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

R

RADIAL - org.graffiti.plugins.views.defaults.GradientFillAttributeEditor.NodeGradientModes

RadialTreeLayout - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree

An implementation of a radial tree layout algorithm.

RadialTreeLayout() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree.RadialTreeLayout

Construct a new RadialTreeLayout algorithm instance.

RadialTreeLayoutPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree

Plugin for a radial tree layouter algorithm

RadialTreeLayoutPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree.RadialTreeLayoutPlugin

Creates a new GraphTreeLayoutPlugin object.

RainbowPalette - Class in org.jfree.chart.ui

Contains the data to constuct an 8-bit rainbow palette This come from an old application which ran on 8-bit graphics device.

RainbowPalette() - Constructor for class org.jfree.chart.ui.RainbowPalette

Default constructor.

RandomLayouterAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.random

This algorithm performs a random placement of the nodes on the visible area.

RandomLayouterAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.random.RandomLayouterAlgorithm

RandomLayouterPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.random

Plugin container for the RandomLayouterAlgorithm.

RandomLayouterPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.random.RandomLayouterPlugin

Creates a new RandomLayouterPlugin object.

RandomMerger - Class in org.vanted.plugins.layout.multilevelframework

Merger that randomly merges edges.

RandomMerger() - Constructor for class org.vanted.plugins.layout.multilevelframework.RandomMerger

RandomPlacer - Class in org.vanted.plugins.layout.multilevelframework

Implementation of the Placer Interface that reduces Coarsening Levels by randomly placing the inner nodes randomly around their MergedNode

RandomPlacer() - Constructor for class org.vanted.plugins.layout.multilevelframework.RandomPlacer

rang_AA - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation

Range - Class in org.jfree.data

Represents an immutable range of values.

Range(double, double) - Constructor for class org.jfree.data.Range

Creates a new range.

RANGE - Static variable in class org.jfree.chart.axis.CategoryLabelWidthType

Percentage of range.

rangeAxis - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions

RangeInfo - Interface in org.jfree.data

An interface (optional) that can be implemented by a dataset to assist in determining the minimum and maximum values.

RangeType - Class in org.jfree.chart.renderer

An enumeration of the 'range types' for a renderer.

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

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

ratioCalculationCount - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview.SubstanceRatioCalculationAlgorithm

RatioViewAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview

RatioViewAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview.RatioViewAlgorithm

RatioViewPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview

RatioViewPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview.RatioViewPlugin

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

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

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

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

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

reaction - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.EntryType

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

Reaction(String, ReactionType, Collection<Entry>, Collection<Entry>) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Reaction

Reaction(String, ReactionType, Collection<Entry>, Collection<Entry>, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Reaction

REACTION - de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.KeggDatabases

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

ReactionAndInfo(Reaction, boolean, boolean, String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.ReactionAndInfo

ReactionEntry - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg_reaction

ReactionEntry() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg_reaction.ReactionEntry

ReactionIdEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui

ReactionIdEditor(Reaction, Pathway) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui.ReactionIdEditor

ReactionIDSpeciesIDWrapper - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml

ReactionIDSpeciesIDWrapper(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.sbml.ReactionIDSpeciesIDWrapper

ReactionLabel - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg

ReactionLabel(Reaction, HashMap<Entry, Node>, Pathway, Collection<Gml2PathwayWarningInformation>, Collection<Gml2PathwayErrorInformation>, Graph) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.ReactionLabel

ReactionService - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg_reaction

ReactionService() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg_reaction.ReactionService

ReactionType - Enum in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes

ReactionTypeSelection - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui

ReactionTypeSelection(Reaction) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui.ReactionTypeSelection

read() - Method in class org.graffiti.plugins.ios.exporters.graphml.Base64.InputStream

Reads enough of the input stream to convert to/from Base64 and returns the next byte.

read() - Method in class org.graffiti.plugins.ios.importers.graphml.parser.Base64.InputStream

Reads enough of the input stream to convert to/from Base64 and returns the next byte.

read(byte[], int, int) - Method in class org.graffiti.plugins.ios.exporters.graphml.Base64.InputStream

Calls read repeatedly until the end of stream is reached or len bytes are read.

read(byte[], int, int) - Method in class org.graffiti.plugins.ios.importers.graphml.parser.Base64.InputStream

Calls read repeatedly until the end of stream is reached or len bytes are read.

read(File) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.TextFile

read(InputStream) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLReader

Reads a graph from the given input stream.

read(InputStream) - Method in class org.graffiti.plugin.io.AbstractInputSerializer

Reads in a graph from the given input stream.

read(InputStream) - Method in class org.graffiti.plugin.io.AbstractIOSerializer

Reads in a graph from the given input stream.

read(InputStream) - Method in interface org.graffiti.plugin.io.InputSerializer

Reads in a graph from the given input stream.

read(InputStream) - Method in class org.graffiti.plugins.ios.importers.gml.GMLReader

Reads in a graph from the given input stream.

read(InputStream, int) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.TextFile

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.metatool.MetaToolReader

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.BioPAX_OWL_Reader

main read method

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kegg_xml.KEGG_XML_Reader

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kegg_xml.KEGG2_XML_Reader

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kgml.KEGG_XML_Reader_g

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.pajek.PajekReader

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.petri_ina_pnt.PNTReader

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_XML_Reader

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.text_list.SIFreader

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.text_list.TextListReader

read(InputStream, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLReader

Reads a graph from the given input stream.

read(InputStream, Graph) - Method in class org.graffiti.plugin.io.AbstractInputSerializer

Reads in a graph from the given input stream.

read(InputStream, Graph) - Method in class org.graffiti.plugin.io.AbstractIOSerializer

Reads in a graph from the given input stream.

read(InputStream, Graph) - Method in interface org.graffiti.plugin.io.InputSerializer

Reads in a graph from the given input stream.

read(InputStream, Graph) - Method in class org.graffiti.plugins.ios.exporters.graphviz.DOTreader

read(InputStream, Graph) - Method in class org.graffiti.plugins.ios.importers.gml.GMLReader

Reads in a graph from the given input stream.

read(InputStream, Graph) - Method in class org.graffiti.plugins.ios.importers.graphml.GraphMLReader

read(Reader) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.TextFile

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.exporters.metatool.MetaToolReader

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.BioPAX_OWL_Reader

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kegg_xml.KEGG_XML_Reader

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kegg_xml.KEGG2_XML_Reader

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kgml.KEGG_XML_Reader_g

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.pajek.PajekReader

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.petri_ina_pnt.PNTReader

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_XML_Reader

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.text_list.SIFreader

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.text_list.TextListReader

read(Reader, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLReader

read(Reader, Graph) - Method in interface org.graffiti.plugin.io.InputSerializer

read(Reader, Graph) - Method in class org.graffiti.plugins.ios.exporters.graphviz.DOTreader

read(Reader, Graph) - Method in class org.graffiti.plugins.ios.importers.gml.GMLReader

read(Reader, Graph) - Method in class org.graffiti.plugins.ios.importers.graphml.GraphMLReader

read(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.TextFile

read(String, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kegg_xml.KEGG_XML_Reader

read(String, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kegg_xml.KEGG2_XML_Reader

read(String, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.kgml.KEGG_XML_Reader_g

read(String, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.pajek.PajekReader

read(String, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.text_list.SIFreader

read(String, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.text_list.TextListReader

read(String, Graph) - Method in class org.graffiti.plugin.io.AbstractInputSerializer

Reads in a graph from the given filename.

read(String, Graph) - Method in class org.graffiti.plugin.io.AbstractIOSerializer

Reads in a graph from the given filename.

read(String, Graph) - Method in interface org.graffiti.plugin.io.InputSerializer

Reads in a graph from the given filename.

