

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

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

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest with type arguments of type Node

Modifier and Type	Method	Description
static void	ColorizeAlgorithm.colorizeNodes(List<Node> nodes, Color minC, Color maxC, double gamma, double min, double max, boolean useRatioCalculation)
static List<Node>	GrubbsTestAlgorithm.doGrubbsTest(List<Node> nodes, Graph g, double alpha, boolean removeOutliers)

Uses of Node 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 Node

Modifier and Type	Method	Description
Node[]	UllmannSubraphIsomAdjMatrixState.getMatchingNodesOfPattern()
Node[]	UllmannSubraphIsomAdjMatrixState.getMatchingNodesOfTarget()

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

Modifier and Type	Method	Description
static void	PatternAttributeUtils.addAGNWContainer(Node n)	Adds the top level container attribute "AGNW" to the given node.
static void	PatternAttributeUtils.addPattern(Node n, int position)	Adds the pattern container for the given pattern position at the given node.
static void	PatternAttributeUtils.addPatternContainer(Node n)	Adds the pattern container attribute "AGNW.PATTERN" to the given node.
static void	PatternAttributeUtils.addPatternInformation(Node n, int position, String patternName, Integer patternIndex, Integer nodeIndex, Node patternNode)	Adds a set of pattern information to the given node.
static void	PatternAttributeUtils.checkAndAddAGNWContainer(Node n)	Adds the top level container attribute "AGNW" to the given node, if it is not already there.
static void	PatternAttributeUtils.checkAndAddPattern(Node n, int position)	Adds the pattern container for the pattern position to the given node, if it is not already there.
static void	PatternAttributeUtils.checkAndAddPatternContainer(Node n)	Adds the pattern container attribute "AGNW.PATTERN" to the given node, if it is not already there.
static boolean	PatternAttributeUtils.checkExistenceAGNWContainer(Node n)	Checks, if the top level container attribute "AGNW" exists at the given node.
static boolean	PatternAttributeUtils.checkExistenceOfAnyPattern(Node n)	Checks if a pattern exists at the given node.
static boolean	PatternAttributeUtils.checkExistencePattern(Node n, int position)	Checks, if the pattern container for the pattern position exists at the given node.
static boolean	PatternAttributeUtils.checkExistencePatternContainer(Node n)	Checks, if the pattern container attribute "AGNW.PATTERN" exists at the given node.
static int	PatternAttributeUtils.findPatternPosition(Node n, String patternName, Integer patternIndex)	Returns the position of the given pattern name and pattern index for the given node.
static Integer	PatternAttributeUtils.getInternalNodeIndex(Node n, int position)	Returns the internal node index for the given node and position.
static int	PatternAttributeUtils.getMaxAddIncEdges(Node n)	Returns the maximal value for the additional incoming edges.
static int	PatternAttributeUtils.getMaxAddOutEdges(Node n)	Returns the maximal value for the additional outgoing edges.
static int	PatternAttributeUtils.getMaximumPatternPosition(Node n)	Returns the maximal position value of the pattern container.
static int	PatternAttributeUtils.getMinAddIncEdges(Node n)	Returns the minimal value for the additional incoming edges.
static int	PatternAttributeUtils.getMinAddOutEdges(Node n)	Returns the minimal value for the additional outgoing edges.
static Integer	PatternAttributeUtils.getNodeIndex(Node n, int position)	Returns the node index for the given node and position.
static Integer	PatternAttributeUtils.getPatternIndex(Node n, int position)	Returns the pattern index for the given node and position.
static String	PatternAttributeUtils.getPatternName(Node n, int position)	Returns the pattern name for the given node and position.
static void	UllmannSubraphIsomAdjMatrixState.printAdjacencyMatrix(Node[] nodes, byte[][] createAdjacencyMatrix)
boolean	PatternVistorLayouter.visitPattern(int numberOfNodesInMatch, Node[] matchInPattern, Node[] matchInTarget, String patternName, boolean allowOverlap)
boolean	SelectResultsVisitor.visitPattern(int numberOfNodesInMatch, Node[] matchInPattern, Node[] matchInTarget, String patternName, boolean allowOverlap)

Uses of Node 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 Node

Modifier and Type	Method	Description
Node	DistanceInfo.getNode()

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

Modifier and Type	Method	Description
Collection<Node>	DistanceInfo.getSourceNodes()

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

Modifier and Type	Method	Description
static Collection<GraphElement>	AllPathsSelectionAlgorithm.getPathElements(Collection<Node> validNodes, Node sourceNode, Collection<Node> targetNodes, boolean includeInnerEdges, boolean directed, boolean includeEdges, int maxDistance)
void	DistanceInfo.updateSourceIfValid(Node workNode, double minDistanceCheck)

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

Modifier and Type	Method	Description
static Collection<GraphElement>	AllPathsSelectionAlgorithm.getPathElements(Collection<Node> validNodes, Node sourceNode, Collection<Node> targetNodes, boolean includeInnerEdges, boolean directed, boolean includeEdges, int maxDistance)

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

Constructor	Description
DistanceInfo(double distance, Node sourceNode, Node thisNode)

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

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath that return Node

Modifier and Type	Method	Description
Node	TranspathMolecule.getGraphNode(Graph g, String clusterID, HashMap<String,Node> graphElementId2graphNode)

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

Modifier and Type	Method	Description
static void	TranspathMolecule.connectMoleculeNodes(Graph g, Node moleculeNode1, Node moleculeNode2)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath with type arguments of type Node

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)
Node	TranspathMolecule.getGraphNode(Graph g, String clusterID, HashMap<String,Node> graphElementId2graphNode)

Uses of Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image with parameters of type Node

Modifier and Type	Method	Description
static boolean	CompoundImagePositionAttributeEditor.isCenteredFitPosition(Node n)
static boolean	CompoundImagePositionAttributeEditor.isCenteredPosition(Node n)

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

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type with type arguments of type Node

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)

Uses of Node 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 Node

Modifier and Type	Method	Description
static void	PathwayKeggLoading.collapsePathway(Graph graph, String curVal, Node sourceNode)

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

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui with type arguments of type Node

Constructor	Description
CompoundListEditor(Reaction currReaction, Pathway p, boolean sub, boolean enz, boolean prod, HashMap<Entry,Node> entry2graphNode)

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

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui with type arguments of type Node

Constructor	Description
SrcTargetEditor(String title, Relation initialRelation, List<Entry> entries, HashMap<Entry,Node> entry2graphNode)
SubtypeCompoundEditor(String title, Relation initialRelation, List<Entry> entries, HashMap<Entry,Node> entry2graphNode)

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

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe that return Node

Modifier and Type	Method	Description
static Node	MergeNodes.mergeNode(Graph graph, Collection<Node> toBeMerged, Vector2d center, boolean retainClusterIDs)

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

Modifier and Type	Method	Description
static SplitResult	SplitNodeForSingleMappingData.splitNodes(Node graphNode, int mMinimumDegree, Graph graph, boolean mProcessSelfLoops, boolean mRepositionOfNodes)

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

Modifier and Type	Method	Description
static void	CombineMappingData.mergeMultipleMappingsIntoSingleMapping(Collection<Node> workNodes)
static Node	MergeNodes.mergeNode(Graph graph, Collection<Node> toBeMerged, Vector2d center, boolean retainClusterIDs)
static void	MergeNodes.mergeNodesIntoSingleNode(Graph graph, Collection<Node> workNodes)

Uses of Node 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 that return Node

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)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go with type arguments of type Node

Modifier and Type	Method	Description
JMenuItem[]	InterpreteParentGOtermsAlgorithm.getCurrentNodeContextMenuItem(Collection<Node> selectedNodes)
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 Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram that return Node

Modifier and Type	Method	Description
Node	MyEntry.getKey()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram with parameters of type Node

Modifier and Type	Method	Description
void	CreateGOchildrenClustersHistogramAlgorithm.processUpstreamNodes(Node n, HashSet<Node> processedNodes)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram with type arguments of type Node

Modifier and Type	Method	Description
static Collection<String>	CreateGOchildrenClustersHistogramAlgorithm.getLeafNodesClusterIDs(HashSet<Node> processedNodes, NodeHelper nh)
void	CreateGOchildrenClustersHistogramAlgorithm.processUpstreamNodes(Node n, HashSet<Node> processedNodes)
static void	PruneTreeAlgorithm.pruneFromTheseNodes(HashSet<Node> significantNodes)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram with parameters of type Node

Constructor	Description
MyEntry(Node graphNode, int res)

Uses of Node 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 Node

Modifier and Type	Method	Description
static Collection<Node>	ContextMenuHelper.getActiveNodeSelection()

Uses of Node 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 Node

Modifier and Type	Class	Description
class	NodeHelper

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

Modifier and Type	Method	Description
Node	NodeHelper.getGraphNode()

