A-Index (Vanted 2.8.3 API)

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A

a - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors.LineModeSetting
a - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.ResultPair
a - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kgml.NodePair
a() - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(Object) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(String, boolean) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(String, char) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(String, double) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(String, double[]) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(String, double[][]) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(String, float) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(String, int) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(String, Object) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(String, String[]) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
a(String, Vector) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
A - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_ABS - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_B_MAX - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_B_MIN - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_DIV_B - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_EXP - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_LOG - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_LOG10 - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_MINUS_B - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_MULT_B - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_PLUS_B - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_POW_B - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_POW_INV_B - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
A_SGN - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
aAll - Variable in class qmwi.kseg.som.diagram.DiagrammPaneData
ABOUT_COMMAND - Static variable in class org.jfree.chart.demo.JFreeChartDemo: About action command.
ABOVE - org.AlignmentSetting
ABOVE - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants: Constant used to specify the position of a label according to a node.
ABOVELEFT - org.AlignmentSetting
ABOVELEFT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants: Constant used to specify the position of a label according to a node.
ABOVERIGHT - org.AlignmentSetting
ABOVERIGHT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants: Constant used to specify the position of a label according to a node.
ABSHOR - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
ABSOLUTE - org.graffiti.plugins.views.defaults.ThicknessAttributeEditor.ArrowHeadModes
absoluteInhibitorArrow - Static variable in class org.graffiti.plugins.editcomponents.defaults.EdgeArrowShapeEditComponent
AbsoluteInhibitorArrowShape - Class in org.graffiti.plugins.views.defaults
AbsoluteInhibitorArrowShape() - Constructor for class org.graffiti.plugins.views.defaults.AbsoluteInhibitorArrowShape
AbsoluteInhibitorArrowShape(float) - Constructor for class org.graffiti.plugins.views.defaults.AbsoluteInhibitorArrowShape
absoluteStimulationArrow - Static variable in class org.graffiti.plugins.editcomponents.defaults.EdgeArrowShapeEditComponent
AbsoluteStimulationArrowShape - Class in org.graffiti.plugins.views.defaults: DOCUMENT ME!
AbsoluteStimulationArrowShape() - Constructor for class org.graffiti.plugins.views.defaults.AbsoluteStimulationArrowShape: Constructs a new arrow.
AbsoluteStimulationArrowShape(float) - Constructor for class org.graffiti.plugins.views.defaults.AbsoluteStimulationArrowShape
AbstractAlgorithm - Class in org.graffiti.plugin.algorithm: Implements some empty versions of non-obligatory methods.
AbstractAlgorithm() - Constructor for class org.graffiti.plugin.algorithm.AbstractAlgorithm
AbstractAnimatedAlgorithm - Class in org.graffiti.plugin.algorithm: Gives a standard implementation for the execute() method.
AbstractAnimatedAlgorithm() - Constructor for class org.graffiti.plugin.algorithm.AbstractAnimatedAlgorithm
AbstractAnnotationProvider - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe
AbstractAnnotationProvider() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.AbstractAnnotationProvider
AbstractArrowShape - Class in org.graffiti.plugins.views.defaults: DOCUMENT ME!
AbstractArrowShape() - Constructor for class org.graffiti.plugins.views.defaults.AbstractArrowShape
AbstractAttributable - Class in org.graffiti.attributes: Provides common functionality for Attributable classes.
AbstractAttributable() - Constructor for class org.graffiti.attributes.AbstractAttributable: Constructs a new AbstractAttribute instance.
AbstractAttributable(CollectionAttribute) - Constructor for class org.graffiti.attributes.AbstractAttributable: Constructs a new AbstractAttribute instance.
AbstractAttribute - Class in org.graffiti.attributes: Provides common functionality for classes implementing the Attribute interface.
AbstractAttribute() - Constructor for class org.graffiti.attributes.AbstractAttribute
AbstractAttribute(String) - Constructor for class org.graffiti.attributes.AbstractAttribute: Constructor for setting the id of an AbstractAttribute.
AbstractAttributeComponent - Class in org.graffiti.plugin.attributecomponent: This component represents a org.graffiti.attributes.Attribute.
AbstractAttributeComponent() - Constructor for class org.graffiti.plugin.attributecomponent.AbstractAttributeComponent: Instantiates an AttributeComponent
AbstractAttributeListener - Class in org.graffiti.event: An abstract adapter class for receiving attribute events.
AbstractAttributeListener() - Constructor for class org.graffiti.event.AbstractAttributeListener
AbstractButtonScaler - Class in org.vanted.scaling.scalers.component: An AbstractButton-specific extension of ComponentScaler.
AbstractButtonScaler(float) - Constructor for class org.vanted.scaling.scalers.component.AbstractButtonScaler
AbstractCategoryItemLabelGenerator - Class in org.jfree.chart.labels: A base class that can be used to create a label or tooltip generator that can be assigned to a CategoryItemRenderer.
AbstractCategoryItemRenderer - Class in org.jfree.chart.renderer: An abstract base class that you can use to implement a new CategoryItemRenderer.
AbstractCellEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model
AbstractCellEditor() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.AbstractCellEditor
AbstractCollectionAttribute - Class in org.graffiti.attributes: Provides common functionality for CollectionAttribute instances.
AbstractCollectionAttribute(String) - Constructor for class org.graffiti.attributes.AbstractCollectionAttribute: Constructor for setting the id of an AbstractCollectionAttribute.
AbstractDataset - Class in org.jfree.data: An abstract implementation of the Dataset interface, containing a mechanism for registering change listeners.
AbstractDialogableEditComponent - Class in org.graffiti.plugin.editcomponent: AbstractDialogableEditComponent provides some default extensions of the AbstractValueEditComponent for those instances of ValueEditComponent which offer an arbitrary dialog for specifying the corresponding attribute value.
AbstractEdge - Class in org.graffiti.graph: Provides default implementations of methods on edges.
AbstractEdge(Graph) - Constructor for class org.graffiti.graph.AbstractEdge: Constructs a new AbstractEdge.
AbstractEdge(Graph, CollectionAttribute) - Constructor for class org.graffiti.graph.AbstractEdge: Constructs a new AbstractEdge.
AbstractEdgeListener - Class in org.graffiti.event: An abstract adapter class for receiving edge events.
AbstractEdgeListener() - Constructor for class org.graffiti.event.AbstractEdgeListener
AbstractEditorAlgorithm - Class in org.graffiti.plugin.algorithm
AbstractEditorAlgorithm() - Constructor for class org.graffiti.plugin.algorithm.AbstractEditorAlgorithm
AbstractEvent - Class in org.graffiti.event: This class is merely meant to group all the Node-/Edge-/ etc.
AbstractEvent(Object) - Constructor for class org.graffiti.event.AbstractEvent: Constructs an AbstractEvent with object o as source.
AbstractEvent.EVENTTYPE - Enum in org.graffiti.event
AbstractExperimentDataProcessor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe: Management of action commands for data mapping.
AbstractExperimentDataProcessor() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.AbstractExperimentDataProcessor
AbstractExperimentDataProcessor(boolean) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.AbstractExperimentDataProcessor
AbstractGraffitiComponent - Class in org.graffiti.plugin.gui: Abstract class for default containers.
AbstractGraffitiContainer - Class in org.graffiti.plugin.gui: Abstract class for default containers.
AbstractGraffitiValueEditContainer - Class in org.graffiti.editor.dialog: Provides an abstract implementation of the interface ValueEditContainer in graffiti style.
AbstractGraffitiValueEditContainer() - Constructor for class org.graffiti.editor.dialog.AbstractGraffitiValueEditContainer: Constructor for AbstractGraffitiValueEditContainer.
AbstractGraph - Class in org.graffiti.graph: Provides further functionality for graphs.
AbstractGraph() - Constructor for class org.graffiti.graph.AbstractGraph: Constructs a new instance of an AbstractGraph.
AbstractGraph(CollectionAttribute) - Constructor for class org.graffiti.graph.AbstractGraph: Constructs a new instance of an AbstractGraph.
AbstractGraph(ListenerManager) - Constructor for class org.graffiti.graph.AbstractGraph: Constructs a new instance of an AdjListGraph.
AbstractGraph(ListenerManager, CollectionAttribute) - Constructor for class org.graffiti.graph.AbstractGraph: Constructs a new instance of an AdjListGraph.
AbstractGraphElement - Class in org.graffiti.graph: GraphElements are Attributables which know the graph they belong to.
AbstractGraphElement() - Constructor for class org.graffiti.graph.AbstractGraphElement: Constructs a new AbstrctGraphElement.
AbstractGraphElement(CollectionAttribute) - Constructor for class org.graffiti.graph.AbstractGraphElement: Constructs a new AbstrctGraphElement.
AbstractGraphElement(Graph) - Constructor for class org.graffiti.graph.AbstractGraphElement: Constructs a new AbstrctGraphElement.
AbstractGraphElement(Graph, CollectionAttribute) - Constructor for class org.graffiti.graph.AbstractGraphElement: Constructs a new AbstrctGraphElement.
AbstractGraphElementComponent - Class in org.graffiti.plugins.views.defaults: Class that shares common members for all GraphElementComponents.
AbstractGraphListener - Class in org.graffiti.event: An abstract adapter class for receiving graph events.
AbstractGraphListener() - Constructor for class org.graffiti.event.AbstractGraphListener
AbstractInputSerializer - Class in org.graffiti.plugin.io: Provides additional methods to access a graph file from different kinds of input.
AbstractInputSerializer() - Constructor for class org.graffiti.plugin.io.AbstractInputSerializer
AbstractIntervalXYDataset - Class in org.jfree.data: An base class that you can use to create new implementations of the XYDataset interface.
AbstractIntervalXYDataset() - Constructor for class org.jfree.data.AbstractIntervalXYDataset
AbstractIOSerializer - Class in org.graffiti.plugin.io: Provides additional methods to read and write from/to different kinds of targets.
AbstractIOSerializer() - Constructor for class org.graffiti.plugin.io.AbstractIOSerializer
AbstractLimitableParameter - Class in org.graffiti.plugin.parameter: This abstract class provides a default implementation for the toXMLString method and specifies an interval size between the limitable parameter's values to be implemented for finer input control.
AbstractLimitableParameter(String, String) - Constructor for class org.graffiti.plugin.parameter.AbstractLimitableParameter: Constructs a new abstract limitable parameter.
AbstractMode - Class in org.graffiti.plugin.mode: This class provides a skeletal implementation of the interface Mode.
AbstractNode - Class in org.graffiti.graph: Abstract class AbstractNode common functionality for Node implementations.
AbstractNode(Graph) - Constructor for class org.graffiti.graph.AbstractNode: Constructs a new AbstractNode.
AbstractNode(Graph, CollectionAttribute) - Constructor for class org.graffiti.graph.AbstractNode: Constructs a new AbstractNode.
AbstractNodeListener - Class in org.graffiti.event: An abstract adapter class for receiving node events.
AbstractNodeListener() - Constructor for class org.graffiti.event.AbstractNodeListener
AbstractOptionPane - Class in org.graffiti.options: The default implementation of the option pane interface.
AbstractOutputSerializer - Class in org.graffiti.plugin.io: Provides additional methods to write a graph object.
AbstractOutputSerializer() - Constructor for class org.graffiti.plugin.io.AbstractOutputSerializer
AbstractParameterDialog - Class in org.graffiti.editor.dialog: AbstractParameterDialog provides an abstract implementation of the ParamterDialog for editing name-value pairs.
AbstractParameterDialog(Frame, boolean) - Constructor for class org.graffiti.editor.dialog.AbstractParameterDialog: Constructs a new abstract parameter dialog.
AbstractRenderer - Class in org.jfree.chart.renderer: Base class providing common services for renderers.
AbstractRenderer() - Constructor for class org.jfree.chart.renderer.AbstractRenderer: Default constructor.
AbstractResourceIOHandler - Class in org.graffiti.plugin.io.resources
AbstractResourceIOHandler() - Constructor for class org.graffiti.plugin.io.resources.AbstractResourceIOHandler
AbstractSeriesDataset - Class in org.jfree.data: An abstract implementation of the SeriesDataset interface, containing a mechanism for registering change listeners.
AbstractSingleParameter - Class in org.graffiti.plugin.parameter: Implements functions that are common in all SingleParameters.
AbstractSingleParameter(Object, String, String) - Constructor for class org.graffiti.plugin.parameter.AbstractSingleParameter: Constructs a new abstract single parameter class.
AbstractSingleParameter(String, String) - Constructor for class org.graffiti.plugin.parameter.AbstractSingleParameter: Constructs a new abstract single parameter class.
AbstractTab - Class in org.graffiti.plugins.inspectors.defaults: Represents an inspector tab.
AbstractTab() - Constructor for class org.graffiti.plugins.inspectors.defaults.AbstractTab: Creates a new AbstractTab object.
AbstractThreadSaveLayoutAlgorithm - Class in org.graffiti.plugin.algorithm: Basis for Thread Safe (layout) Plugins and communication to the MainFrame
AbstractThreadSaveLayoutAlgorithm() - Constructor for class org.graffiti.plugin.algorithm.AbstractThreadSaveLayoutAlgorithm
AbstractTool - Class in org.graffiti.plugin.tool: Provides an abstract implementation of the Tool interface.
AbstractTool() - Constructor for class org.graffiti.plugin.tool.AbstractTool
AbstractTreeTableModel - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model: An abstract implementation of the TreeTableModel interface, handling the list of listeners.
AbstractTreeTableModel(Object) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.AbstractTreeTableModel
AbstractUndoableTool - Class in org.graffiti.plugin.tool: Superclass for all tools that provide undo information for their actions.
AbstractUndoableTool() - Constructor for class org.graffiti.plugin.tool.AbstractUndoableTool
AbstractValueEditComponent - Class in org.graffiti.plugin.editcomponent: The class AbstractValueEditComponent provides some generic implementation for ValueEditComponents.
AbstractValueEditContainer - Class in org.graffiti.editor.dialog: This class provides an abstract implementation of the ValueEditComponent-interface.
AbstractView - Class in org.graffiti.plugin.view: enclosing_type
AbstractView() - Constructor for class org.graffiti.plugin.view.AbstractView: Constructs a new GraffitiView.
AbstractView(Graph) - Constructor for class org.graffiti.plugin.view.AbstractView: Constructs a new GraffitiView for the specified Graph.
AbstractXYDataset - Class in org.jfree.data: An base class that you can use to create new implementations of the XYDataset interface.
AbstractXYDataset() - Constructor for class org.jfree.data.AbstractXYDataset
AbstractXYItemLabelGenerator - Class in org.jfree.chart.labels: A base class for creating item label generators.
AbstractXYItemRenderer - Class in org.jfree.chart.renderer: A base class that can be used to create new XYItemRenderer implementations.
AbstractXYZDataset - Class in org.jfree.data: An base class that you can use to create new implementations of the XYZDataset interface.