read(URL) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.TextFile

Tools to read and write files as single strings:

read(URL, Graph) - Method in class org.graffiti.plugin.io.AbstractInputSerializer

Reads in the graph from the given url.

read(URL, Graph) - Method in class org.graffiti.plugin.io.AbstractIOSerializer

Reads in the graph from the given url.

read(URL, Graph) - Method in interface org.graffiti.plugin.io.InputSerializer

Reads in the graph from the given url.

read(Level2Element) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.BPbiochemicalReaction

read(Level2Element) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.BPcatalysis

read(Level2Element) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.BPcomplexAssembly

read(Level2Element) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.BPcontrol

read(Level2Element) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.BPconversion

read(Level2Element) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.BPmodulation

read(Level2Element) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.BPphysicalInteraction

read(Level2Element) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.BPtransport

read(Level2Element) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.BPtransportWithBiochemicalReaction

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPBiochemicalReaction

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPCatalysis

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPComplexAssembly

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPControl

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPConversion

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPDegradation

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPGeneticInteraction

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPModulation

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPMolecularInteraction

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPTemplateReaction

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPTemplateReactionRegulation

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPTransport

read(Interaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.BPTransportWithBiochemicalReaction

read(SBMLDocument, Graph, BackgroundTaskStatusProviderSupportingExternalCallImpl) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_XML_Reader

Method controls the import of the SBML document.

readAttributes(GraphElement) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UBioChemicalReaction

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UCatalysis

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UComplex

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UComplexAssembly

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UControl

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UConversion

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UDegradation

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UDna

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UDnaRegion

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UGene

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UGeneticInteraction

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UModulation

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UMolecularInteraction

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UPathway

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UPhysicalEntity

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UProtein

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.URna

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.URnaRegion

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.USmallMolecule

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTemplateReaction

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTemplateReactionRegulation

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTransport

readAttributesFromNode(GraphElement, Graph, Model) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTransportWithBiochemicalReaction

readCategoryDatasetFromXML(File) - Static method in class org.jfree.data.xml.DatasetReader

Reads a CategoryDataset from a file.

readCategoryDatasetFromXML(InputStream) - Static method in class org.jfree.data.xml.DatasetReader

Reads a CategoryDataset from a stream.

reAddChangeListener() - Static method in class org.vanted.scaling.vanted.GraphScaler

To subsequent new ScalingSlider instance.

readFile(String) - Static method in class qmwi.kseg.som.CSVreader

readFromClipboardAsText() - Static method in class org.graffiti.editor.actions.ClipboardService

readGraph(Model, Graph) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.LVL3ModelConverter

reads all nodes and edges of the graph first all physical entities will be read so pointing in interactions to them is possible afterwards the interactions will be read

readInteractionsFromPathway(Model, ArrayList<MyPathWay>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.LVL3ModelConverter

made for partial import of one or more pathway components

readInteractionsFromPathway(Model, ArrayList<MyPathWay>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2interactions.LVL2ModelConverter

made for reading all interactions in a biopax level 3 model and writing it to the graph

readParticipantStoichiometry(PhysicalEntity, Conversion, Edge, Model) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.StoichiometryWriter

readPathwaysFromGraphAndWriteToModel() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3interactions.PathWayHandler

use while export to write PathWays into the model

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

DOCUMENT ME!

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

Init cache entry for a node (get pattern nodes-call cache)

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

Init cache entry for a node (get pattern nodes-call cache)

readPieDatasetFromXML(File) - Static method in class org.jfree.data.xml.DatasetReader

Reads a PieDataset from an XML file.

readPieDatasetFromXML(InputStream) - Static method in class org.jfree.data.xml.DatasetReader

Reads a PieDataset from a stream.

readPluginDescription(URL) - Static method in class org.graffiti.util.PluginHelper

Reads and returns the plugin description of the plugin from the given URL.

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

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

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

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

Receives and returns the data contained in a broadcast message.

ReceiveHighlightInfo - Interface in org.graffiti.plugin.tool

RecentEntry - Class in org.graffiti.editor

RecentEntry(File, boolean, Icon) - Constructor for class org.graffiti.editor.RecentEntry

RecentEntry(String, boolean, Icon) - Constructor for class org.graffiti.editor.RecentEntry

RecentEntry(RecentEntry) - Constructor for class org.graffiti.editor.RecentEntry

ReceptorDownShape - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes

ReceptorDownShape() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes.ReceptorDownShape

ReceptorLeftShape - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes

ReceptorLeftShape() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes.ReceptorLeftShape

ReceptorRightShape - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes

ReceptorRightShape() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes.ReceptorRightShape

ReceptorUpShape - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes

ReceptorUpShape() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes.ReceptorUpShape

reColor() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ReColorBars

ReColorBars - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent

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

RecolorEdgesAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms

RecolorEdgesAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.RecolorEdgesAlgorithm

recordStart() - Static method in class scenario.ScenarioService

recordStop() - Static method in class scenario.ScenarioService

recreate() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartAttributeComponent

recreate() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image.CompoundImageAttributeComponent

recreate() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.PathwayLinkVisualizationComponent

recreate() - Method in class org.graffiti.plugin.attributecomponent.AbstractAttributeComponent

Used when the shape changed in the datastructure.

recreate() - Method in class org.graffiti.plugin.view.AttributeComponent

Used when the shape changed in the datastructure.

recreate() - Method in class org.graffiti.plugins.attributecomponents.simplelabel.LabelComponent

Used when the shape changed in the datastructure.

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

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

rectangle - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.kgmlGraphicsType

RECTANGLE - org.LabelFrameSetting

RECTANGLE_BOTTOM_ROUND - org.LabelFrameSetting

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

rectangle node shape class name

RECTANGLE_CORNER_CUT - org.LabelFrameSetting

RECTANGLE_ROUNDED - org.LabelFrameSetting

RectangleDrawerFrame - Class in placement

RectangleDrawerPanel - Class in placement

RectangleDrawerPanel() - Constructor for class placement.RectangleDrawerPanel

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

Class representing a rectangle.

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

The constructor creates a rectangle using default values.

RectanglePlacement - Interface in placement

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

An implementation of NodeShape representing rectangular shapes.

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

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

redo() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.KeggNavigationToolbarCommand

redo() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.zoomfit.AlignNodesCommand

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

Default behaviour is to run execute() again.

redo() - Method in class org.graffiti.undo.AddEdgeEdit

Adds the same edge that was added through the method that created this edit.

redo() - Method in class org.graffiti.undo.AddNodeEdit

Adds the same node that was added through the method that created this edit.

redo() - Method in class org.graffiti.undo.ChangeAttributesEdit

redo() - Method in class org.graffiti.undo.GraphElementsDeletionEdit

Deletes the GraphElements stored in this edit.

redraw - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.springembedder_1.SpringEmbedderAlgorithm

redraw - Variable in class org.graffiti.plugin.algorithm.ThreadSafeOptions

If set to true, a redraw should be done.

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

redrawActive() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.NullView

redrawActive() - Method in class org.graffiti.plugin.view.AbstractView

redrawActive() - Method in interface org.graffiti.plugin.view.Zoomable

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

RedrawViewAction - Class in org.graffiti.editor.actions

The action for a new graph.

RedrawViewAction(MainFrame) - Constructor for class org.graffiti.editor.actions.RedrawViewAction

Creates a new RedrawViewAction object.

reduce_table() - Method in class org.graffiti.plugins.ios.importers.gml.parser

Access to reduce_goto table.

reduceCoarseningLevel(MultilevelGraph) - Method in interface org.vanted.plugins.layout.multilevelframework.Placer

Remove a coarsening level from the MultilevelGraph by calling MultilevelGraph.popCoarseningLevel() and but the nodes represented by the MergedNode at positions close to the MergedNode they were represented by.

