Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _
All Classes|All Packages

I

i - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance.WorkTask

IAPnodeTools - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som

IAPnodeTools() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.IAPnodeTools

IContextMenuManager - Interface in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools

The Interface a custom ContextManager should implement.

id - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.IdAndGraphNode

Id - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes

Id() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.Id

Id(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.Id

ID - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathMolecule

ID - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathPathway

ID - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathReaction

ID - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathReference

ID - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.info_dialog_dbe.MenuItemInfoDialog

DOCUMENT ME!

ID - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.info_dialog_example.MenuItemInfoDialog

Deprecated.

DOCUMENT ME!

ID - Static variable in class org.graffiti.plugins.ios.importers.gml.sym

ID_ATTRIBUTE_LITERAL - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLConstants

id_ttestCircleSize - Static variable in class org.AttributeHelper

IdAndGraphNode - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes

IdAndGraphNode(String, Node) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.IdAndGraphNode

IDLE - org.vanted.plugins.layout.stressminimization.BackgroundStatus

IdRef - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes

IdRef(Entry, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.IdRef

IdRef(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.IdRef

IGNORE - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.GroupLinkProcessingMode

IGNORED_FIELD - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition.ConditionInfo

IllegalIdException - Exception in org.graffiti.attributes

The IllegalIdException will be thrown if a method tries to add an attribute at a location where another attribute already exists.

IllegalIdException(String) - Constructor for exception org.graffiti.attributes.IllegalIdException

Constructs an IllegalIdException with the specified detail message.

IMAGE - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants

ImageAssignmentCommand - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image

Algorithm to assign an image to a node.

ImageAssignmentCommand() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.ImageAssignmentCommand

ImageAttribute - Class in org.graffiti.graphics

Contains the graphic attribute image.

ImageAttribute(String) - Constructor for class org.graffiti.graphics.ImageAttribute

Constructor for Image.

ImageAttribute(String, boolean, boolean, Image, String) - Constructor for class org.graffiti.graphics.ImageAttribute

Constructor for Image.

ImageAttribute(String, boolean, boolean, AWTImageAttribute, String) - Constructor for class org.graffiti.graphics.ImageAttribute

Constructor for Image.

ImageAttribute(String, BooleanAttribute, BooleanAttribute, AWTImageAttribute, StringAttribute) - Constructor for class org.graffiti.graphics.ImageAttribute

Constructor for Image.

ImageBundle - Class in org.graffiti.core

The resource bundle for the images used in the system.

ImageFileResultProcessor - Interface in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter

ImageMapDemo1 - Class in org.jfree.chart.demo

A demo showing how to create an HTML image map for a bar chart.

ImageMapDemo1() - Constructor for class org.jfree.chart.demo.ImageMapDemo1

Default constructor.

ImageMapDemo2 - Class in org.jfree.chart.demo

A demo showing how to create an HTML image map for a pie chart.

ImageMapDemo2() - Constructor for class org.jfree.chart.demo.ImageMapDemo2

Default constructor.

ImageMapDemo3 - Class in org.jfree.chart.demo

A demo showing the construction of HTML image maps for a time series chart.

ImageMapDemo3() - Constructor for class org.jfree.chart.demo.ImageMapDemo3

Default constructor.

ImageMapDemo4 - Class in org.jfree.chart.demo

A demo showing how to create an HTML image map for a 3D bar chart.

ImageMapDemo4() - Constructor for class org.jfree.chart.demo.ImageMapDemo4

Default constructor.

ImageMapDemo5 - Class in org.jfree.chart.demo

Creates an HTML image map for an area chart.

ImageMapDemo5() - Constructor for class org.jfree.chart.demo.ImageMapDemo5

Default constructor.

ImageMapDemo6 - Class in org.jfree.chart.demo

Creates an HTML image map for a multiple pie chart.

ImageMapDemo6() - Constructor for class org.jfree.chart.demo.ImageMapDemo6

Default constructor.

ImageMapDemo7 - Class in org.jfree.chart.demo

A demo showing how to create an HTML image map for a scatter plot.

ImageMapDemo7() - Constructor for class org.jfree.chart.demo.ImageMapDemo7

Default constructor.

IMAGES - Static variable in class org.jfree.chart.renderer.StandardXYItemRenderer

Constant for the type of rendering (images only).

ImageTitle - Class in org.jfree.chart.title

A chart title that displays an image.

ImageTitle(Image) - Constructor for class org.jfree.chart.title.ImageTitle

Creates a new image title.

ImageTitle(Image, int, int, RectangleEdge, HorizontalAlignment, VerticalAlignment, Spacer) - Constructor for class org.jfree.chart.title.ImageTitle

Creates a new image title with the given image scaled to the given width and height in the given location.

ImageTitle(Image, RectangleEdge, HorizontalAlignment, VerticalAlignment) - Constructor for class org.jfree.chart.title.ImageTitle

Creates a new image title.

IMAGING - org.graffiti.plugin.algorithm.Category

ImmutableCheckBox - Class in org.vanted.scaling.resources

A JCheckBox that remains unchanged regardless of the scaling.

ImmutableCheckBox() - Constructor for class org.vanted.scaling.resources.ImmutableCheckBox

ImmutableSlider - Class in org.vanted.scaling.resources

A JSlider that remains unchanged regardless of the scaling.

ImmutableSlider() - Constructor for class org.vanted.scaling.resources.ImmutableSlider

ImmutableSlider(int) - Constructor for class org.vanted.scaling.resources.ImmutableSlider

ImmutableSlider(int, int) - Constructor for class org.vanted.scaling.resources.ImmutableSlider

ImmutableSlider(int, int, int) - Constructor for class org.vanted.scaling.resources.ImmutableSlider

ImmutableSlider(int, int, int, int) - Constructor for class org.vanted.scaling.resources.ImmutableSlider

ImmutableSlider(BoundedRangeModel) - Constructor for class org.vanted.scaling.resources.ImmutableSlider

IMPORT - org.graffiti.plugin.algorithm.Category

IN - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants

inc() - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment

Increments the internal attributes of this segment by one segment.

inc(long) - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment

Increments the internal attributes of this segment by a number of segments.

inch - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.SizeSettingDPIunit

INCH - Static variable in class org.graffiti.editor.Rule

include - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.SearchOperation

includeEmptyAttributes - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance

INCONSISTENT_NUMBER_OF_REACTIONNAMES_AND_TYPES - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Gml2PathwayError

inConstraintCounter - Variable in class placement.Variable

increaseInCount() - Method in class de.ipk_gatersleben.ag_nw.graffiti.services.network.BroadCastService

increaseKey(PNode<T>, T) - Method in class placement.MaxPairingHeap

Change the value of the item stored in the pairing heap.

incrementCount() - Method in class org.jfree.data.statistics.HistogramBin

Increments the item count.

incrementValue(double, Comparable, Comparable) - Method in class org.jfree.data.DefaultCategoryDataset

Adds the specified value to an existing value in the dataset (if the existing value is null, it is treated as if it were 0.0).

inDavidRange(double, int, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.TabStatistics

IndexAndString - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml

IndexAndString(int, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.IndexAndString

IndexAttribute - Class in org.vanted.indexednodes

Stores indices for nodes to allow fast index finding.

IndexedComponent - Class in org.vanted.indexednodes

IndexedComponent(IndexedNodeSet, IndexedEdgeList) - Constructor for class org.vanted.indexednodes.IndexedComponent

IndexedEdgeList - Class in org.vanted.indexednodes

A list of edges

IndexedEdgeList() - Constructor for class org.vanted.indexednodes.IndexedEdgeList

IndexedEdgeListAccumulator - Class in org.vanted.indexednodes.accumulators

IndexedEdgeListAccumulator() - Constructor for class org.vanted.indexednodes.accumulators.IndexedEdgeListAccumulator

IndexedEdgeListAccumulator(IndexedEdgeList) - Constructor for class org.vanted.indexednodes.accumulators.IndexedEdgeListAccumulator

IndexedGraphOperations - Class in org.vanted.indexednodes

Some graph operations backed by org.vanted.addons.indexednodes.IndexedNodeSet.

IndexedNodeSet - Class in org.vanted.indexednodes

A node collection that supports indexed access and fast index finding as well as speedy set operations.

IndexedNodeSet.NodeNotContainedException - Exception in org.vanted.indexednodes

IndexedNodeSet.NotIndexedException - Exception in org.vanted.indexednodes

IndexedNodeSetAccumulator - Class in org.vanted.indexednodes.accumulators

IndexedNodeSetAccumulator(IndexedNodeSet) - Constructor for class org.vanted.indexednodes.accumulators.IndexedNodeSetAccumulator

indexOf(Number) - Method in class org.jfree.data.XYSeries

Returns the index of the item with the specified x-value.

indexOf(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment

indexOf(Object) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface

indexOf(XYDataset) - Method in class org.jfree.chart.plot.XYPlot

Returns the index of the specified dataset, or -1 if the dataset does not belong to the plot.

indexX() - Method in interface org.jfree.data.ContourDataset

Returns an int array contain the index into the x values.

indexX() - Method in class org.jfree.data.DefaultContourDataset

Returns an int array contain the index into the x values.

indexX(int) - Method in class org.jfree.data.DefaultContourDataset

Given index k, returns the column index containing k.

indexY(int) - Method in class org.jfree.data.DefaultContourDataset

Given index k, return the row index containing k.

indexZ(int, int) - Method in class org.jfree.data.DefaultContourDataset

Given column and row indices, returns the k index.

indirect - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.SubtypeName

indirectEffect - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.SubtypeName

inExceptionSegments() - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment

Returns true if we are an exception segment.

inExcludeSegments() - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment

Returns true if we are an excluded segment.

