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

U

UbioChemicalReaction - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

UbioChemicalReaction() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UbioChemicalReaction

UBioChemicalReaction - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UBioChemicalReaction() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UBioChemicalReaction

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

Ucatalysis - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Ucatalysis() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Ucatalysis

UCatalysis - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UCatalysis() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UCatalysis

Ucomplex - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Ucomplex() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Ucomplex

UComplex - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UComplex() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UComplex

UcomplexAssembly - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

UcomplexAssembly() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UcomplexAssembly

UComplexAssembly - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UComplexAssembly() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UComplexAssembly

Ucontrol - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Ucontrol() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Ucontrol

UControl - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UControl() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UControl

Uconversion - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Uconversion() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Uconversion

UConversion - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UConversion() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UConversion

UDegradation - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UDegradation() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UDegradation

Udna - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Udna() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Udna

UDna - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UDna() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UDna

UDnaRegion - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UDnaRegion() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UDnaRegion

UDPreceiveStructure - Class in de.ipk_gatersleben.ag_nw.graffiti

UDPreceiveStructure(InetAddress, byte[]) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.UDPreceiveStructure

UGene - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UGene() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UGene

UGeneticInteraction - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UGeneticInteraction() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UGeneticInteraction

UI - org.graffiti.plugin.algorithm.Category

UL_TYPE_CIRCLE - Static variable in class org.vanted.scaling.Toolbox

UL_TYPE_DISC - Static variable in class org.vanted.scaling.Toolbox

UL_TYPE_EXTRA - Static variable in class org.vanted.scaling.Toolbox

UL_TYPE_SQUARE - Static variable in class org.vanted.scaling.Toolbox

UllmannSubraphIsomAdjMatrixState - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder

UllmannSubraphIsomAdjMatrixState(Graph, Graph, boolean) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder.UllmannSubraphIsomAdjMatrixState

Umodulation - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Umodulation() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Umodulation

UModulation - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UModulation() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UModulation

UMolecularInteraction - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UMolecularInteraction() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UMolecularInteraction

UNCFileLocationCheck - Class in org

UNCFileLocationCheck() - Constructor for class org.UNCFileLocationCheck

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

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

UNDIRECTED - Static variable in interface org.graffiti.graph.Edge

Indicates that an Edge is undirected.

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

Call unDisplayAsMarked(GraphElementComponent geComp) on every element of the provided list.

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

Remove anything that specifies a graph element component as being marked.

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

undo() - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms.RemoveMappingDataAlgorithm

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

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

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

Extend with your Undo functionality.

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

Deletes the edge whose addition is stored in this edit.

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

Deletes the node that is stored in this edit.

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

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

Adds the deleted GraphElements stored in this edit.

Undoable - Interface in org.graffiti.undo

This interface should be implemented by all classes that provide UndoableEdits for their actions.

undoableEditHappened(UndoableEditEvent) - Method in class org.graffiti.editor.MainFrame

This method is called when an undoableEdit happened.

Unicode - Static variable in class org.StringManipulationTools

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

UnicodeToHtml(String, HashSet<Character>) - Static method in class org.StringManipulationTools

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

UnificationException - Exception in org.graffiti.attributes

Thrown in the context of unification failures (e.g.: during the merge of two collection attributes in an addAttributeConsumer call).

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

Constructor for UnificationException.

UnificationException(Throwable) - Constructor for exception org.graffiti.attributes.UnificationException

Constructor for UnificationException.

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

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

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

UNIPROT - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.biomodels.BiomodelsAccessAdapter.QueryType

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

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

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

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

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

unit_test_support - package unit_test_support

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

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

A constant for unit type 'Celcius'.

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

A constant for unit type 'Fahrenheit'.

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

A constant for unit type 'Kelvin'.

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

A constant for unit type 'None'.

UNKNOWN - org.UpdateInfoResult

unmarkAll() - Method in class org.graffiti.plugins.modes.defaults.MegaTools

Clears the selection.