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

Places the internal Nodes of the topmost Coarsening Level of the given MultilevelGraph randomly around their average Position

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

REDUCED - org.graffiti.plugins.views.defaults.DrawMode

RedundantMultipleIterator - Class in org.graffiti.util

Deprecated.

RedundantMultipleIterator(Iterator[]) - Constructor for class org.graffiti.util.RedundantMultipleIterator

Deprecated.

Constructs a new MultipleIterator instance.

RedundantMultipleIterator(Iterator<?>) - Constructor for class org.graffiti.util.RedundantMultipleIterator

Deprecated.

Constructs a new MultipleIterator instance.

RedundantMultipleIterator(Iterator<?>, Iterator<?>) - Constructor for class org.graffiti.util.RedundantMultipleIterator

Deprecated.

Constructs a new MultipleIterator instance.

RedundantMultipleIterator(Iterator<?>, Iterator<?>, Iterator<?>) - Constructor for class org.graffiti.util.RedundantMultipleIterator

Deprecated.

Constructs a new MultipleIterator instance.

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

REFERENCE - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.TtestInfo

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

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

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

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

REFERENCES_ITEM - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathGene

ReferencesPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references

ReferencesPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references.ReferencesPlugin

refresh() - Method in class org.graffiti.util.AllPermissionPolicy

refreshGUI(Container) - Static method in class org.vanted.scaling.ScalingCoordinator

Call after each major scaling operation.

refreshHorizontalTicks(Graphics2D, double, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.CyclicNumberAxis

Builds a list of ticks for the axis.

refreshNews(RSSFeedManager, Runnable, JButton) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow.NewsHelper

refreshTicks(Graphics2D, AxisState, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.Axis

Calculates the positions of the ticks for the axis, storing the results in the tick list (ready for drawing).

refreshTicks(Graphics2D, AxisState, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.CategoryAxis

Creates a temporary list of ticks that can be used when drawing the axis.

refreshTicks(Graphics2D, AxisState, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.DateAxis

Calculates the positions of the tick labels for the axis, storing the results in the tick label list (ready for drawing).

refreshTicks(Graphics2D, AxisState, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.LogarithmicAxis

Calculates the positions of the tick labels for the axis, storing the results in the tick label list (ready for drawing).

refreshTicks(Graphics2D, AxisState, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.NumberAxis

Calculates the positions of the tick labels for the axis, storing the results in the tick label list (ready for drawing).

refreshTicks(Graphics2D, AxisState, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.SymbolicAxis

Calculates the positions of the tick labels for the axis, storing the results in the tick label list (ready for drawing).

refreshTicksHorizontal(Graphics2D, double, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.DateAxis

Recalculates the ticks for the date axis.

refreshTicksHorizontal(Graphics2D, double, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.LogarithmicAxis

Calculates the positions of the tick labels for the axis, storing the results in the tick label list (ready for drawing).

refreshTicksHorizontal(Graphics2D, double, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.SymbolicAxis

Calculates the positions of the tick labels for the axis, storing the results in the tick label list (ready for drawing).

refreshTicksVertical(Graphics2D, double, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.DateAxis

Recalculates the ticks for the date axis.

refreshTicksVertical(Graphics2D, double, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.LogarithmicAxis

Calculates the positions of the tick labels for the axis, storing the results in the tick label list (ready for drawing).

refreshTicksVertical(Graphics2D, double, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.SymbolicAxis

Calculates the positions of the tick labels for the axis, storing the results in the tick label list (ready for drawing).

refreshVerticalTicks(Graphics2D, double, Rectangle2D, Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.CyclicNumberAxis

Builds a list of ticks for the axis.

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

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

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

registerChangeListeners(ChangeListener[]) - Static method in class org.vanted.scaling.ScalingSlider

This method could be used to add any number of ChangeListeners, so that you could synchronize any actions with the movement of the slider, i.e.

registerChartComponent(ChartComponent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartComponentManager

registerFileHandlingListener(FileHandlingListeners) - Method in class org.graffiti.editor.actions.FileHandlingManager

registerIOHandler(ResourceIOHandler) - Static method in class org.graffiti.plugin.io.resources.ResourceIOManager

registerLoader() - Method in class de.ipk_gatersleben.ag_pbi.datahandling.TemplateLoader

registerMemoryHog() - Method in interface org.graffiti.editor.MemoryHog

To enable free-up on application clear memory event, when the user requests such, the hog has to be registered beforehand.

registerNewFeed(String, String[]) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow.RSSFeedManager

registerNewScaler(Class<?>, ComponentScaler) - Static method in class org.vanted.scaling.ComponentRegulator

Registers new ComponentScaler to use.

registerScaler(Class<?>, ComponentScaler) - Static method in class org.vanted.scaling.Toolbox

Adds a new component scaler to the automatic scaling routine.

registerSessionListener() - Static method in class org.vanted.scaling.vanted.GraphScaler

registerSessionListenerPostponed() - Static method in class org.vanted.scaling.vanted.GraphScaler

registerSliderChangeListeners(ChangeListener[]) - Static method in class org.vanted.scaling.Toolbox

This method could be used to add any number of ChangeListeners, so that you could synchronize any actions with the movement of the slider, i.e.

registerTemplate() - Method in class de.ipk_gatersleben.ag_pbi.datahandling.Template

Regression - Class in org.jfree.data

A utility class for fitting regression curves to data.

Regression() - Constructor for class org.jfree.data.Regression

RegularTimePeriod - Class in org.jfree.data.time

An abstract class representing a unit of time.

RegularTimePeriod() - Constructor for class org.jfree.data.time.RegularTimePeriod

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

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

Relation(IdRef, IdRef, RelationType, Collection<Subtype>) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Relation

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

RelationLabel - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg

RelationLabel(Relation, HashMap<Entry, Node>, Pathway, Collection<Gml2PathwayWarningInformation>, Collection<Gml2PathwayErrorInformation>, Graph) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.kegg.RelationLabel

RelationType - Enum in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes

RelationTypeEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui

RelationTypeEditor(Relation, JLabel) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui.RelationTypeEditor

RELATIVE - org.graffiti.plugins.views.defaults.ThicknessAttributeEditor.ArrowHeadModes

RELATIVE_FREQUENCY - Static variable in class org.jfree.data.statistics.HistogramType

Relative frequency.

RelativePolyShape - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes

RelativePolyShape() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes.RelativePolyShape

Release - Enum in org

RELEASE_CLUSTERVIS - org.Release

RELEASE_IPK - org.Release

RELEASE_PUBLIC - org.Release

ReleaseInfo - Class in org

ReleaseInfo() - Constructor for class org.ReleaseInfo

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

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

remove() - Method in class org.graffiti.util.MultipleIterator

The method remove() of the interface java.util.Iterator will not be supported in this implementation.

remove() - Method in class org.graffiti.util.RedundantMultipleIterator

Deprecated.

The method remove() of the interface java.util.Iterator will not be supported in this implementation.

remove(double, String) - Method in class org.jfree.data.CategoryTableXYDataset

Removes a value from the dataset.

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

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

remove(int) - Method in class org.jfree.data.gantt.TaskSeriesCollection

Removes a series from the collection.

remove(int) - Method in class org.jfree.data.XYSeries

Removes the item at the specified index.

remove(int) - Method in class org.vanted.indexednodes.IndexedNodeSet

Removed the node at index from this set.

remove(Component) - Static method in class net.iharder.dnd.FileDrop

Removes the drag-and-drop hooks from the component and optionally from the all children.

remove(Component) - Method in class org.graffiti.plugins.views.defaults.GraffitiView

remove(PrintStream, Component, boolean) - Static method in class net.iharder.dnd.FileDrop

Removes the drag-and-drop hooks from the component and optionally from the all children.