INFINITY - org.vanted.animation.LoopDuration

INFINITY - org.vanted.animation.NumberOfLoops

info - Variable in class org.jfree.chart.demo.PanScrollZoomDemo

INFO - org.graffiti.editor.MessageType

INFO - Static variable in class org.jfree.chart.JFreeChart

Information about the project.

info.clearthought.layout - package info.clearthought.layout

inhibition - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.SubtypeName

INHIBITOR - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathReaction

inhibitorArrow - Static variable in class org.graffiti.plugins.editcomponents.defaults.EdgeArrowShapeEditComponent

InhibitorArrowShape - Class in org.graffiti.plugins.views.defaults

InhibitorArrowShape() - Constructor for class org.graffiti.plugins.views.defaults.InhibitorArrowShape

InhibitorArrowShape(float) - Constructor for class org.graffiti.plugins.views.defaults.InhibitorArrowShape

INHIBITS - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathMolecule

inIncludeSegments() - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment

Returns true if we are an included segment and we are not an exception.

init() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants

init(Container) - Method in class org.vanted.scaling.ComponentRegulator

Global system DPI scaling init! Scan and scale the components specifics.

init(Container, Class<? extends Container>) - Static method in class org.vanted.scaling.ScalerLoader

Global init for LAF and External (Component) scaling operations.

init(String, String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.database.dbe.ProgressManager

init(JComponent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.IPKGraffitiView

init(JComponent) - Method in class org.graffiti.editor.options.LoadSaveOptionsPane

init(JComponent) - Method in class org.graffiti.editor.options.ShortcutsOptionPane

init(JComponent) - Method in class org.graffiti.editor.options.ToolBarOptionPane

init(JComponent) - Method in class org.graffiti.options.AbstractOptionPane

This method is called every time this option pane is displayed.

init(JComponent) - Method in interface org.graffiti.options.OptionPane

This method is called every time this option pane is displayed.

init(Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.ClusterBackgroundDraw

INIT - org.vanted.plugins.layout.stressminimization.BackgroundStatus

initAlgorithmPreferencesPanel(JDialog, Algorithm, Graph, Selection, HandlesAlgorithmData, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.plugin_settings.PreferencesDialog

initApplication(String[], SplashScreenInterface, ClassLoader, String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.GravistoMainHelper

initApplicationExt(String[], SplashScreenInterface, ClassLoader, String, String[]) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.GravistoMainHelper

InitClusterForce - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.myOp

INITIAL_AMOUNT - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants

INITIAL_ASSIGNMENT_FUNCTION - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants

INITIAL_CONCENTRATION - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants

INITIAL_VALUE - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants

initialise(Graphics2D, Rectangle2D, CategoryPlot, int, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.AbstractCategoryItemRenderer

Initialises the renderer and returns a state object that will be used for the remainder of the drawing process for a single chart.

initialise(Graphics2D, Rectangle2D, CategoryPlot, int, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.BarRenderer

Initialises the renderer and returns a state object that will be passed to subsequent calls to the drawItem method.

initialise(Graphics2D, Rectangle2D, CategoryPlot, int, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.BoxAndWhiskerRenderer

Initialises the renderer.

initialise(Graphics2D, Rectangle2D, CategoryPlot, int, PlotRenderingInfo) - Method in interface org.jfree.chart.renderer.CategoryItemRenderer

Initialises the renderer.

initialise(Graphics2D, Rectangle2D, CategoryPlot, int, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.LevelRenderer

Initialises the renderer and returns a state object that will be passed to subsequent calls to the drawItem method.

initialise(Graphics2D, Rectangle2D, PiePlot, Integer, PlotRenderingInfo) - Method in class org.jfree.chart.plot.PiePlot

Initialises the drawing procedure.

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.AbstractXYItemRenderer

Initialises the renderer and returns a state object that should be passed to all subsequent calls to the drawItem() method.

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.AreaXYRenderer

Deprecated.

Initialises the renderer and returns a state object that should be passed to all subsequent calls to the drawItem(...) method.

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.CandlestickRenderer

Initialises the renderer then returns the number of 'passes' through the data that the renderer will require (usually just one).

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.ClusteredXYBarRenderer

Initialises the renderer.

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.StackedXYAreaRenderer

Initialises the renderer.

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.StackedXYBarRenderer

Initialises the renderer and returns a state object that should be passed to all subsequent calls to the drawItem() method.

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.XYAreaRenderer

Initialises the renderer and returns a state object that should be passed to all subsequent calls to the drawItem(...) method.

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.XYBarRenderer

Initialises the renderer and returns a state object that should be passed to all subsequent calls to the drawItem() method.

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.XYDifferenceRenderer

Initialises the renderer and returns a state object that should be passed to subsequent calls to the drawItem() method.

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in interface org.jfree.chart.renderer.XYItemRenderer

Initialises the renderer then returns the number of 'passes' through the data that the renderer will require (usually just one).

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.XYLineAndShapeRenderer

Initialises the renderer.

initialise(Graphics2D, Rectangle2D, XYPlot, XYDataset, PlotRenderingInfo) - Method in class org.jfree.chart.renderer.XYStepAreaRenderer

Initialises the renderer.

INITIALIZATION - org.ApplicationStatus

initialize() - Method in class org.jfree.chart.ui.ColorPalette

Called to initialize the palette's color indexes

initialize() - Method in class org.jfree.chart.ui.GreyPalette

Intializes the palette's indices.

initialize() - Method in class org.jfree.chart.ui.RainbowPalette

Intializes the palettes indexes

initialize(Object[], Object[], Object[]) - Method in class org.jfree.data.DefaultContourDataset

Initialises the dataset.

initializeGUIforGivenContainer(boolean, Algorithm[]) - Method in class de.ipk_gatersleben.ag_nw.graffiti.services.algorithms.AlgorithmPanelFactory

initializeGUIforGivenContainer(Container, JDialog, boolean, boolean, boolean, boolean, boolean, boolean, boolean, Graph, Selection, HandlesAlgorithmData, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.plugin_settings.PreferencesDialog

initializeMacOSX(Action, Action, Action, OpenFileAction, Image, Window) - Static method in class org.vanted.osx.OSXSupport

Initializes various Mac OS X adaptations, using reflection and proxies in order to be compilable on other platforms.

initializeValueCount(int) - Method in class qmwi.kseg.som.diagram.AttributsAttribut

Insert the method's description here.

initialScaling() - Method in class org.vanted.scaling.scalers.BasicScaler

initialScaling() - Method in class org.vanted.scaling.scalers.NimbusScaler

initialScaling() - Method in interface org.vanted.scaling.scalers.Scaler

Used for synchronized LAFs, where only one change (e.g.

initLernrate - Variable in class qmwi.kseg.som.Map

initLinearMarkSequence(MarkComponent, MarkComponent...) - Static method in class org.MarkComponent

initNiceIds() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLNodesNiceIdHelper

Sets the niceIDs if they are not initialized yet.

initNodeCache(ArrayList<NodeCacheEntry>, HashMap<Node, NodeCacheEntry>, Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache.MyTools

As the attribute access is very slow, this method initializes the NodeCacheEntry structures.

initNodeCache(ArrayList<NodeCacheEntry>, HashMap<Node, NodeCacheEntry>, Graph, Selection, ArrayList<Graph>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.MyTools

As the attribute access is very slow, this method initializes the NodeCacheEntry structures.

initNodeCache3d(ArrayList<NodeCacheEntry3d>, HashMap<Node, NodeCacheEntry3d>, Graph, Selection) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.MyTools

initProductEdge(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

initReactantEdge(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

initReactionNode(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

initSOM(int, int, double, int, int, boolean) - Method in class qmwi.kseg.som.DataSet

initSpeciesNode(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

This method converts a node into a species node

initWindowResizer() - Static method in class org.vanted.scaling.DPIHelper

Attaches a WindowResizer listener that will resize any newly opened windows.

inkValueCount(int) - Method in class qmwi.kseg.som.diagram.AttributsAttribut

Insert the method's description here.

inputNeuronsNeededFor(int) - Method in class qmwi.kseg.som.DataSet

inputNeuronsNeededFor(Vector<SOMdataEntry>, String[]) - Method in class qmwi.kseg.som.DataSet

InputSerializer - Interface in org.graffiti.plugin.io

Interfaces a serializer, which is able to reconstruct a graph from a given input.

inputSerializerAdded(InputSerializer) - Method in class org.graffiti.editor.MainFrame

inputSerializerAdded(InputSerializer) - Method in interface org.graffiti.managers.IOManager.IOManagerListener

Called, if an input serializer is added to the io manager.

InputStream(InputStream) - Constructor for class org.graffiti.plugins.ios.exporters.graphml.Base64.InputStream

Constructs a Base64.InputStream in DECODE mode.

InputStream(InputStream) - Constructor for class org.graffiti.plugins.ios.importers.graphml.parser.Base64.InputStream

Constructs a Base64.InputStream in DECODE mode.

InputStream(InputStream, int) - Constructor for class org.graffiti.plugins.ios.exporters.graphml.Base64.InputStream

Constructs a Base64.InputStream in either ENCODE or DECODE mode.

InputStream(InputStream, int) - Constructor for class org.graffiti.plugins.ios.importers.graphml.parser.Base64.InputStream

Constructs a Base64.InputStream in either ENCODE or DECODE mode.

inputv - Variable in class qmwi.kseg.som.Map

insert(T) - Method in class placement.MinPairingHeap

Insert into the priority queue, and return a PNode that can be used by decreaseKey.

insertColumn(int, double) - Method in class info.clearthought.layout.TableLayout

Inserts a column in this layout.

insertRow(int, double) - Method in class info.clearthought.layout.TableLayout

Inserts a row in this layout.

INSIDE - org.graffiti.plugins.views.defaults.DockingAttributeEditor.DockingModes

INSIDE1 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE1.

INSIDE10 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE10.

INSIDE11 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE11.

INSIDE12 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE12.

INSIDE2 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE2.

INSIDE3 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE3.

INSIDE4 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE4.

INSIDE5 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE5.

INSIDE6 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE6.

INSIDE7 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE7.

INSIDE8 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE8.

INSIDE9 - Static variable in class org.jfree.chart.labels.ItemLabelAnchor

INSIDE9.

INSIDEBOTTOM - org.AlignmentSetting

INSIDEBOTTOM - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants

Constant used to specify the position of a label according to a node.

INSIDEBOTTOMLEFT - org.AlignmentSetting

INSIDEBOTTOMLEFT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants

INSIDEBOTTOMRIGHT - org.AlignmentSetting

INSIDEBOTTOMRIGHT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants

INSIDELEFT - org.AlignmentSetting

INSIDELEFT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants

INSIDERIGHT - org.AlignmentSetting

INSIDERIGHT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants

INSIDETOP - org.AlignmentSetting

INSIDETOP - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants

Constant used to specify the position of a label according to a node.

INSIDETOPLEFT - org.AlignmentSetting

INSIDETOPLEFT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants

INSIDETOPRIGHT - org.AlignmentSetting

INSIDETOPRIGHT - Static variable in interface org.graffiti.graphics.GraphicAttributeConstants

Inspector - Class in org.graffiti.plugins.inspectors.defaults

Represents the main class of the inspector plugin.

Inspector() - Constructor for class org.graffiti.plugins.inspectors.defaults.Inspector

Constructs a new inspector instance.

InspectorContainer - Class in org.graffiti.plugins.inspectors.defaults

Represents the central gui component of the inspector plugin.

InspectorContainer() - Constructor for class org.graffiti.plugins.inspectors.defaults.InspectorContainer

Creates a new InspectorContainer object.

InspectorPlugin - Interface in org.graffiti.plugin.inspector

Provides a general interface for components to be plugged into an inspector.

InspectorTab - Class in org.graffiti.plugin.inspector

An InspectorTab is a generic component for an InspectorPlugin.