AbstractXYZDataset() - Constructor for class org.jfree.data.AbstractXYZDataset
ABSVERT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
ac() - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
ac(Object) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
ac(String, boolean) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
ac(String, char) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
ac(String, double) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
ac(String, double[][]) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
ac(String, float) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
ac(String, int) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
ac(String, Object) - Static method in class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
accept(File) - Method in class org.graffiti.core.GenericFileFilter: Whether the given file is accepted by this filter.
accept(File) - Method in class org.graffiti.managers.pluginmgr.PluginFileFilter
accept(GuiRow, String) - Method in interface org.SearchFilter
accept(IndexedComponent) - Method in class org.vanted.indexednodes.accumulators.DistanceAccumulator
accept(IndexedComponent) - Method in class org.vanted.indexednodes.accumulators.EdgeCountAccumulator
accept(IndexedComponent) - Method in class org.vanted.indexednodes.accumulators.IndexedEdgeListAccumulator
accept(IndexedComponent) - Method in class org.vanted.indexednodes.accumulators.IndexedNodeSetAccumulator
accept(IndexedComponent) - Method in class org.vanted.indexednodes.accumulators.NodeCountAccumulator
ACCNOS - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathGene
action_table() - Method in class org.graffiti.plugins.ios.importers.gml.parser: Access to parse-action table.
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggGroupPartAttributeEditor
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggReactionIdAttributeEditor
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggReactionTypeAttributeEditor
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggRelationTypeAttributeEditor
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.KeggTypeAttributeEditor
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.enhanced_attribute_editors.EnhDoubleEditComponent
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.ClusterHelperToolbarComponent
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsPanel
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.FileOpenAction
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.FileSaveAsAction
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.FontChooser
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.MessageBox
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.TabKegg
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.TabStatistics
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate.RotateAlgorithm
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.set_background_color.SetBackgroundColorAlgorithm
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.set_background_color.WindowSettings
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit.AlignNodesComponent
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit.ZoomFitChangeComponent
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover.CenterLayouterAlgorithm
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid_placement.GridPlacementAlgorithm
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.DebugSelectionCheck
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup.DeleteNodesAlgorithm
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy.HierarchyAlgorithm
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy.SelectLeafNodesAlgorithm
actionPerformed(ActionEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskWindow
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.AddAttributeAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.ChangeAttributeValueAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.CloneViewAction: Executes this action.
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.CloseViewAction: Executes this action.
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.CopyAction: Executes this action.
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.CutAction: Executes this action.
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.DeleteAction: Executes this action.
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.DeleteAttributeAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.EditRedoAction: Implementation Note: The status of the GUIComponents has to be updated after actionPerformed was executed.
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.EditUndoAction: Implementation Note: The status of the GUIComponents has to be updated after actionPerformed was executed.
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.ExitAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.FileCloseAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.FileNewAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.FileOpenAction
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.FileSaveAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.FileSaveAllAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.FileSaveAsAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.PasteAction: Executes this action.
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.PluginManagerEditAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.RedrawViewAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.RunAlgorithm
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.SelectAllAction: Executes this action.
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.ShowPreferencesAction
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.actions.ViewNewAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.dialog.DefaultParameterDialog
actionPerformed(ActionEvent) - Method in class org.graffiti.editor.ViewTypeChooser
actionPerformed(ActionEvent) - Method in class org.graffiti.managers.pluginmgr.PluginManagerDialog: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class org.graffiti.managers.pluginmgr.PluginSelector
actionPerformed(ActionEvent) - Method in class org.graffiti.options.OptionsDialog: Called, if a button in the dialog is pressed.
actionPerformed(ActionEvent) - Method in class org.graffiti.plugin.actions.PopupAction: Executes this action.
actionPerformed(ActionEvent) - Method in class org.graffiti.plugin.gui.ToolButton
actionPerformed(ActionEvent) - Method in class org.graffiti.plugins.guis.switchselections.SelectionChangeAction
actionPerformed(ActionEvent) - Method in class org.graffiti.plugins.guis.switchselections.SelectionSaveAction
actionPerformed(ActionEvent) - Method in class org.graffiti.plugins.tools.enhancedzoomtool.ZoomChangeComponent
actionPerformed(ActionEvent) - Method in class org.graffiti.plugins.tools.zoomtool.ZoomChangeComponent: Deprecated.
actionPerformed(ActionEvent) - Method in class org.graffiti.plugins.views.matrix.MatrixView
actionPerformed(ActionEvent) - Method in class org.graffiti.session.EditorSession: Registrates the selected Tool as an MouseInputListener at the view.
actionPerformed(ActionEvent) - Method in class org.graffiti.util.MaximizeManager
actionPerformed(ActionEvent) - Method in class org.jfree.chart.ChartPanel: Handles action events generated by the popup menu.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.ChartTiming1: Receives notification of action events (in this case, from the Timer).
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.ChartTiming2: Receives notification of action events (in this case, from the Timer).
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.ChartTiming3: Receives notification of action events (in this case, from the Timer).
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.ChartTiming4: Receives notification of action events (in this case, from the Timer).
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.CyclicXYPlotDemo: Receives notification of an action event.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.DynamicDataDemo: Handles a click on the button by adding new (random) data.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.DynamicDataDemo2: Handles a click on the button by adding new (random) data.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.DynamicDataDemo3: Handles a click on the button by adding new (random) data.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.JFreeChartDemo: Handles menu selections by passing control to an appropriate method.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.MultipleDatasetDemo1: Handles a click on the button by adding new (random) data.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.PanScrollZoomDemo: Handles an action event.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.SecondaryDatasetDemo2: Handles a click on the button by adding new (random) data.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.SerializationTest1: Handles a click on the button by adding new (random) data.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.XYStepAreaChartDemo: Change options according to settings.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.demo.XYTickLabelDemo: When a checkbox is changed ...
actionPerformed(ActionEvent) - Method in class org.jfree.chart.PolarChartPanel: Handles action events generated by the popup menu.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.ui.AxisPropertyEditPanel: Handles user interaction with the property panel.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.ui.ChartPropertyEditPanel: Handles user interactions with the panel.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.ui.ColorBarPropertyEditPanel: Handles actions from within the property panel.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.ui.PlotPropertyEditPanel: Handles user actions generated within the panel.
actionPerformed(ActionEvent) - Method in class org.jfree.chart.ui.TitlePropertyEditPanel: Handles button clicks by passing control to an appropriate handler method.
actionPerformed(ActionEvent) - Method in class org.vanted.osx.OpenFileAction
activate() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.IPK_MegaCreateTool
activate() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.IPK_MegaMoveTool
activate() - Method in class org.graffiti.plugin.tool.AbstractTool: Classes that overwrite this method should call super.active first.
activate() - Method in interface org.graffiti.plugin.tool.Tool: Called when the tool is activated.
activate() - Method in class org.graffiti.plugins.modes.defaults.AdvancedLabelTool
activate() - Method in class org.graffiti.plugins.modes.defaults.LabelTool
activate() - Method in class org.graffiti.plugins.modes.defaults.MegaCreateTool: The method additionally registers a key used to delete graph elements.
activate() - Method in class org.graffiti.plugins.modes.defaults.MegaMoveTool: The method additionally registers a key used to delete graph elements.
activateAddon(int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonManagerPlugin: Activate deactivated addon.
activateAddon(String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonManagerPlugin
activateTool(String) - Static method in class org.graffiti.plugin.tool.AbstractTool
activation - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.SubtypeName
ACTIVE - Static variable in class org.graffiti.selection.SelectionModel: DOCUMENT ME!
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.data_mapping.DataMapping
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.CloseAllWindows
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.RecreateView
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.launch_gui.LaunchGui
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.PutIntoSidePanel
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.set_background_color.SetBackgroundColorAlgorithm
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph.ShowLayoutTab
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.DuplicateEdge
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.RemoveParallelEdges
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ResetEdgeSourceOrTarget
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.SelectClusterAlgorithm
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ChangeEdgeStyle
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ChangeElementStyle
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ChangeNodeStyle
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ExportDataTableAlgorithm
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.SearchAndSelecAlgorithm
activeForView(View) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.WebsiteGeneration
activeForView(View) - Method in interface org.graffiti.plugin.algorithm.EditorAlgorithm
activeForView(View) - Method in class org.vanted.plugins.layout.stressminimization.StressMinimizationLayout
ActiveSetPlacement - Class in placement
ActiveSetPlacement(Variable[]) - Constructor for class placement.ActiveSetPlacement
activeStartLayoutButton - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.plugin_settings.PreferencesDialog
AdaptagramsLibrary - Class in org.vanted.plugins.layout.adaptagrams
AdaptagramsLibrary() - Constructor for class org.vanted.plugins.layout.adaptagrams.AdaptagramsLibrary
AdaptagramsRouting - Class in org.vanted.plugins.layout.adaptagrams.edgerouting
AdaptagramsRouting() - Constructor for class org.vanted.plugins.layout.adaptagrams.edgerouting.AdaptagramsRouting
add(double, double) - Method in class org.jfree.data.XYSeries: Adds a data item to the series and sends a SeriesChangeEvent to all registered listeners.
add(double, double, boolean) - Method in class org.jfree.data.XYSeries: Adds a data item to the series and, if requested, sends a SeriesChangeEvent to all registered listeners.
add(double, double, Comparable, Comparable) - Method in class org.jfree.data.statistics.DefaultStatisticalCategoryDataset
add(double, double, Comparable, Comparable, boolean) - Method in class org.jfree.data.statistics.DefaultStatisticalCategoryDataset: Adds a mean and standard deviation to the table.
add(double, double, Comparable, Comparable, boolean, boolean, String, String, boolean, boolean) - Method in class org.BioStatisticalCategoryDataset: Adds a mean, a standard deviation and the info about the t test to the table.
add(double, double, Comparable, Comparable, boolean, boolean, String, String, boolean, Color, Color, boolean) - Method in class org.BioStatisticalCategoryDataset
add(double, double, String) - Method in class org.jfree.data.CategoryTableXYDataset: Adds a data item to this data set.
add(double, Number) - Method in class org.jfree.data.XYSeries: Adds a data item to the series and sends a SeriesChangeEvent to all registered listeners.
add(double, Number, boolean) - Method in class org.jfree.data.XYSeries: Adds a data item to the series and, if requested, sends a SeriesChangeEvent to all registered listeners.
add(double, RectangleEdge) - Method in class org.jfree.chart.axis.AxisSpace: Adds some space to the edge corresponding to the specified axis location.
add(int) - Method in class org.vanted.indexednodes.IndexedNodeSet: Adds the node at index to this set.
add(int, int) - Method in class org.vanted.indexednodes.IndexedEdgeList: Add an edge indicated by indices.
add(int, SubstanceInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
add(int, SubstanceInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface
add(ConditionInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
add(ConditionInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface
add(NumericMeasurementInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample
add(NumericMeasurementInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface
add(SampleInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
add(SampleInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface
add(SubstanceInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
add(SubstanceInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface
add(Component) - Method in class org.graffiti.plugin.gui.ModeToolbar: This function add the specified component to this toolbar.
add(Number, Number) - Method in class org.jfree.data.XYSeries: Adds new data to the series and sends a SeriesChangeEvent to all registered listeners.
add(Number, Number, boolean) - Method in class org.jfree.data.XYSeries: Adds new data to the series and, if requested, sends a SeriesChangeEvent to all registered listeners.
add(Number, Number, String, boolean) - Method in class org.jfree.data.CategoryTableXYDataset: Adds a data item to this data set.
add(String) - Method in exception org.graffiti.plugin.algorithm.PreconditionException: Adds a new cause message without a source.
add(String, Object) - Method in exception org.graffiti.plugin.algorithm.PreconditionException: Adds a new cause message, together with the responsible source.
add(Date, BoxAndWhiskerItem) - Method in class org.jfree.data.statistics.DefaultBoxAndWhiskerXYDataset: Adds an item to the dataset.
add(List, Comparable, Comparable) - Method in class org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset: Adds a list of values relating to one Box and Whisker entity to the table.
add(Attribute) - Method in class org.graffiti.attributes.AbstractCollectionAttribute: Adds a given attribute to the collection.
add(Attribute) - Method in interface org.graffiti.attributes.CollectionAttribute: Adds a given Attribute to the list.
add(Attribute) - Method in class org.graffiti.graphics.LabelAttribute
add(Attribute) - Method in class org.graffiti.graphics.NodeGraphicAttribute
add(Attribute, boolean) - Method in class org.graffiti.attributes.AbstractCollectionAttribute: Adds a given attribute to the collection.
add(Attribute, boolean) - Method in interface org.graffiti.attributes.CollectionAttribute: Adds a given attribute to the collection.
add(Attribute, boolean) - Method in class org.graffiti.graphics.LabelAttribute
add(Attribute, boolean) - Method in class org.graffiti.graphics.NodeGraphicAttribute
add(Edge) - Method in class org.graffiti.selection.Selection: Adds the given edge to the list of selected edges.
add(GraphElement) - Method in class org.graffiti.selection.Selection: Adds the given node or edge to the selection.
add(Node) - Method in class org.graffiti.selection.Selection: Adds the given node to the list of selected nodes.
add(Node) - Method in class org.vanted.indexednodes.IndexedNodeSet: Adds a node from the basis collection passed on construction to this set.
add(Selection) - Method in class org.graffiti.selection.SelectionModel: Adds the given selection to the list of selections.
add(Axis, RectangleEdge) - Method in class org.jfree.chart.axis.AxisCollection: Adds an axis to the collection.
add(TickUnit) - Method in class org.jfree.chart.axis.TickUnits: Adds a tick unit to the collection.
add(LegendItem) - Method in class org.jfree.chart.LegendItemCollection: Adds a legend item to the collection.
add(CategoryPlot, int) - Method in class org.jfree.chart.plot.CombinedDomainCategoryPlot: Adds a subplot to the combined chart.
add(CategoryPlot, int) - Method in class org.jfree.chart.plot.CombinedRangeCategoryPlot: Adds a subplot.
add(XYPlot) - Method in class org.jfree.chart.plot.CombinedDomainXYPlot: Adds a subplot, with a default 'weight' of 1.
add(XYPlot) - Method in class org.jfree.chart.plot.CombinedRangeXYPlot: Adds a subplot, with a default 'weight' of 1.
add(XYPlot, int) - Method in class org.jfree.chart.plot.CombinedDomainXYPlot: Adds a subplot with a particular weight (greater than or equal to one).
add(XYPlot, int) - Method in class org.jfree.chart.plot.CombinedRangeXYPlot: Adds a subplot with a particular weight (greater than or equal to one).
add(Outlier) - Method in class org.jfree.chart.renderer.OutlierList: Adds an outlier to the list.
add(Outlier) - Method in class org.jfree.chart.renderer.OutlierListCollection: Appends the specified element as a new OutlierList to the end of this list if it does not overlap an outlier in an existing list.
add(Task) - Method in class org.jfree.data.gantt.TaskSeries: Adds a task to the series.
add(TaskSeries) - Method in class org.jfree.data.gantt.TaskSeriesCollection: Adds a series to the dataset.
add(SeriesDataset) - Method in class org.jfree.data.CombinedDataset: Adds one SeriesDataset to the combination.
add(SeriesDataset[]) - Method in class org.jfree.data.CombinedDataset: Adds an array of SeriesDataset's to the combination.
add(SeriesDataset, int) - Method in class org.jfree.data.CombinedDataset: Adds one series from a SeriesDataset to the combination.
add(BoxAndWhiskerItem, Comparable, Comparable) - Method in class org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset: Adds a list of values relating to one Box and Whisker entity to the table.
add(RegularTimePeriod, double) - Method in class org.jfree.data.time.TimeSeries: Adds a new data item to the series and sends a SeriesChangeEvent to all registerd listeners.