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

Removes the item(s) with the specified x-value.

remove(Number, String, boolean) - Method in class org.jfree.data.CategoryTableXYDataset

Removes an item from the dataset.

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

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

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

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

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

Don't forget to call updateSampleAverage after removing a measurement.

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

Don't forget to call updateSampleAverage after removing a measurement.

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

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

remove(String) - Method in class org.graffiti.attributes.AbstractCollectionAttribute

Removes the attribute with the given id from the collection.

remove(String) - Method in interface org.graffiti.attributes.CollectionAttribute

Removes the Attribute with the given id from the list.

remove(Attribute) - Method in class org.graffiti.attributes.AbstractCollectionAttribute

Removes the given attribute from the collection by calling remove(String id) with the attribute's id as parameter.

remove(Attribute) - Method in interface org.graffiti.attributes.CollectionAttribute

Removes the given Attribute from the list.

remove(GraphElement) - Method in class org.graffiti.selection.Selection

Removes the given node or edge from the selection.

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

Removes a node from the basis collection passed on construction from this set.

remove(ToolButton) - Method in class org.graffiti.editor.GraffitiButtonGroup

Removes the button from the group.

remove(Selection) - Method in class org.graffiti.selection.SelectionModel

Removes the given selection for the list of selections.

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

Removes a subplot from the combined chart.

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

Removes a subplot from the combined chart.

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

Removes a subplot from the combined chart and sends a PlotChangeEvent to all registered listeners.

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

Removes a subplot from the combined chart.

remove(Task) - Method in class org.jfree.data.gantt.TaskSeries

Removes a task from the series.

remove(TaskSeries) - Method in class org.jfree.data.gantt.TaskSeriesCollection

Removes a series from the collection.

remove(RegularTimePeriod, String) - Method in class org.jfree.data.time.TimeTableXYDataset

Removes an existing data item from the dataset.

remove(RegularTimePeriod, String, boolean) - Method in class org.jfree.data.time.TimeTableXYDataset

Removes an existing data item from the dataset.

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

removeActionListener(ActionListener) - Method in interface org.graffiti.plugin.gui.GraffitiToolComponent

DOCUMENT ME!

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

removeAddon(File) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.addons.AddonManagerPlugin

Removes the Add-on by renaming it.

removeAll() - Method in class org.jfree.data.gantt.TaskSeries

Removes all tasks.

removeAll() - Method in class org.jfree.data.gantt.TaskSeriesCollection

Removes all the series from the collection.

removeAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition

removeAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface

removeAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment

removeAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface

removeAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample

removeAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface

removeAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance

removeAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface

removeAll(Collection<?>) - Method in class org.graffiti.selection.Selection

removeAllBends(Graph, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

Deprecated.

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

Removes all the series from the collection and sends a DatasetChangeEvent to all registered listeners.

removeAllSeries() - Method in class org.jfree.data.MatrixSeriesCollection

Removes all the series from the collection.

removeAllSeries() - Method in class org.jfree.data.time.TimeSeriesCollection

Removes all the series from the collection.

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

Removes all the series from the collection.

removeAllValuesForX(Number) - Method in class org.jfree.data.DefaultTableXYDataset

Removes the items from all series for a given x value.

removeAnimation(Animation) - Method in class org.vanted.animation.Animator

Call this method any time you want to remove an animation.
Can be called while animations are taking place.

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

removeAttribute(String) - Method in class org.graffiti.attributes.AbstractAttributable

Deletes the Attribute attr from the attributes.

removeAttribute(String) - Method in interface org.graffiti.attributes.Attributable

Deletes the Attribute located at the given path from the attributes.

removeAttributeComponent(Attribute) - Method in interface org.graffiti.plugin.view.GraphElementComponentInterface

Removes a GraffitiViewComponent of an Attribute from collection of attribute components.

removeAttributeComponent(Attribute) - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent

Removes a GraffitiViewComponent of an Attribute from collection of attribute components.

removeAttributeConsumer(AttributeConsumer) - Method in class org.graffiti.graph.AbstractGraph

Returns true, if the given attribute consumer was in the list of attribute consumers and could be removed.

removeAttributeConsumer(AttributeConsumer) - Method in interface org.graffiti.graph.Graph

Returns true, if the given attribute consumer was in the list of attribute consumers and could be removed.

removeAttributeListener(AttributeListener) - Method in class org.graffiti.event.ListenerManager

Unregisters AttributeListener l by removing it from the list of AttributeListeners.

removeBends(Graph, Collection<Edge>, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

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

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

removeBendsBetweenSelectedNodes(Collection<Node>, boolean) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

Deprecated.

removeCategoryLabelToolTip(Comparable) - Method in class org.jfree.chart.axis.CategoryAxis

Removes the tooltip for the specified category and sends an AxisChangeEvent to all registered listeners.

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

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

Deregisters an object for notification of changes to the axis.

removeChangeListener(ChartChangeListener) - Method in class org.jfree.chart.JFreeChart

Deregisters an object for notification of changes to the chart.

removeChangeListener(LegendChangeListener) - Method in class org.jfree.chart.Legend

Deregisters an object for notification of changes to the legend.

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

Unregisters an object for notification of changes to the plot.

removeChangeListener(RendererChangeListener) - Method in class org.jfree.chart.renderer.AbstractRenderer

Deregisters an object so that it no longer receives notification of changes to the renderer.

removeChangeListener(RendererChangeListener) - Method in interface org.jfree.chart.renderer.CategoryItemRenderer

Removes a change listener.

removeChangeListener(RendererChangeListener) - Method in interface org.jfree.chart.renderer.PolarItemRenderer

Removes a change listener.

removeChangeListener(RendererChangeListener) - Method in interface org.jfree.chart.renderer.XYItemRenderer

Removes a change listener.

removeChangeListener(TitleChangeListener) - Method in class org.jfree.chart.title.Title

Unregisters an object for notification of changes to the chart title.

removeChangeListener(DatasetChangeListener) - Method in class org.jfree.chart.demo.SampleSignalDataset

Deregisters an object so that it no longer receives notification of changes to the dataset.

removeChangeListener(DatasetChangeListener) - Method in class org.jfree.chart.demo.SimpleIntervalXYDataset

Deregisters an object for notification of changes to the dataset.

removeChangeListener(DatasetChangeListener) - Method in class org.jfree.chart.demo.SimpleIntervalXYDataset2

Deregisters an object for notification of changes to the dataset.

removeChangeListener(DatasetChangeListener) - Method in class org.jfree.data.AbstractDataset

Deregisters an object so that it no longer receives notification of changes to the dataset.

removeChangeListener(DatasetChangeListener) - Method in interface org.jfree.data.Dataset

Deregisters an object for notification of changes to the dataset.

removeChangeListener(SeriesChangeListener) - Method in class org.jfree.data.Series

Deregisters an object, so that it not longer receives notification whenever the series changes.

removeChartComponent(ChartComponent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.chart_settings.ChartComponentManager

removeChartMouseListener(ChartMouseListener) - Method in class org.jfree.chart.ChartPanel

Removes a listener from the list of objects listening for chart mouse events.

removeClusterColoringOnGraph(Graph) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.PajekClusterColor

Re-colours graph elements to their default fill and outline colours.

removeColumn(int) - Method in class org.jfree.data.DefaultCategoryDataset

Removes a column from the dataset.

removeColumn(int) - Method in class org.jfree.data.DefaultKeyedValues2D

Removes a column.

removeColumn(int) - Method in class org.jfree.data.KeyedObjects2D

Removes a column.

removeColumn(Comparable) - Method in class org.jfree.data.DefaultCategoryDataset

Removes a column from the dataset.

removeColumn(Comparable) - Method in class org.jfree.data.DefaultKeyedValues2D

Removes a column.

removeColumn(Comparable) - Method in class org.jfree.data.KeyedObjects2D

Removes a column.

removeConstraint(GraphConstraint) - Method in class org.graffiti.session.GraphConstraintChecker

Removes the specified GraphConstraint from the set of constraints of this constraint checker.