UnresolvableDependenyException - Class in org.graffiti.managers.pluginmgr

An UnresolvableDependencyException will be thrown whever there is a dependency of a plugin to another which cannot be resolved.

UnresolvableDependenyException() - Constructor for class org.graffiti.managers.pluginmgr.UnresolvableDependenyException

UnsatisfiedConstraintException - Exception in org.graffiti.session

An UnsatisfiedConstraintException is thrown when a constraint to a graph is not satisfied.

UnsatisfiedConstraintException() - Constructor for exception org.graffiti.session.UnsatisfiedConstraintException

Constructs a new UnsatisfiedConstraintException with null as its detail message.

UnsatisfiedConstraintException(String) - Constructor for exception org.graffiti.session.UnsatisfiedConstraintException

Constructs a new UnsatisfiedConstraintException with the specifiecd detail message.

unselectGraphElements(Collection<? extends GraphElement>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.GraphHelper

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

UNSPECIFIED_ATTRIBUTE_STRING - Static variable in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface

UNSPECIFIED_EXPERIMENTNAME - Static variable in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface

UNSPECIFIED_SUBSTANCE - Static variable in interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.ExperimentInterface

UNSPECIFIED_TIME_STRING - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Sample

unzipFile(File) - Static method in class org.graffiti.editor.GravistoService

UP_45 - Static variable in class org.jfree.chart.axis.CategoryLabelPositions

UP_45 category label positions.

UP_90 - Static variable in class org.jfree.chart.axis.CategoryLabelPositions

UP_90 category label positions.

Upathway - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Upathway() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Upathway

UPathway - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UPathway() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UPathway

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

Updates the state of this action.

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

Updates the state of this action.

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

Updates the state of the action.

update(double, boolean) - Method in class org.vanted.animation.Animation

Modifies a particular attribute in a node relative to the time elapsed.

update(double, boolean) - Method in class org.vanted.animation.ContinuousAnimation

update(int, int, double) - Method in class org.jfree.data.MatrixSeries

Updates the value of the specified item in this matrix series.

update(int, int, double) - Method in class org.jfree.data.NormalizedMatrixSeries

update(int, Number) - Method in class org.jfree.data.time.TimePeriodValues

Updates (changes) the value of a data item.

update(int, Number) - Method in class org.jfree.data.time.TimeSeries

Updates (changes) the value of a data item.

update(int, Number) - Method in class org.jfree.data.XYSeries

Updates the value of an item in the series and sends a SeriesChangeEvent to all registered listeners.

update(Observable, Object) - Method in class placement.QPRectanglePlacement

update(Observable, Object) - Method in class placement.RectangleDrawerPanel

update(RegularTimePeriod, Number) - Method in class org.jfree.data.time.TimeSeries

Updates (changes) the value for a time period.

UPDATE_CLUSTER_NODES - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar.KeggNavigationToolbarCommand.Command

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

Updates the state of the actions.

updateAllActions() - Static method in class org.graffiti.plugin.actions.GraffitiAction

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

Updates the averaged outlier.

updateChartProperties(JFreeChart) - Method in class org.jfree.chart.ui.ChartPropertyEditPanel

Updates the properties of a chart to match the properties defined on the panel.

updateClusterList(Collection<String>) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.cluster_colors.ClusterColorAttribute

Must be called on an existing ClusterColorAttribute to update the cluster information.

updateCrosshairPoint(double, double, double, double, PlotOrientation) - Method in class org.jfree.chart.plot.CrosshairState

Evaluates a data point and if it is the closest to the anchor point it becomes the new crosshair point.

updateCrosshairX(double) - Method in class org.jfree.chart.plot.CrosshairState

Evaluates an x-value and if it is the closest to the anchor point it becomes the new crosshair point.

updateCrosshairY(double) - Method in class org.jfree.chart.plot.CrosshairState

Evaluates a y-value and if it is the closest to the anchor point it becomes the new crosshair point.