add(RegularTimePeriod, double, String) - Method in class org.jfree.data.time.TimeTableXYDataset: Adds a new data item to the dataset.
add(RegularTimePeriod, Number) - Method in class org.jfree.data.time.TimeSeries: Adds a new data item to the series and sends a SeriesChangeEvent to all registerd listeners.
add(RegularTimePeriod, Number, String, boolean) - Method in class org.jfree.data.time.TimeTableXYDataset: Adds a new data item to the dataset.
add(TimePeriod, double) - Method in class org.jfree.data.time.TimePeriodValues: Adds a new data item to the series.
add(TimePeriod, Number) - Method in class org.jfree.data.time.TimePeriodValues: Adds a new data item to the series.
add(TimePeriodValue) - Method in class org.jfree.data.time.TimePeriodValues: Adds a data item to the series.
add(TimeSeriesDataItem) - Method in class org.jfree.data.time.TimeSeries: Adds a data item to the series and sends a SeriesChangeEvent to all registerd listeners.
add(XYDataItem) - Method in class org.jfree.data.XYSeries: Adds a data item to the series and sends a SeriesChangeEvent to all registered listeners.
add(XYDataItem, boolean) - Method in class org.jfree.data.XYSeries: Adds a data item to the series and, if requested, sends a SeriesChangeEvent to all registered listeners.
add(PNode<T>) - Method in class placement.MaxPairingHeap
add(T) - Method in class placement.MaxPairingHeap: Insert into the priority queue, and return a PNode that can be used by decreaseKey.
add(T) - Method in interface placement.MaxPriorityQueue
add(T) - Method in class placement.ScanListPriorityQueue
add(T) - Method in class placement.SlowPriorityQueue
ADD_PARENTHESIS - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.GroupLinkProcessingMode
addActionListener(ActionListener) - Method in interface org.graffiti.plugin.gui.GraffitiToolComponent: DOCUMENT ME!
addActionOnKeystroke(JDialog, ActionListener, KeyStroke) - Static method in class org.graffiti.editor.GravistoService
addAddon(PluginDescription, File, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonManagerPlugin: Adds the addon to Vanted.
addAGNWContainer(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the top level container attribute "AGNW" to the given edge.
addAGNWContainer(Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the top level container attribute "AGNW" to the given graph.
addAGNWContainer(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the top level container attribute "AGNW" to the given node.
addAlgebraicRule(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addAlgebraicRule(Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRuleHelper
addAlgebraicRule(Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRuleHelper
addAlgebraicRules(Graph, List<String>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRuleHelper
addAlgorithm(Algorithm) - Method in interface org.graffiti.managers.AlgorithmManager: Adds the given algorithm to the list of algorithms.
addAlgorithm(Algorithm) - Method in class org.graffiti.managers.DefaultAlgorithmManager
addAll(int, Collection<? extends SubstanceInterface>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
addAll(int, Collection<? extends SubstanceInterface>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface
addAll(ExperimentInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
addAll(ExperimentInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface
addAll(Collection<?>) - Method in class org.graffiti.selection.Selection: Adds all (graph)elements of the given collection to this selection.
addAll(Collection<? extends ConditionInterface>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
addAll(Collection<? extends ConditionInterface>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface
addAll(Collection<? extends NumericMeasurementInterface>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample
addAll(Collection<? extends NumericMeasurementInterface>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface
addAll(Collection<? extends SampleInterface>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
addAll(Collection<? extends SampleInterface>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface
addAll(Collection<? extends SubstanceInterface>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
addAll(Collection<? extends SubstanceInterface>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface
addAll(LegendItemCollection) - Method in class org.jfree.chart.LegendItemCollection: Adds the legend items from another collection to this collection.
addAllTimeAttributeListener(AttributeListener) - Method in class org.graffiti.event.ListenerManager: Registers AttributeListener l by adding it to the list of nonstrict and strict transaction AttributeListeners.
addAllTimeEdgeListener(EdgeListener) - Method in class org.graffiti.event.ListenerManager: Registers EdgeListener l by adding it to the list of nonstrict transaction EdgeListeners.
addAllTimeGraphListener(GraphListener) - Method in class org.graffiti.event.ListenerManager: Registers GraphListener l by adding it to the list of GraphListeners.
addAllTimeNodeListener(NodeListener) - Method in class org.graffiti.event.ListenerManager: Registers NodeListener l by adding it to the list of nonstrict transaction NodeListeners.
addAndMerge(ExperimentInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment
addAndMerge(ExperimentInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface
addAndMerge(ExperimentInterface, ExperimentInterface) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment: Deprecated.
addAndMerge(ExperimentInterface, SubstanceInterface) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
addAndMerge(SampleInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition
addAndMerge(SampleInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface
addAndMergeData(ConditionInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance
addAndMergeData(ConditionInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface
addAndOrUpdate(TimeSeries) - Method in class org.jfree.data.time.TimeSeries: Adds or updates data from one series to another.
addAnimation(Animation) - Method in class org.vanted.animation.Animator: Call this method any time you want to add an animation.
Can be called while animations are taking place.
Call it whenever you want.
addAnnotation(CategoryAnnotation) - Method in class org.jfree.chart.plot.CategoryPlot: Adds an annotation to the plot.
addAnnotation(XYAnnotation) - Method in class org.jfree.chart.plot.ContourPlot: Adds an annotation to the plot.
addAnnotation(XYAnnotation) - Method in class org.jfree.chart.plot.XYPlot: Adds an annotation to the plot and sends a PlotChangeEvent to all registered listeners.
addAnnotationProvider(AnnotationProvider) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ExperimentDataInfoPane
addAnnotationsToGraphElements(Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop.TabMetaCrop
addAssignmentRule(Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRuleHelper
addAssignmentRule(Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRuleHelper
addAssignmentRuleFunction(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addAssignmentRules(Graph, List<String>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRuleHelper
addAssignmentRuleVariable(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addAttribut(AttributsAttribut) - Method in class qmwi.kseg.som.diagram.AttributsClass: Insert the method's description here.
addAttribute(Attribute, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addAttribute(Attribute, String) - Method in class org.graffiti.attributes.AbstractAttributable: Adds attr to the attributes at position indicated by path.
addAttribute(Attribute, String) - Method in interface org.graffiti.attributes.Attributable: Adds attr to the attributes at position indicated by path.
AddAttributeAction - Class in org.graffiti.editor.actions: Represents an action to add an attribute to the selected item.
AddAttributeAction(MainFrame) - Constructor for class org.graffiti.editor.actions.AddAttributeAction: Constructs a new add attribute action.
addAttributeComponent(Attribute, GraffitiViewComponent) - Method in interface org.graffiti.plugin.view.GraphElementComponentInterface: Adds an Attribute and its GraffitiViewComponent to the list of registered attributes that can be displayed.
addAttributeComponent(Attribute, GraffitiViewComponent) - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent: Adds an Attribute and its GraffitiViewComponent to the list of registered attributes that can be displayed.
addAttributeConsumer(AttributeConsumer) - Method in class org.graffiti.graph.AbstractGraph: Adds the given attribute consumer to the list of attribute consumers.
addAttributeConsumer(AttributeConsumer) - Method in interface org.graffiti.graph.Graph: Adds the given attribute consumer to the list of attribute consumers.
addAttributeFolder(Attributable, String) - Static method in class org.AttributeHelper
addAttributeFolder(Attributable, String, boolean) - Static method in class org.AttributeHelper
addAttributesToNode(GraphElement, biochemicalReaction) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UbioChemicalReaction
addAttributesToNode(GraphElement, catalysis) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Ucatalysis
addAttributesToNode(GraphElement, complex) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Ucomplex
addAttributesToNode(GraphElement, complexAssembly) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UcomplexAssembly
addAttributesToNode(GraphElement, control) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Ucontrol
addAttributesToNode(GraphElement, conversion) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Uconversion
addAttributesToNode(GraphElement, dna) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Udna
addAttributesToNode(GraphElement, modulation) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Umodulation
addAttributesToNode(GraphElement, pathway) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Upathway
addAttributesToNode(GraphElement, physicalEntity) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UphysicalEntity
addAttributesToNode(GraphElement, physicalInteraction) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UphysicalInteraction
addAttributesToNode(GraphElement, protein) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Uprotein
addAttributesToNode(GraphElement, rna) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Urna
addAttributesToNode(GraphElement, smallMolecule) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UsmallMolecule
addAttributesToNode(GraphElement, transport) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Utransport
addAttributesToNode(GraphElement, transportWithBiochemicalReaction) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UtransportWithBiochemicalReaction
addAttributesToNode(GraphElement, BiochemicalReaction) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UBioChemicalReaction: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Catalysis) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UCatalysis: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Complex) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UComplex: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, ComplexAssembly) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UComplexAssembly: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Control) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UControl: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Conversion) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UConversion: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Degradation) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UDegradation: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Dna) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UDna: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, DnaRegion) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UDnaRegion: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Gene) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UGene: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, GeneticInteraction) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UGeneticInteraction: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Modulation) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UModulation: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, MolecularInteraction) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UMolecularInteraction: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Pathway) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UPathway: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, PhysicalEntity) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UPhysicalEntity: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Protein) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UProtein: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Rna) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.URna: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, RnaRegion) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.URnaRegion: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, SmallMolecule) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.USmallMolecule: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, TemplateReaction) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTemplateReaction: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, TemplateReactionRegulation) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTemplateReactionRegulation: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, Transport) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTransport: adds all information within the biopax class to the attribute set of the node
addAttributesToNode(GraphElement, TransportWithBiochemicalReaction) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTransportWithBiochemicalReaction: adds all information within the biopax class to the attribute set of the node
addAttributeType(Class) - Method in class org.graffiti.attributes.AttributeTypesManager: Adds a given Attribute type class to the list of attribute types.
addAttributsNames(Vector) - Method in class qmwi.kseg.som.diagram.ClassesAll: Insert the method's description here.
addAttributsSelected(Vector) - Method in class qmwi.kseg.som.diagram.ClassesAll: Zuweisung der ausgew�hlte Elemente Speicherung der Indexe der ausgew�hlten Attribute der Parameter a ist ein Vector mit den Namen dieser Attribute Creation date: (17.12.2001 00:29:37)
addAttributsValue(int, String) - Method in class qmwi.kseg.som.diagram.AttributsAll: Insert the method's description here.
addBaseTimelineException(long) - Method in class org.jfree.chart.axis.SegmentedTimeline: Adds a segment relative to the baseTimeline as an exception.
addBaseTimelineException(Date) - Method in class org.jfree.chart.axis.SegmentedTimeline: Adds a segment relative to the baseTimeline as an exception.
addBaseTimelineExclusions(long, long) - Method in class org.jfree.chart.axis.SegmentedTimeline: Adds all excluded segments from the BaseTimeline as exceptions to our timeline.
addBendPointForNodePosition(ArrayList<Vector2d>, int, int, Vector2d) - Static method in class org.vanted.plugins.layout.adaptagrams.edgerouting.AdaptagramsRouting: Adds an edge bend point for the node position.
addBends(Edge, Collection<Vector2d>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper
addBoolean(String, String, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addBoolean(String, String, boolean) - Method in class org.graffiti.attributes.AbstractAttributable: Adds an BooleanAttribute with the given value and id to a CollectionAttribute at path.
addBoolean(String, String, boolean) - Method in interface org.graffiti.attributes.Attributable: Adds a BooleanAttribute with the given value and id to a CollectionAttribute at path.
addBriteEntry(String, Set<BriteEntry>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.KoEntry
addBriteEntryToECEntryMap(String, BriteEntry) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.BriteHierarchy
addBriteEntryToEntryMap(String, BriteEntry) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.BriteHierarchy
addButton(ToolButton) - Method in class org.graffiti.editor.GraffitiButtonGroup: Adds the given button to the button group.
addByte(String, String, byte) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addByte(String, String, byte) - Method in class org.graffiti.attributes.AbstractAttributable: Adds an ByteAttribute with the given value and id to a CollectionAttribute at path.
addByte(String, String, byte) - Method in interface org.graffiti.attributes.Attributable: Adds an ByteAttribute with the given value and id to a CollectionAttribute at path.
addCategoryLabelToolTip(Comparable, String) - Method in class org.jfree.chart.axis.CategoryAxis: Adds a tooltip to the specified category and sends an AxisChangeEvent to all registered listeners.
addCellData(int, int, Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.TableData
addCellEditorListener(CellEditorListener) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.AbstractCellEditor
addChangeListener(AxisChangeListener) - Method in class org.jfree.chart.axis.Axis: Registers an object for notification of changes to the axis.
addChangeListener(ChartChangeListener) - Method in class org.jfree.chart.JFreeChart: Registers an object for notification of changes to the chart.
addChangeListener(LegendChangeListener) - Method in class org.jfree.chart.Legend: Registers an object for notification of changes to the legend.
addChangeListener(PlotChangeListener) - Method in class org.jfree.chart.plot.Plot: Registers an object for notification of changes to the plot.
addChangeListener(RendererChangeListener) - Method in class org.jfree.chart.renderer.AbstractRenderer: Registers an object to receive notification of changes to the renderer.
addChangeListener(RendererChangeListener) - Method in interface org.jfree.chart.renderer.CategoryItemRenderer: Adds a change listener.
addChangeListener(RendererChangeListener) - Method in interface org.jfree.chart.renderer.PolarItemRenderer: Adds a change listener.
addChangeListener(RendererChangeListener) - Method in interface org.jfree.chart.renderer.XYItemRenderer: Add a renderer change listener.
addChangeListener(TitleChangeListener) - Method in class org.jfree.chart.title.Title: Registers an object for notification of changes to the title.
addChangeListener(DatasetChangeListener) - Method in class org.jfree.chart.demo.SampleSignalDataset: Registers an object to receive notification of changes to the dataset.
addChangeListener(DatasetChangeListener) - Method in class org.jfree.chart.demo.SimpleIntervalXYDataset: Registers an object for notification of changes to the dataset.
addChangeListener(DatasetChangeListener) - Method in class org.jfree.chart.demo.SimpleIntervalXYDataset2: Registers an object for notification of changes to the dataset.
addChangeListener(DatasetChangeListener) - Method in class org.jfree.data.AbstractDataset: Registers an object to receive notification of changes to the dataset.
addChangeListener(DatasetChangeListener) - Method in interface org.jfree.data.Dataset: Registers an object for notification of changes to the dataset.
addChangeListener(SeriesChangeListener) - Method in class org.jfree.data.Series: Registers an object with this series, to receive notification whenever the series changes.
addChartMouseListener(ChartMouseListener) - Method in class org.jfree.chart.ChartPanel: Adds a listener to the list of objects listening for chart mouse events.
addChartPanel(JComponent, int, int, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.MyScatterBlock
addChild(BriteEntry) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.BriteEntry
addChild(PluginEntry) - Method in class org.graffiti.managers.pluginmgr.PluginDescription
addClass(AttributsClass) - Method in class qmwi.kseg.som.diagram.AttributsAll: Insert the method's description here.
addClass(ClassesClass) - Method in class qmwi.kseg.som.diagram.ClassesAll: Insert the method's description here.
addClasses(Vector[]) - Method in class qmwi.kseg.som.diagram.ClassesAll: Insert the method's description here.