InspectorTab() - Constructor for class org.graffiti.plugin.inspector.InspectorTab

install(JEditorPane) - Method in class de.ipk_gatersleben.ag_nw.graffiti.services.PatchedHTMLEditorKit

installAddon(String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonManagerPlugin

Install Add-on by copying the jarfile and loading it.

installDragNDrop(JButton) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.TabDBE

installDragNDropForAnnotationFiles(JButton, JButton) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ExperimentDataInfoPane

installDragNDropForArrayFiles(JButton, JButton) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ExperimentDataInfoPane

installDragNDropForGraphFiles(JButton) - Method in class org.graffiti.editor.MainFrame

InstalledAndActive - de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddOnInstallResult

InstalledAndIncompatible - de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddOnInstallResult

InstanceCreationException - Exception in org.graffiti.util

An exception, which is thrown, iff the instantiation of a given class fails.

InstanceCreationException(Exception) - Constructor for exception org.graffiti.util.InstanceCreationException

Creates a new InstanceCreationException object.

InstanceCreationException(String) - Constructor for exception org.graffiti.util.InstanceCreationException

Creates a new InstanceCreationException object.

InstanceLoader - Class in org.graffiti.util

Represents an instance loader, which can be used to instantiate a class with the given name.

InstanceLoader() - Constructor for class org.graffiti.util.InstanceLoader

instantiateEdge() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLContentHandler

Instantiates a new edge and add it to teh graph.

instantiateEdge() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLHandler

instantiateGraph() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLContentHandler

Instantiates a new graph.

instantiateGraph() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLHandler

instantiateNode() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLContentHandler

Instantiates a new node and add it to teh graph.

instantiateNode() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLHandler

INTEGER - Static variable in class org.graffiti.plugins.ios.importers.gml.sym

IntegerAttribute - Class in org.graffiti.attributes

Contains an integer.

IntegerAttribute(String) - Constructor for class org.graffiti.attributes.IntegerAttribute

Constructs a new instance of an IntegerAttribute.

IntegerAttribute(String, int) - Constructor for class org.graffiti.attributes.IntegerAttribute

Constructs a new instance of an IntegerAttribute with the given value.

IntegerAttribute(String, Integer) - Constructor for class org.graffiti.attributes.IntegerAttribute

Constructs a new instance of a IntegerAttribute with the given value.

IntegerEditComponent - Class in org.graffiti.plugins.editcomponents.defaults

Represents a GUI component, which handles integer values.

IntegerEditComponent(Displayable) - Constructor for class org.graffiti.plugins.editcomponents.defaults.IntegerEditComponent

Creates a new IntegerEditComponent object.

IntegerParameter - Class in org.graffiti.plugin.parameter

Parameter that can contain Integer/int values.

IntegerParameter(Integer, Integer, Integer, Integer, String, String) - Constructor for class org.graffiti.plugin.parameter.IntegerParameter

Constructs a new Integer parameter.

IntegerParameter(Integer, Integer, Integer, String, String) - Constructor for class org.graffiti.plugin.parameter.IntegerParameter

Constructs a new Integer parameter.

IntegerParameter(Integer, Integer, String, String) - Constructor for class org.graffiti.plugin.parameter.IntegerParameter

Constructs a new Integer parameter.

IntegerParameter(Integer, String, String) - Constructor for class org.graffiti.plugin.parameter.IntegerParameter

Constructs a new Integer parameter.

INTERNAL_EDGE_INDEX - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils

The attribute name for the internal edge index.

INTERNAL_NODE_INDEX - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.PatternAttributeUtils

The attribute name for the internal node index.

INTERNAL_RELATION_SRC_OR_TGT_NOT_FOUND - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Gml2PathwayError

internalFrameActivated(InternalFrameEvent) - Method in class org.graffiti.util.MaximizeManager

internalFrameDeiconified(InternalFrameEvent) - Method in class org.graffiti.util.MaximizeManager

InternalFrameDemo - Class in org.jfree.chart.demo

A simple internal frame demo.

InternalFrameDemo(String) - Constructor for class org.jfree.chart.demo.InternalFrameDemo

Creates a new instance of the demo.

InterpolatableTimePoint<T> - Class in org.vanted.animation.data

Inherit from this class instead of TimePoint if the data point is capable of being interpolated

InterpolatableTimePoint(double, T) - Constructor for class org.vanted.animation.data.InterpolatableTimePoint

interpolate(double, double...) - Method in class org.vanted.animation.interpolators.SmoothCubicInterpolator

interpolate(double, double, int, List<T>, Looper) - Method in class org.vanted.animation.interpolators.BezierInterpolator

interpolate(double, double, int, List<T>, Looper) - Method in class org.vanted.animation.interpolators.Interpolator

interpolateColor(double, double, int, List<ColorTimePoint>, Looper, ColorMode) - Method in class org.vanted.animation.interpolators.Interpolator

Colors can interpolate in special ways.
It is recommended that you call this method instead of interpolate() to interpolate between values.

Interpolator - Class in org.vanted.animation.interpolators

Interpolator() - Constructor for class org.vanted.animation.interpolators.Interpolator

Interpolator classes specify how data is interpolated between datapoints.

InterpreteGOtermsAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go

InterpreteGOtermsAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go.InterpreteGOtermsAlgorithm

InterpreteParentGOtermsAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go

InterpreteParentGOtermsAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go.InterpreteParentGOtermsAlgorithm

INTERPRODESCRIPTION - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathMolecule

INTERPROID - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathMolecule

interrupt() - Method in interface org.graffiti.plugin.GenericPlugin

Interrupts the running plugin.

interrupt() - Method in class org.graffiti.plugin.GenericPluginAdapter

Interrupts the running plugin.

intersect(long, long) - Method in class org.jfree.chart.axis.SegmentedTimeline.Segment

Returns a segment that is the intersection of this segment and the interval.

intersection(IndexedNodeSet) - Method in class org.vanted.indexednodes.IndexedNodeSet

Performs the intersection operation with the given other org.vanted.addons.indexednodes.IndexedNodeSet.

intersects(double, double) - Method in class org.jfree.data.Range

Returns true if the range intersects with the specified range, and false otherwise.

intersects(double, double, double, double) - Method in class org.graffiti.plugins.views.defaults.AbstractArrowShape

DOCUMENT ME!

intersects(double, double, double, double) - Method in class org.graffiti.plugins.views.defaults.LineEdgeShape

DOCUMENT ME!

intersects(double, double, double, double) - Method in class org.graffiti.plugins.views.defaults.PolygonalNodeShape

intersects(double, double, double, double) - Method in class org.graffiti.plugins.views.defaults.RectangularNodeShape

DOCUMENT ME!

intersects(Rectangle2D) - Method in class org.graffiti.plugins.views.defaults.AbstractArrowShape

DOCUMENT ME!

intersects(Rectangle2D) - Method in class org.graffiti.plugins.views.defaults.LineEdgeShape

DOCUMENT ME!

intersects(Rectangle2D) - Method in class org.graffiti.plugins.views.defaults.PolygonalNodeShape

intersects(Rectangle2D) - Method in class org.graffiti.plugins.views.defaults.RectangularNodeShape

DOCUMENT ME!

IntervalBarChartDemo1 - Class in org.jfree.chart.demo

An interval bar chart.

IntervalBarChartDemo1() - Constructor for class org.jfree.chart.demo.IntervalBarChartDemo1

Creates a new demo.

IntervalBarRenderer - Class in org.jfree.chart.renderer

A renderer that handles the drawing of bars for a bar plot where each bar has a high and low value.

IntervalBarRenderer() - Constructor for class org.jfree.chart.renderer.IntervalBarRenderer

Constructs a new renderer.

IntervalCategoryDataset - Interface in org.jfree.data

A category dataset that defines a value range for each series/category combination.

IntervalCategoryLabelGenerator - Class in org.jfree.chart.labels

A label generator for plots that use data from an IntervalCategoryDataset.

IntervalCategoryLabelGenerator() - Constructor for class org.jfree.chart.labels.IntervalCategoryLabelGenerator

Creates a new generator with a default number formatter.

IntervalCategoryLabelGenerator(String, DateFormat) - Constructor for class org.jfree.chart.labels.IntervalCategoryLabelGenerator

Creates a new generator with the specified date formatter.

IntervalCategoryLabelGenerator(String, NumberFormat) - Constructor for class org.jfree.chart.labels.IntervalCategoryLabelGenerator

Creates a new generator with the specified number formatter.

IntervalCategoryToolTipGenerator - Class in org.jfree.chart.labels

A tooltip generator for plots that use data from an IntervalCategoryDataset.

IntervalCategoryToolTipGenerator() - Constructor for class org.jfree.chart.labels.IntervalCategoryToolTipGenerator

Creates a new generator with a default number formatter.

IntervalCategoryToolTipGenerator(String, DateFormat) - Constructor for class org.jfree.chart.labels.IntervalCategoryToolTipGenerator

Creates a new generator with the specified date formatter.

IntervalCategoryToolTipGenerator(String, NumberFormat) - Constructor for class org.jfree.chart.labels.IntervalCategoryToolTipGenerator

Creates a new generator with the specified number formatter.

IntervalMarker - Class in org.jfree.chart.plot

Represents an interval to be highlighted in some way.

IntervalMarker(double, double) - Constructor for class org.jfree.chart.plot.IntervalMarker

Constructs an interval marker.

IntervalMarker(double, double, Paint, Stroke, Paint, Stroke, float) - Constructor for class org.jfree.chart.plot.IntervalMarker

Constructs an interval marker.

IntervalXYDataset - Interface in org.jfree.data

An extension of the XYDataset interface that allows a range of data to be defined for the X values, the Y values, or both the X and Y values.

IntervalXYZDataset - Interface in org.jfree.data

An extension of the XYZDataset interface that allows a range of data to be defined for any of the X values, the Y values, and the Z values.

inTrash() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentHeader

inTrash() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentHeaderInterface

IntroduceBendsAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands

IntroduceBendsAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.IntroduceBendsAlgorithm

introduceNewBends(Graph, HashSet<Edge>, int, String, int, boolean, String, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

Add new bends to a graph

introduceNewBends(Graph, HashSet<Edge>, int, String, int, String, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

IntroduceParallelEdgeBends - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands

IntroduceParallelEdgeBends() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.IntroduceParallelEdgeBends

IntroduceSelfEdgeBends - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands

IntroduceSelfEdgeBends() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.IntroduceSelfEdgeBends

INVALID_BACKGROUNDCOLOR - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Gml2PathwayError

INVALID_FOREGROUNDCOLOR - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Gml2PathwayError

INVALID_GRAPHICS_TYPE - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Gml2PathwayError

INVALID_RELATION_TYPE - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Gml2PathwayError

invalidateLayout(Container) - Method in class info.clearthought.layout.TableLayout

Invalidates the layout, indicating that if the layout manager has cached information it should be discarded.

invalidateRangeInfo() - Method in class org.jfree.data.time.DynamicTimeSeriesCollection

Invalidates the range info.

InverseGraphPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.inverse_graph

InverseGraphPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.inverse_graph.InverseGraphPlugin

InverseGraphPluginAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.inverse_graph

InverseGraphPluginAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.inverse_graph.InverseGraphPluginAlgorithm

invertPalette() - Method in class org.jfree.chart.ui.ColorPalette

Inverts Palette

InvertSelectionAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection

Labels all selected nodes with unique numbers.

InvertSelectionAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.InvertSelectionAlgorithm

Constructs a new instance.

InvertSelectionPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection

InvertSelectionPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.InvertSelectionPlugin

IOManager - Interface in org.graffiti.managers

Handles the editor's IO serializers.

IOManager.IOManagerListener - Interface in org.graffiti.managers

Interfaces an io manager listener.

IOurl - Class in org.graffiti.plugin.io.resources

IOurl(String) - Constructor for class org.graffiti.plugin.io.resources.IOurl

IOurl(String, String) - Constructor for class org.graffiti.plugin.io.resources.IOurl

IOurl(String, String, String) - Constructor for class org.graffiti.plugin.io.resources.IOurl

IOurl(IOurl) - Constructor for class org.graffiti.plugin.io.resources.IOurl

IPK_AdvancedLabelTool - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools

A modified editing tool

IPK_AdvancedLabelTool() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.IPK_AdvancedLabelTool

IPK_EditorPluginAdapter - Class in de.ipk_gatersleben.ag_nw.graffiti

IPK_EditorPluginAdapter() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.IPK_EditorPluginAdapter

IPK_MegaCreateTool - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools

A modified editing tool

IPK_MegaCreateTool() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.IPK_MegaCreateTool

IPK_MegaMoveTool - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools

A modified editing tool.

IPK_MegaMoveTool() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.IPK_MegaMoveTool

IPK_PluginAdapter - Class in de.ipk_gatersleben.ag_nw.graffiti

IPK_PluginAdapter() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.IPK_PluginAdapter

IPK_StandardTools - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools

This plugin contains the modified standard editing tools.

IPK_StandardTools() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.IPK_StandardTools

Creates a new StandardTools object.

IPKDefaultView - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview

PlugIn for default view of graffiti graph editor

IPKDefaultView() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.IPKDefaultView

Constructor for DefaultView.

IPKeditComponents - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.enhanced_attribute_editors

This class is a plugin providing some default value edit components.

IPKeditComponents() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.enhanced_attribute_editors.IPKeditComponents

IPKGraffitiView - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview

An implementation of org.graffiti.plugin.view.View2D, that displays a graph.

IPKGraffitiView() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.IPKGraffitiView

IPKnodeComponent - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview

IPKnodeComponent(GraphElement) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.IPKnodeComponent

irreversible - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.ReactionType

isAbort() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsAccessAdapter

isAbortWanted() - Method in class org.graffiti.plugin.algorithm.ThreadSafeOptions

Check if the plugin should stop.

isActive() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.Addon

isActive() - Method in class org.graffiti.plugin.tool.AbstractTool

Returns true if this tool has been activated and since then not been deactivated.

isActive() - Method in interface org.graffiti.plugin.tool.Tool

Returns true if the tool is active.

isAddon() - Method in class org.graffiti.managers.pluginmgr.PluginDescription

isAdvanceLineVisible() - Method in class org.jfree.chart.axis.CyclicNumberAxis

The advance line is the line drawn at the limit of the current cycle, when erasing the previous cycle.

isAlreadyNormalized() - Method in class qmwi.kseg.som.CSV_SOM_dataEntry

isAlreadyNormalized() - Method in interface qmwi.kseg.som.SOMdataEntry

isAlwaysExecutable() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation.ErdosRenyiGraphGenerator

isAlwaysExecutable() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation.WattsStrogatzGraphGenerator

isAlwaysExecutable() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.SelectWindowsAlgorithm

isAlwaysExecutable() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.RemoveSelectedNodesPreserveEdgesAlgorithm

isAlwaysExecutable() - Method in class org.graffiti.plugin.algorithm.AbstractAlgorithm

Indicates, if an algorithm is always executable - even without an active session.

isAngleGridlinesVisible() - Method in class org.jfree.chart.plot.PolarPlot

Returns true if the angular gridlines are visible, and false otherwise.

isAngleLabelsVisible() - Method in class org.jfree.chart.plot.PolarPlot

Returns a flag that controls whether or not the angle labels are visible.

isAnyOneSignificant(double) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.CorrelationResult

isAskBeforeOverwrite() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithm

isAutoPrune() - Method in class org.jfree.data.DefaultTableXYDataset

Returns the flag that controls whether or not x-values are removed from the dataset when the corresponding y-values are all null.

isAutoRange() - Method in class org.jfree.chart.axis.ValueAxis

Returns true if the axis range is automatically adjusted to fit the data.

isAutoRange() - Method in class org.jfree.chart.ui.ColorBarPropertyEditPanel

Returns the current setting of the auto-range property.

isAutoTickUnitSelection() - Method in class org.jfree.chart.axis.ValueAxis

Returns a flag indicating whether or not the tick unit is automatically selected from a range of standard tick units.

isAutoWidth() - Method in class org.jfree.data.CategoryTableXYDataset

Returns wether the interval width is automatically calculated or not.

isAutoWidth() - Method in class org.jfree.data.DefaultTableXYDataset

Returns wether the interval width is automatically calculated or not.

isAutoWidth() - Method in class org.jfree.data.XYSeriesCollection

Returns wether the interval width is automatically calculated or not.

isAvailable() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsAccessAdapter

isAvoidable() - Static method in class org.vanted.scaling.DPIHelper

Test whether scaling is currently necessary.

isAxisLineVisible() - Method in class org.jfree.chart.axis.Axis

A flag that controls whether or not the axis line is drawn.

isBiologicalAndTechnicalReplicateDataAvailable(ExperimentInterface) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment

isBorderOpaque() - Method in class org.graffiti.plugin.tool.EdgeBorder

DOCUMENT ME!

isBorderOpaque() - Method in class org.graffiti.plugin.tool.NodeBorder

DOCUMENT ME!

isBorderVisible() - Method in class org.jfree.chart.JFreeChart

Returns a flag that controls whether or not a border is drawn around the outside of the chart.

isBoundMappedToLastCycle() - Method in class org.jfree.chart.axis.CyclicNumberAxis

The cycle bound can be associated either with the current or with the last cycle.

isCacheURL(URL) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.CachedWebDownload

isCacheURL(URL) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.FileDownloadCache

isCellEditable(int, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonTableModel

isCellEditable(int, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.TreeTableModelAdapter

isCellEditable(int, int) - Method in class org.graffiti.plugins.views.matrix.MatrixModel

isCellEditable(int, int) - Method in class org.jfree.data.TimeSeriesTableModel

Returns a flag indicating whether or not the specified cell is editable.

isCellEditable(int, int) - Method in class org.jfree.data.XYDatasetTableModel

Returns a flag indicating whether or not the specified cell is editable.

isCellEditable(Object, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.AbstractTreeTableModel

By default, make the column with the Tree in it the only editable one.

isCellEditable(Object, int) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.TreeTableModel

Indicates whether the the value for node node, at column number column is editable.

isCellEditable(EventObject) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.AbstractCellEditor

isCenteredFitPosition(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundImagePositionAttributeEditor

isCenteredPosition(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundImagePositionAttributeEditor

isCircular() - Method in class org.jfree.chart.plot.PiePlot

Returns a flag indicating whether the pie chart is circular, or stretched into an elliptical shape.

isClip() - Method in class org.jfree.chart.ClipPath

Returns the clip.

isClosing() - Method in class org.graffiti.session.EditorSession

Returns true, if the session is currently closing.

isClusterAnalysisRunning() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.ClusterAnalysisMain

isColorEnzymesAndUseReferencePathway() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggPathwayEntry

isCompatibleDomainAxis(ValueAxis) - Method in class org.jfree.chart.plot.ContourPlot

Checks the compatibility of a domain axis, returning true if the axis is compatible with the plot, and false otherwise.

isComplete() - Method in class org.vanted.plugins.layout.multilevelframework.MultilevelGraph

Checks whether the top level is complete, i.e.

isComponentScaled(JComponent) - Static method in class org.vanted.scaling.Toolbox

A shortcut method for ComponentRegulator.isScaled(JComponent) that checks at runtime whether a component has been scaled with the most recent scaling procedure.

isContainedBasisCollectionAndSet(Node) - Method in class org.vanted.indexednodes.IndexedNodeSet

Returns true if node is contained in this sets basis collection as well as in this set itself.

isCpdChemicalCompound() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.KeggId

isCreateHTMLmap() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithmParams

isCreateJPG() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithmParams

isCreatingEdge() - Method in class org.graffiti.plugins.modes.defaults.MegaCreateTool

isCustomTarget() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithmParams

isDatabaseAvailable(boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes.EnzymeService

isDataFlavorSupported(DataFlavor) - Method in class net.iharder.dnd.TransferableObject

Returns true if flavor is one of the supported flavors.

isDateAfterUpdateDate(Date, Preferences) - Static method in class org.vanted.updater.CheckUpdateDate

isDateAxis(int) - Method in interface org.jfree.data.ContourDataset

Returns true if axis are dates.

isDateAxis(int) - Method in class org.jfree.data.DefaultContourDataset

Returns true if axis are dates.

isDBEinputForm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.TableData

isDBEtransposedInputForm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.TableData

isDead() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.UllmannSubraphIsomAdjMatrixState

isDeleted() - Method in class org.graffiti.attributes.AbstractAttribute

isDeleted() - Method in interface org.graffiti.attributes.Attribute

isDirected() - Method in class org.graffiti.graph.AbstractGraph

Indicates whether the graph is directed.

isDirected() - Method in class org.graffiti.graph.AdjListEdge

Returns true, if the Edge is directed, false otherwise.

isDirected() - Method in interface org.graffiti.graph.Edge

Returns true, if the Edge is directed, false otherwise.

isDirected() - Method in interface org.graffiti.graph.Graph

Indicates whether the Graph is directed.

isDirected() - Method in class org.graffiti.graph.OptAdjListGraph

Indicates whether the graph is directed.

isDirectedRelationDefinedBySubtypes() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Relation

isDomainCrosshairLockedOnData() - Method in class org.jfree.chart.plot.ContourPlot

Returns a flag indicating whether or not the crosshair should "lock-on" to actual data values.

isDomainCrosshairLockedOnData() - Method in class org.jfree.chart.plot.XYPlot

Returns a flag indicating whether or not the crosshair should "lock-on" to actual data values.

isDomainCrosshairVisible() - Method in class org.jfree.chart.plot.ContourPlot

Returns a flag indicating whether or not the domain crosshair is visible.

isDomainCrosshairVisible() - Method in class org.jfree.chart.plot.XYPlot

Returns a flag indicating whether or not the domain crosshair is visible.

isDomainGridlinesVisible() - Method in class org.jfree.chart.plot.CategoryPlot

Returns the flag that controls whether the domain grid-lines are visible.