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

Modifier and Type	Method	Description
Collection<Node>	NodeHelper.getAllInNeighbors()
HashSet<Node>	NodeHelper.getAllOutChildNodes()
Collection<Node>	NodeHelper.getAllOutNeighbors()
Set<Node>	NodeHelper.getInNeighbors()
Iterator<Node>	NodeHelper.getInNeighborsIterator()
Set<Node>	NodeHelper.getNeighbors()
Iterator<Node>	NodeHelper.getNeighborsIterator()
Set<Node>	NodeHelper.getOutNeighbors()
Iterator<Node>	NodeHelper.getOutNeighborsIterator()
Collection<Node>	NodeHelper.getUndirectedNeighbors()
Iterator<Node>	NodeHelper.getUndirectedNeighborsIterator()

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper with type arguments of type Node

Modifier and Type	Method	Description
static List<NodeHelper>	NodeHelper.getNodeHelperList(Collection<Node> nodes)

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

Constructor	Description
NodeHelper(Node workNode)
NodeHelper(Node n, boolean isLastNode)

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

Fields in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview with type parameters of type Node

Modifier and Type	Field	Description
HashMap<Node,String>	ClusterBackgroundDraw.node2cluster
HashMap<Node,Vector2df>	ClusterBackgroundDraw.node2position

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

Modifier and Type	Method	Description
static String	IPKnodeComponent.getTooltipForNode(Node n, boolean includeClickHelp)

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

Fields in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes declared as Node

Modifier and Type	Field	Description
Node	IdAndGraphNode.graphNode

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

Modifier and Type	Method	Description
static void	Experiment2GraphHelper.addMappingData2Node(SubstanceInterface xmlSubstanceNode, Node graphNode)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes with parameters of type Node

Constructor	Description
IdAndGraphNode(String id2, Node graphNode)

Uses of Node 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 with parameters of type Node

Modifier and Type	Method	Description
static String	KeggHelper.getKeggId(Node n)
static boolean	KeggHelper.isEnzymeNode(Node n)
static boolean	KeggHelper.isMapNode(Node n)
static boolean	KeggHelper.isMapTitleNode(Node n)
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)

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg with type arguments of type Node

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 Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.special

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

Constructor	Description
EnzymeStatisticInformation(Node n)

Uses of Node 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 that return types with arguments of type Node

Modifier and Type	Method	Description
static List<Node>	TabStatistics.doDavidSchnellTest(List<Node> nodes, Graph g, int probab_123)	Returns all nodes which contain samples which are not normaly distributed.

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

Modifier and Type	Method	Description
static List<Node>	TabStatistics.doDavidSchnellTest(List<Node> nodes, Graph g, int probab_123)	Returns all nodes which contain samples which are not normaly distributed.

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics with type arguments of type Node

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 Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions with type arguments of type Node

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)

Uses of Node 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 Node

Modifier and Type	Method	Description
void	StoichiometryWriter.writeParticipantStoichiometry(Node physicalEntityNode, Node reactionNode, Edge e, Set<org.biopax.paxtools.model.level3.Stoichiometry> Stoichiometry)

Uses of Node 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 Node

Modifier and Type	Method	Description
static String	MetatoolWriter.getNodeLabel(Node nd)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.metatool with parameters of type Node

Constructor	Description
SBMLReaction(Node enzyme)

Uses of Node 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 Node

Modifier and Type	Method	Description
void	SBML_SBase_Writer.addSBaseAttributes(org.sbml.jsbml.AbstractSBase sbase, Node node)	Method adds all sBase attributes to an object of a model
Object	SBML_SBase_Writer.getAttribute(Node n, String headline, String attributeName)	Shortens the statement for getting the value of an attribute
ArrayList<String>	SBML_SBase_Writer.headlineHelper(Node n, String pattern)	Method returns all headlines in the node tab which begin with a certain pattern

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

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions with type arguments of type Node

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)

Uses of Node 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 Node

Modifier and Type	Method	Description
void	StoichiometryWriter.writeParticipantStoichiometry(Node node, Node center, Edge e, Set<org.biopax.paxtools.model.level2.physicalEntityParticipant> set)

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

Fields in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kgml declared as Node

Modifier and Type	Field	Description
Node	NodePair.a
Node	NodePair.b

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kgml with parameters of type Node

Constructor	Description
NodePair(Node a, Node b)

Uses of Node 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 Node

Modifier and Type	Method	Description
void	SBML_SBase_Reader.addNotes(org.sbml.jsbml.xml.XMLNode notesObject, String notesString, Node node, String path, String notesName)	This method adds notes to the current object in the node tab
void	SBML_SBase_Reader.setAttributes(Node node, Color color, String label, Point2D point, int size_multiplier)	Method helps to set Attributes Creates nodes with 20, 20 height/width

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

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

Modifier and Type	Method	Description
Node	Entry.addGraphNode(Graph graph)
Node	NodeCombination.getNodeA()
Node	NodeCombination.getNodeB()
Node	Entry.getSourceGraphNode()	In case this entry has been created from a Graph node, the souce graph node may be retrieved with this function.

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml that return types with arguments of type Node

Modifier and Type	Method	Description
static Set<Node>	KeggGmlHelper.getNodesInsideThisNode(Node bigNode, Collection<Node> nodes, HashMap<Node,Vector2d> node2upperLeftPos, HashMap<Node,Vector2d> node2lowerRightPos)	Find those nodes, which are located inside the "bigNode".

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

Modifier and Type	Method	Description
static Collection<Entry>	Reaction.getDistanceSubset(Collection<Entry> substratesOrProducts, Node b, HashMap<Entry,Node> entry2graphNode)
static Graphics	Graphics.getGraphicsFromGraphNode(Node graphNode, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors)
static boolean	KeggGmlHelper.getIsPartOfGroup(Node n)
static Color	KeggGmlHelper.getKeggGraphicsBgColor(Node n)
static Color	KeggGmlHelper.getKeggGraphicsFgColor(Node n)
static int	KeggGmlHelper.getKeggGraphicsHeight(Node n)
static String	KeggGmlHelper.getKeggGraphicsTitle(Node n)
static kgmlGraphicsType	KeggGmlHelper.getKeggGraphicsType(Node n)
static int	KeggGmlHelper.getKeggGraphicsWidth(Node n)
static int	KeggGmlHelper.getKeggGraphicsX(Node n)
static int	KeggGmlHelper.getKeggGraphicsY(Node n)
static String	KeggGmlHelper.getKeggId(Node n)
static ArrayList<IndexAndString>	KeggGmlHelper.getKeggIds(Node n)
static String	KeggGmlHelper.getKeggImageUrl(Node n)
static String	KeggGmlHelper.getKeggLinkUrl(Node n)
static String	KeggGmlHelper.getKeggLinkUrl(Node n, int index)
static ArrayList<IndexAndString>	KeggGmlHelper.getKeggReactions(Node n)
static String	KeggGmlHelper.getKeggType(Node n)
static String	KeggGmlHelper.getKeggType(Node n, int index)
static Set<Node>	KeggGmlHelper.getNodesInsideThisNode(Node bigNode, Collection<Node> nodes, HashMap<Node,Vector2d> node2upperLeftPos, HashMap<Node,Vector2d> node2lowerRightPos)	Find those nodes, which are located inside the "bigNode".
static void	Graphics.processDefaultNodeDesign(Node n, Entry entry)
void	Graphics.processNodeDesign(Node n, boolean hasComponents)
static void	KeggGmlHelper.setIsPartOfGroup(Node n, boolean value)
static void	KeggGmlHelper.setKeggGraphicsBgColor(Node n, Color bgcolor)
static void	KeggGmlHelper.setKeggGraphicsFgColor(Node n, Color fgcolor)
static void	KeggGmlHelper.setKeggGraphicsHeight(Node n, int height)
static void	KeggGmlHelper.setKeggGraphicsTitle(Node n, String name)
static void	KeggGmlHelper.setKeggGraphicsType(Node n, kgmlGraphicsType type)
static void	KeggGmlHelper.setKeggGraphicsWidth(Node n, int width)
static void	KeggGmlHelper.setKeggGraphicsX(Node n, int xPosition)
static void	KeggGmlHelper.setKeggGraphicsY(Node n, int yPosition)
static void	KeggGmlHelper.setKeggId(Node n, String id)
static void	KeggGmlHelper.setKeggId(Node n, String id, int index)
static void	KeggGmlHelper.setKeggLinkUrl(Node n, int index, String linkURL)
static void	KeggGmlHelper.setKeggLinkUrl(Node n, String linkURL)
static void	KeggGmlHelper.setKeggReaction(Node n, int index, String id)
static void	KeggGmlHelper.setKeggType(Node n, int index, String type)
static void	KeggGmlHelper.setKeggType(Node n, String type)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml with type arguments of type Node