addCloneToList(String, Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper
addCloseActionListener(ActionListener) - Method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskPanelEntry
addCollapseListener(ActionListener) - Method in class org.FolderPanel
addCollapseListenerDialogSizeUpdate() - Method in class org.FolderPanel
addCommands(String[]) - Method in class scenario.Scenario
addCommands(Collection<String>) - Method in class scenario.Scenario
addComp(JComponent) - Method in class org.FolderPanel
addComp(JComponent, int) - Method in class org.FolderPanel
addCompartment(Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLCompartmentHelper
addCompartment(Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLCompartmentHelper
addCompartment(ListOf<Compartment>, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_Compartment_Reader: Method reads in compartments and is called from class SBML_XML_Reader.java
addCompartment(Model, Graph, String, SBMLCompartmentHelper) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_Compartment_Writer: Adds a compartment and its attributes to the model.
addCompartmentConstant(Graph, String, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addCompartmentName(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addCompartments(Graph, List<String>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLCompartmentHelper
addCompartmentSize(Graph, String, Double) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addCompartmentSpatialDimensions(Graph, String, Double) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addCompartmentUnits(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addComponent(IdRef) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Entry
addComponent(Component) - Method in class org.graffiti.options.AbstractOptionPane: Adds the given component to the option pane.
addComponent(Component, int) - Method in class org.graffiti.options.AbstractOptionPane: Adds a component according to an anchor.
addComponent(String, Component) - Method in class org.graffiti.options.AbstractOptionPane: Adds the given label and component to the option pane.
addConstraint(String, String, double) - Method in class placement.ActiveSetPlacement
addConstraint(String, String, double) - Method in interface placement.Placement
addConstraint(Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLConstraintHelper
addConstraint(Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLConstraintHelper
addConstraint(Graph, Model, String, SBMLConstraintHelper) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_Constraint_Writer: Adds a constraint and its variables to the model
addConstraint(GraphConstraint) - Method in class org.graffiti.session.GraphConstraintChecker: Adds another constraint to the set of constraints in this constraint checker.
addConstraint(ListOf<Constraint>, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_Constraint_Reader: Method reads in constraints and is called from class SBML_XML_Reader.java
addConstraintConstraint(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addConstraintMessage(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addConstraints(Graph, List<String>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLConstraintHelper
addCornerTextItem(String) - Method in class org.jfree.chart.plot.PolarPlot: Add text to be displayed in the lower right hand corner.
addData(SubstanceInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.xml_attribute.XMLAttribute
addData(ValueDataset) - Method in class org.jfree.chart.plot.CompassPlot: Adds a dataset to the compass.
addData(ValueDataset, MeterNeedle) - Method in class org.jfree.chart.plot.CompassPlot: Adds a dataset to the compass.
addDataColumn(int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.SubstanceColumnInformation
addDataMapping(SubstanceInterface) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addDataMapping(Collection<DataSetRow>, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addDatapoint(String, Double, Double, Double, Double, Double, Double, Double, Double, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.kegg_expression.KeggExpressionDataset
addDbLinkValue(String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.KoEntry
addDefaultTextSearchFilter() - Method in class org.FolderPanel
addDefaultTextSearchFilterFixed(String) - Method in class org.FolderPanel
addDelayedAttributeListener(AttributeListener) - Method in class org.graffiti.event.ListenerManager: Registers AttributeListener l by adding it to the list of strict transaction AttributeListeners.
addDelayedEdgeListener(EdgeListener) - Method in class org.graffiti.event.ListenerManager: Registers EdgeListener l by adding it to the list of strict transaction EdgeListeners.
addDelayedGraphListener(GraphListener) - Method in class org.graffiti.event.ListenerManager: Registers GraphListener l by adding it to the list of strict transaction GraphListeners.
addDelayedNodeListener(NodeListener) - Method in class org.graffiti.event.ListenerManager: Registers NodeListener l by adding it to the list of strict transaction NodeListeners.
addDelayToEvent(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addDelayToEvent(Graph, String, Delay) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addDependency(PluginDependency) - Method in class org.graffiti.managers.pluginmgr.PluginDescription: Adds the given dependency to the list of dependencies.
addDependentComponent(GraphElementComponent) - Method in interface org.graffiti.plugin.view.GraphElementComponentInterface: Adds a GraphElementComponent to the list of dependent GraphElementComponents.
addDependentComponent(GraphElementComponent) - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent: Adds a GraphElementComponent to the list of dependent GraphElementComponents.
addDependentParameters(BooleanParameter[]) - Method in class org.graffiti.plugin.parameter.BooleanParameter
addDetachedFrame(GraffitiFrame) - Method in class org.graffiti.editor.MainFrame
AddDiagramLegendAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms
AddDiagramLegendAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.AddDiagramLegendAlgorithm
addDomainMarker(int, Marker, Layer) - Method in class org.jfree.chart.plot.XYPlot: Adds a marker for a renderer and sends a PlotChangeEvent to all registered listeners.
addDomainMarker(Marker) - Method in class org.jfree.chart.plot.ContourPlot: Adds a marker for the domain axis.
addDomainMarker(Marker) - Method in class org.jfree.chart.plot.XYPlot: Adds a marker for the domain axis and sends a PlotChangeEvent to all registered listeners.
addDomainMarker(Marker, Layer) - Method in class org.jfree.chart.plot.XYPlot: Adds a marker for the domain axis in the specified layer and sends a PlotChangeEvent to all registered listeners.
addDouble(double) - Method in class org.graffiti.plugin.algorithm.ThreadSafeOptions
addDouble(String, String, double) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addDouble(String, String, double) - Method in class org.graffiti.attributes.AbstractAttributable: Adds a DoubleAttribute with the given value and id to a CollectionAttribute at path.
addDouble(String, String, double) - Method in interface org.graffiti.attributes.Attributable: Adds a DoubleAttribute with the given value and id to a CollectionAttribute at path.
addDragAndDropHandler(DragAndDropHandler) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.GravistoMainHelper
addEdge(String, String) - Method in class placement.Graph
addEdge(Node, Node) - Method in class org.vanted.plugins.layout.multilevelframework.MultilevelGraph: Adds an undirected AdjListEdge to the topmost level (i.e.
addEdge(Node, Node, boolean) - Method in class org.graffiti.graph.AbstractGraph: Adds a new edge to the current graph.
addEdge(Node, Node, boolean) - Method in interface org.graffiti.graph.Graph: Adds a new Edge to the current Graph.
addEdge(Node, Node, boolean, CollectionAttribute) - Method in class org.graffiti.graph.AbstractGraph: Adds a new edge to the current graph.
addEdge(Node, Node, boolean, CollectionAttribute) - Method in interface org.graffiti.graph.Graph: Adds a new Edge to the current Graph.
addEdgeAttributeType(String, Class<? extends Attribute>) - Static method in class org.graffiti.attributes.AbstractAttribute
addEdgeBend(Edge, double, double) - Static method in class org.AttributeHelper
addEdgeBend(Edge, double, double, boolean) - Static method in class org.AttributeHelper
addEdgeBend(Edge, Vector2d) - Static method in class org.AttributeHelper
addEdgeBends(Edge, Collection<Vector2d>) - Static method in class org.AttributeHelper
addEdgeCopy(Edge, Node, Node) - Method in class org.graffiti.graph.AbstractGraph: Adds a copy of the specified edge to the graph as a new edge between the specified source and target node.
addEdgeCopy(Edge, Node, Node) - Method in interface org.graffiti.graph.Graph: Adds a copy of the specified Edge to the Graph as a new Edge between the specified source and target Node.
addEdgeCopyIfNotExistant(Edge, Node, Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelperBio
AddEdgeEdit - Class in org.graffiti.undo: Class AddNodeEdit makes the add edge action undoable.
AddEdgeEdit(Edge, Graph, Map<GraphElement, GraphElement>) - Constructor for class org.graffiti.undo.AddEdgeEdit: Constructor for AddEdgeEdit.
addEdgeIfNotExistant(Graph, Node, Node, boolean, CollectionAttribute) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelperBio
addEdgeShape(String, String) - Static method in class org.AttributeHelper
addEdit(UndoableEdit) - Method in class org.graffiti.plugin.algorithm.AbstractAlgorithm
addElementsToGraph(Graph, String, HashMap<String, Node>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathPathway
addElementsToGraph(Graph, String, HashMap<String, Node>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathReaction
addEntities(EntityCollection) - Method in interface org.jfree.chart.entity.EntityCollection: Adds the entities from another collection to this collection.
addEntities(EntityCollection) - Method in class org.jfree.chart.entity.StandardEntityCollection: Adds all the entities from the specified collection.
addEntity(ChartEntity) - Method in interface org.jfree.chart.entity.EntityCollection: Adds an entity to the collection.
addEntity(ChartEntity) - Method in class org.jfree.chart.entity.StandardEntityCollection: Adds an entity.
addEntry(String) - Method in class qmwi.kseg.som.DataSet
addEntry(String, boolean) - Method in class qmwi.kseg.som.DataSet
addEntry(SOMdataEntry) - Method in class qmwi.kseg.som.DataSet
addErrorMessage(Exception) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Logger: dummy method, catching errors
addErrorMessage(Exception) - Static method in class org.ErrorMsg: Adds exception to the global exception list, which is then reported to the user and prepared for reporting.
addErrorMessage(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Logger: dummy method, catching errors
addErrorMessage(String) - Static method in class org.ErrorMsg: Adds a errorMessage to a global list.
addErrorMessage(Thread, StackTraceElement[]) - Static method in class org.ErrorMsg
addErrorMessage(Throwable) - Static method in class org.ErrorMsg
addEvent(Graph, Model, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_Event_Writer: Adds an event to the model
addEventAssignment(Graph, String, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventHelper
addEventAssignment(Graph, String, String, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventHelper
addEventAssignmentToEvent(Graph, String, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addEventAssignmentToEvent(Graph, String, EventAssignment) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addEventName(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addEvents(List<Event>, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_Event_Reader: Adds an events to the graph tab
addEventUseValuesFromTriggerTime(Graph, String, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addException(long) - Method in class org.jfree.chart.axis.SegmentedTimeline: Adds a segment as an exception.
addException(long, long) - Method in class org.jfree.chart.axis.SegmentedTimeline: Adds a segment range as an exception.
addException(Date) - Method in class org.jfree.chart.axis.SegmentedTimeline: Adds a segment as an exception.
addExceptions(List) - Method in class org.jfree.chart.axis.SegmentedTimeline: Adds a list of dates as segment exceptions.
addExperimentDataProcessor(ExperimentDataProcessor) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ExperimentDataProcessingManager
addExperimentNameInfoToAllLinesForThisSubstanceNode(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.Experiment2GraphHelper
addFan(int, IndexedNodeSet) - Method in class org.vanted.indexednodes.IndexedEdgeList: Add edges from `source` to all nodes in `targets`.
addFileDropListener(FileDropListener) - Method in class net.iharder.dnd.FileDropBean: Register a listener for FileDropEvents.
addFileDropTarget(Component) - Method in class net.iharder.dnd.FileDropBean: Registers a component as a drop target.
addFirstGuiComponentRow(JComponent, JComponent, boolean, int) - Method in class org.FolderPanel
addFloat(String, String, float) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addFloat(String, String, float) - Method in class org.graffiti.attributes.AbstractAttributable: Adds a FloatAttribute with the given value and id to a CollectionAttribute at path.
addFloat(String, String, float) - Method in interface org.graffiti.attributes.Attributable: Adds a FloatAttribute with the given value and id to a CollectionAttribute at path.
addFolderPanel(String, double) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow.RSSFeedManager
addFrame(GraffitiInternalFrame) - Method in class org.graffiti.editor.GravistoService: Adds a new internal frame to the list of pattern editor frames.
addFunctionDefinition(Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLFunctionDefinitionHelper
addFunctionDefinition(Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLFunctionDefinitionHelper
addFunctionDefinition(Model, Graph, String, SBMLFunctionDefinitionHelper) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_FunctionDefinition_Writer: Adds a function definition and its variables to the model
addFunctionDefinitionFunction(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addFunctionDefinitionName(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addFunctionDefinitions(Graph, List<String>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLFunctionDefinitionHelper
addFunktionDefinition(ListOf<FunctionDefinition>, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_FunctionDefinition_Reader: Method reads in function definitions and is called from class SBML_XML_Reader.java
addGeneForSpecies(String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.KoEntry
addGraph(Graph) - Method in class org.graffiti.graph.AbstractGraph: Adds a Graph g to the current graph.
addGraph(Graph) - Method in interface org.graffiti.graph.Graph: Adds a Graph g to the current Graph.
addGraphNode(Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Entry
addGuiComponentRow(JComponent, JComponent, boolean) - Method in class org.FolderPanel
addGuiComponentRow(JComponent, JComponent, boolean, int) - Method in class org.FolderPanel
addGuiComponentRow(GuiRow, boolean) - Method in class org.FolderPanel
addImport(String) - Method in class scenario.Scenario
addImports(String[]) - Method in class scenario.Scenario
addImports(Collection<String>) - Method in class scenario.Scenario
addInConstraint(Constraint) - Method in class placement.Variable
addInformation(EnzymeStatisticInformation) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.special.EnzymeStatisticInformation
addInitialAssignment(Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLInitialAssignmentHelper
addInitialAssignment(Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLInitialAssignmentHelper
addInitialAssignment(Graph, Model, String, SBMLInitialAssignmentHelper) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_InitialAssignment_Writer: Adds an initial assignment and its variables to the model
addInitialAssignmentFunction(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addInitialAssignments(Graph, List<String>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLInitialAssignmentHelper
addInitialAssignments(ListOf<InitialAssignment>, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_InitialAssignment_Reader: Method reads in initial assignments and is called from class SBML_XML_Reader.java
addInnerNode(Node) - Method in class org.vanted.plugins.layout.multilevelframework.MergedNode: Deprecated.
addInputSerializer(InputSerializer) - Method in class org.graffiti.managers.DefaultIOManager
addInputSerializer(InputSerializer) - Method in interface org.graffiti.managers.IOManager: Registers the given input serializer.
addInt(int) - Method in class org.graffiti.plugin.algorithm.ThreadSafeOptions
addInteger(String, String, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addInteger(String, String, int) - Method in class org.graffiti.attributes.AbstractAttributable: Adds an IntegerAttribute with the given value and id to a CollectionAttribute at path.
addInteger(String, String, int) - Method in interface org.graffiti.attributes.Attributable: Adds an IntegerAttribute with the given value and id to a CollectionAttribute at path.
AddInterestingAttributes - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes
AddInterestingAttributes() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AddInterestingAttributes
addItem(Comparable, Comparable, Number) - Method in class org.jfree.data.xml.CategoryDatasetHandler: Adds an item to the dataset.
addItem(Comparable, Number) - Method in class org.jfree.data.xml.CategorySeriesHandler: Adds an item to the temporary storage for the series.
addItem(Comparable, Number) - Method in class org.jfree.data.xml.PieDatasetHandler: Adds an item to the dataset under construction.
AdditionalIdentifiersAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids
AdditionalIdentifiersAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids.AdditionalIdentifiersAlgorithm
ADDITIVE - org.vanted.scaling.scalers.component.HTMLScaleSupport.Tags
addKineticLaw(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addKineticLaw(Node, KineticLaw) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addKnownMemoryHog(MemoryHog) - Static method in class org.graffiti.editor.GravistoService
addKnownModeToolBar(ModeToolbar) - Static method in class org.graffiti.plugin.gui.ToolButton
addKnownOptionPane(Object, OptionPane) - Method in class org.graffiti.editor.GravistoService: Adds a optionPane to the list of known options-panes.
addLast(Object) - Method in class org.graffiti.util.Queue: Adds the given object to the end of the queue.
addLayoutComponent(Component, Object) - Method in class info.clearthought.layout.TableLayout: Adds the specified component with the specified name to the layout.
addLayoutComponent(String, Component) - Method in class info.clearthought.layout.SingleFiledLayout: Adds the specified component with the specified name to the layout.
addLayoutComponent(String, Component) - Method in class info.clearthought.layout.TableLayout: Adds the specified component with the specified name to the layout.
addLayoutComponent(String, Component) - Method in class org.graffiti.util.MaximizeLayout
addLegendItem(LegendItem) - Method in class org.jfree.chart.title.LegendTitle: Adds a legend item to the LegendTitle.
addLinkProcessor(LinkProcessor) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithm
addListDataListener(ListDataListener) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.MyDynamicObjectListModel
addListener(BiomodelsAccessAdapter.BiomodelsLoaderCallback) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsAccessAdapter
addListener(IOManager.IOManagerListener) - Method in class org.graffiti.managers.DefaultIOManager
addListener(IOManager.IOManagerListener) - Method in interface org.graffiti.managers.IOManager: Adds the given IOManagerListener to the list of io manager listeners.
addListener(ViewManager.ViewManagerListener) - Method in class org.graffiti.managers.DefaultViewManager
addListener(ViewManager.ViewManagerListener) - Method in interface org.graffiti.managers.ViewManager: Registers the given ViewManagerListener.
addListener(AnimatorListener) - Method in class org.vanted.animation.Animator
addLocalParameter(Graph, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.KineticLawHelper
addLocalParameter(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addLocalParameter(Node, LocalParameter) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addLocalParameterName(Node, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addLocalParameterUnits(Node, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addLocalParameterValue(Node, String, Double) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addLocalParemeter(Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.KineticLawHelper
addLong(long) - Method in class org.graffiti.plugin.algorithm.ThreadSafeOptions
addLong(long) - Method in class org.ObjectRef
addLong(String, String, long) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addLong(String, String, long) - Method in class org.graffiti.attributes.AbstractAttributable: Adds an LongAttribute with the given value and id to a CollectionAttribute at path.
addLong(String, String, long) - Method in interface org.graffiti.attributes.Attributable: Adds an LongAttribute with the given value and id to a CollectionAttribute at path.
addMapLinkNode(String, Graph, Node, ActionEvent, boolean, boolean, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.PathwayReferenceAutoCreationAlgorithm
addMapNode(Graph, KeggPathwayEntry) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelperBio
addMappingData2Node(SubstanceInterface, GraphElement, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.Experiment2GraphHelper
addMappingData2Node(SubstanceInterface, Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.Experiment2GraphHelper
addMarker(IntervalMarker) - Method in class org.jfree.chart.axis.MarkerAxisBand: Adds a marker to the band.
addMeasurementsToHierarchy(SampleInterface, String) - Method in class de.ipk_gatersleben.ag_pbi.datahandling.TemplateLoaderInstance
addMeasurementsToHierarchy(SampleInterface, String) - Method in interface de.ipk_gatersleben.ag_pbi.datahandling.TemplateLoaderInterface
addMenuItemForAlgorithmOrExtension(JMenuItem, String) - Method in class org.graffiti.editor.MainFrame: Adds a menu item to the menu given a category The menuitem's action should be a GraffitiAction with the implemented Action that is called, when the user clicks on that menu item The category string defines the place, where this item is places The category string is a '.'-separated string, where each token represents a parental level of the items path e.g.
addMerger(Merger) - Static method in class org.vanted.plugins.layout.multilevelframework.MultilevelFrameworkLayout: Add a new Merger that will be available for the user to choose.
addMessageListener(MessageListener) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view.FastView
addMessageListener(MessageListener) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.NullView
addMessageListener(MessageListener) - Method in class org.graffiti.plugin.view.AbstractView: Adds a message listener to the view.
addMessageListener(MessageListener) - Method in interface org.graffiti.plugin.view.View: Adds a message listener to the view.
addMessageListener(MessageListener) - Method in class org.graffiti.plugins.views.defaults.GraffitiView: Adds a message listener to the view.
addMessageListener(MessageListener) - Method in class org.graffiti.plugins.views.matrix.MatrixView
addMessageToBeSent(String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.network.BroadCastTask
addMode(Mode) - Method in class org.graffiti.managers.DefaultModeManager: Adds the given mode to the list of modes.
addMode(Mode) - Method in interface org.graffiti.managers.ModeManager: Adds the specified mode to the list of modes this manager contains.
addModel(Model, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_Model_Writer: Add attributes to the model.
addModifier(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addModifier(Node, ModifierSpeciesReference) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addModifierCloneToList(String, String, Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper
addMouseListener(MouseListener) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.gui.TristateCheckBox: No one may add mouse listeners, not even Swing!
addMouseListener(MouseListener) - Method in class org.graffiti.plugins.views.defaults.GraffitiView
addMouseMotionListener(MouseMotionListener) - Method in class org.graffiti.plugins.views.defaults.GraffitiView
addNamespaces(Map<String, String>, Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_SBase_Reader: Adds a map of namespaces (namespace, URL) to the graph tab.
addNamespaces(XMLNode, Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_SBase_Reader: Adds the namespaces of an XMLNode to the graph tab
addNeurons(double[][]) - Method in class qmwi.kseg.som.diagram.ClassesAll: Insert the method's description here.
addNewAttribute(Element, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.KGMLhelper
addNewRecentFileMenuItem(File) - Method in class org.graffiti.editor.MainFrame
addNode() - Method in class org.graffiti.graph.AbstractGraph: Adds a new node to the graph.
addNode() - Method in interface org.graffiti.graph.Graph: Adds a new Node to the Graph.
addNode(String, int, int, int, int) - Method in class placement.Graph
addNode(Set<Node>) - Method in class org.vanted.plugins.layout.multilevelframework.MultilevelGraph: Add a new MergedNode to the topmost coarsening level (i.e.
addNode(CollectionAttribute) - Method in class org.graffiti.graph.AbstractGraph: Adds a new node to the graph.
addNode(CollectionAttribute) - Method in interface org.graffiti.graph.Graph: Adds a new node to the graph.
addNodeAttributeType(String, Class<? extends Attribute>) - Static method in class org.graffiti.attributes.AbstractAttribute
addNodeCopy(Node) - Method in class org.graffiti.graph.AbstractGraph: Adds a copy of the specified node to the graph and returns the copy.
addNodeCopy(Node) - Method in interface org.graffiti.graph.Graph: Adds a copy of the specified Node to the Graph.
AddNodeEdit - Class in org.graffiti.undo: Class AddNodeEdit makes the add node action undoable.
AddNodeEdit(Node, Graph, Map<GraphElement, GraphElement>) - Constructor for class org.graffiti.undo.AddNodeEdit: Constructor for AddNodeEdit.
addNodeToGraph(Graph, double, double, double, double, double, Color, Color) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper: Adds a new node to a graph.
addNotes(XMLNode, String, Edge, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_SBase_Reader
addNotes(XMLNode, String, Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_SBase_Reader: This method adds notes to the current object in the graph tab
addNotes(XMLNode, String, Node, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_SBase_Reader: This method adds notes to the current object in the node tab
addObject(Comparable, Object) - Method in class org.jfree.data.KeyedObjects: Adds a new object to the collection, or overwrites an existing object.
addObject(Object, Comparable, Comparable) - Method in class org.jfree.data.KeyedObjects2D: Adds an object to the table.
addObject(ClassesObject) - Method in class qmwi.kseg.som.diagram.ClassesClass: Insert the method's description here.
addObjects(ClassesClass, Vector, int) - Method in class qmwi.kseg.som.diagram.ClassesAll: Insert the method's description here.
addObserver(Observer) - Method in class placement.QPRectanglePlacement
Addon - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.addons
Addon(File, URL, PluginDescription, boolean, ImageIcon) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.Addon
ADDON - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow.FeedDownloadType
ADDON_LOADING - org.FeatureSet
AddonAdapter - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.addons: Use to set up the Add-on initialization and icon.
AddonAdapter() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonAdapter: Default constructor.
addOnAddonLoadingFinishedAction(Runnable) - Static method in class org.ErrorMsg
addOnAppLoadingFinishedAction(Runnable) - Static method in class org.ErrorMsg
AddOnInstallResult - Enum in de.ipk_gatersleben.ag_nw.graffiti.plugins.addons: Type of response upon add-on installation.
AddonInstantiationRuntimeException - Exception in de.ipk_gatersleben.ag_nw.graffiti.plugins.addons
AddonInstantiationRuntimeException(Exception) - Constructor for exception de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonInstantiationRuntimeException
AddonManagerPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.addons: This class manages Add-ons, which are Vanted-plugins loaded during runtime.
AddonManagerPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonManagerPlugin: Creates a new menu-entry for the Add-ons and waits for all plugins to be started.
ADDONS_LOADED - org.ApplicationStatus
addonsLoaded() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonManagerPlugin
AddonsOptionsPane - Class in org.graffiti.options
AddonTableModel - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.addons
AddonTableModel() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonTableModel
addOptionGroup(OptionGroup) - Method in class org.graffiti.options.OptionGroup: Adds the given option group to this option group.
addOptionPane(OptionPane) - Method in class org.graffiti.options.OptionGroup: Adds the given option pane to this option group.
addOrUpdate(RegularTimePeriod, double) - Method in class org.jfree.data.time.TimeSeries: Adds or updates an item in the times series and sends a SeriesChangeEvent to all registered listenrs.
addOrUpdate(RegularTimePeriod, Number) - Method in class org.jfree.data.time.TimeSeries: Adds or updates an item in the times series and sends a SeriesChangeEvent to all registered listenrs.
addOrUpdateExperimentPane(ProjectEntity) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.TabDBE
addOSXHandler(String, String, String, Action) - Static method in class org.vanted.osx.OSXSupport: Adds an OS X handler to the application
addOutConstraint(Constraint) - Method in class placement.Variable
addOutputSerializer(OutputSerializer) - Method in class org.graffiti.managers.DefaultIOManager
addOutputSerializer(OutputSerializer) - Method in interface org.graffiti.managers.IOManager: Registers the given output serializer.
addPair(int, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.UllmannSubraphIsomAdjMatrixState
addParameter(Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLParameterHelper
addParameter(Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLParameterHelper
addParameter(Graph, Model, String, SBMLParameterHelper) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_Parameter_Writer: Adds a parameter and its variables to the model
addParameter(SingleParameter) - Method in interface org.graffiti.plugin.parameter.ParameterList: Adds a SingleParameter to the list.
addParameter(ListOf<Parameter>, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_Parameter_Reader: Method reads in parameter and is called from class SBML_XML_Reader.java
addParameterConstant(Graph, String, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addParameterName(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addParameters(Graph, List<String>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLParameterHelper
addParameterUnits(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addParameterValue(Graph, String, Double) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addPath(String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.services.web.RestService
addPattern(Edge, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the pattern container for the given pattern position at the given edge.
addPattern(Node, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the pattern container for the given pattern position at the given node.
addPatternContainer(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the pattern container attribute "AGNW.PATTERN" to the given edge.
addPatternContainer(Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the pattern container attribute "AGNW.PATTERN" to the given graph.
addPatternContainer(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds the pattern container attribute "AGNW.PATTERN" to the given node.
addPatternInformation(Edge, int, String, Integer, Integer) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds a set of pattern information to the given edge.
addPatternInformation(Node, int, String, Integer, Integer, Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils: Adds a set of pattern information to the given node.
addPatternSession(Session) - Method in class org.graffiti.editor.GravistoService: Adds a Session to the list of patternSessions.
addPieLabelRecord(PieLabelRecord) - Method in class org.jfree.chart.plot.PieLabelDistributor: Adds a label record.
addPlacer(Placer) - Static method in class org.vanted.plugins.layout.multilevelframework.MultilevelFrameworkLayout: Add a new Placer that will be available for the user to choose.
addPluginCommand(ProvidesScenarioSupportCommands) - Method in class scenario.Scenario
addPluginDependency(PluginDependency) - Method in class org.graffiti.managers.pluginmgr.PluginDescription: Adds the given plugin dependency to the list of dependencies.
addPluginManagerListener(PluginManagerListener) - Method in class org.graffiti.managers.pluginmgr.DefaultPluginManager: Adds the given plugin manager listener to the list of listeners.
addPluginManagerListener(PluginManagerListener) - Method in interface org.graffiti.managers.pluginmgr.PluginManager: Adds the given plugin manager listener to the list of listeners.
addPostProcessor(List<Runnable>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.AbstractExperimentDataProcessor
addPostProcessor(List<Runnable>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ExperimentDataProcessor
addPreferencingClass(Class<? extends PreferencesInterface>) - Method in class org.graffiti.managers.PreferenceManager: Another way of adding custom classes that implement the PreferencesInterface which will be added to the list of preferencing classes.
addPriorityToEvent(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addPriorityToEvent(Graph, String, Priority) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addProduct(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addProduct(Node, SpeciesReference) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addProductCloneToList(String, String, Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper
addProgressListener(ChartProgressListener) - Method in class org.jfree.chart.JFreeChart: Registers an object for notification of progress events relating to the chart.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.jfree.data.Series: Adds a property change listener to the series.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.vanted.plugins.layout.stressminimization.BackgroundAlgorithm: add new PropertyChangeListener to the listener list
addPropertyChangeListeners(PropertyChangeListener[]) - Method in class org.vanted.plugins.layout.stressminimization.BackgroundAlgorithm: add elements of an array to the property change list
addR(float, double, int, String, String, double) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.CorrelationResult
AddRandomClusterInformationAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands
AddRandomClusterInformationAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.AddRandomClusterInformationAlgorithm
addRangeMarker(int, Marker, Layer) - Method in class org.jfree.chart.plot.CategoryPlot: Adds a marker for display by a particular renderer.
addRangeMarker(int, Marker, Layer) - Method in class org.jfree.chart.plot.XYPlot: Adds a marker for a renderer and sends a PlotChangeEvent to all registered listeners.
addRangeMarker(Marker) - Method in class org.jfree.chart.plot.CategoryPlot: Adds a marker for display (in the foreground) against the range axis and sends a PlotChangeEvent to all registered listeners.
addRangeMarker(Marker) - Method in class org.jfree.chart.plot.ContourPlot: Adds a marker for the range axis.
addRangeMarker(Marker) - Method in class org.jfree.chart.plot.XYPlot: Adds a marker for the range axis and sends a PlotChangeEvent to all registered listeners.
addRangeMarker(Marker, Layer) - Method in class org.jfree.chart.plot.CategoryPlot: Adds a marker for display against the range axis and sends a PlotChangeEvent to all registered listeners.
addRangeMarker(Marker, Layer) - Method in class org.jfree.chart.plot.XYPlot: Adds a marker for the range axis in the specified layer and sends a PlotChangeEvent to all registered listeners.