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

Remove the given text from the list of corner text items.

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

removedEdges - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.SplitResult

removeDependentComponent(GraphElementComponent) - Method in interface org.graffiti.plugin.view.GraphElementComponentInterface

Removes a GraphElementComponent from the list of dependent GraphElementComponents.

removeDependentComponent(GraphElementComponent) - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent

Removes a GraphElementComponent from the list of dependent GraphElementComponents.

removeDetachedFrame(GraffitiFrame) - Method in class org.graffiti.editor.MainFrame

removedNodes - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.SplitResult

removeDragAndDropHandler(DragAndDropHandler) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.webstart.GravistoMainHelper

removeEdgeBends(Edge) - Static method in class org.AttributeHelper

removeEdgeListener(EdgeListener) - Method in class org.graffiti.event.ListenerManager

Unregisters EdgeListener l by removing it from the list of EdgeListeners.

removeEmptyConditions - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.chartDrawComponent.ChartOptions

removeFileDropListener(FileDropListener) - Method in class net.iharder.dnd.FileDropBean

Unregister a listener for FileDropEvents.

removeFileDropTarget(Component) - Method in class net.iharder.dnd.FileDropBean

Unregisters a component as a drop target.

removeFileHandlingListener(FileHandlingListeners) - Method in class org.graffiti.editor.actions.FileHandlingManager

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

Returns and removes the first element in the queue.

removeFrame(GraffitiInternalFrame) - Method in class org.graffiti.editor.GravistoService

removeGraphElementComponent(GraphElement) - Method in class org.graffiti.plugin.view.AbstractView

removeGraphListener(GraphListener) - Method in class org.graffiti.event.ListenerManager

Unregisters GraphListener l by removing it from the list of non-strict and strict transaction GraphListeners.

removeGuiComponentRow(GuiRow, boolean) - Method in class org.FolderPanel

RemoveHiddenLabelsAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing

RemoveHiddenLabelsAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing.RemoveHiddenLabelsAlgorithm

removeHiddenPatterns() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.TabPatternLayout

Removes all pattern graph - sessions from the global pattern graph session list.

removeHTMLtags(String) - Static method in class org.StringManipulationTools

removeIOHandler(ResourceIOHandler) - Static method in class org.graffiti.plugin.io.resources.ResourceIOManager

removeLayoutComponent(Component) - Method in class info.clearthought.layout.SingleFiledLayout

Removes the specified component with the specified name from the layout.

removeLayoutComponent(Component) - Method in class info.clearthought.layout.TableLayout

Removes the specified component from the layout.

removeLayoutComponent(Component) - Method in class org.graffiti.util.MaximizeLayout

removeListDataListener(ListDataListener) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.MyDynamicObjectListModel

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

removeListener(IOManager.IOManagerListener) - Method in class org.graffiti.managers.DefaultIOManager

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

Returns true, if the given io manager listener was in the list of listeners and could be removed.

removeListener(ViewManager.ViewManagerListener) - Method in class org.graffiti.managers.DefaultViewManager

removeListener(ViewManager.ViewManagerListener) - Method in interface org.graffiti.managers.ViewManager

Returns true, if the given view manager listener was in the list of listeners and could be removed.

removeListener(AnimatorListener) - Method in class org.vanted.animation.Animator

RemoveMappingDataAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms

RemoveMappingDataAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.RemoveMappingDataAlgorithm

removeMappingDataFrom(GraphElement) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.RemoveMappingDataAlgorithm

removeMergeTheseEntriesIfPossible(Collection<Entry>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Pathway

removeMessageListener(MessageListener) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.fast_view.FastView

removeMessageListener(MessageListener) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.NullView

removeMessageListener(MessageListener) - Method in class org.graffiti.plugin.view.AbstractView

Removes a message listener from the view.

removeMessageListener(MessageListener) - Method in interface org.graffiti.plugin.view.View

Removes a message listener from the view.If the view have been started without editor instance, this method may be empty.

removeMessageListener(MessageListener) - Method in class org.graffiti.plugins.views.defaults.GraffitiView

Removes a message listener from the view.

removeMessageListener(MessageListener) - Method in class org.graffiti.plugins.views.matrix.MatrixView

removeMode(Mode) - Method in class org.graffiti.managers.DefaultModeManager

removeMode(Mode) - Method in interface org.graffiti.managers.ModeManager

Removes the specified mode from the list of modes the manager contains.

removeMouseListener(MouseListener) - Method in class org.graffiti.plugins.views.defaults.GraffitiView

removeMouseMotionListener(MouseMotionListener) - Method in class org.graffiti.plugins.views.defaults.GraffitiView

removeNodeListener(NodeListener) - Method in class org.graffiti.event.ListenerManager

Unregisters NodeListener l by removing it from the list of NodeListeners

removeNodesPreserveEdges(ArrayList<Node>, Graph, boolean, boolean, BackgroundTaskStatusProviderSupportingExternalCall) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.RemoveSelectedNodesPreserveEdgesAlgorithm

removeNonValidElementsFromSelection(Selection) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

removeNumbersFromString(String) - Static method in class org.StringManipulationTools

removeObject(Comparable, Comparable) - Method in class org.jfree.data.KeyedObjects2D

Removes an object.

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

The following algorithm deletes additional parallel edges, leaving only a single edge.

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

removeParameter(SingleParameter) - Method in interface org.graffiti.plugin.parameter.ParameterList

Removes a SingleParameter from the list.

RemoveParenthesisLabels - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing

RemoveParenthesisLabels() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing.RemoveParenthesisLabels

removePathwayReferences(Attributable, boolean) - Static method in class org.AttributeHelper

removePluginManagerListener(PluginManagerListener) - Method in class org.graffiti.managers.pluginmgr.DefaultPluginManager

Removes the given plugin manager listener from the list of listeners.

removePluginManagerListener(PluginManagerListener) - Method in interface org.graffiti.managers.pluginmgr.PluginManager

Removes the given plugin manager listener from the list of listeners.

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

removePostProcessor(List<Runnable>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.AbstractExperimentDataProcessor

removePostProcessor(List<Runnable>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ExperimentDataProcessor

removeProgressListener(ChartProgressListener) - Method in class org.jfree.chart.JFreeChart

Deregisters an object for notification of changes to the chart.

removePropertyChangeListener(PropertyChangeListener) - Method in class org.jfree.data.Series

Removes a property change listener from the series.

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

remove PropertyChangeListener from the listener list

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

removeRow(int) - Method in class org.jfree.data.DefaultCategoryDataset

Removes a row from the dataset.

removeRow(int) - Method in class org.jfree.data.DefaultKeyedValues2D

Removes a row.

removeRow(int) - Method in class org.jfree.data.KeyedObjects2D

Removes a row.

removeRow(Comparable) - Method in class org.jfree.data.DefaultCategoryDataset

Removes a row from the dataset.

removeRow(Comparable) - Method in class org.jfree.data.DefaultKeyedValues2D

Removes a row.

removeRow(Comparable) - Method in class org.jfree.data.KeyedObjects2D

Removes a row.

removeScalingListener(PropertyChangeListener) - Static method in class org.vanted.scaling.Toolbox

Remove a previously add PropertyChangeListener.

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

Labels all selected nodes with unique numbers.

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

removeSelectionListener(SelectionListener) - Method in class org.graffiti.editor.MainFrame

Removes a SelectionListener.

removeSelectionListener(SelectionListener) - Method in class org.graffiti.selection.SelectionModel

Removes the given selection listener from the list of listeners.