Modifier and Type	Method	Description
Collection<NodeCombination>	Reaction.getDesiredNodeCombinations(HashMap<Entry,Node> entry2graphNode, Collection<Entry> entryElements, Collection<Relation> relationElements, Collection<NodeCombination> relationNodeCombinations)
Collection<NodeCombination>	Relation.getDesiredNodeCombinations(HashMap<Entry,Node> entry2graphNode, Collection<Entry> entries)
static Collection<Entry>	Reaction.getDistanceSubset(Collection<Entry> substratesOrProducts, Node b, HashMap<Entry,Node> entry2graphNode)
static Collection<Entry>	Entry.getEntryElementsFromGraphNodes(de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.KgmlIdGenerator idGenerator, List<Node> nodes, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, HashMap<Entry,Node> entry2graphNode)
static Collection<Entry>	Entry.getEntryElementsFromGraphNodes(de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.KgmlIdGenerator idGenerator, List<Node> nodes, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, HashMap<Entry,Node> entry2graphNode)
static Set<Node>	KeggGmlHelper.getNodesInsideThisNode(Node bigNode, Collection<Node> nodes, HashMap<Node,Vector2d> node2upperLeftPos, HashMap<Node,Vector2d> node2lowerRightPos)	Find those nodes, which are located inside the "bigNode".
static Set<Node>	KeggGmlHelper.getNodesInsideThisNode(Node bigNode, Collection<Node> nodes, HashMap<Node,Vector2d> node2upperLeftPos, HashMap<Node,Vector2d> node2lowerRightPos)	Find those nodes, which are located inside the "bigNode".
static Pathway	Pathway.getPathwayFromGraph(Graph graph, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors, HashMap<Entry,Node> entry2graphNode)
static Collection<Reaction>	Reaction.getReactionElementsFromGraphNodes(Collection<Entry> entries, List<Node> graphNodes, Collection<Gml2PathwayWarningInformation> warnings, Collection<Gml2PathwayErrorInformation> errors)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml with parameters of type Node

Constructor	Description
NodeCombination(Node a, Node b, boolean isProductRequest, boolean isSubstrateRequest, ReactionType reactionType)

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

Fields in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml with type parameters of type Node

Modifier and Type	Field	Description
static Map<String,Node>	SBMLSpeciesHelper.speciesMap

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml that return Node

Modifier and Type	Method	Description
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 Node	SBMLHelper.getReactionNode(Graph g, String id)	Returns the reaction node with a distinct id
Node	SBMLReactionHelper.getReactionNode(String layoutId, String reactionId)
static Node	SBMLHelper.getSpeciesNode(Graph g, String id)	Returns the species node with a distinct id
static Node	SBMLSpeciesHelper.getSpeciesNode(String id)	Returns the species with a distinct id
Node	SBMLSpeciesHelper.getSpeciesNode(String layoutId, String speciesId)
static Node	SBMLHelper.initReactionNode(Node n)
static Node	SBMLHelper.initSpeciesNode(Node n)	This method converts a node into a species node

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml that return types with arguments of type Node

Modifier and Type	Method	Description
Map<String,List<Node>>	SBMLReactionHelper.getReactionClones()
static List<Node>	SBMLHelper.getReactionNodes(Graph g)	Returns all reaction nodes of the graph
static List<Node>	SBMLHelper.getSpeciesNodes(Graph g)	Returns all species nodes of the graph
List<Node>	SBMLSpeciesHelper.getSpeciesNodes()	Returns all species nodes of the graph
Map<String,List<Node>>	SBMLSpeciesHelper.getSpeicesClones()