addRateRule(Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRuleHelper
addRateRule(Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRuleHelper
addRateRuleFunction(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addRateRules(Graph, List<String>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRuleHelper
addRateRuleVariable(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addReactant(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addReactant(Node, SpeciesReference) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addReactantCloneToList(String, String, Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper
addReaction(KeggId) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Entry
addReactionCloneToList(String, Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper
addReactions(Graph, ListOf<Reaction>, String, PositionGridGenerator, SBMLReactionHelper) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_Reaction_Reader: Method reads in function definitions and is called from class SBML_XML_Reader.java.
addReactions(Graph, Model) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_Reaction_Writer: This method adds the reactions to a model
addRow(String, String, String, String, String, String, String, int, String, String, int, Double, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.DataSetTable
addRows(File) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.FileHandlerUserDecision
addRule(ListOf<Rule>, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_Rule_Reader: Method reads in rules and is called from class SBML_XML_Reader.java
addRules(Graph, Model) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_Rule_Writer: Controls the processing of rules
addSBaseAttributes(AbstractSBase, Edge, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_SBase_Writer
addSBaseAttributes(AbstractSBase, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_SBase_Writer
addSBaseAttributes(AbstractSBase, Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_SBase_Writer: This Method helps processing the attributes with a variable headline inherited by SBase
addSBaseAttributes(AbstractSBase, Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_SBase_Writer: Method adds all sBase attributes to an object of a model
addSBML(OutputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_SBML_Writer: Processes the reading in an model
addSBML(SBMLDocument, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_SBML_Reader: Method reads in the model tag information and is called from class SBML_XML_Reader.java
addScaledComponent(JComponent) - Static method in class org.vanted.scaling.ComponentRegulator: Add the component to the set of already scaled components.
addScalingComponents(AbstractOptionPane, Container, int, int) - Static method in class org.vanted.scaling.DPIHelper: Insert the preferencing Components into the specified pane.
addScalingListener(PropertyChangeListener) - Static method in class org.vanted.scaling.Toolbox: Add a PropertyChangeListener to be informed about the workflow of the scaling procedures.
addSearchFilter(SearchFilter) - Method in class org.FolderPanel
addSelection(Selection) - Method in class org.graffiti.selection.Selection: Adds all elements from the given selection to this selection.
addSelectionListener(SelectionListener) - Method in class org.graffiti.editor.MainFrame: Adds a SelectionListener.
addSelectionListener(SelectionListener) - Method in class org.graffiti.selection.SelectionModel: Adds the given selection listener to the list of listeners.
addSelectionPaths(TreePath[]) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.gui.CheckTreeSelectionModel
addSeparator(String) - Method in class org.graffiti.options.AbstractOptionPane: Adds a separator to the option pane.
addSeries(float[], int, String) - Method in class org.jfree.data.time.DynamicTimeSeriesCollection: Adds a series to the dataset.
addSeries(String, double[], int) - Method in class org.jfree.data.statistics.HistogramDataset: Adds a series to the dataset, using the specified number of bins.
addSeries(String, double[], int, double, double) - Method in class org.jfree.data.statistics.HistogramDataset: Adds a series to the dataset.
addSeries(MatrixSeries) - Method in class org.jfree.data.MatrixSeriesCollection: Adds a series to the collection.
addSeries(TimePeriodValues) - Method in class org.jfree.data.time.TimePeriodValuesCollection: Adds a series to the collection.
addSeries(TimeSeries) - Method in class org.jfree.data.time.TimeSeriesCollection: Adds a series to the collection.
addSeries(XYSeries) - Method in class org.jfree.data.DefaultTableXYDataset: Adds a series to the collection and sends a DatasetChangeEvent to all registered listeners.
addSeries(XYSeries) - Method in class org.jfree.data.XYSeriesCollection: Adds a series to the collection and sends a DatasetChangeEvent to all registered listeners.
addSession(Session) - Method in class org.graffiti.editor.MainFrame: Adds the given session to the list of sessions.
addSession(Session) - Method in interface org.graffiti.session.SessionManager: Adds the given session to the list of sessions.
addSessionListener(SessionListener) - Method in class org.graffiti.editor.MainFrame: Adds a SessionListener.
addSessionListener(SessionListener) - Method in interface org.graffiti.session.SessionManager: Adds a SelectionListener.
addShort(String, String, short) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addShort(String, String, short) - Method in class org.graffiti.attributes.AbstractAttributable: Adds an ShortAttribute with the given value and id to a CollectionAttribute at path.
addShort(String, String, short) - Method in interface org.graffiti.attributes.Attributable: Adds an ShortAttribute with the given value and id to a CollectionAttribute at path.
addSpecies(Graph, ListOf<Species>, PositionGridGenerator, SBMLSpeciesHelper) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_Species_Reader: reads in species and is called from class SBML_XML_Reader.java.
addSpecies(Model, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_Species_Writer: Adds a species and its variables to the model
addSpeciesBoundaryConsition(Node, Boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Sets the attribute boundary condition of a species node
addSpeciesCompartment(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Sets the compartment of a node
addSpeciesConstant(Node, Boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Sets the attribute constant of a species node
addSpeciesConversionFactor(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Sets the attribute conversion factor of a species node
addSpeciesGlyph(Model, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_Species_Writer
addSpeciesHasOnlySubstanceUnits(Node, Boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Sets the attribute hasOnlySubstanceUnits of a species node
addSpeciesID(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Sets the id of a species node
addSpeciesInitialAmount(Node, Double) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Sets the initial amount of a node
addSpeciesInitialConcentration(Node, Double) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Sets the initial concentration of a node
addSpeciesName(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addSpeciesSubstanceUnits(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Sets the substance units of a species node
addStatusPanel(JPanel) - Method in class org.graffiti.editor.MainFrame
addString(String, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper
addString(String, String, String) - Method in class org.graffiti.attributes.AbstractAttributable: Adds a StringAttribute with the given value and id to a CollectionAttribute at path.
addString(String, String, String) - Method in interface org.graffiti.attributes.Attributable: Adds an StringAttribute with the given value and id to a CollectionAttribute at path.
addSubCategory(Comparable) - Method in class org.jfree.chart.axis.SubCategoryAxis: Adds a sub-category to the axis.
addSubitle(Title) - Method in class org.jfree.chart.plot.JThermometer: Adds a subtitle to the chart.
addSubLabel(Comparable, String) - Method in class org.jfree.chart.axis.ExtendedCategoryAxis: Adds a sublabel for a category.
addSubplotInfo(PlotRenderingInfo) - Method in class org.jfree.chart.plot.PlotRenderingInfo: Adds the info for a subplot.
addSubtask(Task) - Method in class org.jfree.data.gantt.Task: Adds a sub-task to the task.
addSubtitle(String) - Method in class org.jfree.chart.plot.JThermometer: Adds a subtitle to the chart.
addSubtitle(String, Font) - Method in class org.jfree.chart.plot.JThermometer: Adds a subtitle to the chart.
addSubtitle(Title) - Method in class org.jfree.chart.JFreeChart: Adds a chart subtitle, and notifies registered listeners that the chart has been modified.
addSubtypeName(SubtypeName) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Relation
addSubtypeRef(Entry) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Relation
addTab(InspectorTab) - Method in interface org.graffiti.plugin.inspector.InspectorPlugin: Adds another InspectorTab to the current InspectorPlugin.
addTab(InspectorTab) - Method in class org.graffiti.plugins.inspectors.defaults.Inspector: Adds another InspectorTab to the current InspectorPlugin.
addTab(InspectorTab, ImageIcon) - Method in class org.graffiti.plugin.inspector.SubtabHostTab: Adds a tab to the inspector.
addTab(InspectorTab, ImageIcon) - Method in class org.graffiti.plugins.inspectors.defaults.InspectorContainer: Adds a tab to the inspector.
addTemplate(Template) - Method in class de.ipk_gatersleben.ag_pbi.datahandling.TemplateManager
addTemplate(String, URL, RunnableForFile) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.TemplateFileManager
addTemplateChartComponent(ChartComponent) - Method in class de.ipk_gatersleben.ag_pbi.datahandling.Template
addTemplateFile(TemplateFile) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.TemplateFileManager
addTemplateFile(TemplateFile) - Method in class de.ipk_gatersleben.ag_pbi.datahandling.Template: Don't forget to register the created TemplateFile after creating this object.
addThickness(Rectangle2D, double) - Static method in class org.graffiti.plugins.views.defaults.AbstractArrowShape
addToDate(Date) - Method in class org.jfree.chart.axis.DateTickUnit: Calculates a new date by adding this unit to the base date.
addTool(Tool) - Method in class org.graffiti.managers.DefaultToolManager
addTool(Tool) - Method in interface org.graffiti.managers.ToolManager: Adds the specified tool to the list of tools of this manager.
addTool(Tool) - Method in class org.graffiti.plugin.mode.AbstractMode: Adds the given tool to the mode.
addTool(Tool) - Method in interface org.graffiti.plugin.mode.Mode: Adds the given tool to the mode.
addToolTip(JComponent, String) - Static method in class org.graffiti.plugin.ToolTipHelper
addToolTipSeries(List) - Method in class org.jfree.chart.labels.CustomXYToolTipGenerator: Adds a list of tooltips for a series.
addToResult(String, Object) - Method in interface org.graffiti.plugin.algorithm.AlgorithmResult: Adds a key-value pair to the Map.
addToResult(String, Object) - Method in class org.graffiti.plugin.algorithm.DefaultAlgorithmResult
addTreeModelListener(TreeModelListener) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.AbstractTreeTableModel
addTriggerFunction(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addTriggerInitialValue(Graph, String, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addTriggerPersistent(Graph, String, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addTriggerToEvent(Graph, String, boolean, boolean, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addTriggerToEvent(Graph, String, Trigger) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addUnit(int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLUnitDefinition
addUnitDefinition(Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLUnitDefinitionHelper
addUnitDefinition(Graph, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLUnitDefinitionHelper
addUnitDefinition(Model, Graph, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_UnitDefinition_Writer: Adds an unit definition and its variables to the model
addUnitDefinitionID(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addUnitDefinitionName(Graph, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addUnitDefinitions(Graph, List<String>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLUnitDefinitionHelper
addUnitDefinitions(ListOf<UnitDefinition>, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_UnitDefinition_Reader: Method reads in unit definitions and is called from class SBML_XML_Reader.java
addUnitToUnitDefinition(Graph, String, Unit) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addUnitToUnitDefinition(Graph, String, Unit.Kind, double, double, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
addUnwrittenAttribute(String) - Method in class org.graffiti.attributes.AttributeManager
addURLs(Map) - Method in class org.jfree.chart.urls.CustomPieURLGenerator: Adds a map of URLs.
addURLSeries(List) - Method in class org.jfree.chart.urls.CustomXYURLGenerator: Adds a list of URLs.
addValue(double, Comparable, Comparable) - Method in class org.jfree.data.DefaultCategoryDataset: Adds a value to the table.
addValue(int, int, float) - Method in class org.jfree.data.time.DynamicTimeSeriesCollection: Adds a value to a series.
addValue(int, int, int) - Method in class org.jfree.data.WaferMapDataset: Adds a value to the dataset.
addValue(Comparable, Number) - Method in class org.jfree.data.DefaultKeyedValues: Adds a new value to the collection, or updates an existing value.
addValue(Number, Comparable, Comparable) - Method in class org.jfree.data.DefaultCategoryDataset: Adds a value to the table.
addValue(Number, Comparable, Comparable) - Method in class org.jfree.data.DefaultKeyedValues2D: Adds a value to the table.
addValue(Number, Comparable, Comparable) - Method in class org.jfree.data.WaferMapDataset: Sets a value in the dataset.
addValue(String, double) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.DataRowExcelExport
addValueEditComponent(ValueEditComponent) - Method in class org.graffiti.editor.dialog.AbstractGraffitiValueEditContainer: Adds a ValueEditComponent to the value edit container.
addValueEditComponent(ValueEditComponent) - Method in class org.graffiti.editor.dialog.AbstractValueEditContainer: Adds another ValueEditComponent to the current dialog.
addValueEditComponent(ValueEditComponent) - Method in interface org.graffiti.editor.dialog.ValueEditContainer: Adds another ValueEditComponent to the dialog.
addValues(String) - Method in class qmwi.kseg.som.CSV_SOM_dataEntry
addValues(String) - Method in interface qmwi.kseg.som.SOMdataEntry
addValues(String, boolean) - Method in class qmwi.kseg.som.CSV_SOM_dataEntry
addValues(String, boolean) - Method in interface qmwi.kseg.som.SOMdataEntry
addValues(ClassesAll) - Method in class qmwi.kseg.som.diagram.AttributsAll: Insert the method's description here.
addView(String) - Method in class org.graffiti.managers.DefaultViewManager
addView(String) - Method in interface org.graffiti.managers.ViewManager: Adds the given view type (class name) to the map of view types.
addView(View) - Method in class org.graffiti.session.Session: Adds a new View to the inner list of views.
addViewListener(ViewListener) - Method in class org.graffiti.editor.MainFrame
addViewListener(ViewListener) - Method in class org.graffiti.managers.DefaultViewManager
addViewListener(ViewListener) - Method in interface org.graffiti.managers.ViewManager: Registers the given ViewListener.
addViews(String[]) - Method in class org.graffiti.managers.DefaultViewManager
addViews(String[]) - Method in interface org.graffiti.managers.ViewManager: Adds the given list of views types (class names) to the list of available view types.
addXmlDataSeries(SubstanceInterface, SubstanceInterface, String, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.MyXML_XYDataset: Adds the corresponding data points from the specified mapping data.
addXmlDataSeriesXY(SubstanceInterface, SubstanceInterface, String, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.MyXML_XYDataset
AdjListEdge - Class in org.graffiti.graph: Implementation of the Edge interface for a Graph with adjacency list representation.
AdjListGraph - Class in org.graffiti.graph: Implements the Graph -interface using an adjacency list representation of the graph.
AdjListGraph() - Constructor for class org.graffiti.graph.AdjListGraph: Constructs a new instance of an AdjListGraph.
AdjListGraph(CollectionAttribute) - Constructor for class org.graffiti.graph.AdjListGraph: Constructs a new instance of an AdjListGraph.
AdjListGraph(ListenerManager) - Constructor for class org.graffiti.graph.AdjListGraph: Constructs a new instance of an AdjListGraph.
AdjListGraph(ListenerManager, CollectionAttribute) - Constructor for class org.graffiti.graph.AdjListGraph: Constructs a new instance of an AdjListGraph.
AdjListGraph(Graph, ListenerManager) - Constructor for class org.graffiti.graph.AdjListGraph: Constructs a new instance of an AdjListGraph from an instance of any Graph implementation.
AdjListGraph(Graph, ListenerManager, CollectionAttribute) - Constructor for class org.graffiti.graph.AdjListGraph: Constructs a new instance of an AdjListGraph from an instance of any Graph implementation.