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

removeSeries(int) - Method in class org.jfree.data.DefaultTableXYDataset

Removes a series from the collection and sends a DatasetChangeEvent to all registered listeners.

removeSeries(int) - Method in class org.jfree.data.MatrixSeriesCollection

Removes a series from the collection.

removeSeries(int) - Method in class org.jfree.data.time.TimePeriodValuesCollection

Removes a series from the collection.

removeSeries(int) - Method in class org.jfree.data.time.TimeSeriesCollection

Removes a series from the collection.

removeSeries(int) - Method in class org.jfree.data.XYSeriesCollection

Removes a series from the collection.

removeSeries(MatrixSeries) - Method in class org.jfree.data.MatrixSeriesCollection

Removes a series from the collection.

removeSeries(TimePeriodValues) - Method in class org.jfree.data.time.TimePeriodValuesCollection

Removes the specified series from the collection.

removeSeries(TimeSeries) - Method in class org.jfree.data.time.TimeSeriesCollection

Removes the specified series from the collection.

removeSeries(XYSeries) - Method in class org.jfree.data.DefaultTableXYDataset

Removes a series from the collection and sends a DatasetChangeEvent to all registered listeners.

removeSeries(XYSeries) - Method in class org.jfree.data.XYSeriesCollection

Removes a series from the collection.

removeSession(Session) - Method in class org.graffiti.editor.MainFrame

Removes the session from the list of sessions.

removeSessionListener(SessionListener) - Method in class org.graffiti.editor.MainFrame

Removes a SessionListener.

removeSessionListener(SessionListener) - Method in interface org.graffiti.session.SessionManager

Removes a SelectionListener.

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

removeSubtask(Task) - Method in class org.jfree.data.gantt.Task

Removes a sub-task from the task.

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

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

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

removeTab(InspectorTab) - Method in class org.graffiti.plugin.inspector.SubtabHostTab

Removes a tab from the inspector.

removeTab(InspectorTab) - Method in class org.graffiti.plugins.inspectors.defaults.InspectorContainer

Removes a tab from the inspector.

removeTagFromString(String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_SBase_Reader

This method processes an string with xhtml content

removeTags(String, String, String) - Static method in class org.StringManipulationTools

removeTagsGetTextAndRemovedTexts(String, String, String) - Static method in class org.StringManipulationTools

Removes the tags from a html-text and gives back the striped text.

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

removeValue(int) - Method in class org.jfree.data.DefaultKeyedValues

Removes a value from the collection.

removeValue(int) - Method in class org.jfree.data.KeyedObjects

Removes a value from the collection.

removeValue(Comparable) - Method in class org.jfree.data.DefaultKeyedValues

Removes a value from the collection.

removeValue(Comparable) - Method in class org.jfree.data.KeyedObjects

Removes a value from the collection.

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

Removes a value from the dataset.

removeValue(Comparable, Comparable) - Method in class org.jfree.data.DefaultKeyedValues2D

Removes a value.

removeView(View) - Method in class org.graffiti.session.Session

Removes the given view from this session.

removeViewListener(ViewListener) - Method in class org.graffiti.managers.DefaultViewManager

removeViewListener(ViewListener) - Method in interface org.graffiti.managers.ViewManager

Returns true, if the given view listener was in the list of listeners and could be removed.

removeViews() - Method in class org.graffiti.managers.DefaultViewManager

removeViews() - Method in interface org.graffiti.managers.ViewManager

Removes the known list of views from the internal memory.

render(int, int, Graphics2D) - Method in class placement.RectangleDrawerPanel

render(Graphics2D, Rectangle2D, int, PlotRenderingInfo) - Method in class org.jfree.chart.plot.CategoryPlot

Draws a representation of a dataset within the dataArea region using the appropriate renderer.

render(Graphics2D, Rectangle2D, int, PlotRenderingInfo, CrosshairState) - Method in class org.jfree.chart.plot.XYPlot

Draws a representation of the data within the dataArea region, using the current renderer.

render(Graphics2D, Rectangle2D, PlotRenderingInfo) - Method in class org.jfree.chart.plot.PolarPlot

Draws a representation of the data within the dataArea region, using the current m_Renderer.

render(Graphics2D, Rectangle2D, PlotRenderingInfo, CrosshairState) - Method in class org.jfree.chart.plot.ContourPlot

Draws a representation of the data within the dataArea region, using the current renderer.

render(Graphics2D, Rectangle2D, PlotRenderingInfo, CrosshairState) - Method in class org.jfree.chart.plot.FastScatterPlot

Draws a representation of the data within the dataArea region.

rendererChanged(RendererChangeEvent) - Method in interface org.jfree.chart.event.RendererChangeListener

Receives notification of a renderer change event.

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

Receives notification of a renderer change event.

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

Notifies all registered listeners of a property change.

rendererChanged(RendererChangeEvent) - Method in class org.jfree.chart.plot.WaferMapPlot

Notifies all registered listeners of a renderer change.

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

Receives notification of a renderer change event.

RendererChangeEvent - Class in org.jfree.chart.event

An event that can be forwarded to any RendererChangeListener to signal a change to a plot.

RendererChangeEvent(Object) - Constructor for class org.jfree.chart.event.RendererChangeEvent

Creates a new event.

RendererChangeListener - Interface in org.jfree.chart.event

The interface that must be supported by classes that wish to receive notification of changes to a renderer.

RendererState - Class in org.jfree.chart.renderer

Represents the current state of a renderer.

RendererState(PlotRenderingInfo) - Constructor for class org.jfree.chart.renderer.RendererState

Creates a new state object.

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

repaint(long, int, int, int, int) - Method in class org.graffiti.plugins.views.defaults.AbstractGraphElementComponent

Overrides the original method to deal with zoomable containers It will not call the original repaint, which will call the repaintmanager with unzoomed coordinates and local coordinates relativ to this graphcomponent so x and y are always 0 to create the correct repaint region we call the parent frame with new coordinates, which regard the zoom the parent will then call its repaintmanager, which will have then the correct coordinates to paint.

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

repaint(GraphElement) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.ipk_graffitiview.NullView

repaint(GraphElement) - Method in interface org.graffiti.plugin.view.View

Repaints the given graph element

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

repaint(GraphElement) - Method in class org.graffiti.plugins.views.matrix.MatrixView

repaintGraphElementComponent(GraphElementComponent) - Method in class org.graffiti.plugins.views.defaults.GraffitiView

replaceBottomPosition(CategoryLabelPositions, CategoryLabelPosition) - Static method in class org.jfree.chart.axis.CategoryLabelPositions

Returns a new instance based on an existing instance but with the bottom position changed.

ReplaceDiagramTitleFromAlternativeSubstanceNames - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe

ReplaceDiagramTitleFromAlternativeSubstanceNames() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.ReplaceDiagramTitleFromAlternativeSubstanceNames

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

replaceExtension(String, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter.PngJpegAlgorithm

replaceLabel - de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.ModeOfAttributeOperation

ReplaceLabelAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing

ReplaceLabelAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing.ReplaceLabelAlgorithm

ReplaceLabelFromAlternativeSubstanceNames - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids

ReplaceLabelFromAlternativeSubstanceNames() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids.ReplaceLabelFromAlternativeSubstanceNames

ReplaceLabelPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing

ReplaceLabelPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing.ReplaceLabelPlugin

replaceLeftPosition(CategoryLabelPositions, CategoryLabelPosition) - Static method in class org.jfree.chart.axis.CategoryLabelPositions

Returns a new instance based on an existing instance but with the left position changed.

replaceRightPosition(CategoryLabelPositions, CategoryLabelPosition) - Static method in class org.jfree.chart.axis.CategoryLabelPositions

Returns a new instance based on an existing instance but with the right position changed.

replaceTopPosition(CategoryLabelPositions, CategoryLabelPosition) - Static method in class org.jfree.chart.axis.CategoryLabelPositions

Returns a new instance based on an existing instance but with the top position changed.