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

Modifier and Type	Method	Description
void	SBMLSpeciesHelper.addCloneToList(String speciesId, Node speciesNode)
static void	SBMLHelper.addKineticLaw(Node reactionNode, String function)
static void	SBMLHelper.addKineticLaw(Node reactionNode, org.sbml.jsbml.KineticLaw kineticLaw)
static void	SBMLHelper.addLocalParameter(Node node, String id)
static void	SBMLHelper.addLocalParameter(Node node, org.sbml.jsbml.LocalParameter lp)
static void	SBMLHelper.addLocalParameterName(Node node, String lpID, String name)
static void	SBMLHelper.addLocalParameterUnits(Node node, String lpID, String units)
static void	SBMLHelper.addLocalParameterValue(Node node, String lpID, Double value)
static Edge	SBMLHelper.addModifier(Node node, String speciesID)
static Edge	SBMLHelper.addModifier(Node node, org.sbml.jsbml.ModifierSpeciesReference ref)
static Edge	SBMLHelper.addProduct(Node node, String speciesID)
static Edge	SBMLHelper.addProduct(Node node, org.sbml.jsbml.SpeciesReference ref)
static Edge	SBMLHelper.addReactant(Node node, String speciesID)
static Edge	SBMLHelper.addReactant(Node node, org.sbml.jsbml.SpeciesReference ref)
void	SBMLReactionHelper.addReactionCloneToList(String reactionId, Node reactionNode)
static void	SBMLHelper.addSpeciesBoundaryConsition(Node speciesNode, Boolean boundaryCondition)	Sets the attribute boundary condition of a species node
static void	SBMLHelper.addSpeciesCompartment(Node speciesNode, String compartment)	Sets the compartment of a node
static void	SBMLHelper.addSpeciesConstant(Node speciesNode, Boolean constant)	Sets the attribute constant of a species node
static void	SBMLHelper.addSpeciesConversionFactor(Node speciesNode, String conversionFactor)	Sets the attribute conversion factor of a species node
static void	SBMLHelper.addSpeciesHasOnlySubstanceUnits(Node speciesNode, Boolean hasOnlySubstanceUnits)	Sets the attribute hasOnlySubstanceUnits of a species node
static void	SBMLHelper.addSpeciesID(Node speciesNode, String id)	Sets the id of a species node
static void	SBMLHelper.addSpeciesInitialAmount(Node speciesNode, Double initialAmount)	Sets the initial amount of a node
static void	SBMLHelper.addSpeciesInitialConcentration(Node speciesNode, Double initialConcentration)	Sets the initial concentration of a node
static void	SBMLHelper.addSpeciesName(Node speciesNode, String name)
static void	SBMLHelper.addSpeciesSubstanceUnits(Node speciesNode, String substanceUnits)	Sets the substance units of a species node
void	KineticLawHelper.deleteAnnotation(Node reactionNode)
void	SBMLLocalParameter.deleteAnnotation(Node node)
void	SBMLReactionHelper.deleteAnnotation(Node reactinNode)
void	SBMLSpeciesHelper.deleteAnnotation(Node speciesNode)
static void	SBMLHelper.deleteKineticLawFunction(Node node)
static void	SBMLHelper.deleteLocalParameter(Node node, String lpID)
static void	SBMLHelper.deleteLocalParameterID(Node node, String lpID)
static void	SBMLHelper.deleteLocalParameterName(Node node, String lpID)
static void	SBMLHelper.deleteLocalParameterUnits(Node node, String lpID)
static void	SBMLHelper.deleteLocalParameterValue(Node node, String lpID)
void	KineticLawHelper.deleteMetaID(Node reactionNode)
void	SBMLLocalParameter.deleteMetaID(Node node)
void	SBMLReactionHelper.deleteMetaID(Node reactinNode)
void	SBMLSpeciesHelper.deleteMetaID(Node speciesNode)
void	KineticLawHelper.deleteNonRDFAnnotation(Node reactionNode)
void	SBMLLocalParameter.deleteNonRDFAnnotation(Node node)
void	SBMLReactionHelper.deleteNonRDFAnnotation(Node reactinNode)
void	SBMLSpeciesHelper.deleteNonRDFAnnotation(Node speciesNode)
void	KineticLawHelper.deleteNotes(Node reactionNode)
void	SBMLLocalParameter.deleteNotes(Node node)
void	SBMLReactionHelper.deleteNotes(Node reactinNode)
void	SBMLSpeciesHelper.deleteNotes(Node speciesNode)
static void	SBMLHelper.deleteReactionCompartment(Node reactionNode)
static void	SBMLHelper.deleteReactionFast(Node reactionNode)
static void	SBMLHelper.deleteReactionID(Node reactionNode)
static void	SBMLHelper.deleteReactionName(Node reactionNode)
static void	SBMLHelper.deleteReactionReversible(Node reactionNode)
void	KineticLawHelper.deleteSBOTerm(Node reactionNode)
void	SBMLLocalParameter.deleteSBOTerm(Node node)
void	SBMLReactionHelper.deleteSBOTerm(Node reactinNode)
void	SBMLSpeciesHelper.deleteSBOTerm(Node speciesNode)
static void	SBMLHelper.deleteSpecies(Node node)
static void	SBMLHelper.deleteSpeciesBoundaryCondition(Node node)
static void	SBMLHelper.deleteSpeciesCompartment(Node node)
static void	SBMLHelper.deleteSpeciesConstant(Node node)
static void	SBMLHelper.deleteSpeciesConversionFactor(Node node)
static void	SBMLHelper.deleteSpeciesHasOnlySubstanceUnits(Node node)
static void	SBMLHelper.deleteSpeciesID(Node node)
static void	SBMLHelper.deleteSpeciesInitialAmount(Node node)
static void	SBMLHelper.deleteSpeciesInitialConcentration(Node node)
static void	SBMLHelper.deleteSpeciesName(Node node)
static void	SBMLHelper.deleteSpeciesSubstanceUnits(Node node)
org.sbml.jsbml.Annotation	KineticLawHelper.getAnnotation(Node reactionNode)
org.sbml.jsbml.Annotation	SBMLLocalParameter.getAnnotation(Node node)
org.sbml.jsbml.Annotation	SBMLReactionHelper.getAnnotation(Node reactionNode)
org.sbml.jsbml.Annotation	SBMLSpeciesHelper.getAnnotation(Node speciesNode)
Boolean	SBMLSpeciesHelper.getBoundaryCondition(Node speciesNode)	Returns the boolean value boundaryCondition of the species
String	SBMLReactionHelper.getCompartment(Node reactionNode)
String	SBMLSpeciesHelper.getCompartment(Node speciesNode)	Returns the compartment id of a species
String	SBMLSpeciesHelper.getCompartmentName(Node speciesNode)
Boolean	SBMLSpeciesHelper.getConstant(Node speciesNode)	Returns the boolean value constant of the species
String	SBMLSpeciesHelper.getConversionFactor(Node speciesNode)	Returns the conversion factor units of a species
Boolean	SBMLReactionHelper.getFast(Node reactionNode)
String	KineticLawHelper.getFunction(Node reactionNode)
Boolean	SBMLSpeciesHelper.getHasOnlySubstanceUnits(Node speciesNode)	Returns the boolean value hasOnlySubstanceUnits of the species
String	SBMLLocalParameter.getID(Node reactionNode)
String	SBMLReactionHelper.getID(Node reactionNode)
String	SBMLSpeciesHelper.getID(Node speciesNode)	Returns the id of the species
Double	SBMLSpeciesHelper.getInitialAmount(Node speciesNode)	Returns the initial amount of a species
Double	SBMLSpeciesHelper.getInitialConcentration(Node speciesNode)	Returns the initial concentration of a species
static String	SBMLHelper.getKineticLawFunction(Node reactionNode)	Returns the function of a kinetic law
static String	SBMLHelper.getLocalParameterID(Node reactionNode, int localParameterCount)	Returns the value of the attribute id
static String	SBMLHelper.getLocalParameterName(Node reactionNode, int localParameterCount)	Returns the value of the attribute name
static String	SBMLHelper.getLocalParameterUnits(Node reactionNode, int localParameterCount)	Returns the value of the attribute units
static Double	SBMLHelper.getLocalParameterValue(Node reactionNode, int localParameterCount)	Returns the value of the attribute value
String	KineticLawHelper.getMetaID(Node reactionNode)
String	SBMLLocalParameter.getMetaID(Node node)
String	SBMLReactionHelper.getMetaID(Node reactionNode)
String	SBMLSpeciesHelper.getMetaID(Node speciesNode)
static List<Edge>	SBMLHelper.getModifier(Node node)	Returns the modifier edges
String	SBMLLocalParameter.getName(Node reactionNode)
String	SBMLReactionHelper.getName(Node reactionNode)
String	SBMLSpeciesHelper.getName(Node speciesNode)	Returns the name of the species
org.sbml.jsbml.xml.XMLNode	KineticLawHelper.getNonRDFAnnotation(Node reactionNode)
org.sbml.jsbml.xml.XMLNode	SBMLLocalParameter.getNonRDFAnnotation(Node node)
org.sbml.jsbml.Annotation	SBMLReactionHelper.getNonRDFAnnotation(Node reactionNode)
org.sbml.jsbml.Annotation	SBMLSpeciesHelper.getNonRDFAnnotation(Node speciesNode)
org.sbml.jsbml.xml.XMLNode	KineticLawHelper.getNotes(Node reactionNode)
String	SBMLLocalParameter.getNotes(Node node)
org.sbml.jsbml.xml.XMLNode	SBMLReactionHelper.getNotes(Node reactionNode)
org.sbml.jsbml.xml.XMLNode	SBMLSpeciesHelper.getNotes(Node speciesNode)
static List<Edge>	SBMLHelper.getProducts(Node node)	The edges with the simple species references will be returned
static List<Edge>	SBMLHelper.getReactants(Node node)	The edges with the simple species references will be returned
static org.sbml.jsbml.Reaction	SBMLHelper.getReaction(Node node)	Returns a JSBML Reaction object belonging to a reaction node
static String	SBMLHelper.getReactionCompartment(Node reactionNode)	Returns the compartment of a reaction
static Boolean	SBMLHelper.getReactionFast(Node reactionNode)	Returns the attribute fast of a reaction
static String	SBMLHelper.getReactionID(Node reactionNode)	Returns the id of a reaction
static String	SBMLHelper.getReactionName(Node reactionNode)	Returns the name of a reaction
static Boolean	SBMLHelper.getReactionReversible(Node reactionNode)	Returns the attribute reversible of a reaction
Boolean	SBMLReactionHelper.getReversible(Node reactionNode)
String	KineticLawHelper.getSBOTerm(Node reactionNode)
String	SBMLLocalParameter.getSBOTerm(Node node)
String	SBMLReactionHelper.getSBOTerm(Node reactionNode)
String	SBMLSpeciesHelper.getSBOTerm(Node speciesNode)
static org.sbml.jsbml.Species	SBMLHelper.getSpecies(Node node)	Returns a JSBML Species object belonging to a species node
static Boolean	SBMLHelper.getSpeciesBoundaryCondition(Node speciesNode)	Returns the boolean value boundaryCondition of the species
static String	SBMLHelper.getSpeciesCompartment(Node speciesNode)	Returns the compartment id of a species
static Boolean	SBMLHelper.getSpeciesConstant(Node speciesNode)	Returns the boolean value constant of the species
static String	SBMLHelper.getSpeciesConversionFactor(Node speciesNode)	Returns the conversion factor units of a species
static Boolean	SBMLHelper.getSpeciesHasOnlySubstanceUnits(Node speciesNode)	Returns the boolean value hasOnlySubstanceUnits of the species
static String	SBMLHelper.getSpeciesID(Node speciesNode)	Returns the id of the species
static Double	SBMLHelper.getSpeciesInitialAmount(Node speciesNode)	Returns the initial amount of a species
static Double	SBMLHelper.getSpeciesInitialConcentration(Node speciesNode)	Returns the initial concentration of a species
static String	SBMLHelper.getSpeciesName(Node speciesNode)	Returns the name of the species
static String	SBMLHelper.getSpeciesSubstanceUnits(Node speciesNode)	Returns the substance units of a species
String	SBMLSpeciesHelper.getSubstanceUnits(Node speciesNode)	Returns the substance units of a species