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

UPDATED - org.graffiti.event.AbstractEvent.EVENTTYPE

UPDATED - org.UpdateInfoResult

UPDATED_DATASET - Static variable in class org.jfree.chart.event.ChartChangeEvent

Event type indicating that the chart's data source has been modified.

updateDrawing() - Method in class placement.DebugPanel

updateGUI() - Method in class org.graffiti.managers.pluginmgr.PluginManagerDialog

Called, if the selection changed and/or the ui elements have to be updated.

updateGUIforUpdatedExperimentData(String, ExperimentInterface, JComponent) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe.ExperimentDataInfoPane

UpdateInfoResult - Enum in org

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

Using the information from the associated LabelAttribute and the shape and position of the GraphElement to calculate and set the position of the label.

UpdateMessageDialog - Class in org.vanted.updater

updatePanels(FolderPanel, FolderPanel, Collection<Gml2PathwayWarningInformation>, Collection<Gml2PathwayErrorInformation>) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.kgml.gui.KGMLerrorWindow

updatePlotProperties(Plot) - Method in class org.jfree.chart.ui.PlotPropertyEditPanel

Updates the plot properties to match the properties defined on the panel.

updatePositionForEdgeMapping(Attribute, GraphElementShape, String, String, double, int, int, Point) - Static method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.viewcomponents.EdgeComponentHelper

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

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

updatePreferences(Preferences) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop.RimasTab

updatePreferences(Preferences) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.metacrop.TabMetaCrop

updatePreferences(Preferences) - Method in interface org.graffiti.options.PreferencesInterface

This method will be called, when preferences for this class have changed and the implementing class gets the chance of setting class (static) variables having the values of the parameters.

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

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

updatePreferences(Preferences) - Method in class org.vanted.scaling.vanted.HighDPISupport

updatePreferences(Preferences) - Method in class org.vanted.updater.ScanForUpdate

updatePreferences(Preferences) - Method in class org.vanted.VantedPreferences

updatePreferencesForClass(Class<? extends PreferencesInterface>, Preferences) - Static method in class org.graffiti.managers.PreferenceManager

This method will instantiate an Object from the given class and call the updatePreferences method, which must be implemented by any PreferencesInterface implementing class.

updateReactionInfo(Reaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui.MyReactionList

updateReactionSelection(Reaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui.CompoundListEditor

updateReactionSelection(Reaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui.ReactionIdEditor

updateReactionSelection(Reaction) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.reaction_gui.ReactionTypeSelection

updateRelationInfo(Relation) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui.MyRelationList

updateRelationSelection(Relation) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui.RelationTypeEditor

updateRelationSelection(Relation) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui.SrcTargetEditor

updateRelationSelection(Relation) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui.SubComponentNameCheckBox

updateRelationSelection(Relation) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui.SubComponentTypesEditor

updateRelationSelection(Relation) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.kegg.kegg_type.relation_gui.SubtypeCompoundEditor

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

updateShape() - Method in interface org.graffiti.plugin.view.EdgeComponentInterface

Calls buildShape if no NodeShapes have changed.

updateShape() - Method in class org.graffiti.plugins.views.defaults.EdgeComponent

Calls buildShape if no NodeShapes have changed.

updateSize(double) - Method in interface org.graffiti.plugin.view.ArrowShape

updateSize(double) - Method in class org.graffiti.plugins.views.defaults.AbsoluteInhibitorArrowShape

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

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

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

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

updateSize(double) - Method in class org.graffiti.plugins.views.defaults.CircleConnectArrowShape

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

updateSize(double) - Method in class org.graffiti.plugins.views.defaults.InhibitorArrowShape

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

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

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

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

updateSourceIfValid(Node, double) - Method in class de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths.DistanceInfo

updateTable(Attribute) - Method in class org.graffiti.plugin.inspector.EditPanel

DOCUMENT ME!

updateTable(Attribute) - Method in class org.graffiti.plugins.inspectors.defaults.DefaultEditPanel

DOCUMENT ME!

updateValue(Number) - Method in class org.jfree.data.DefaultKeyedValueDataset

Updates the value.