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

ReplicateDouble - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe

ReplicateDouble(Object, String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ReplicateDouble

replicateID - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.DataSetRow

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

requestToolButtonFocus() - Static method in class org.graffiti.plugin.gui.ToolButton

requestUserData(ExperimentInterface) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.AnnotationProvider

requiresMultipleA() - Method in enum de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes.AttributeCalculation

reserved(Rectangle2D, RectangleEdge) - Method in class org.jfree.chart.axis.AxisSpace

Calculates the reserved area.

reserveSpace(Graphics2D, Plot, Rectangle2D, Rectangle2D, RectangleEdge, AxisSpace) - Method in class org.jfree.chart.axis.ColorBar

Reserves the space required to draw the color bar.

reserveSpace(Graphics2D, Plot, Rectangle2D, RectangleEdge, AxisSpace) - Method in class org.jfree.chart.axis.CyclicNumberAxis

Reserve some space on each axis side because we draw a centered label at each extremity.

reserveSpace(Graphics2D, Plot, Rectangle2D, RectangleEdge, AxisSpace) - Method in class org.jfree.chart.axis.SubCategoryAxis

Estimates the space required for the axis, given a specific drawing area.

reserveSpace(Graphics2D, Plot, Rectangle2D, RectangleEdge, AxisSpace, boolean) - Method in class org.jfree.chart.axis.Axis

Estimates the space (height or width) required to draw the axis.

reserveSpace(Graphics2D, Plot, Rectangle2D, RectangleEdge, AxisSpace, boolean) - Method in class org.jfree.chart.axis.CategoryAxis

Estimates the space required for the axis, given a specific drawing area.

reserveSpace(Graphics2D, Plot, Rectangle2D, RectangleEdge, AxisSpace, boolean) - Method in class org.jfree.chart.axis.ValueAxis

Returns the space required to draw the axis.

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.data_mapping.DataMapping

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

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

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

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths.AllPathsSelectionAlgorithm

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths.WeightedShortestPathSelectionAlgorithm

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.SOMclusterAnalysis

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.SOMprintDataset

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

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

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

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

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

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

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

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

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

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

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.AddRandomClusterInformationAlgorithm

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

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

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

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

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup.DeleteNodesAlgorithm

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

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy.HierarchyAlgorithm

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy.SelectLeafNodesAlgorithm

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.ExpandSelectionAlgorithm

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.FindReplaceDialog

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.InvertSelectionAlgorithm

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

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.SearchAndSelecAlgorithm

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

Resets the algorithm state.

reset() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.scripting.BeanShellDesktopAlgorithm

No special reset implemented.

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

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

Resets the internal state of the algorithm.

reset() - Method in class org.graffiti.plugins.modes.defaults.LabelTool

DOCUMENT ME!

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

Resets the tool to initial values.

reset() - Method in class org.graffiti.plugins.modes.defaults.MegaMoveTool

Resets the tool to initial values.

reset() - Method in class org.vanted.animation.Animation

Should be called whenever an animation wants to be restarted.

reset() - Method in class org.vanted.animation.Animator

Stops the animation and rests it.

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

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

Calls super.reset() and updates the parameters.

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

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

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

Resets the internal state of the algorithm.

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

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

DOCUMENT ME!

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

Initialized the node cache structures.

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

Initialized the node cache structures.

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

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

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

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

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

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

resetIdGen() - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.Pathway

resetScalingOf(JComponent, float) - Static method in class org.vanted.scaling.Toolbox

Reset the scaling of component and its children.

ResizeAndGridLayoutPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout

Plugin for Gridlayouter algorithm

ResizeAndGridLayoutPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout.ResizeAndGridLayoutPlugin

Creates a new GridLayouterPlugin object.

ResizeFromMappingCountLayoutAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout

ResizeFromMappingCountLayoutAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout.ResizeFromMappingCountLayoutAlgorithm

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

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

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

Increases or decreases the axis range by the specified percentage about the central value and sends an AxisChangeEvent to all registered listeners.

resizeRange(double, double) - Method in class org.jfree.chart.axis.ValueAxis

Increases or decreases the axis range by the specified percentage about the specified anchor value and sends an AxisChangeEvent to all registered listeners.

resizeWindow(Component, boolean) - Static method in class org.vanted.scaling.scalers.component.WindowScaler

Resizes window components.

resolveDomainAxisLocation(AxisLocation, PlotOrientation) - Static method in class org.jfree.chart.plot.Plot

Resolves a domain axis location for a given plot orientation.

resolveEntity(String, String) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.xgmml.XGMMLDTDResolver

Resolves the entity.

resolveEntity(String, String) - Method in class org.graffiti.plugins.ios.importers.graphml.parser.GraphMLEntityResolver

Redirects the external system identifiers pointing to graphML schema locations to the locally cached schemas.

resolveRangeAxisLocation(AxisLocation, PlotOrientation) - Static method in class org.jfree.chart.plot.Plot

Resolves a range axis location for a given plot orientation.

ResourceIOConfigObject - Interface in org.graffiti.plugin.io.resources

ResourceIOHandler - Interface in org.graffiti.plugin.io.resources

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

respectNodeDimensionsForLayout - Variable in class org.graffiti.plugin.algorithm.ThreadSafeOptions

If true, distances are calculated with respect to node dimensions.

RestApiBiomodels - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels

API for establishing a connection to the Biomodels database with the functionality of retrieving Simple Models and SBML Models.

RestApiBiomodels() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.RestApiBiomodels

restart() - Method in class org.vanted.animation.Animator

Resets the animation and starts it again.

restoreDefintions() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection.SearchAttributeHelper

RestoreLabelAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing

RestoreLabelAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing.RestoreLabelAlgorithm

RestService - Class in de.ipk_gatersleben.ag_nw.graffiti.services.web

Klasse zum Auslesen von Rest-Resourcen.

RestService() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.services.web.RestService

RestService(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.services.web.RestService

RestService(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.services.web.RestService

RestService(String, ArrayList<String>) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.services.web.RestService

resultError(Exception) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.TabBiomodels

resultForSBML() - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsAccessAdapter.BiomodelsLoaderCallback

resultForSBML() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsPanel

resultForSBML(SimpleModel, String) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.TabBiomodels

resultForSimpleModelQuery(List<SimpleModel>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsAccessAdapter.BiomodelsLoaderCallback

resultForSimpleModelQuery(List<SimpleModel>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsPanel

ResultPair - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics

ResultPair(Object, Object, CorrelationResult) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.ResultPair

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

Resumes execution of this algorithm, if the algorithm has been paused.

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

resumeEncoding() - Method in class org.graffiti.plugins.ios.exporters.graphml.Base64.OutputStream

Resumes encoding of the stream.

resumeEncoding() - Method in class org.graffiti.plugins.ios.importers.graphml.parser.Base64.OutputStream

Resumes encoding of the stream.

retainAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Condition

retainAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ConditionInterface

retainAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Experiment

retainAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface

retainAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample

retainAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SampleInterface

retainAll(Collection<?>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance

retainAll(Collection<?>) - Method in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.SubstanceInterface

returnAttributeByPath(GraphElement, Pattern, ArrayList<Attribute>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.HelperClass

finds Attributes in GraphElements

returnAttributeByPath(Graph, Pattern, ArrayList<Attribute>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.HelperClass

written by Hendrik Mehlhorn it is looking for all attributes that match a specific pattern and putting the result into the set passed into the function

returnScriptMenu(JMenu) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.DefaultContextMenuManager

reverse() - Method in class org.graffiti.graph.AbstractEdge

Swaps source and target of the edge.