String	SBMLLocalParameter.getUnits(Node reactionNode)
Double	SBMLLocalParameter.getValue(Node reactionNode)
static Node	SBMLHelper.initReactionNode(Node n)
static Node	SBMLHelper.initSpeciesNode(Node n)	This method converts a node into a species node
static Boolean	SBMLHelper.isKineticLawFunction(Node reactionNode)	Indicates if the function of a kinetic law is set
static Boolean	SBMLHelper.isLocalParameterID(Node reactionNode, int localParameterCount)	Indicates if the attribute id is set
static Boolean	SBMLHelper.isLocalParameterName(Node reactionNode, int localParameterCount)	Indicates if the attribute name is set
static Boolean	SBMLHelper.isLocalParameterUnits(Node reactionNode, int localParameterCount)	Indicates if the attribute units is set
static Boolean	SBMLHelper.isLocalParameterValue(Node reactionNode, int localParameterCount)	Indicates if the attribute value is set
static Boolean	SBMLHelper.isReactionCompartment(Node reactionNode)	Indicates if compartment of a reaction is set
static Boolean	SBMLHelper.isReactionFast(Node reactionNode)	Indicates if fast of a reaction is set
static Boolean	SBMLHelper.isReactionID(Node reactionNode)	Indicates if id of a reaction is set
static Boolean	SBMLHelper.isReactionName(Node reactionNode)	Indicates if name of a reaction is set
static Boolean	SBMLHelper.isReactionReversible(Node reactionNode)	Indicates if reversible of a reaction is set
Boolean	KineticLawHelper.isSetAnnotation(Node reactionNode)
Boolean	SBMLLocalParameter.isSetAnnotation(Node reactionNode)
Boolean	SBMLReactionHelper.isSetAnnotation(Node reactionNode)
Boolean	SBMLSpeciesHelper.isSetAnnotation(Node speciesNode)
Boolean	SBMLSpeciesHelper.isSetBoundaryCondition(Node speciesNode)	Indicates if boundary condition of a species is set
Boolean	SBMLReactionHelper.isSetCompartment(Node reactionNode)
Boolean	SBMLSpeciesHelper.isSetCompartment(Node speciesNode)	Indicates if the compartment id of a species is set
Boolean	SBMLSpeciesHelper.isSetConstant(Node speciesNode)	Indicates if constant of a species is set
Boolean	SBMLSpeciesHelper.isSetConversionFactor(Node speciesNode)	Indicates if conversion factor of a species is set
Boolean	SBMLReactionHelper.isSetFast(Node reactionNode)
Boolean	KineticLawHelper.isSetFunction(Node reactionNode)
Boolean	SBMLSpeciesHelper.isSetHasOnlySubstanceUnits(Node speciesNode)	Indicates if hasOnlySubstanceUnits of a species is set
Boolean	SBMLLocalParameter.isSetID(Node reactionNode)
Boolean	SBMLReactionHelper.isSetID(Node reactionNode)
Boolean	SBMLSpeciesHelper.isSetID(Node speciesNode)	Indicates if the id of a species is set
Boolean	SBMLSpeciesHelper.isSetInitialAmount(Node speciesNode)	Indicates if the initial amount of a species is set
Boolean	SBMLSpeciesHelper.isSetInitialConcentration(Node speciesNode)	Indicates if the initial concentration of a species is set
static boolean	SBMLHelper.isSetLayoutID(Graph g, Node node)
static boolean	SBMLHelper.isSetLocalParameterName(Node node, String lpID)
static boolean	SBMLHelper.isSetLocalParameterUnits(Node node, String lpID)
static boolean	SBMLHelper.isSetLocalParameterValue(Node node, String lpID)
Boolean	KineticLawHelper.isSetMetaID(Node reactionNode)
Boolean	SBMLLocalParameter.isSetMetaID(Node reactionNode)
Boolean	SBMLReactionHelper.isSetMetaID(Node reactionNode)
Boolean	SBMLSpeciesHelper.isSetMetaID(Node speciesNode)
Boolean	SBMLLocalParameter.isSetName(Node reactionNode)
Boolean	SBMLReactionHelper.isSetName(Node reactionNode)
Boolean	SBMLSpeciesHelper.isSetName(Node speciesNode)	Indicates if the name of a species is set
Boolean	KineticLawHelper.isSetNonRDFAnnotation(Node reactionNode)
Boolean	SBMLLocalParameter.isSetNonRDFAnnotation(Node reactionNode)
Boolean	SBMLReactionHelper.isSetNonRDFAnnotation(Node reactionNode)
Boolean	SBMLSpeciesHelper.isSetNonRDFAnnotation(Node speciesNode)
Boolean	KineticLawHelper.isSetNotes(Node reactionNode)
Boolean	SBMLLocalParameter.isSetNotes(Node reactionNode)
Boolean	SBMLReactionHelper.isSetNotes(Node reactionNode)
Boolean	SBMLSpeciesHelper.isSetNotes(Node speciesNode)
Boolean	SBMLReactionHelper.isSetReversible(Node reactionNode)
Boolean	KineticLawHelper.isSetSBOTerm(Node reactionNode)
Boolean	SBMLLocalParameter.isSetSBOTerm(Node reactionNode)
Boolean	SBMLReactionHelper.isSetSBOTerm(Node reactionNode)
Boolean	SBMLSpeciesHelper.isSetSBOTerm(Node speciesNode)
Boolean	SBMLSpeciesHelper.isSetSubstanceUnits(Node speciesNode)	Indicates if substance units of a species is set
Boolean	SBMLLocalParameter.isSetUnits(Node reactionNode)
Boolean	SBMLLocalParameter.isSetValue(Node reactionNode)
static Boolean	SBMLHelper.isSpeciesBoundaryCondition(Node speciesNode)	Indicates if boundary condition of a species is set
static Boolean	SBMLHelper.isSpeciesCompartment(Node speciesNode)	Indicates if the compartment id of a species is set
static Boolean	SBMLHelper.isSpeciesConstant(Node speciesNode)	Indicates if constant of a species is set
static Boolean	SBMLHelper.isSpeciesConversionFactor(Node speciesNode)	Indicates if conversion factor of a species is set
static Boolean	SBMLHelper.isSpeciesHasOnlySubstanceUnits(Node speciesNode)	Indicates if hasOnlySubstanceUnits of a species is set
static Boolean	SBMLHelper.isSpeciesID(Node speciesNode)	Indicates if the id of a species is set
static Boolean	SBMLHelper.isSpeciesInitialAmount(Node speciesNode)	Indicates if the initial amount of a species is set
static Boolean	SBMLHelper.isSpeciesInitialConcentration(Node speciesNode)	Indicates if the initial concentration of a species is set
static Boolean	SBMLHelper.isSpeciesName(Node speciesNode)	Indicates if the name of a species is set
static Boolean	SBMLHelper.isSpeciesSubstanceUnits(Node speciesNode)	Indicates if substance units of a species is set
static int	SBMLHelper.localParameterCount(Node node)	Returns the number of local parameter
void	KineticLawHelper.setAnnotation(Node reactionNode, org.sbml.jsbml.Annotation annotation)
void	SBMLLocalParameter.setAnnotation(Node reactionNode, org.sbml.jsbml.Annotation annotation)
void	SBMLReactionHelper.setAnnotation(Node reactionNode, org.sbml.jsbml.Annotation annotation)
void	SBMLSpeciesHelper.setAnnotation(Node speciesNode, org.sbml.jsbml.Annotation annotation)
void	SBMLSpeciesHelper.setBoundaryConsition(Node speciesNode, Boolean boundaryCondition)	Sets the attribute boundary condition of a species node
void	SBMLSpeciesHelper.setCharge(Node speciesNode, Integer charge)	Sets the deprecated attribute charge of a species node
void	SBMLReactionHelper.setCompartment(Node reactionNode, String compartment)
void	SBMLSpeciesHelper.setCompartment(Node speciesNode, String compartment)	Sets the compartment of a node
void	SBMLSpeciesHelper.setCompartmentName(Node speciesNode)
void	SBMLSpeciesHelper.setConstant(Node speciesNode, Boolean constant)	Sets the attribute constant of a species node
void	SBMLSpeciesHelper.setConversionFactor(Node speciesNode, String conversionFactor)	Sets the attribute conversion factor of a species node
void	SBMLReactionHelper.setFast(Node reactionNode, Boolean fast)
void	KineticLawHelper.setFunction(Node reactionNode, String function)
void	SBMLSpeciesHelper.setHasOnlySubstanceUnits(Node speciesNode, Boolean hasOnlySubstanceUnits)	Sets the attribute hasOnlySubstanceUnits of a species node
void	SBMLSpeciesHelper.setHiddenLabel(Node speciesNode, String id)	Sets the hidden label of a species node
void	SBMLLocalParameter.setID(Node reactionNode, String ID)
void	SBMLReactionHelper.setID(Node reactionNode, String ID)
void	SBMLSpeciesHelper.setID(Node speciesNode, String id)	Sets the id of a species node
void	SBMLSpeciesHelper.setInitialAmount(Node speciesNode, Double initialAmount)	Sets the initial amount of a node
void	SBMLSpeciesHelper.setInitialConcentration(Node speciesNode, Double initialConcentration)	Sets the initial concentration of a node
void	SBMLReactionHelper.setLabel(Node reactionNode, String name, String id, PositionGridGenerator pgg)
void	SBMLSpeciesHelper.setLabel(Node speciesNode, String name, String id, PositionGridGenerator pgg)	Sets the label of a node.
void	KineticLawHelper.setMetaId(Node reactionNode, String metaID)
void	SBMLLocalParameter.setMetaID(Node reactionNode, String metaID)
void	SBMLReactionHelper.setMetaID(Node reactionNode, String metaID)
void	SBMLSpeciesHelper.setMetaID(Node speciesNode, String metaID)	Sets the attribute meta id of a species node
void	SBMLLocalParameter.setName(Node reactionNode, String name)
void	KineticLawHelper.setNonRDFAnnotation(Node reactionNode, org.sbml.jsbml.xml.XMLNode xmlNode)
void	SBMLLocalParameter.setNonRDFAnnotation(Node reactionNode, org.sbml.jsbml.xml.XMLNode nonRDFAnnotation)
void	SBMLReactionHelper.setNonRDFAnnotation(Node reactionNode, org.sbml.jsbml.xml.XMLNode nonRDFAnnotation)
void	SBMLSpeciesHelper.setNonRDFAnnotation(Node speciesNode, org.sbml.jsbml.xml.XMLNode xmlNode)
void	KineticLawHelper.setNotes(Node reactionNode, String notes, org.sbml.jsbml.xml.XMLNode notesObj)
void	SBMLLocalParameter.setNotes(Node reactionNode, String notes, org.sbml.jsbml.xml.XMLNode notesObj)
void	SBMLReactionHelper.setNotes(Node reactionNode, String notes, org.sbml.jsbml.xml.XMLNode notesObj)
void	SBMLSpeciesHelper.setNotes(Node speciesNode, String notes, org.sbml.jsbml.xml.XMLNode notesObj)	Sets the attribute notes of a species node
static void	SBMLHelper.setReactionCompartment(Node reactionNode, String compartment)	Sets the compartment of a node
static void	SBMLHelper.setReactionFast(Node reactionNode, Boolean fast)	Sets the attribute fast of a node
static void	SBMLHelper.setReactionID(Node reactionNode, String ID)	Sets the attribute id of a node
static void	SBMLHelper.setReactionLabel(Node reactionNode, String name, String id, PositionGridGenerator pgg)	Sets the attribute name of a node
static void	SBMLHelper.setReactionName(Node reactionNode, String name)
static void	SBMLHelper.setReactionReversible(Node reactionNode, Boolean reversible)	Sets the attribute reversible of a node
void	SBMLReactionHelper.setReversible(Node reactionNode, Boolean reversible)
void	KineticLawHelper.setSBOTerm(Node reactionNode, String sboTerm)
void	SBMLLocalParameter.setSBOTerm(Node reactionNode, String sboTerm)
void	SBMLReactionHelper.setSBOTerm(Node reactionNode, String sboTerm)
void	SBMLSpeciesHelper.setSBOTerm(Node speciesNode, String sboTerm)	Sets the attribute sboTerm of a species node
static void	SBMLHelper.setSpeciesAttributes(Node sbmlNode, String niceID, Object value)
void	SBMLSpeciesHelper.setSubstanceUnits(Node speciesNode, String substanceUnits)	Sets the substance units of a species node
void	SBMLLocalParameter.setUnits(Node reactionNode, String units)
void	SBMLLocalParameter.setValue(Node reactionNode, Double value)