isDomainGridlinesVisible() - Method in class org.jfree.chart.plot.FastScatterPlot

Returns true if the domain gridlines are visible, and false otherwise.

isDomainGridlinesVisible() - Method in class org.jfree.chart.plot.XYPlot

Returns true if the domain gridlines are visible, and false otherwise.

isDrawBarOutline() - Method in class org.jfree.chart.renderer.BarRenderer

Returns a flag that controls whether or not bar outlines are drawn.

isDrawLines() - Method in class org.jfree.chart.renderer.LineAndShapeRenderer

Returns true if a line should be drawn from the previous to the current data point, and false otherwise.

isDrawLines() - Method in class org.jfree.chart.renderer.MinMaxCategoryRenderer

Gets whether or not lines are drawn between category points.

isDrawPath() - Method in class org.jfree.chart.ClipPath

Returns the drawPath.

isDrawShapes() - Method in class org.jfree.chart.renderer.LineAndShapeRenderer

Returns true if a shape should be drawn to represent each data point, and false otherwise.

isEcEnzyme() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.KeggId

isEdgeAttributeDescription() - Method in class org.graffiti.attributes.AttributeDescription

isEditorFrameSelected() - Method in class org.graffiti.editor.GravistoService

Checks if an editor frame in the main view is selected.

isEmpty() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition

isEmpty() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface

isEmpty() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment

isEmpty() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface

isEmpty() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample

isEmpty() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface

isEmpty() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance

isEmpty() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface

isEmpty() - Method in class org.graffiti.attributes.AbstractCollectionAttribute

Returns true if the HashMapAttribute is empty.

isEmpty() - Method in interface org.graffiti.attributes.CollectionAttribute

Returns true if the CollectionAttribute is empty.

isEmpty() - Method in class org.graffiti.editor.ViewTypeChooser

Returns true, if the list is empty.

isEmpty() - Method in class org.graffiti.graph.AbstractGraph

Returns true if the graph is empty.

isEmpty() - Method in interface org.graffiti.graph.Graph

Returns true if the Graph is empty.

isEmpty() - Method in class org.graffiti.graph.OptAdjListGraph

Returns true if the graph is empty.

isEmpty() - Method in class org.graffiti.managers.pluginmgr.PluginSelector

Returns true, if the list is empty.

isEmpty() - Method in exception org.graffiti.plugin.algorithm.PreconditionException

Checks, if this PreconditionException contains any error entries.

isEmpty() - Method in class org.graffiti.selection.Selection

Returns true if no nodes or edges are selected.

isEmpty() - Method in class org.graffiti.util.Queue

Returns true, if the queue is empty.

isEmpty() - Method in class org.vanted.indexednodes.IndexedNodeSet

isEmpty() - Method in class placement.MaxPairingHeap

Test if the priority queue is logically empty.

isEmpty() - Method in class placement.MinPairingHeap

Test if the priority queue is logically empty.

isEmptyOrNull(CategoryDataset) - Static method in class org.jfree.data.DatasetUtilities

Returns true if the dataset is empty (or null), and false otherwise.

isEmptyOrNull(PieDataset) - Static method in class org.jfree.data.DatasetUtilities

Returns true if the dataset is empty (or null), and false otherwise.

isEmptyOrNull(XYDataset) - Static method in class org.jfree.data.DatasetUtilities

Returns true if the dataset is empty (or null), and false otherwise.

isEmptyValue() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_colors.LineModeSetting

isEnabled() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.FileOpenAction

This action is enabled, if the editor's io manager contains an input serializer.

isEnabled() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.FileSaveAsAction

isEnabled() - Method in class org.graffiti.editor.actions.AddAttributeAction

isEnabled() - Method in class org.graffiti.editor.actions.ChangeAttributeValueAction

isEnabled() - Method in class org.graffiti.editor.actions.CloneViewAction

isEnabled() - Method in class org.graffiti.editor.actions.CloseViewAction

isEnabled() - Method in class org.graffiti.editor.actions.CopyAction

isEnabled() - Method in class org.graffiti.editor.actions.CutAction

isEnabled() - Method in class org.graffiti.editor.actions.DeleteAction

isEnabled() - Method in class org.graffiti.editor.actions.DeleteAttributeAction

isEnabled() - Method in class org.graffiti.editor.actions.EditRedoAction

isEnabled() - Method in class org.graffiti.editor.actions.EditUndoAction

isEnabled() - Method in class org.graffiti.editor.actions.ExitAction

isEnabled() - Method in class org.graffiti.editor.actions.FileCloseAction

DOCUMENT ME!

isEnabled() - Method in class org.graffiti.editor.actions.FileNewAction

isEnabled() - Method in class org.graffiti.editor.actions.FileOpenAction

This action is enabled, if the editor's io manager contains an input serializer.

isEnabled() - Method in class org.graffiti.editor.actions.FileSaveAction

DOCUMENT ME!

isEnabled() - Method in class org.graffiti.editor.actions.FileSaveAllAction

DOCUMENT ME!

isEnabled() - Method in class org.graffiti.editor.actions.FileSaveAsAction

DOCUMENT ME!

isEnabled() - Method in class org.graffiti.editor.actions.PasteAction

isEnabled() - Method in class org.graffiti.editor.actions.PluginManagerEditAction

isEnabled() - Method in class org.graffiti.editor.actions.RedrawViewAction

isEnabled() - Method in class org.graffiti.editor.actions.RunAlgorithm

isEnabled() - Method in class org.graffiti.editor.actions.SelectAllAction

DOCUMENT ME!

isEnabled() - Method in class org.graffiti.editor.actions.ShowPreferencesAction

isEnabled() - Method in class org.graffiti.editor.actions.ViewNewAction

isEnabled() - Method in class org.graffiti.plugin.actions.GraffitiAction

Returns true, if this action is enabled.

isEnabled() - Method in class org.graffiti.plugin.actions.PopupAction

isEnabled() - Method in class org.graffiti.plugin.actions.SelectionAction

isEnabled() - Method in class org.graffiti.plugin.editcomponent.AbstractValueEditComponent

isEnabled() - Method in class org.graffiti.plugin.editcomponent.JComponentParameterEditor

isEnabled() - Method in interface org.graffiti.plugin.editcomponent.ValueEditComponent

Returns whether this component allows editing.

isEnabled() - Method in class org.graffiti.plugins.guis.switchselections.SelectionChangeAction

isEnabled() - Method in class org.graffiti.plugins.guis.switchselections.SelectionSaveAction

isEnabled(String) - Method in class org.SettingsHelperDefaultIsFalse

isEnabled(String) - Method in class org.SettingsHelperDefaultIsTrue

isEnforceFileExtensions() - Method in class org.jfree.chart.ChartPanel

Returns true if file extensions should be enforced, and false otherwise.

isEnzymeNode(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggHelper

isEqualPrefix(String) - Method in class org.graffiti.plugin.io.resources.IOurl

isFeasiblePair(int, int) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.UllmannSubraphIsomAdjMatrixState

isFileUrl(IOurl) - Static method in class org.graffiti.plugin.io.resources.FileSystemHandler

isFillPath() - Method in class org.jfree.chart.ClipPath

Returns the fillPath.

isFinished() - Method in interface org.graffiti.plugin.algorithm.AnimatedAlgorithm

Returns true if the algorithm has another step (that means that nextStep() will not throw an Exception).

isFinished() - Method in class org.vanted.updater.ScanForAddonUpdates

isFinished(double) - Method in class org.vanted.animation.Animation

isFinishingTransacation - Variable in class org.graffiti.plugins.views.defaults.GraffitiView

components can use this variable to check, if this view is currently finishing a transaction and thus can behave differently as ususal Currently it is used to selectively NOT update dependent components on each node

isFirstRun() - Static method in class org.ReleaseInfo

isFixPath2Models() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_XML_Reader

isGeneExpressionFileFormatForm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.TableData

isGeneProductOfGivenOrganism() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.KeggId

isGlGlycan() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.KeggId

isGoal() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.UllmannSubraphIsomAdjMatrixState

isGraphLoadingInProgress() - Method in class org.graffiti.editor.MainFrame

isGridLinesVisible() - Method in class org.jfree.chart.axis.SymbolicAxis

Returns true if the symbolic grid lines are showing, and false otherwise.

isGroupComplexOfKOs() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.KeggId

isHidden(GraphElement) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view.FastView

isHidden(GraphElement) - Method in interface org.graffiti.plugin.view.GraphView

isHidden(GraphElement) - Method in class org.graffiti.plugins.views.defaults.GraffitiView

isHiddenGraphElement(GraphElement) - Static method in class org.AttributeHelper

isHiddenValue(long) - Method in class org.jfree.chart.axis.DateAxis

Returns true if the axis hides this value, and false otherwise.

isHide(String) - Static method in enum de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.GraffitiCharts

isHighlight() - Method in class org.graffiti.plugins.attributecomponents.simplelabel.ViewLabel

isHighlighted(GraphElement) - Method in interface org.graffiti.plugin.tool.ReceiveHighlightInfo

isHollow() - Method in class org.graffiti.plugins.views.defaults.AbsoluteStimulationArrowShape

isHollow() - Method in class org.graffiti.plugins.views.defaults.AssignmentArrowShape

isHollow() - Method in class org.graffiti.plugins.views.defaults.CircleArrowShape

isHollow() - Method in class org.graffiti.plugins.views.defaults.DiamondArrowShape

isHollow() - Method in class org.graffiti.plugins.views.defaults.StandardArrowShape

isHollow() - Method in class org.graffiti.plugins.views.defaults.StandardArrowShapeLeft

isHollow() - Method in class org.graffiti.plugins.views.defaults.StandardArrowShapeRight

isHollow() - Method in interface org.graffiti.plugins.views.defaults.SupportsHollowDrawing

isHollow() - Method in class org.graffiti.plugins.views.defaults.TriggerArrowShape

isHumanPathwayUsingOMIMids() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.MapOrg

isIncludeTooltip() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithmParams

isIncludeURLinTooltip() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithmParams

isIndividualNodeCommand() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.BSHscriptMenuEntry

isInEdge() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.AttributePathNameSearchType

isInFullscreen() - Method in interface org.graffiti.plugin.view.CustomFullscreenView

isInitialized() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLNodesNiceIdHelper

isInNode() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.AttributePathNameSearchType

isInputSerializerKnown(File) - Method in class org.graffiti.editor.MainFrame

isInstalled() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.DotLayoutAlgorithm

isInstalled(String) - Method in class org.graffiti.managers.pluginmgr.DefaultPluginManager

Checks if the plugin is already installed, i.e.

isInstalled(String) - Method in interface org.graffiti.managers.pluginmgr.PluginManager

Returns true, if the plugin with the given name is in the list of currently installed plugins.

isInverse() - Method in class org.jfree.chart.ui.ColorPalette

Returns the inverse flag.