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

Changes source and target of the Edge, that means if the Edge is directed the direction will be changed.

reverse(String) - Static method in class org.StringManipulationTools

REVERSE - Static variable in class org.jfree.chart.LegendRenderingOrder

In reverse order.

REVERSE - Static variable in class org.jfree.chart.plot.DatasetRenderingOrder

Render datasets in the order N-1, N-2, ..., 2, 1, 0, where N is the number of datasets.

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

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

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

RGB - org.vanted.animation.data.ColorMode

right - Variable in class org.GuiRow

RIGHT - org.AlignmentSetting

RIGHT - org.CondenseButtonLayout

RIGHT - org.graffiti.plugins.attributecomponents.simplelabel.Quadrant

RIGHT - org.graffiti.plugins.views.defaults.Line

RIGHT - Static variable in class info.clearthought.layout.SingleFiledLayout

Right justify components

RIGHT - Static variable in interface info.clearthought.layout.TableLayoutConstants

Indicates that the component is right justified in its cell

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

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

RIGHT - Static variable in class org.jfree.chart.plot.ThermometerPlot

A constant for the value label position (right of the thermometer).

RIGHT - Static variable in class org.jfree.chart.renderer.LineAndShapeRenderer

Constant indicating that labels are to be shown right of data points

RIGHT - Static variable in class org.jfree.chart.title.Title

Useful constant for the title position (also used for horizontal alignment).

RightSkewedRectShape - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes

RightSkewedRectShape() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.shapes.RightSkewedRectShape

RIMAS_ACCESS - org.FeatureSet

RimasTab - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop

RimasTab() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop.RimasTab

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

RKINS_ITEM - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathGene

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

RKOUTS_ITEM - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.TranspathGene

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

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

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

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

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

rollDate(Date) - Method in class org.jfree.chart.axis.DateTickUnit

Rolls the date forward by the amount specified by the roll unit and count.

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

Check whether the tree is rooted.

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

Check whether the tree is rooted.

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

Check whether the tree is rooted.

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

Check whether the tree is rooted.

RootHandler - Class in org.jfree.data.xml

A SAX handler that delegates work to sub-handlers.

RootHandler() - Constructor for class org.jfree.data.xml.RootHandler

Creates a new handler.

ROTATE_DEFAULT - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.VTextIcon

ROTATE_LEFT - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.VTextIcon

ROTATE_NONE - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.VTextIcon

ROTATE_RIGHT - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.helper_classes.VTextIcon

RotateAlgorithm - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate

RotateAlgorithm() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate.RotateAlgorithm

RotatePlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate

RotatePlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate.RotatePlugin

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

RoundGradientContext(Point2D, Color, Point2D, Color) - Constructor for class org.graffiti.plugins.views.defaults.RoundGradientContext

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

roundrectangle - de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.datatypes.kgmlGraphicsType

RouterWithProgress - Class in org.vanted.plugins.layout.adaptagrams.edgerouting

RouterWithProgress(long) - Constructor for class org.vanted.plugins.layout.adaptagrams.edgerouting.RouterWithProgress

RouterWithProgress(long, boolean) - Constructor for class org.vanted.plugins.layout.adaptagrams.edgerouting.RouterWithProgress

RouterWithProgress(long, boolean, BackgroundTaskStatusProviderSupportingExternalCall) - Constructor for class org.vanted.plugins.layout.adaptagrams.edgerouting.RouterWithProgress

RouterWithProgress(long, BackgroundTaskStatusProviderSupportingExternalCall) - Constructor for class org.vanted.plugins.layout.adaptagrams.edgerouting.RouterWithProgress

row - Variable in class qmwi.kseg.som.diagram.DiagrammData

ROW - Static variable in class info.clearthought.layout.SingleFiledLayout

Align components in a row

ROW - Static variable in class org.jfree.data.CategoryToPieDataset

Deprecated.

Use the TableOrder class.

row1 - Variable in class info.clearthought.layout.TableLayoutConstraints

Cell in which the upper left corner of the component lays

row2 - Variable in class info.clearthought.layout.TableLayoutConstraints

Cell in which the lower right corner of the component lays

rowLabel - Variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.DataSetRow

RSSfeedDefinition - Class in org.graffiti.managers.pluginmgr

RSSfeedDefinition(String, String) - Constructor for class org.graffiti.managers.pluginmgr.RSSfeedDefinition

RSSFeedManager - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow

RSSFeedManager(double) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow.RSSFeedManager

RTTreeLayout - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree

An implementation of a tree layout algorithm.

RTTreeLayout() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree.RTTreeLayout

Construct a new GraphTreeLayout algorithm instance.

RTTreeLayoutPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree

Plugin for a tree layouter algorithm

RTTreeLayoutPlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree.RTTreeLayoutPlugin

Creates a new GraphTreeLayoutPlugin object.

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

This class provides the menu entries for the jRuby-Script Menu Items.

RubyScriptMenuEntry(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.RubyScriptMenuEntry

Creates a new ScriptMenuEntry object.

Rule - Class in org.graffiti.editor

Rule(int, boolean) - Constructor for class org.graffiti.editor.Rule

run() - Method in class de.ipk_gatersleben.ag_nw.graffiti.KeggSoapAndPathwayService

run() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance.HammingCalculator

run() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som.SOMservice

run() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.AllSuperGraphsCreator

run() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.network.BroadCastTask

run() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.network.TabAglet

run() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.statistics.MyCorrlationFinder

run() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands.MyClusterGraphBasedReLayoutService

run() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.MyNonInteractiveSpringEmb

run() - Method in class org.graffiti.util.DelayThread

run() - Method in class org.jfree.chart.demo.ChartTiming1

Runs the timing.

run() - Method in class org.jfree.chart.demo.ChartTiming2

Runs the test.

run() - Method in class org.jfree.chart.demo.ChartTiming3

Runs the test.

run() - Method in class org.jfree.chart.demo.ChartTiming4

Runs the test.

run() - Method in class org.jfree.chart.demo.SampleXYDatasetThread

Runs the thread.

run(String, ActionEvent) - Static method in class org.graffiti.editor.GravistoService

runAlgorithm(Algorithm, boolean, ActionEvent) - Method in class org.graffiti.editor.GravistoService

runAlgorithm(Algorithm, ActionEvent) - Method in class org.graffiti.editor.GravistoService

runAlgorithm(Algorithm, Graph, Selection, boolean, ActionEvent) - Method in class org.graffiti.editor.GravistoService

runAlgorithm(Algorithm, Graph, Selection, ActionEvent) - Method in class org.graffiti.editor.GravistoService

RunAlgorithm - Class in org.graffiti.editor.actions

Runs an algorithm.

RunAlgorithm(String, String, MainFrame, EditComponentManager, Algorithm) - Constructor for class org.graffiti.editor.actions.RunAlgorithm

Constructor for RunAlgorithm.

RunAlgorithmDialog - Class in de.ipk_gatersleben.ag_nw.graffiti.services

RunAlgorithmDialog(String, Graph, Selection, boolean, boolean) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.services.RunAlgorithmDialog

RunnableForFile - Interface in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe

RunnableWithMappingData - Interface in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe

RunnableWithXMLexperimentData - Interface in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe

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

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

runPlugin(String, Graph, ActionEvent) - Method in class org.graffiti.editor.GravistoService

Starts a plugin and returns, as soon as the plugin execution has finished.

runStatus - Variable in class org.graffiti.plugin.algorithm.ThreadSafeOptions

Can be interpreted by the algorithm like desired.

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