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml with type arguments of type Node

Constructor	Description
KineticLawHelper(Graph g, Map<String,List<Node>> reactionClones)	Constructor.

Uses of Node 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 that return types with arguments of type Node

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

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

Modifier and Type	Method	Description
static int	ApplyGraphLayout.calcNodeDifferenceDistance(Node n, Node layoutedNode)

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

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle that return types with arguments of type Node

Modifier and Type	Method	Description
static Collection<Node>	CircleLayouterAlgorithm.createCircleOrder(Collection<Node> nodes)	Creates an ordered list of a given list of nodes for creation of circular layouts, without the disruption of the order of nodes.

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

Modifier and Type	Method	Description
static double	CircleLayouterAlgorithm.energyOfNode(Node node, double newX, double newY)
static double	CircleLayouterAlgorithm.getDistance(double x, double y, Node b)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle with type arguments of type Node

Modifier and Type	Method	Description
static Collection<Node>	CircleLayouterAlgorithm.createCircleOrder(Collection<Node> nodes)	Creates an ordered list of a given list of nodes for creation of circular layouts, without the disruption of the order of nodes.
void	CircleLayouterAlgorithm.layoutOnCircles(Collection<Node> workNodes, double defaultRadius, String operationname)

Uses of Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_reduce_space

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_reduce_space with type arguments of type Node

Modifier and Type	Method	Description
static void	ExpandReduceLayouterAlgorithm.doOperation(Collection<Node> selectedNodes, double factorX, double factorY, String description)
JMenuItem[]	ExpandReduceLayouterAlgorithm.getCurrentNodeContextMenuItem(Collection<Node> selectedNodes)

Uses of Node 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 Node

Modifier and Type	Method	Description
boolean	FishEyeLayout.rootedTree(Node rootNode)	Check whether the tree is rooted.

Uses of Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid with type arguments of type Node

Modifier and Type	Method	Description
static void	GridLayouterAlgorithm.layoutOnGrid(Collection<Node> workNodes, double widthHeightRatio, double xDistance, double yDistance)
static void	GridLayouterAlgorithm.layoutOnGrid(Collection<Node> workNodes, double widthHeightRatio, double xDistance, double yDistance, int nodesOnLine, Point location)

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

Fields in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder declared as Node

Modifier and Type	Field	Description
Node	NodeCacheEntry.node	Reference to the node in the graph.
Node	NodeCacheEntry3d.node	Reference to the node in the graph.
Node	NodeCacheEntry.patternNode	Reference to a node in the pattern graph.
Node	NodeCacheEntry3d.patternNode	Reference to a node in the pattern graph.

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

Modifier and Type	Method	Description
static String	MyTools.getLabelFromNode(Node n)
static double	MyTools.getX(Node a)	For geting the x position of a node through attribute access,
static double	MyTools.getY(Node a)	For geting the y position of a node through attribute access,
static void	MyTools.setXY(Node a, double x, double y)
static void	MyTools.setXYZ(Node a, double x, double y, double z)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder with type arguments of type Node

Modifier and Type	Method	Description
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)

Uses of Node 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 Node

Modifier and Type	Method	Description
static String	MyTools.getLabelFromNode(Node n)
static void	MyTools.getPosition(Node a, Vector2d result)
static double	MyTools.getX(Node a)	For geting the x position of a node through attribute access,
static double	MyTools.getY(Node a)	For geting the y position of a node through attribute access,
static void	MyTools.setXY(Node a, double x, double y)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache with type arguments of type Node

Modifier and Type	Method	Description
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 Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree with parameters of type Node

Modifier and Type	Method	Description
boolean	RadialTreeLayout.rootedTree(Node rootNode)	Check whether the tree is rooted.

Uses of Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout with type arguments of type Node

Modifier and Type	Method	Description
void	GridLayoutAlgorithm.layoutOnGrid(Collection<Node> workNodes, double widthHeightRatio, double xDistance, double yDistance)

Uses of Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree that return types with arguments of type Node

Modifier and Type	Method	Description
HashMap<Node,Integer>	TreeContainer.getBfsNum()
HashMap<Node,Integer>	TreeContainer.getBfsNumUpsideDown()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree with parameters of type Node

Modifier and Type	Method	Description
boolean	RTTreeLayout.rootedTree(Node rootNode)	Check whether the tree is rooted.

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree with type arguments of type Node

Modifier and Type	Method	Description
void	TreeContainer.setBfsNum(HashMap<Node,Integer> map)

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree with type arguments of type Node

Constructor	Description
TreeContainer(HashMap<Node,Integer> bfsNum, HashMap<Integer,Double> maxNodeHeight)
TreeContainer(HashMap<Node,Integer> bfsNum, HashMap<Integer,Double> maxNodeHeight, HashSet<Edge> edges)

Uses of Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.tree_simple

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.tree_simple with parameters of type Node

Modifier and Type	Method	Description
void	GraphTreeLayout.computeAppropriateDepth(Node startNode)	Initialize the appropriate level of each node
boolean	GraphTreeLayout.rootedTree(Node rootNode)	Check whether the tree is rooted.

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

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup with type arguments of type Node

Modifier and Type	Method	Description
JMenuItem[]	NumberNodesAndEdgesAlgorithm.getCurrentNodeContextMenuItem(Collection<Node> selectedNodes)

Uses of Node in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy with type arguments of type Node

Modifier and Type	Method	Description
JMenuItem[]	HideOrShowChildNodes.getCurrentNodeContextMenuItem(Collection<Node> selectedNodes)
JMenuItem[]	HierarchyAlgorithm.getCurrentNodeContextMenuItem(Collection<Node> selectedNodes)
JMenuItem[]	SelectLeafNodesAlgorithm.getCurrentNodeContextMenuItem(Collection<Node> selectedNodes)

Uses of Node 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 Node

Modifier and Type	Method	Description
static ArrayList<String>	SearchDialog.getAlternativePaths(Node nd, String path)

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

Modifier and Type	Method	Description
static int	RemoveSelectedNodesPreserveEdgesAlgorithm.removeNodesPreserveEdges(ArrayList<Node> workNodes, Graph graph, boolean ignoreDirection, boolean layoutParallelEdges, BackgroundTaskStatusProviderSupportingExternalCall optStatus)

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

Fields in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references declared as Node

Modifier and Type	Field	Description
Node	TargetYandNewNodeResult.linkNode

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

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

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

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

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

Constructor	Description
TargetYandNewNodeResult(double targetY, Node linkNode)

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

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

Modifier and Type	Method	Description
static void	AlgorithmServices.doCircularEdgeCrossingsMinimization(Object referenceObject, ArrayList<Node> nodes, Runnable threadUnsafePostTask)
static int	AlgorithmServices.getNumberOfCircularEdgeCrossings(Collection<Node> nodes)