isInverted() - Method in class org.jfree.chart.axis.ValueAxis

Returns a flag that controls the direction of values on the axis.

isItemLabelVisible(int, int) - Method in class org.jfree.chart.renderer.AbstractRenderer

Returns true if an item label is visible, and false otherwise.

isItemLabelVisible(int, int) - Method in interface org.jfree.chart.renderer.CategoryItemRenderer

Returns true if an item label is visible, and false otherwise.

isItemLabelVisible(int, int) - Method in interface org.jfree.chart.renderer.XYItemRenderer

Returns true if an item label is visible, and false otherwise.

isKEGGAccepted() - Static method in class org.vanted.KeggAccess

Whether the KEGG License agreement has been accepted by the user.

isKineticLawFunction(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the function of a kinetic law is set

isKoOrthologGroup() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.KeggId

isLabelAlignmentKnownConstant(int, Node) - Static method in class org.AttributeHelper

isLastNode() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper

isLayoutActive - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_Constants

switch, to activate readout of layout information

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.circle_search.CircleSearchAndLayoutAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest.ColorizeAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest.DavidTestAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest.GrubbsTestAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.lines_as_substances.LinesToSubstancesAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview.ExchangeNodePositionsAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview.RatioViewAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview.SubstanceRatioCalculationAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.MultiDataView

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.AddDiagramLegendAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.ColorScaleLegendAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate.RotateAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.startlayout.StartLayoutAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph.ApplyGraphLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.CircleLayouterWithMinimumCrossingsAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.DotLayoutAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle.NullLayoutAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components.ConnectedComponentLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout.CopyPatternLayoutAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_no_overlapp.NoOverlappLayoutAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_reduce_space.ExpandReduceLayouterAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fd_edge_routing.ForceDirectedEdgeLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fish_eye.FishEyeLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid_placement.GridPlacementAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid_placement.IterateGridPlacementLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid.GridLayouterAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.no_overlapp_as_tim.NoOverlappLayoutAlgorithmAS

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache.PatternSpringembedder

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.BundleParallelEdges

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ClusterGraphLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ClusterIndividualLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.PatternSpringembedder

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.PatternSpringembedder3d

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree.RadialTreeLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.random.RandomLayouterAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout.ArrayLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout.GridLayoutAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout.ResizeFromMappingCountLayoutAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree.MultiTreeLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree.RTTreeLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.tree_simple.GraphTreeLayout

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AddInterestingAttributes

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup.NumberNodesAndEdgesAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.RemoveSelectedNodesPreserveEdgesAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.SetToolTipAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.SetURLAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.PathwayReferenceAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.PathwayReferenceAutoCreationAlgorithm

isLayoutAlgorithm() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.printer.PrintAlgorithm

isLayoutAlgorithm() - Method in class org.graffiti.plugin.algorithm.AbstractAlgorithm

isLayoutAlgorithm() - Method in interface org.graffiti.plugin.algorithm.Algorithm

A LayoutAlgorithm should return true.

isLayoutAlgorithm() - Method in class org.vanted.plugins.layout.adaptagrams.edgerouting.EdgeRoutingAlgorithm

isLayoutAlgorithm() - Method in class org.vanted.plugins.layout.multilevelframework.ForceDirectedLayoutWrapper

isLayoutAlgorithm() - Method in class org.vanted.plugins.layout.multilevelframework.MultilevelFrameworkLayout

This makes sure the algorithm is moved to the layout-tab of VANTED

isLayoutAlgorithm() - Method in class org.vanted.plugins.layout.stressminimization.BackgroundExecutionAlgorithm

isLayoutAlgorithm() - Method in class org.vanted.plugins.layout.stressminimization.StressMinimizationLayout

isLeaf(Object) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.AbstractTreeTableModel

isLeftAligned() - Method in class org.graffiti.plugin.parameter.AbstractSingleParameter

isLinux() - Static method in class org.SystemInfo

isLocalParameterID(Node, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the attribute id is set

isLocalParameterName(Node, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the attribute name is set

isLocalParameterUnits(Node, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the attribute units is set

isLocalParameterValue(Node, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the attribute value is set

isLogscale() - Method in class org.jfree.chart.ui.ColorPalette

Returns the log-scale flag.

isMac() - Static method in class org.SystemInfo

isMapLink(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelperBio

isMapNode(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggHelper

isMapTitleNode(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggHelper

isMarked() - Method in class org.MarkComponent

isMarkerFilled() - Method in class org.jfree.chart.DrawableLegendItem

Returns a flag that controls whether or not the marker is filled.

isMaxValue(Number) - Method in class org.jfree.data.WaferMapDataset

Tests to see if the passed value is larger than the stored maxvalue.

isMeanValue - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.MyComparableDataPoint

isMetric - Variable in class org.graffiti.editor.Rule

isMetric() - Method in class org.graffiti.editor.Rule

isMinValue(Number) - Method in class org.jfree.data.WaferMapDataset

Tests to see if the passed value is smaller than the stored minvalue.

isModal() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.SOManalysis

isModal() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.launch_gui.LaunchGui

By default all LaunchGui Windows are modal.

isModal() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.ClusterOverviewNetworkLaunchGui

isModal() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.SetClusterLaunchGui

isModal() - Method in class vanted_feature.SelectAlgorithm

Deprecated.

isModified() - Method in class org.graffiti.graph.AdjListGraph

isModified() - Method in interface org.graffiti.graph.Graph

Indicates whether the Graph has been modified.

isModified() - Method in class org.graffiti.session.Session

Returns true, if the graph in this session has been modified.

isModifiedPoolRefilled() - Static method in class org.vanted.scaling.ComponentRegulator

True, when the modified pool has been recently cleared and re-created.

isMultiple() - Method in class org.jfree.chart.renderer.OutlierList

Returns true if the list contains multiple outliers, and false otherwise.

isNeg() - Method in class org.vanted.plugins.layout.stressminimization.parameters.SliderOptions

isNegativeArrowVisible() - Method in class org.jfree.chart.axis.ValueAxis

Returns a flag that controls whether or not the axis line has an arrow drawn that points in the negative direction for the axis.

isNoAutoOrHide(String) - Static method in enum de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.GraffitiCharts

isNodeAttributeDescription() - Method in class org.graffiti.attributes.AttributeDescription

isNodeCommand(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.BSHscriptMenuEntry

isNotEnoughMetabolites() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.metatool.SBMLReaction

isNotHeatmap(String) - Static method in enum de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.GraffitiCharts

isNotify() - Method in class org.jfree.chart.JFreeChart

Returns a flag that controls whether or not change events are sent to registered listeners.

isObsolete() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go.GOinformation

isOkSelected() - Method in class org.graffiti.editor.dialog.DefaultParameterDialog

DOCUMENT ME!

isOkSelected() - Method in interface org.graffiti.editor.dialog.ParameterDialog

Returns true, if the user selected the ok button.

isOptional() - Method in class org.graffiti.managers.pluginmgr.PluginDescription

isOptionalDefaultTrue() - Method in class org.graffiti.managers.pluginmgr.PluginDescription

isOSX() - Static method in class org.vanted.osx.OSXSupport

Determine whether we are running on MAC OS X or not

isOutlier() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.MyComparableDataPoint

isOutline() - Method in class org.jfree.chart.renderer.AreaXYRenderer

Deprecated.

Returns a flag that controls whether or not outlines of the areas are drawn.

isOutline() - Method in class org.jfree.chart.renderer.XYAreaRenderer

Returns a flag that controls whether or not outlines of the areas are drawn.

isOutline() - Method in class org.jfree.chart.renderer.XYAreaRenderer2

Returns a flag that controls whether or not outlines of the areas are drawn.

isOutline() - Method in class org.jfree.chart.renderer.XYStepAreaRenderer

Returns a flag that controls whether or not outlines of the areas are drawn.

isOverlapped(Outlier) - Method in class org.jfree.chart.renderer.OutlierList

Returns true if the outlier overlaps, and false otherwise.

isPartiallySelected(TreePath) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.gui.CheckTreeSelectionModel

isPartOfGroup() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Entry

isPathSelected(TreePath, boolean) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.gui.CheckTreeSelectionModel

isPathwayMap() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.KeggId

isPaused() - Method in class org.vanted.plugins.layout.stressminimization.BackgroundAlgorithm

isPlotShowing() - Method in class org.jfree.chart.plot.Plot

isPos() - Method in class org.vanted.plugins.layout.stressminimization.parameters.SliderOptions

isPositiveArrowVisible() - Method in class org.jfree.chart.axis.ValueAxis

Returns a flag that controls whether or not the axis line has an arrow drawn that points in the positive direction for the axis.

isPowerOf(int, int) - Static method in class org.graffiti.util.GeneralUtils

Returns true iff first parameter is a power of second, i.e.

isPrintFooter() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.PrintEnvironment

isPrintHeader() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.PrintEnvironment

isPriorityPlugin() - Method in class org.graffiti.managers.pluginmgr.PluginDescription

isProductReq() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.ReactionAndInfo

isProgressViewVisible() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskGUIprovider

isProgressViewVisible() - Method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskPanelEntry

isProgressViewVisible() - Method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskWindow

isRadiusGridlinesVisible() - Method in class org.jfree.chart.plot.PolarPlot

Returns true if the radius axis grid is visible, and false otherwise.

isRandomTop() - Method in class org.vanted.plugins.layout.multilevelframework.MLFParamModel.LayoutAlgGroup

isRangeCrosshairLockedOnData() - Method in class org.jfree.chart.plot.CategoryPlot

Returns a flag indicating whether or not the crosshair should "lock-on" to actual data values.

isRangeCrosshairLockedOnData() - Method in class org.jfree.chart.plot.ContourPlot

Returns a flag indicating whether or not the crosshair should "lock-on" to actual data values.

isRangeCrosshairLockedOnData() - Method in class org.jfree.chart.plot.XYPlot

Returns a flag indicating whether or not the crosshair should "lock-on" to actual data values.

isRangeCrosshairVisible() - Method in class org.jfree.chart.plot.CategoryPlot

Returns a flag indicating whether or not the range crosshair is visible.

isRangeCrosshairVisible() - Method in class org.jfree.chart.plot.ContourPlot

Returns a flag indicating whether or not the range crosshair is visible.

isRangeCrosshairVisible() - Method in class org.jfree.chart.plot.XYPlot

Returns a flag indicating whether or not the range crosshair is visible.

isRangeGridlinesVisible() - Method in class org.jfree.chart.plot.CategoryPlot

Returns the flag that controls whether the range grid-lines are visible.

isRangeGridlinesVisible() - Method in class org.jfree.chart.plot.FastScatterPlot

Returns true if the range axis grid is visible, and false otherwise.

isRangeGridlinesVisible() - Method in class org.jfree.chart.plot.XYPlot

Returns true if the range axis grid is visible, and false otherwise.