AdjListNode - Class in org.graffiti.graph: Implements a graph node with adjacency list representation.
adjustComponentPosition() - Method in class org.graffiti.plugin.attributecomponent.AbstractAttributeComponent
adjustComponentPosition() - Method in class org.graffiti.plugin.view.AttributeComponent: adjust the component position only
adjustComponentPosition() - Method in class org.graffiti.plugins.attributecomponents.simplelabel.LabelComponent
adjustComponentSize() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttributeComponent
adjustComponentSize() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundImageAttributeComponent
adjustComponentSize() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.PathwayLinkVisualizationComponent
adjustComponentSize() - Method in class org.graffiti.plugin.attributecomponent.AbstractAttributeComponent
adjustComponentSize() - Method in class org.graffiti.plugin.view.AttributeComponent: adjust the component size and position
adjustComponentSize() - Method in class org.graffiti.plugins.attributecomponents.simplelabel.LabelComponent
adjustData(double) - Method in class org.jfree.chart.demo.CompassDemo: Updates the data.
adjustDefaults(Scaler) - Method in class org.vanted.scaling.ScalingCoordinator: Scan Defaults and re-scale the appropriate values.
adjustedLog10(double) - Method in class org.jfree.chart.axis.LogarithmicAxis: Returns an adjusted log10 value for graphing purposes.
adjustmentValueChanged(AdjustmentEvent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.navigation.NavigationComponentView: listener that listens to value changes of the scrollbar and simply repaint
adjustWindowDecoratations() - Static method in class org.vanted.scaling.DPIHelper: By transferring all Window decorations from OS to LookAndFeel, those could be now scaled too.
AdvancedLabelTool - Class in org.graffiti.plugins.modes.defaults: A tool for creating and editing labels of graphelements.
AdvancedLabelTool() - Constructor for class org.graffiti.plugins.modes.defaults.AdvancedLabelTool
advanceTime() - Method in class org.jfree.data.time.DynamicTimeSeriesCollection: Adjust the array offset as needed when a new time-period is added: Increments the indices "oldestAt" and "newestAt", mod(array length), zeroes the series values at newestAt, returns the new TimePeriod.
affix(Point2D, Point2D, double) - Method in interface org.graffiti.plugin.view.ArrowShape: Sets this arrow to the target point and rotates it according to the line given by the connection between points target and other.
affix(Point2D, Point2D, double) - Method in class org.graffiti.plugins.views.defaults.AbstractArrowShape: Sets this arrow to the target point and rotates it according to the line given by the connection between points target and other.
after(SegmentedTimeline.Segment) - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment: Returns true if this segment is wholly after another segment.
ageHistoryCountItems() - Method in class org.jfree.data.time.TimeSeries: Age items in the series.
ageHistoryCountItems(long) - Method in class org.jfree.data.time.TimeSeries: Age items in the series.
AGLET_NETWORK - org.FeatureSet
AGNW_PATH - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.AttributeConstants: Unique identifier for the group in Gatersleben.
alg - Static variable in class vanted_feature.PluginFeatureClusterCommands
ALGEBRAIC_FUNCTION - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
Algorithm - Interface in org.graffiti.plugin.algorithm: An Algorithm has to provide a function that returns an array of Parameters it needs, in order to give user interfaces the possibility to provide the Algorithm with appropriate.
algorithmAttachData(Algorithm) - Method in class org.graffiti.editor.GravistoService
AlgorithmListCellRenderer - Class in de.ipk_gatersleben.ag_nw.graffiti.services.algorithms
AlgorithmListCellRenderer() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.services.algorithms.AlgorithmListCellRenderer
AlgorithmManager - Interface in org.graffiti.managers: Provides a generic interface for a component managing a set of algorithms.
AlgorithmPanelFactory - Class in de.ipk_gatersleben.ag_nw.graffiti.services.algorithms: The factory class initializes any algorithms, belonging to the Network.Analysis tab category.
AlgorithmPanelFactory(boolean, List<Algorithm>) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.services.algorithms.AlgorithmPanelFactory
AlgorithmResult - Interface in org.graffiti.plugin.algorithm: An AlgorithmResult is a map of results that were computed by a CalculatingAlgorithm.
AlgorithmServices - Class in de.ipk_gatersleben.ag_nw.graffiti.services
AlgorithmServices() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.services.AlgorithmServices
AlgorithmWithComponentDescription - Interface in org.graffiti.plugin.algorithm
ALIASES - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathMolecule
ALIASES - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathPathway
alignJEP(JTextComponent) - Static method in class org.vanted.scaling.scalers.component.JTextComponentScaler: JEditorPane has a couple of intrinsic properties, with the help of which, one could control to a certain extent, the layout (e.g.
ALIGNMENT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
AlignmentSetting - Enum in org
AlignNodesCommand - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit
AlignNodesCommand(AlignNodesCommand.Command, EditorSession) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit.AlignNodesCommand: Creates a Alignment Command, used for aligning nodes.
AlignNodesCommand.Command - Enum in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit
AlignNodesComponent - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit: DOCUMENT ME!
AlignNodesComponent(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit.AlignNodesComponent
ALIGNSEGMENT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
ALL - org.vanted.scaling.scalers.component.HTMLScaleSupport.Tags
AllPathsSelectionAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths
AllPathsSelectionAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths.AllPathsSelectionAlgorithm: Constructs a new instance.
AllPermissionPolicy - Class in org.graffiti.util
AllPermissionPolicy() - Constructor for class org.graffiti.util.AllPermissionPolicy
allPossibleSourcePathsTraversed(boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths.WeightedDistanceInfo
allRelevantEdgesProcessed(boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths.DistanceInfo
AllSuperGraphsCreator - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar
AllSuperGraphsCreator(Graph, String, OrganismEntry[], boolean, boolean, boolean, boolean, boolean) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.AllSuperGraphsCreator
AlternativeIDannotationStatistics - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.alt_id_statistics
AlternativeIDannotationStatistics() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.alt_id_statistics.AlternativeIDannotationStatistics
AlternativeIdentifiersPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids
AlternativeIdentifiersPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids.AlternativeIdentifiersPlugin
AlternativeIdentifierTableData - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe
AlternativeIdentifierTableData() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.AlternativeIdentifierTableData
ANALYSIS - org.graffiti.plugin.algorithm.Category
analyzeNewInput(int, int, int, double, double[]) - Method in class qmwi.kseg.som.Map
analyzeSystem() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.threading.SystemAnalysis
ANCHOR - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
AND - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsAccessAdapter.QueryAdvanced
AND - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.LogicConnection
AND - de.ipk_gatersleben.ag_nw.graffiti.services.algorithms.SearchAlgorithms.LogicalOp
animate(double) - Method in class org.vanted.animation.animations.VisibilityAnimation
animate(double, T) - Method in class org.vanted.animation.animations.SizeAnimation
animate(Graph) - Method in interface org.graffiti.plugin.algorithm.AnimatedAlgorithm: Starts the animation of the algorithm.
AnimatedAlgorithm - Interface in org.graffiti.plugin.algorithm: An AnimatedAlgorithm provides the possibility to execute the underlying algorithm in steps, so that the intermediate results can be seen.
Animation<T extends TimePoint> - Class in org.vanted.animation: The Animation class represents DISCRETE Animation.
Animation(Attributable, List<T>, double) - Constructor for class org.vanted.animation.Animation: Creates an animation with a StandardLooper, infinite loops and starts immediately
Animation(Attributable, List<T>, double, double) - Constructor for class org.vanted.animation.Animation: Creates an animation with a StandardLooper that loops forever
Animation(Attributable, List<T>, double, double, int) - Constructor for class org.vanted.animation.Animation: Creates an animation with a StandardLooper
Animation(Attributable, List<T>, double, double, int, Looper) - Constructor for class org.vanted.animation.Animation: Creates an animation
Animator - Class in org.vanted.animation
Animator(Graph) - Constructor for class org.vanted.animation.Animator: Creates an animator will perform a single loop forever.
Animator(Graph, int) - Constructor for class org.vanted.animation.Animator: Creates an animator that will automatically calculate the loop duration to be the same as the animation who's loop duration is largest
Animator(Graph, int, double) - Constructor for class org.vanted.animation.Animator: Creates an animator that needs to have its loop duration manually specified.
Animator(Graph, int, int, TimeUnit) - Constructor for class org.vanted.animation.Animator: Creates an animator that needs to have its loop duration manually specified.
Animator(Graph, int, LoopDuration) - Constructor for class org.vanted.animation.Animator: Creates an animator that needs to have its loop duration manually specified.
Animator(Graph, NumberOfLoops) - Constructor for class org.vanted.animation.Animator: Creates an animator that will automatically calculate the loop duration to be the same as the animation who's loop duration is largest
AnimatorAdapter<T> - Class in org.vanted.animation: Adapter for the AnimatorListener interface, providing default empty implementation.
AnimatorAdapter() - Constructor for class org.vanted.animation.AnimatorAdapter
AnimatorData - Class in org.vanted.animation
AnimatorData(double, int, double, int, boolean) - Constructor for class org.vanted.animation.AnimatorData
AnimatorListener<T> - Interface in org.vanted.animation
ANNO_DIV - Static variable in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.MappingDataEntity
Annotation - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe
Annotation(String, int) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.Annotation
ANNOTATION - org.graffiti.plugin.algorithm.Category
ANNOTATION - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
AnnotationProvider - Interface in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe
appendData(float[]) - Method in class org.jfree.data.time.DynamicTimeSeriesCollection: Appends new data.
appendData(float[], int, int) - Method in class org.jfree.data.time.DynamicTimeSeriesCollection: Appends data at specified index, for loading up with data from file(s).
appendLabel - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.ModeOfAttributeOperation
appletDragStarted() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.GravistoMain: Deprecated.
ApplicationStatus - Enum in org
apply(O) - Method in class org.vanted.indexednodes.accumulators.StatefulAccumulator: Interface method to apply a value to the accumulator, additionally calling the next accumulator if set.
ApplyAlternativeIdentifiersTo - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe
ApplyAlternativeIdentifiersTo() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.ApplyAlternativeIdentifiersTo
ApplyGraphLayout - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph
ApplyGraphLayout() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph.ApplyGraphLayout
ApplyGraphLayoutPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph
ApplyGraphLayoutPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph.ApplyGraphLayoutPlugin
applyGrid(int, int) - Method in class org.Vector2d
applyLayoutFromGraphToGraph(Selection, Graph, Graph, String, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph.ApplyGraphLayout
applyUndoableClusterIdAssignment(Graph, HashMap<GraphElement, String>, String, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper
applyUndoableEdgeReversal(Graph, Collection<Edge>, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper
applyUndoableNodeAndBendPositionUpdate(HashMap<Node, Vector2d>, HashMap<CoordinateAttribute, Vector2d>, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper
applyUndoableNodePositionAndSizeUpdate(HashMap<Node, Vector2d>, HashMap<Node, Vector2d>, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper
applyUndoableNodePositionUpdate(HashMap<Node, Vector2d>, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper
applyUndoableNodeSizeUpdate(HashMap<Node, Vector2d>, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper
AREA - Static variable in class org.jfree.chart.renderer.AreaXYRenderer: Deprecated.

Useful constant for specifying the type of rendering (area only).
AREA - Static variable in class org.jfree.chart.renderer.XYAreaRenderer: Useful constant for specifying the type of rendering (area only).
AREA - Static variable in class org.jfree.chart.renderer.XYStepAreaRenderer: Useful constant for specifying the type of rendering (area only).
AREA_AND_SHAPES - Static variable in class org.jfree.chart.renderer.AreaXYRenderer: Deprecated.

Useful constant for specifying the type of rendering (area and shapes).
AREA_AND_SHAPES - Static variable in class org.jfree.chart.renderer.XYAreaRenderer: Useful constant for specifying the type of rendering (area and shapes).
AREA_AND_SHAPES - Static variable in class org.jfree.chart.renderer.XYStepAreaRenderer: Useful constant for specifying the type of rendering (area and shapes).
AREA_UNITS - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
AreaChartDemo - Class in org.jfree.chart.demo: A simple demonstration application showing how to create an area chart using data from a CategoryDataset.
AreaChartDemo(String) - Constructor for class org.jfree.chart.demo.AreaChartDemo: Creates a new demo application.
AreaManager - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands
AreaManager(Graph) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.AreaManager
areApploadingAndFinishActionsCompleted() - Static method in class org.ErrorMsg
AreaRenderer - Class in org.jfree.chart.renderer: A category item renderer that draws area charts.
AreaRenderer() - Constructor for class org.jfree.chart.renderer.AreaRenderer: Creates a new renderer.
AreaRendererEndType - Class in org.jfree.chart.renderer: An enumeration of the 'end types' for an area renderer.
AreaXYRenderer - Class in org.jfree.chart.renderer: Deprecated.
Use XYAreaRenderer.
AreaXYRenderer() - Constructor for class org.jfree.chart.renderer.AreaXYRenderer: Deprecated.

Constructs a new renderer.
AreaXYRenderer(int) - Constructor for class org.jfree.chart.renderer.AreaXYRenderer: Deprecated.

Constructs a new renderer.
AreaXYRenderer(int, XYToolTipGenerator, XYURLGenerator) - Constructor for class org.jfree.chart.renderer.AreaXYRenderer: Deprecated.

Constructs a new renderer.
areConnected(Node, Node) - Method in class org.graffiti.graph.AbstractGraph: Returns true, if the graph contains an edge between the nodes n1 and n2, false otherwise.
ArrayLayout - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout
ArrayLayout() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout.ArrayLayout
ARROWHEAD - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
ArrowNeedle - Class in org.jfree.chart.needle: A needle in the shape of an arrow.
ArrowNeedle(boolean) - Constructor for class org.jfree.chart.needle.ArrowNeedle: Constructs a new arrow needle.
ArrowShape - Interface in org.graffiti.plugin.view: DOCUMENT ME!
ArrowShapeAttribute - Class in org.graffiti.attributes
ArrowShapeAttribute() - Constructor for class org.graffiti.attributes.ArrowShapeAttribute
ArrowShapeAttribute(String, String) - Constructor for class org.graffiti.attributes.ArrowShapeAttribute
ArrowShapeCellRenderer - Class in org.graffiti.plugins.editcomponents.defaults
ArrowShapeCellRenderer() - Constructor for class org.graffiti.plugins.editcomponents.defaults.ArrowShapeCellRenderer
ArrowShapeEditComponent - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.enhanced_attribute_editors: Class used to display different node shapes.
ArrowShapeEditComponent(Displayable) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.enhanced_attribute_editors.ArrowShapeEditComponent: Constructor sets the correct entries of the combo box.
ArrowSizeAnimation - Class in org.vanted.animation.animations: Animates the size of an edge arrow
ArrowSizeAnimation(Edge, List<DoubleTimePoint>, double) - Constructor for class org.vanted.animation.animations.ArrowSizeAnimation
ArrowSizeAnimation(Edge, List<DoubleTimePoint>, double, double) - Constructor for class org.vanted.animation.animations.ArrowSizeAnimation
ArrowSizeAnimation(Edge, List<DoubleTimePoint>, double, double, int) - Constructor for class org.vanted.animation.animations.ArrowSizeAnimation
ArrowSizeAnimation(Edge, List<DoubleTimePoint>, double, double, int, Looper) - Constructor for class org.vanted.animation.animations.ArrowSizeAnimation
ArrowSizeAnimation(Edge, List<DoubleTimePoint>, double, double, int, Looper, Interpolator) - Constructor for class org.vanted.animation.animations.ArrowSizeAnimation
ARROWTAIL - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
ASSIGNMENT_FUNCTION - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
ASSIGNMENT_VARIABLE - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants
assignmentArrow - Static variable in class org.graffiti.plugins.editcomponents.defaults.EdgeArrowShapeEditComponent
AssignmentArrowShape - Class in org.graffiti.plugins.views.defaults: DOCUMENT ME!