Uses of Node in org

Methods in org with parameters of type Node

Modifier and Type	Method	Description
static double	AttributeHelper.getDepth(Node node, double defaultReturn, boolean setDefault)
static double	AttributeHelper.getHeight(Node myNode)
static NodeLabelAttribute	AttributeHelper.getLabel(int index, Node node)	Get NodeLabelAttribute (if available)
static AlignmentSetting	AttributeHelper.getLabelAlignment(int index, Node node)
static Color	AttributeHelper.getLabelColor(Node n)
static Rectangle2D.Double	AttributeHelper.getNodeRectangle(Node node)
static Rectangle	AttributeHelper.getNodeRectangleAWT(Node node)
static Point2D	AttributeHelper.getPosition(Node a)	Returns the position of a node
static Vector2d	AttributeHelper.getPositionVec2d(Node a)	Returns the position of a node
static Vector2df	AttributeHelper.getPositionVec2df(Node a)	Returns the position of a node
static Vector3d	AttributeHelper.getPositionVec3d(Node node, boolean setDefault)	If setDefault is true, values will be initilized, saved and returned as 0.
static Vector3d	AttributeHelper.getPositionVec3d(Node node, double zReturnIfNotAvailable, boolean setDefaultZ)
static double	AttributeHelper.getPositionX(Node a)	For getting the x position of a node through attribute access,
static double	AttributeHelper.getPositionY(Node a)	For geting the y position of a node through attribute access,
static double	AttributeHelper.getPositionZ(Node node, boolean setDefault)
static double	AttributeHelper.getPositionZ(Node node, double defaultReturn, boolean setDefault)
static double	AttributeHelper.getRoundedEdges(Node node)
static String	AttributeHelper.getShape(Node node)
static Vector2d	AttributeHelper.getSize(Node myNode)	Gets the size of the Node.
static Vector3d	AttributeHelper.getSize3D(Node myNode, double defaultDepth, boolean setDefault)
static Dimension	AttributeHelper.getSizeD(Node myNode)	Gets the size of the Node.
static double	AttributeHelper.getWidth(Node myNode)
static boolean	AttributeHelper.isLabelAlignmentKnownConstant(int index, Node node)
static void	AttributeHelper.setBorderWidth(Node node, double frameThickness)
static void	AttributeHelper.setDefaultGraphicsAttribute(Node node, double x, double y)
static void	AttributeHelper.setDefaultGraphicsAttribute(Node newNode, Point2D position)
static void	AttributeHelper.setDepth(Node node, double depth)
static void	AttributeHelper.setHeight(Node myNode, double height)
static void	AttributeHelper.setHidden(boolean doHide, Node n, boolean processOutEdges, boolean processInEdges, boolean processUndirEdges)
static void	AttributeHelper.setLabel(Node node, String label)	Sets the Label of a Node.
static void	AttributeHelper.setLabel(Node node, String label, String fontName, String alignment)	Sets the label of a node.
static void	AttributeHelper.setLabelAlignment(int index, Node node, AlignmentSetting align)
static void	AttributeHelper.setLabelFrameStyle(int index, Node n, LabelFrameSetting setting)
static void	AttributeHelper.setLabelPosition(Node node, String pos)
static void	AttributeHelper.setPosition(Node n, double x, double y)	Sets the position of a node
static void	AttributeHelper.setPosition(Node n, Point2D p)	Sets the position of a node
static void	AttributeHelper.setPosition(Node node, Vector2d position)
static void	AttributeHelper.setPosition3d(Node n, double x, double y, double z)
static void	AttributeHelper.setPositionZ(Node node, double z)
static void	AttributeHelper.setRoundedEdges(Node node, double rounding)
static void	AttributeHelper.setShape(Node node, String knownShapeClassName)
static void	AttributeHelper.setShapeEllipse(Node node)
static void	AttributeHelper.setShapeRectangle(Node node)
static void	AttributeHelper.setSize(Node myNode, double width, double height)	Sets the size of the Node.
static void	AttributeHelper.setSize(Node myNode, int width, int height)	Sets the size of the Node.
static void	AttributeHelper.setSize(Node myNode, Vector2d newSize)	Sets the size of the Node.
static void	AttributeHelper.setWidth(Node myNode, double width)

Method parameters in org with type arguments of type Node

Modifier and Type	Method	Description
static void	AttributeHelper.setVisibilityOfChildElements(Collection<Node> nodes, boolean doHide)
static void	AttributeHelper.switchVisibilityOfChildElements(Collection<Node> nodes)

Uses of Node in org.graffiti.event

Methods in org.graffiti.event that return Node

Modifier and Type	Method	Description
Node	GraphEvent.getNode()	Returns the node that is concerned with that event, e.g.: the node that has been / is to be removed.
Node	NodeEvent.getNode()	Returns the node that has been changed by this event.
Node	GraphEvent.getSecondNode()	Returns the node that is concerned with that event, e.g.: the node that has been / is to be removed.

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

Constructor	Description
GraphEvent(Node node)	Constructs a graph event object with the specified source component.
GraphEvent(Node node, Node secondNode)	Constructs a graph event object with the graph of the first node as source and saves the two given nodes.
NodeEvent(Node node, Edge edge)	Constructs a graph event object with the specified source components.

Uses of Node in org.graffiti.graph

Classes in org.graffiti.graph that implement Node

Modifier and Type	Class	Description
class	AbstractNode	Abstract class AbstractNode common functionality for Node implementations.
class	AdjListNode	Implements a graph node with adjacency list representation.

Methods in org.graffiti.graph that return Node

Modifier and Type	Method	Description
Node	AbstractGraph.addNode()	Adds a new node to the graph.
Node	AbstractGraph.addNode(CollectionAttribute col)	Adds a new node to the graph.
Node	Graph.addNode()	Adds a new Node to the Graph.
Node	Graph.addNode(CollectionAttribute col)	Adds a new node to the graph.
Node	AbstractGraph.addNodeCopy(Node node)	Adds a copy of the specified node to the graph and returns the copy.
Node	Graph.addNodeCopy(Node node)	Adds a copy of the specified Node to the Graph.
Node	AdjListEdge.getSource()	Returns the source of the Edge.
Node	Edge.getSource()	Returns the source of the current Edge.
Node	AdjListEdge.getTarget()	Returns the target of the Edge.
Node	Edge.getTarget()	Returns the target of the current Edge.

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

Modifier and Type	Method	Description
List<Node>	NodeHierarchy.getAllChildNodes(List<Node> n)
List<Node>	NodeHierarchy.getAllChildNodes(Node n)
Collection<Node>	AbstractNode.getAllInNeighbors()
Collection<Node>	Node.getAllInNeighbors()	Union of getInNeighbors() and getUndirectedNeighbors() .
Collection<Node>	AbstractNode.getAllOutNeighbors()
Collection<Node>	Node.getAllOutNeighbors()	Union of getOutNeighbors() and getUndirectedNeighbors().
List<Node>	NodeHierarchy.getAllParentNodes(List<Node> n)
List<Node>	NodeHierarchy.getAllParentNodes(Node n)
List<Node>	NodeHierarchy.getDirectChildNodes(List<Node> n)
List<Node>	NodeHierarchy.getDirectChildNodes(Node n)
List<Node>	NodeHierarchy.getDirectParentNodes(List<Node> n)
List<Node>	NodeHierarchy.getDirectParentNodes(Node n)
Set<Node>	AbstractNode.getInNeighbors()	Returns a collection containing the neighbor nodes belonging to incoming edges.
Set<Node>	Node.getInNeighbors()	Returns a collection containing the neighbor nodes belonging to incoming edges.
Iterator<Node>	AbstractNode.getInNeighborsIterator()	Returns an iterator over the neighbor nodes belonging to incoming edges.
Iterator<Node>	Node.getInNeighborsIterator()	Returns an iterator over the neighbor nodes belonging to incoming edges.
Set<Node>	AbstractNode.getNeighbors()	Returns a collection containing all the neighbor nodes of the current Node.
Set<Node>	Node.getNeighbors()	Returns a collection containing all the neighbor nodes of the current Node.
Iterator<Node>	AbstractNode.getNeighborsIterator()	Returns an interator over the neighbor nodes of the current Node.
Iterator<Node>	Node.getNeighborsIterator()	Returns an interator over the neighbor nodes of the current Node.
List<Node>	AdjListGraph.getNodes()
List<Node>	Graph.getNodes()	Returns a java.util.List containing all the nodes of the Graph.
List<Node>	OptAdjListGraph.getNodes()	Returns a list containing a copy of the node list of the graph.
Iterator<Node>	AdjListGraph.getNodesIterator()	Returns an iterator over the nodes of the graph.
Iterator<Node>	Graph.getNodesIterator()	Returns an iterator over the nodes of the Graph.
Iterator<Node>	OptAdjListGraph.getNodesIterator()	Returns an iterator over the nodes of the graph.
Set<Node>	AbstractNode.getOutNeighbors()	Returns a collection containing all the neighbors of the current Node which are connected by an outgoing Edge.
Set<Node>	Node.getOutNeighbors()	Returns a collection containing all the neighbors of the current Node which are connected by an outgoing Edge.
Iterator<Node>	AbstractNode.getOutNeighborsIterator()	Returns an iterator containing all the neighbors of the current Node which are connected by an outgoing Edge.
Iterator<Node>	Node.getOutNeighborsIterator()	Returns an iterator containing all the neighbors of the current Node which are connected by an outgoing Edge.
Collection<Node>	AbstractNode.getUndirectedNeighbors()	Returns a collection containing all the neighbors which are connected to the current Node by an undirected Edge.
Collection<Node>	Node.getUndirectedNeighbors()	Returns a collection containing all the neighbors which are connected to the current Node by an undirected Edge.
Iterator<Node>	AbstractNode.getUndirectedNeighborsIterator()
Iterator<Node>	Node.getUndirectedNeighborsIterator()