isReaction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.KeggId

isReactionCompartment(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if compartment of a reaction is set

isReactionConstant(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if there is set a value for constant

isReactionFast(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if fast of a reaction is set

isReactionID(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if id of a reaction is set

isReactionName(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if name of a reaction is set

isReactionProductReq() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.NodeCombination

isReactionReversible(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if reversible of a reaction is set

isReactionSpecies(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the species attribute is set

isReactionSpeciesID(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the species id attribute is set

isReactionSpeciesName(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the species name attribute is set

isReactionStoichiometry(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if there is set a value for stoichiometry

isReactionSubstrateReq() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.NodeCombination

isRecording() - Static method in class scenario.ScenarioService

isReference - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.BioMeanAndStandardDeviation

isReference - Variable in class org.BioMeanAndStandardDeviation

isReferencePathway() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.KeggPathwayEntry

isReferencePathway() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.MapOrg

isReferencePathwayUsingECids() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.MapOrg

isReferencePathwayUsingKOids() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.MapOrg

isRemoveBendsSelected() - Method in class org.vanted.plugins.layout.stressminimization.StressMinParamModel.PreprocessingGroup

isRenderAsPoints() - Method in class org.jfree.chart.plot.ContourPlot

Returns the renderAsPoints.

isReplicateDataMissing(ExperimentInterface) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment

isReplicateDataMissing(Document) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.XPathHelper

isResizable() - Method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskWindow

isRunningAsApplet() - Static method in class org.ReleaseInfo

Deprecated.

isRunningAsWebstart() - Static method in class org.ReleaseInfo

isSaved() - Method in class org.graffiti.session.EditorSession

isSBMLreaction(GraphElement) - Static method in class org.AttributeHelper

isSBMLreversibleReaction(GraphElement) - Static method in class org.AttributeHelper

isScaled(JComponent) - Static method in class org.vanted.scaling.ComponentRegulator

A rough measure to determine whether component had one of his scaling specifics - Font, Icon, Insets; scaled.

isScaledWith(float) - Method in class org.vanted.scaling.resources.ScaledFontUIResource

Checks whether the resource has already been rescaled with the provided scaling factor.

isScaleFixedUseWidth() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithmParams

isSearchAttributeBoolean() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.SearchOption

isSelected(ButtonModel) - Method in class org.graffiti.editor.GraffitiButtonGroup

Returns whether a ButtonModel is selected.

isSelectionListener() - Method in interface org.graffiti.plugin.GenericPlugin

States whether this class wants to be registered as a SelectionListener.

isSelectionListener() - Method in class org.graffiti.plugin.GenericPluginAdapter

States whether this class wants to be registered as a SelectionListener.

isSelectionListener() - Method in class org.graffiti.plugin.inspector.InspectorTab

isSelectionListener() - Method in class org.graffiti.plugin.inspector.SubtabHostTab

isSelectionListener() - Method in class org.graffiti.plugin.tool.AbstractTool

States whether this class wants to be registered as a SelectionListener.

isSelectionListener() - Method in class org.graffiti.plugin.tool.AbstractUndoableTool

Specifies if this tool wants to receive selectionChanged events.

isSelectionListener() - Method in interface org.graffiti.plugin.tool.Tool

States whether this class wants to be registered as a SelectionListener.

isSelectionListener() - Method in class org.graffiti.plugins.guis.switchselections.SwitchSelectionsPlugin

isSelectionListener() - Method in class org.graffiti.plugins.inspectors.defaults.AbstractTab

isSelectionListener() - Method in class org.graffiti.plugins.inspectors.defaults.Inspector

isSeriesFilled(int) - Method in class org.jfree.chart.renderer.DefaultPolarItemRenderer

Returns true if the renderer should fill the specified series, and false otherwise.

isSeriesItemLabelsVisible(int) - Method in class org.jfree.chart.renderer.AbstractRenderer

Returns true if the item labels for a series are visible, and false otherwise.

isSeriesItemLabelsVisible(int) - Method in interface org.jfree.chart.renderer.CategoryItemRenderer

Returns true if the item labels for a series are visible, and false otherwise.

isSeriesItemLabelsVisible(int) - Method in interface org.jfree.chart.renderer.XYItemRenderer

Returns true if the item labels for a series are visible, and false otherwise.

isSessionActive() - Method in class org.graffiti.editor.MainFrame

Returns true, if a session is active.

isSessionActive() - Method in interface org.graffiti.session.SessionManager

Returns true, if a session is active.

isSessionListener() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.IPK_StandardTools

isSessionListener() - Method in interface org.graffiti.plugin.GenericPlugin

States whether this class wants to be registered as a SessionListener.

isSessionListener() - Method in class org.graffiti.plugin.GenericPluginAdapter

States whether this class wants to be registered as a SessionListener.

isSessionListener() - Method in class org.graffiti.plugin.tool.AbstractTool

States whether this class wants to be registered as a SessionListener.

isSessionListener() - Method in class org.graffiti.plugin.tool.AbstractUndoableTool

Specifies if this tool wants to receive sessionChanged events.

isSessionListener() - Method in interface org.graffiti.plugin.tool.Tool

States whether this class wants to be registered as a SessionListener.

isSessionListener() - Method in class org.graffiti.plugins.inspectors.defaults.Inspector

States whether this class wants to be registered as a SessionListener.

isSessionListener() - Method in class org.graffiti.plugins.modes.defaults.MegaMoveTool

States whether this class wants to be registered as a SessionListener.

isSet() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest.FinalBoolean

isSetAnnotation(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.KineticLawHelper

isSetAnnotation(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLLocalParameter

isSetAnnotation(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetAnnotation(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

isSetAnnotationModifier(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetAnnotationProduct(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetAnnotationReactant(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetAsDefault() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ExperimentDataAnnotation

isSetAssignmentRuleFunction(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetAssignmentRuleVariable(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetBoundaryCondition(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

Indicates if boundary condition of a species is set

isSetCompartment(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetCompartment(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

Indicates if the compartment id of a species is set

isSetCompartmentConstants(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetCompartmentID(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetCompartmentName(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetCompartmentSize(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetCompartmentSpatialDimensions(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetCompartmentUnits(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetConstant() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLCompartment

isSetConstant() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLParameter

isSetConstant(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetConstant(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetConstant(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

Indicates if constant of a species is set

isSetConstraintMessage(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetConversionFactor(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

Indicates if conversion factor of a species is set

isSetDelay(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetDelayFunction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventHelper

isSetDelayFunction(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetEventName(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetEventUseValuesFromTriggerTime(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetFast(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetFunction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLAlgebraicRule

isSetFunction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLAssignmentRule

isSetFunction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLConstraint

isSetFunction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventAssignmentHelper

isSetFunction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLFunctionDefinition

isSetFunction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLInitialAssignment

isSetFunction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRateRule

isSetFunction(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.KineticLawHelper

isSetFunctionDefinitionFunction(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetFunctionDefinitionID(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetFunctionDefinitionName(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetHasOnlySubstanceUnits(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

Indicates if hasOnlySubstanceUnits of a species is set

isSetID() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLCompartment

isSetID() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventHelper

isSetID() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLFunctionDefinition

isSetID() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLParameter

isSetID() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLUnitDefinition

isSetID(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetID(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLLocalParameter

isSetID(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetID(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

Indicates if the id of a species is set

isSetInitialAmount(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

Indicates if the initial amount of a species is set

isSetInitialAssignmentFunction(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetInitialAssignmentSymbol(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetInitialConcentration(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

Indicates if the initial concentration of a species is set

isSetInitialValue() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventHelper

isSetLayoutID(Graph, Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetLocalParameterName(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetLocalParameterUnits(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetLocalParameterValue(Node, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetMessage() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLConstraint

isSetMetaID(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.KineticLawHelper

isSetMetaID(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLLocalParameter

isSetMetaID(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetMetaID(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

isSetMetaIDModifier(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetMetaIDProduct(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetMetaIDReactant(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetName() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLCompartment

isSetName() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventHelper

isSetName() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLFunctionDefinition

isSetName() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLParameter

isSetName() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLUnitDefinition

isSetName(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetName(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLLocalParameter

isSetName(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetName(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

Indicates if the name of a species is set

isSetNonRDFAnnotation(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.KineticLawHelper

isSetNonRDFAnnotation(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLLocalParameter

isSetNonRDFAnnotation(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetNonRDFAnnotation(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

isSetNonRDFAnnotationModifier(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetNonRDFAnnotationProduct(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetNonRDFAnnotationReactant(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetNotes(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.KineticLawHelper

isSetNotes(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLLocalParameter

isSetNotes(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetNotes(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

isSetNotesModifier(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetNotesProduct(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetNotesReactant(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetParameterConstant(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetParameterName(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetParameterUnits(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetParameterValue(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetPersistent() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventHelper

isSetPriority(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetPriorityFunction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventHelper

isSetRateRuleFunction(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetRateRuleVariable(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetReactionSpecies(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetReactionSpeciesID(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetReactionSpeciesName(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetReversible(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetSBOTerm(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.KineticLawHelper

isSetSBOTerm(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLLocalParameter

isSetSBOTerm(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetSBOTerm(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

isSetSBOTermModifier(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetSBOTermProduct(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetSBOTermReactant(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetSize() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLCompartment

isSetSpatialDimensions() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLCompartment

isSetSpecies(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetStoichiometry(Edge) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetStoichiometry(Edge) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLReactionHelper

isSetSubstanceUnits(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLSpeciesHelper

Indicates if substance units of a species is set

isSetSymbol() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLInitialAssignment

isSetTriggerFunction() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventHelper

isSetTriggerFunction(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetTriggerInitialValue(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetTriggerPersistent(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetUnitDefinitionID(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetUnitDefinitionName(Graph, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

isSetUnits() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLCompartment

isSetUnits() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLParameter

isSetUnits(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLLocalParameter

isSetUseValuesFromTriggerTime() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventHelper

isSetValue() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLParameter

isSetValue(Node) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLLocalParameter

isSetVariable() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLAssignmentRule

isSetVariable() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLEventAssignmentHelper

isSetVariable() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLRateRule

isShapeFilled() - Method in class org.jfree.chart.LegendItem

Returns a flag that controls whether or not the shape is filled.

isShapesFilled() - Method in class org.jfree.chart.renderer.XYStepAreaRenderer

Returns the flag that controls whether or not the shapes are filled.

isSignificant() - Method in class org.graffiti.plugin.algorithm.AbstractAlgorithm

Whether this UndoableEdit should be considered on its own for Undo/Redo, when performing any of them.

isSignificantDifferent - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.BioMeanAndStandardDeviation

isSignificantDifferent - Variable in class org.BioMeanAndStandardDeviation

isSpeciesBoundaryCondition(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if boundary condition of a species is set

isSpeciesCompartment(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the compartment id of a species is set

isSpeciesConstant(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if constant of a species is set

isSpeciesConversionFactor(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if conversion factor of a species is set

isSpeciesHasOnlySubstanceUnits(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if hasOnlySubstanceUnits of a species is set

isSpeciesID(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the id of a species is set

isSpeciesInitialAmount(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the initial amount of a species is set

isSpeciesInitialConcentration(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the initial concentration of a species is set

isSpeciesName(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if the name of a species is set

isSpeciesSubstanceUnits(Node) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBMLHelper

Indicates if substance units of a species is set

isStepped() - Method in class org.jfree.chart.ui.ColorPalette

Returns the 'is-stepped' flag.

isStoiWrong() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.metatool.SBMLReaction

isStopped() - Method in class org.vanted.plugins.layout.stressminimization.BackgroundAlgorithm

isSubplot() - Method in class org.jfree.chart.plot.Plot

Returns true if this plot is part of a combined plot structure.

isSubstrateReq() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.ReactionAndInfo

issueCompleteRedrawForActiveView() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

issueCompleteRedrawForAllViews() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

this same method code is duplicated somewhere...

issueCompleteRedrawForGraph(Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

issueCompleteRedrawForView(View, Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

issueCompleteRedrawForView(View, Graph) - Static method in class org.graffiti.plugins.inspectors.defaults.DefaultEditPanel

issueScan(boolean) - Static method in class org.vanted.updater.ScanForUpdate

issueScanAfterStartup() - Static method in class org.vanted.updater.ScanForUpdate

issueSimpleTask(String, String, Runnable, Runnable) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskHelper

issueSimpleTask(String, String, Runnable, Runnable, BackgroundTaskStatusProvider) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskHelper

issueSimpleTask(String, String, Runnable, Runnable, BackgroundTaskStatusProvider, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskHelper

issueSimpleTask(String, String, String, Runnable, Runnable) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskHelper

issueSimpleTask(String, String, String, Runnable, Runnable, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskHelper

issueSimpleTaskInWindow(String, String, Runnable, Runnable, BackgroundTaskStatusProvider) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskHelper

issueSimpleTaskInWindow(String, String, Runnable, Runnable, BackgroundTaskStatusProvider, boolean, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskHelper

isSuperPathWay() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.MyPathWay

isSuperPathWay() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.MyPathWay

isSupressReset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.data_mapping.DataMapping

isTagged(String) - Method in enum org.vanted.scaling.scalers.component.HTMLScaleSupport.Tags

isTaskPanelVisible(String) - Method in class org.graffiti.editor.MainFrame

isTaskWithGivenReferenceRunning(Object) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.services.task.BackgroundTaskHelper

isTemporaryNode(Node) - Static method in class org.graffiti.plugins.modes.defaults.MegaCreateTool

isTestedWithRunningVersion() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.Addon

Tests, if this addon is compatible with the currently running version of VANTED

isTestintMode - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.SBML_XML_ReaderWriterPlugin

isTickLabelsVisible() - Method in class org.jfree.chart.axis.Axis

Returns a flag indicating whether or not the tick labels are visible.

isTickLabelsVisible() - Method in class org.jfree.chart.ui.AxisPropertyEditPanel

Returns a flag that indicates whether or not the tick labels are visible.

isTickMarksVisible() - Method in class org.jfree.chart.axis.Axis

Returns the flag that indicates whether or not the tick marks are showing.

isTickMarksVisible() - Method in class org.jfree.chart.ui.AxisPropertyEditPanel

Returns the current value of the flag that determines whether or not tick marks are visible.

isTight() - Method in class placement.Constraint

isTimeSeries() - Method in class org.jfree.data.JDBCXYDataset

Returns true if the dataset represents time series data, and false otherwise.

isTrueKeggExpressionFormatControlTarget() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.kegg_expression.KeggExpressionDataset

isTypedAttributeFromID(String, boolean) - Static method in class org.graffiti.attributes.AbstractAttribute

isUNCFilePath(File) - Static method in class org.UNCFileLocationCheck

isUNCFilePath(String) - Static method in class org.UNCFileLocationCheck

isUndirected() - Method in class org.graffiti.graph.AbstractGraph

Indicates whether the graph is undirected.

isUndirected() - Method in interface org.graffiti.graph.Graph

Indicates whether the Graph is undirected.

isUndirected() - Method in class org.graffiti.graph.OptAdjListGraph

Indicates whether the graph is undirected.

isUpdated() - Static method in class org.ReleaseInfo

isValid() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg_reaction.ReactionEntry

isValid() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.KoEntry

isValid() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes.EnzymeEntry

isValid() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go.GoProcessing

isValid() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.DataColumnHeader

isValid() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow.LookAndFeelWrapper

isValid() - Method in class org.graffiti.plugin.parameter.BooleanParameter

Returns true, if the current value is valid.

isValid() - Method in class org.graffiti.plugin.parameter.ColorParameter

isValid() - Method in class org.graffiti.plugin.parameter.DoubleParameter

isValid() - Method in class org.graffiti.plugin.parameter.FloatParameter

isValid() - Method in class org.graffiti.plugin.parameter.IntegerParameter

isValid() - Method in interface org.graffiti.plugin.parameter.LimitableParameter

Returns true if the value is between the minimum and the maximum, false otherwise.

isValid() - Method in class scenario.Scenario

isValidatingSBMLOnLoad() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_XML_Reader

isValidEnzymeStart(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes.EnzClassEntry

Determines if a given line is a valid start for a enzyme class entry.

isValidEnzymeStart(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes.EnzymeEntry

isValidInputFileExtension(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ExperimentLoader

isValidMatchFor(QuadNumber) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes.QuadNumber

isValidMatchFor(String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes.EnzClassEntry

If a entry is the same as the given, true is returned.

isValidMatchFor_Inversed(QuadNumber) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes.EnzClassEntry

isValidMatchFor_Inversed(QuadNumber) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes.QuadNumber

isValidMatchFor_Inversed(String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes.EnzClassEntry

isValidQuadNumber() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.sib_enzymes.QuadNumber

isValidReactionStart(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg_reaction.ReactionEntry

isValueValid() - Method in class org.jfree.data.DefaultMeterDataset

Deprecated.

Returns true if the value is valid, and false otherwise.

isValueValid() - Method in interface org.jfree.data.MeterDataset

Deprecated.

Returns true if the value is valid, and false otherwise.

isVersion(String) - Static method in class org.vanted.updater.PreferencesUpdater

Check current version.

isVerticalCategoryLabels() - Method in class org.jfree.chart.axis.CategoryAxis

Deprecated.

Use the get/setXXXCategoryLabelPosition methods.

isVerticalTickLabels() - Method in class org.jfree.chart.axis.ValueAxis

Returns true if the tick labels should be rotated (to vertical), and false otherwise.

isViewListener() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.IPK_StandardTools

isViewListener() - Method in interface org.graffiti.plugin.GenericPlugin

States whether this class wants to be registered as a ViewListener, i.e.

isViewListener() - Method in class org.graffiti.plugin.GenericPluginAdapter

isViewListener() - Method in class org.graffiti.plugin.tool.AbstractTool

States whether this class wants to be registered as a ViewListener, i.e.

isViewListener() - Method in interface org.graffiti.plugin.tool.Tool

States whether this class wants to be registered as a ViewListener, i.e.

isViewListener() - Method in class org.graffiti.plugins.inspectors.defaults.Inspector

isViewOfTypeGraphView(View) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithm

isViewProvidingToolbar(View) - Static method in class org.graffiti.editor.MainFrame

isVisible() - Method in class org.jfree.chart.axis.Axis

Returns true if the axis is visible, and false otherwise.

isWhiteCell - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.xml_data_tree_table_model.SpecialTableValue

isWindowsRunning() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.threading.SystemAnalysis

isZoomToOnePage() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.PrintEnvironment

ITEM_TAG - Static variable in interface org.jfree.data.xml.DatasetTags

The 'Item' element name.

ItemHandler - Class in org.jfree.data.xml

A handler for reading key-value items.

ItemHandler(RootHandler, DefaultHandler) - Constructor for class org.jfree.data.xml.ItemHandler

Creates a new item handler.

ItemLabelAnchor - Class in org.jfree.chart.labels

An enumeration of the positions that a value label can take, relative to an item in a CategoryPlot.

ItemLabelDemo1 - Class in org.jfree.chart.demo

A simple demo showing a label generator that only displays labels for items with a value that is greater than some threshold.

ItemLabelDemo1(String) - Constructor for class org.jfree.chart.demo.ItemLabelDemo1

Creates a new demo instance.

ItemLabelDemo2 - Class in org.jfree.chart.demo

A simple demo showing a label generator that displays labels that include a percentage calculation.

ItemLabelDemo2(String) - Constructor for class org.jfree.chart.demo.ItemLabelDemo2

Creates a new demo instance.

ItemLabelPosition - Class in org.jfree.chart.labels

The attributes that control the position of the label for each data item on a chart.

ItemLabelPosition() - Constructor for class org.jfree.chart.labels.ItemLabelPosition

Creates a new position record with default settings.

ItemLabelPosition(ItemLabelAnchor, TextAnchor) - Constructor for class org.jfree.chart.labels.ItemLabelPosition

Creates a new position record (with zero rotation).

ItemLabelPosition(ItemLabelAnchor, TextAnchor, TextAnchor, double) - Constructor for class org.jfree.chart.labels.ItemLabelPosition

Creates a new position record.

iterateCategoryRangeExtent(CategoryDataset) - Static method in class org.jfree.data.DatasetUtilities

Iterates over the data item of the category dataset to find the range extent.

iterateDomainExtent(XYDataset) - Static method in class org.jfree.data.DatasetUtilities

Iterates over the data item of the xy dataset to find the domain extent.

IterateGridPlacementLayout - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid_placement

IterateGridPlacementLayout() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid_placement.IterateGridPlacementLayout

iterateXYRangeExtent(XYDataset) - Static method in class org.jfree.data.DatasetUtilities

Iterates over the data item of the xy dataset to find the range extent.

iterator() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition

iterator() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface

iterator() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment

iterator() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface

iterator() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample

iterator() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface

iterator() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance

iterator() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface

iterator() - Method in exception org.graffiti.plugin.algorithm.PreconditionException

Returns an iterator over all Errors.

iterator() - Method in interface org.jfree.chart.entity.EntityCollection

Returns an iterator for the entities in the collection.

iterator() - Method in class org.jfree.chart.entity.StandardEntityCollection

Returns an iterator for the entities in the collection.

iterator() - Method in class org.jfree.chart.LegendItemCollection

Returns an iterator that provides access to all the legend items.

iterator() - Method in class org.jfree.chart.renderer.OutlierListCollection

Returns an iterator for the outlier lists.

iterator() - Method in class org.vanted.indexednodes.IndexedNodeSet

Returns an iterator for this set, that iterates in index order.

iterator() - Method in class qmwi.kseg.som.DataSet

Get a iterator for the data.

iterThresholdActive() - Method in class org.vanted.plugins.layout.stressminimization.StressMinParamModel.TerminationCheckboxGroup

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