AssignmentArrowShape() - Constructor for class org.graffiti.plugins.views.defaults.AssignmentArrowShape: Constructs a new arrow.
AssignmentArrowShape(float) - Constructor for class org.graffiti.plugins.views.defaults.AssignmentArrowShape
atLeastOneFileNeedsUserDecision() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.FileHandlerUserDecision
ATT - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.sbml.SBML_SBase_Writer: To make the code shorter
ATT - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_SBase_Reader: To make the code shorter
ATT_ELEMENT_LITERAL - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLConstants: att tag
ATT_ELEMENT_NAME_ATTRIBUTE_VALUE_DAG - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLConstants
ATT_ELEMENT_NAME_ATTRIBUTE_VALUE_GRAPHFACTORY - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLConstants
ATT_ELEMENT_NAME_ATTRIBUTE_VALUE_TRAVERSAL - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLConstants
ATT_ELEMENT_NAME_ATTRIBUTE_VALUE_WEIGHTED - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLConstants: weighted attribute
attach(Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fish_eye.FishEyeLayout
attach(Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache.PatternSpringembedder
attach(Graph, Selection) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate.RotateAlgorithm
attach(Graph, Selection) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph.ApplyGraphLayout
attach(Graph, Selection) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterWithMinimumCrossingsAlgorithm
attach(Graph, Selection) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache.PatternSpringembedder
attach(Graph, Selection) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.PatternSpringembedder
attach(Graph, Selection) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.PatternSpringembedder3d
attach(Graph, Selection) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup.NumberNodesAndEdgesAlgorithm
attach(Graph, Selection) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ExportDataTableAlgorithm
attach(Graph, Selection) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.printer.PrintAlgorithm: Unused for this plugin.
attach(Graph, Selection) - Method in class org.graffiti.plugin.algorithm.AbstractAlgorithm
attach(Graph, Selection) - Method in interface org.graffiti.plugin.algorithm.Algorithm: Attaches the given graph to this algorithm.
attach(Graph, Selection) - Method in class org.vanted.plugins.layout.multilevelframework.ForceDirectedLayoutWrapper
attach(Graph, Selection) - Method in class org.vanted.plugins.layout.multilevelframework.MultilevelFrameworkLayout
attach(Graph, Selection) - Method in class org.vanted.plugins.layout.stressminimization.BackgroundExecutionAlgorithm
attach(Graph, Selection, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.RemoveBendsAlgorithm: See AbstractAlgorithm.attach(Graph, Selection).
attachData(Algorithm) - Static method in class org.graffiti.editor.GravistoService
attachSystemWindowResizer() - Static method in class org.vanted.scaling.scalers.component.WindowScaler: Attach a WindowResizerListener to the default system window Toolkit.
attemptFontSelection() - Method in class org.jfree.chart.ui.TitlePropertyEditPanel: Presents a font selection dialog to the user.
attemptPaintSelection() - Method in class org.jfree.chart.ui.TitlePropertyEditPanel: Allow the user the opportunity to select a Paint object.
attemptTickLabelFontSelection() - Method in class org.jfree.chart.ui.AxisPropertyEditPanel: Presents a tick label font selection dialog to the user.
attReader - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper
Attributable - Interface in org.graffiti.attributes: Interfaces an object that contains a hierarchy of attributes.
Attribute - Interface in org.graffiti.attributes: Interfaces an object, which contains an id and a value.
AttributeAdapter - Class in org.graffiti.event: Adapter for the AttributeListener interface, providing default empty implementation.
AttributeAdapter() - Constructor for class org.graffiti.event.AttributeAdapter
AttributeAndDataMappingEvaluation - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes
AttributeAndDataMappingEvaluation() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeAndDataMappingEvaluation
AttributeCalculation - Enum in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes
attributeChanged(Attribute) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttributeComponent
attributeChanged(Attribute) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundImageAttributeComponent
attributeChanged(Attribute) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view.FastView
attributeChanged(Attribute) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.NullView
attributeChanged(Attribute) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.PathwayLinkVisualizationComponent
attributeChanged(Attribute) - Method in class org.graffiti.plugin.attributecomponent.AbstractAttributeComponent: Called when a graphics attribute of the attribute represented by this component has changed.
attributeChanged(Attribute) - Method in class org.graffiti.plugin.view.AttributeComponent: Called when a graphics attribute of the attribute represented by this component has changed.
attributeChanged(Attribute) - Method in interface org.graffiti.plugin.view.GraffitiViewComponent: Called when a graphics attribute of the GraphElement represented by this component has changed.
attributeChanged(Attribute) - Method in interface org.graffiti.plugin.view.GraphElementComponentInterface: Called when an attribute of the GraphElement represented by this component has changed.
attributeChanged(Attribute) - Method in interface org.graffiti.plugin.view.View: Called when a graphics attributes of the Graph represented by this view has changed.
attributeChanged(Attribute) - Method in class org.graffiti.plugins.attributecomponents.simplelabel.LabelComponent: Called when an attribute of the attribute represented by this component has changed.
attributeChanged(Attribute) - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent: Called when an attribute of the GraphElement represented by this component has changed.
attributeChanged(Attribute) - Method in class org.graffiti.plugins.views.defaults.GraffitiView
attributeChanged(Attribute) - Method in class org.graffiti.plugins.views.matrix.MatrixView
AttributeComponent - Class in org.graffiti.plugin.view: This component represents a org.graffiti.attributes.Attribute.
AttributeComponent() - Constructor for class org.graffiti.plugin.view.AttributeComponent
AttributeComponentManager - Class in org.graffiti.managers: Contains the mapping between attribute classes and their representation as AttributeComponent classes.
AttributeComponentManager() - Constructor for class org.graffiti.managers.AttributeComponentManager: Constructs an AttributeComponentManager.
AttributeComponentNotFoundException - Exception in org.graffiti.editor: DOCUMENT ME!
AttributeComponentNotFoundException(String) - Constructor for exception org.graffiti.editor.AttributeComponentNotFoundException: Constructor for AttributeComponentNotFoundException.
AttributeConstants - Class in de.ipk_gatersleben.ag_nw.graffiti: Useful Attribute Path-Names.
AttributeConstants() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.AttributeConstants
AttributeConsumer - Interface in org.graffiti.attributes: Interfaces an object, which depends on the presence of a set of attributes.
AttributeDescription - Class in org.graffiti.attributes
AttributeDescription(String, Class<? extends Attribute>, String, boolean, boolean) - Constructor for class org.graffiti.attributes.AttributeDescription
AttributeDescription(String, Class<? extends Attribute>, String, boolean, boolean, String) - Constructor for class org.graffiti.attributes.AttributeDescription
AttributeEvent - Class in org.graffiti.event: Contains an attribute event.
AttributeEvent(String, Attribute) - Constructor for class org.graffiti.event.AttributeEvent: Contructor that is called when one composite attribute is concerned, where it is comfortable to pass the path of attribute, too.
AttributeEvent(Attribute) - Constructor for class org.graffiti.event.AttributeEvent: Contructor that is called when one attribute is concerned.
AttributeExistsException - Exception in org.graffiti.attributes: The AttributeExistsException will be thrown if a method tries to add an attribute at a location where another attribute already exists.
AttributeExistsException(String) - Constructor for exception org.graffiti.attributes.AttributeExistsException: Constructs an AttributeExistsException with the specified detail message.
attributeFolder - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors.ChartColorAttribute
attributeFolder - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors.ClusterColorAttribute
AttributeHelper - Class in org: Attribute Helper Class - Makes it more easy to work with graph/node attributes.
AttributeHelper() - Constructor for class org.AttributeHelper
AttributeListener - Interface in org.graffiti.event: Interfaces an attribute events listener.
AttributeManager - Class in org.graffiti.attributes
attributeName - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors.ChartColorAttribute
attributeName - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors.ClusterColorAttribute
AttributeNotFoundException - Exception in org.graffiti.attributes: The AttributeNotFoundException will be thrown if a method tries to access a nonexistent attribute.
AttributeNotFoundException(String) - Constructor for exception org.graffiti.attributes.AttributeNotFoundException: Constructs an AttributeNotFoundException with the specified detail message.
AttributePathNameSearchType - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection
AttributePathNameSearchType(String, String, SearchType, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.AttributePathNameSearchType
attributeSeparator - Static variable in class org.AttributeHelper
AttributeShape - Interface in org.graffiti.plugin.view: DOCUMENT ME!
AttributeTypesManager - Class in org.graffiti.attributes: Provides a type manager for attributes.
AttributeTypesManager() - Constructor for class org.graffiti.attributes.AttributeTypesManager: Constructs a new AttributeTypesManager.
AttributeValuePairSupport - Interface in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper
attributs - Variable in class qmwi.kseg.som.diagram.AttributsClass
AttributsAll - Class in qmwi.kseg.som.diagram: Insert the type's description here.
AttributsAll() - Constructor for class qmwi.kseg.som.diagram.AttributsAll: AllAttributs constructor comment.
AttributsAll(ClassesAll) - Constructor for class qmwi.kseg.som.diagram.AttributsAll: AllAttributs constructor comment.
AttributsAttribut - Class in qmwi.kseg.som.diagram: Insert the type's description here.
AttributsAttribut() - Constructor for class qmwi.kseg.som.diagram.AttributsAttribut: AttributsOneAttribut constructor comment.
AttributsClass - Class in qmwi.kseg.som.diagram: Insert the type's description here.
AttributsClass() - Constructor for class qmwi.kseg.som.diagram.AttributsClass: ClassAttributs constructor comment.
AttributsComputing - Class in qmwi.kseg.som.diagram: Insert the type's description here.
AttributsComputing() - Constructor for class qmwi.kseg.som.diagram.AttributsComputing
attributsValues - Variable in class qmwi.kseg.som.diagram.AttributsAll
attWriter - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper: Provides necessary methods
Aus - Class in qmwi.kseg.som.diagram: Insert the type's description here.
Aus() - Constructor for class qmwi.kseg.som.diagram.Aus: Insert the method's description here.
AUTHORS - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathReference
AUTO_OUTSIDE - org.AlignmentSetting
AUTO_OUTSIDE - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
AUTO_RANGE_BOTH_ACTION_COMMAND - Static variable in interface org.jfree.chart.ChartPanelConstants: Zoom reset (both axes) action command.
AUTO_RANGE_HORIZONTAL_ACTION_COMMAND - Static variable in interface org.jfree.chart.ChartPanelConstants: Zoom reset (horizontal axis only) action command.
AUTO_RANGE_VERTICAL_ACTION_COMMAND - Static variable in interface org.jfree.chart.ChartPanelConstants: Zoom reset (vertical axis only) action command.
autoAdjustRange() - Method in class org.jfree.chart.axis.ColorBar: Rescales the axis to ensure that all data are visible.
autoAdjustRange() - Method in class org.jfree.chart.axis.LogarithmicAxis: Rescales the axis to ensure that all data is visible.
AUTOMATIC - de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.GraffitiCharts
autoRangeBoth() - Method in class org.jfree.chart.ChartPanel: Restores the auto-range calculation on both axes.
autoRangeHorizontal() - Method in class org.jfree.chart.ChartPanel: Restores the auto-range calculation on the horizontal axis.
autoRangeIncludesZero() - Method in class org.jfree.chart.axis.NumberAxis: Returns the flag that indicates whether or not the automatic axis range (if indeed it is determined automatically) is forced to include zero.
autoRangeStickyZero() - Method in class org.jfree.chart.axis.NumberAxis: Returns a flag that affects the auto-range when zero falls outside the data range but inside the margins defined for the axis.
autoRangeVertical() - Method in class org.jfree.chart.ChartPanel: Restores the auto-range calculation on the vertical axis.
autoRedraw - Variable in class org.graffiti.plugin.algorithm.ThreadSafeOptions: If true, the algorithm should auto-update the view.
autoresize(Point) - Method in class org.graffiti.plugin.view.AbstractView: Resizes the panel dynamically so that enough drawing space is available.
autoscroll(Point) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view.FastView
autoscroll(Point) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.NullView
autoscroll(Point) - Method in class org.graffiti.plugin.view.AbstractView
autoscroll(Point) - Method in class org.graffiti.plugins.views.matrix.MatrixView
average - Variable in class qmwi.kseg.som.diagram.AttributsAttribut
average(ClassesAll, AttributsAll) - Static method in class qmwi.kseg.som.diagram.AttributsComputing: Insert the method's description here.
avg_AA - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation
await() - Static method in class org.vanted.scaling.ScalerLoader
awaitMainContainer(Class<? extends Container>) - Static method in class org.vanted.scaling.ScalerLoader: An utility method for waiting on the main container visibility.
AWTImageAttribute - Class in org.graffiti.graphics: Contains the awt image graphic attribute.
AWTImageAttribute(String) - Constructor for class org.graffiti.graphics.AWTImageAttribute: Standard constructor.
AWTImageAttribute(String, Image) - Constructor for class org.graffiti.graphics.AWTImageAttribute: Constructor for AWTImage.
Axis - Class in org.jfree.chart.axis: The base class for all axes in JFreeChart.
axisChanged(AxisChangeEvent) - Method in interface org.jfree.chart.event.AxisChangeListener: Receives notification of an axis change event.
axisChanged(AxisChangeEvent) - Method in class org.jfree.chart.plot.ContourPlot: Receives notification of a change to one of the plot's axes.
axisChanged(AxisChangeEvent) - Method in class org.jfree.chart.plot.Plot: Receives notification of a change to one of the plot's axes.
AxisChangeEvent - Class in org.jfree.chart.event: A change event that encapsulates information about a change to an axis.
AxisChangeEvent(Axis) - Constructor for class org.jfree.chart.event.AxisChangeEvent: Creates a new AxisChangeEvent.
AxisChangeListener - Interface in org.jfree.chart.event: The interface that must be supported by classes that wish to receive notification of changes to an axis.
AxisCollection - Class in org.jfree.chart.axis: A collection of axes that have been assigned to the TOP, BOTTOM, LEFT or RIGHT of a chart.
AxisCollection() - Constructor for class org.jfree.chart.axis.AxisCollection: Creates a new empty collection.
axisColor - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
AXISCOLOR - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants
axisFontSize - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
AxisLocation - Class in org.jfree.chart.axis: Used to indicate the location of an axis on a 2D plot, prior to knowing the orientation of the plot.
AxisPropertyEditPanel - Class in org.jfree.chart.ui: A panel for editing the properties of an axis.
AxisPropertyEditPanel(Axis) - Constructor for class org.jfree.chart.ui.AxisPropertyEditPanel: Standard constructor: builds a panel for displaying/editing the properties of the specified axis.
axisRotation - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions
AxisSpace - Class in org.jfree.chart.axis: A record that contains the space required at each edge of a plot.
AxisSpace() - Constructor for class org.jfree.chart.axis.AxisSpace: Creates a new axis space record.
AxisState - Class in org.jfree.chart.axis: Instances of this class are used to carry state information for an axis during the drawing process.
AxisState() - Constructor for class org.jfree.chart.axis.AxisState: Creates a new axis state.
AxisState(double) - Constructor for class org.jfree.chart.axis.AxisState: Creates a new axis state.
axisWidth - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions

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