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

Updates the x-values for all the series in the dataset.

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

UphysicalEntity - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

UphysicalEntity() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UphysicalEntity

UPhysicalEntity - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UPhysicalEntity() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UPhysicalEntity

UphysicalInteraction - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

UphysicalInteraction() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UphysicalInteraction

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

Uprotein - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Uprotein() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Uprotein

UProtein - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UProtein() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UProtein

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

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

URL - de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow.FeedDownloadType

URL_HELPTEXT - org.FeatureSet

URL_NODE_ANNOTATION - org.FeatureSet

URL_RELEASEINFO - org.FeatureSet

URLAttribute - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute

URLAttribute() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute.URLAttribute

URLAttribute(String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute.URLAttribute

URLAttribute(String, String) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute.URLAttribute

URLattributeAction - Interface in org.graffiti.plugin.actions

URLattributeActionManager - Interface in org.graffiti.managers

URLattributeContextMenuCommandPlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.url_attribute_context_commands

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

URLAttributeEditor - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute

URLAttributeEditor(Displayable) - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute.URLAttributeEditor

URLAttributePlugin - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute

URLAttributePlugin() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.url_attribute.URLAttributePlugin

urlSeparator - Static variable in class de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow.RSSFeedManager

URLTagFragmentGenerator - Interface in org.jfree.chart.imagemap

Interface for generating the URL fragment of an HTML image map area tag.

Urna - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Urna() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Urna

URna - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

URna() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.URna

URnaRegion - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

URnaRegion() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.URnaRegion

usage() - Static method in class org.jfree.chart.demo.ContourPlotDemo

Prints usage information.

usage() - Static method in class org.jfree.chart.demo.ContourPlotDemo2

Prints usage options.

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

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

useDisplayed - org.vanted.plugins.layout.stressminimization.StressMinParamModel.InitialLayoutOption

useIndentation - Static variable in class org.graffiti.plugin.XMLHelper

Indicates whether or not indent XML elements.

useLandmarks() - Method in class org.vanted.plugins.layout.stressminimization.StressMinParamModel.MethodRadioGroup

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

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

useRandom - org.vanted.plugins.layout.stressminimization.StressMinParamModel.InitialLayoutOption

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

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

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

UsmallMolecule - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

UsmallMolecule() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UsmallMolecule

USmallMolecule - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

USmallMolecule() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.USmallMolecule

UTemplateReaction - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UTemplateReaction() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTemplateReaction

UTemplateReactionRegulation - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UTemplateReactionRegulation() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTemplateReactionRegulation

UtilityClassSelectorFromGraph - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

this class and its static method transforms a attributes on a node to an biopax element

UtilityClassSelectorFromGraph() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UtilityClassSelectorFromGraph

UtilityClassSelectorToGraph - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

this class and its static method transforms a biopax element to a node in a graph

UtilityClassSelectorToGraph - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

this class and its static method transforms a biopax element to a node in a graph

UtilityClassSelectorToGraph() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UtilityClassSelectorToGraph

UtilityClassSelectorToGraph() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UtilityClassSelectorToGraph

UtilitySuperClassFromGraph - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

this class's functions gets all available attributes and helps to write them into an owl model

UtilitySuperClassFromGraph() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UtilitySuperClassFromGraph

UtilitySuperClassToGraph - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

this class's functions sets attributes to each node

UtilitySuperClassToGraph - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

this class's functions sets attributes to each node

UtilitySuperClassToGraph() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UtilitySuperClassToGraph

UtilitySuperClassToGraph() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UtilitySuperClassToGraph

Utransport - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

Utransport() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.Utransport

UTransport - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UTransport() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTransport

UtransportWithBiochemicalReaction - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility

UtransportWithBiochemicalReaction() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.biopax.lvl2utility.UtransportWithBiochemicalReaction

UTransportWithBiochemicalReaction - Class in de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility

UTransportWithBiochemicalReaction() - Constructor for class de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.biopax.lvl3utility.UTransportWithBiochemicalReaction

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