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

Modifier and Type	Method	Description
Edge	AbstractGraph.addEdge(Node source, Node target, boolean directed)	Adds a new edge to the current graph.
Edge	AbstractGraph.addEdge(Node source, Node target, boolean directed, CollectionAttribute col)	Adds a new edge to the current graph.
Edge	Graph.addEdge(Node source, Node target, boolean directed)	Adds a new Edge to the current Graph.
Edge	Graph.addEdge(Node source, Node target, boolean directed, CollectionAttribute col)	Adds a new Edge to the current Graph.
Edge	AbstractGraph.addEdgeCopy(Edge edge, Node source, Node target)	Adds a copy of the specified edge to the graph as a new edge between the specified source and target node.
Edge	Graph.addEdgeCopy(Edge edge, Node source, Node target)	Adds a copy of the specified Edge to the Graph as a new Edge between the specified source and target Node.
Node	AbstractGraph.addNodeCopy(Node node)	Adds a copy of the specified node to the graph and returns the copy.
Node	Graph.addNodeCopy(Node node)	Adds a copy of the specified Node to the Graph.
boolean	AbstractGraph.areConnected(Node n1, Node n2)	Returns true, if the graph contains an edge between the nodes n1 and n2, false otherwise.
boolean	AbstractGraph.containsNode(Node n)	Returns true, if the graph contains the specified node, false otherwise.
boolean	Graph.containsNode(Node n)	Returns true, if the Graph contains the specified Node, false otherwise.
boolean	OptAdjListGraph.containsNode(Node n)	Returns true, if the graph contains the specified node, false otherwise.
void	AbstractGraph.deleteNode(Node n)	Deletes the given node.
void	Graph.deleteNode(Node n)	Deletes the Node n.
void	AdjListEdge.doSetTarget(Node target)	Sets the target of the current Edge to target.
List<Node>	NodeHierarchy.getAllChildNodes(Node n)
List<Node>	NodeHierarchy.getAllParentNodes(Node n)
List<Node>	NodeHierarchy.getDirectChildNodes(Node n)
List<Node>	NodeHierarchy.getDirectParentNodes(Node n)
Collection<Edge>	AbstractGraph.getEdges(Node n1, Node n2)	Returns a collection containing all the edges between n1 and n2.
Collection<Edge>	AdjListGraph.getEdges(Node n1, Node n2)
Collection<Edge>	Graph.getEdges(Node n1, Node n2)	Returns a collection containing all the edges between n1 and n2.
void	AdjListGraph.setNodeFirst(Node node)	The given node is moved to the front of the node list.
void	AdjListGraph.setNodeLast(Node node)	The given node is moved to the end of the node list.
void	AbstractEdge.setSource(Node source)	Sets the source of the current Edge to source.
void	Edge.setSource(Node source)	Sets the source of the current Edge to source.
void	AbstractEdge.setTarget(Node target)	Sets the target of the current Edge to target.
void	Edge.setTarget(Node target)	Sets the target of the current Edge to target.

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

Modifier and Type	Method	Description
List<Node>	NodeHierarchy.getAllChildNodes(List<Node> n)
List<Node>	NodeHierarchy.getAllParentNodes(List<Node> n)
List<Node>	NodeHierarchy.getDirectChildNodes(List<Node> n)
List<Node>	NodeHierarchy.getDirectParentNodes(List<Node> n)

Uses of Node in org.graffiti.plugin.algorithm

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

Modifier and Type	Method	Description
void	AbstractThreadSaveLayoutAlgorithm.storeOrSetNodePosition(boolean setAllNodePositions, int index, Node n, double x, double y)	Stores a node position (from the layout thread) or sets the node position of a node to a stored position (from the FrameMain thread).

Method parameters in org.graffiti.plugin.algorithm with type arguments of type Node

Modifier and Type	Method	Description
JMenuItem[]	ProvidesNodeContextMenu.getCurrentNodeContextMenuItem(Collection<Node> selectedNodes)	This method should be implemented, as that it returns the desired Context-MenuItem for the Plugin.

Uses of Node in org.graffiti.plugin.parameter

Methods in org.graffiti.plugin.parameter that return Node

Modifier and Type	Method	Description
Node	NodeParameter.getNode()	Returns the Node contained in this NodeParameter.
Node[]	NodeParameter.getPossibleNodes()

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

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

Uses of Node in org.graffiti.plugins.attributecomponents.simplelabel

Methods in org.graffiti.plugins.attributecomponents.simplelabel with parameters of type Node

Modifier and Type	Method	Description
static String	LabelComponent.getBestAutoOutsideSetting(Node n)

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

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

Modifier and Type	Method	Description
static boolean	MegaCreateTool.isTemporaryNode(Node n)

Uses of Node in org.graffiti.selection

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

Modifier and Type	Method	Description
Collection<Node>	Selection.getNodes()	Returns the list of selected nodes.

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

Modifier and Type	Method	Description
void	Selection.add(Node node)	Adds the given node to the list of selected nodes.

Uses of Node in org.graffiti.undo

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

Constructor	Description
AddNodeEdit(Node node, Graph graph, Map<GraphElement,GraphElement> geMap)	Constructor for AddNodeEdit.

Uses of Node in org.graffiti.util

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

Modifier and Type	Method	Description
boolean	GeneralUtils.existsEdge(Node n1, Node n2)	True iff any edge between n1 (source) and n2 (target) exists.
static Collection<Edge>	GeneralUtils.getEdges(Node n1, Node n2)	Returns a Collection of edges between n1 (source) and n2 (target).

Uses of Node in org.vanted.indexednodes

Methods in org.vanted.indexednodes that return Node

Modifier and Type	Method	Description
Node	IndexedNodeSet.get(int index)

Methods in org.vanted.indexednodes with parameters of type Node

Modifier and Type	Method	Description
void	IndexedNodeSet.add(Node node)	Adds a node from the basis collection passed on construction to this set.
static org.apache.commons.math3.linear.RealVector	IndexedGraphOperations.calcDistances(Node from, IndexedNodeSet inSet)	Calculates the distance vector from the specified node to all other nodes in the given org.vanted.indexednodes.IndexedNodeSet.
boolean	IndexedNodeSet.contains(Node node)	Adds a node from the super set passed on construction to this set.
int	IndexedNodeSet.getIndex(Node node)	Returns the index in this set, based on the indexing of the based collection.
IndexedNodeSet	IndexedNodeSet.getInducedNeighboursOf(Node of)	Returns a org.vanted.addons.indexednodes.IndexedNodeSet containing all neighbors of the node specified node that are also contained in this set.
boolean	IndexedNodeSet.isContainedBasisCollectionAndSet(Node node)	Returns true if node is contained in this sets basis collection as well as in this set itself.
void	IndexedNodeSet.remove(Node node)	Removes a node from the basis collection passed on construction from this set.

Method parameters in org.vanted.indexednodes with type arguments of type Node

Modifier and Type	Method	Description
static IndexedNodeSet	IndexedNodeSet.emptySetOf(Collection<Node> allNodes)	Constructs an empty set with the given node collection as basic collection.
static IndexedNodeSet	IndexedNodeSet.setOfAllIn(Collection<Node> allNodes)	Constructs an set with the given node collection as basic collection, containing all nodes from the basis collection.

Uses of Node in org.vanted.plugins.layout.adaptagrams.edgerouting

Methods in org.vanted.plugins.layout.adaptagrams.edgerouting with parameters of type Node

Modifier and Type	Method	Description
static org.adaptagrams.ShapeRef	AdaptagramsRouting.defineShapeRef(org.adaptagrams.Router router, View view, Node node)	Defines a ShapeRef for a node.
static void	AdaptagramsRouting.fixSourceBendPoints(ArrayList<Vector2d> edgeBends, View view, Node node)	Fixes the edge bend points at the source node.
static void	AdaptagramsRouting.fixTargetBendPoints(ArrayList<Vector2d> edgeBends, View view, Node node)	Fixes the edge bend points at the target node.

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

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

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

Methods in org.vanted.plugins.layout.multilevelframework that return types with arguments of type Node

Modifier and Type	Method	Description
Collection<? extends Node>	MergedNode.getInnerNodes()

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

Modifier and Type	Method	Description
Edge	MultilevelGraph.addEdge(Node source, Node target)	Adds an undirected AdjListEdge to the topmost level (i.e.
void	MergedNode.addInnerNode(Node node)	Deprecated.

Method parameters in org.vanted.plugins.layout.multilevelframework with type arguments of type Node

Modifier and Type	Method	Description
MergedNode	MultilevelGraph.addNode(Set<Node> representedNodes)	Add a new MergedNode to the topmost coarsening level (i.e.
static List<? extends CoarsenedGraph>	MlfHelper.calculateConnectedComponentsOfSelection(Set<Node> selection)	Calculate the subgraph induced by the selection and split it up into its connected components.

Constructor parameters in org.vanted.plugins.layout.multilevelframework with type arguments of type Node

Constructor	Description
MergedNode(Graph g, Set<Node> nodes)	Create a new MergedNode.

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

Methods in org.vanted.plugins.layout.stressminimization that return types with arguments of type Node

Modifier and Type	Method	Description
Supplier<HashMap<Node,Vector2d>>	BackgroundAlgorithm.getLayout()
Supplier<HashMap<Node,Vector2d>>	StressMinimizationImplementation.getLayoutSupplier()