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A B C D E F G H I J K M N O P R S T U

## A

actionPerformed(ActionEvent) - Method in class jp.sbi.celldesigner.plugin.PluginAction
  The action when the plug-in menu is clicked on CellDesigner.
actionPerformed(ActionEvent) - Method in class jp.sbi.celldesigner.plugin.PluginCloneModelDoSthAction
actionPerformed(ActionEvent) - Method in class jp.sbi.celldesigner.plugin.PluginCreateModelDoSthAction
actionPerformed(ActionEvent) - Method in class jp.sbi.celldesigner.plugin.PluginMassShowerAction
actionPerformed(ActionEvent) - Method in class jp.sbi.celldesigner.plugin.PluginOpenFileAndDoSomethingAction
add(PluginAction) - Method in class jp.sbi.celldesigner.plugin.PluginMenu
  Adds a PluginAction to this PluginMenu.
add(PluginMenu) - Method in class jp.sbi.celldesigner.plugin.PluginMenu
  Adds a PluginMenu to this PluginMenu.
add(PluginMenuItem) - Method in class jp.sbi.celldesigner.plugin.PluginMenu
  Adds a PluginMenuItem to this PluginMenu.
ADD_PRODUCT - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  ADD_PRODUCT
ADD_REACTANT - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  ADD_REACTANT
addCellDesignerPluginMenu(PluginMenu) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Adds the menu for this plug-in to CellDesigner.
addCompartment(PluginCompartment) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Adds a PluginCompartment to the list.
addCompartmentPopupMenu(PluginMenu) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Adds the compartment popup menu to CellDesigner.
addCompartmentPopupMenuSeparator() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Adds the boundary to the compartment popup menu of CellDesigner.
addCompartmentType(PluginCompartmentType) - Method in class jp.sbi.celldesigner.plugin.PluginModel
addConstraint(PluginConstraint) - Method in class jp.sbi.celldesigner.plugin.PluginModel
addCVTerm(CVTerm) - Method in class jp.sbi.celldesigner.plugin.PluginSBase
addEvent(PluginEvent) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Adds the PluginEvent to the list.
addEventAssignment(PluginEventAssignment) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
  Adds a PluginEventAssignment to the list.
addFunctionDefinition(PluginFunctionDefinition) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Adds a PluginFunctionDefinition to the list.
addGLogicGate(PluginGLogicGate) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
addInitialAssignment(PluginInitialAssignment) - Method in class jp.sbi.celldesigner.plugin.PluginModel
addMember(InformationDisplayerAbst) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
addMember(InformationDisplayerAbst) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
addModifier(PluginModifierSpeciesReference) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Adds a PluginModifierSpeciesReference to this PluginReaction.
addModifiers(PluginModifierSpeciesReference) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
addParameter(PluginParameter) - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Adds a PluginParameter to the list of PluginParameter of this PluginKineticLaw.
addParameter(PluginParameter) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Adds the PluginParameter to the list.
addPluginBindingRegion(PluginBindingRegion) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Adds a PluginBindingRegion to the list.
addPluginMenu() - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Adds the PluginMenu to CellDesigner.
addPluginModificationRegion(PluginModificationRegion) - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
  Adds PluginModificationRegion
addPluginModificationRegion(PluginModificationRegion) - Method in class jp.sbi.celldesigner.plugin.PluginGene
  Adds a PluginModificationRegion to the list.
addPluginModificationRegion(PluginModificationRegion) - Method in class jp.sbi.celldesigner.plugin.PluginRNA
  Adds a PluginModificationRegion to this PluginRNA.
addPluginModificationResidue(PluginModificationResidue) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Adds a PluginModificationResidue to the list.
addProduct(PluginSpeciesReference) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Adds Product (PluginSpeciesReference) to this PluginReaction.
addReactant(PluginSpeciesReference) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Adds the given Reactant (PluginSpeciesReference) to this PluginReaction.
addReaction(PluginReaction) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Adds a PluginReaction to the list.
addReactionPopupMenu(PluginMenu) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Adds the reaction popup menu to CellDesigner.
addReactionPopupMenuSeparator() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Adds the boundary to the reaction popup menu of CellDesigner.
addRule(PluginRule) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Adds a PluginRule to the list.
addSeparator() - Method in class jp.sbi.celldesigner.plugin.PluginMenu
  Adds the separator of this PluginMenu.
addSpecies(PluginSpecies) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
addSpecies(String) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
addSpecies(PluginSpecies) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Adds a PluginSpecies to the list in this PluginModel.
addSpeciesAlias(PluginSpeciesAlias) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
addSpeciesAlias(PluginSpeciesAlias) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Adds the PluginSpeciesAlias to this Species.
addSpeciesPopupMenu(PluginMenu) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Adds the species popup menu to CellDesigner.
addSpeciesPopupMenuSeparator() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Adds the boundary to the species popup menu of CellDesigner.
addSpeciesType(PluginSpeciesType) - Method in class jp.sbi.celldesigner.plugin.PluginModel
addUnit(PluginUnit) - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
  Sets the PluginUnit of this PluginUnitDefinition.
addUnitDefinition(PluginUnitDefinition) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Adds a PluginUnitDefinition to the list.
ANNOTATION - Static variable in class jp.sbi.celldesigner.plugin.PluginModelBuilder
ANTISENSE_RNA - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  ANTISENSE_RNA
append(PluginSBase) - Method in class jp.sbi.celldesigner.plugin.PluginListOf
  Adds a PluginSBase to this PluginListOf
appendProtein(PluginProtein) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Adds the PluginProtein to the list.

## B

BOOLEAN_LOGIC_GATE_AND - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  BOOLEAN_LOGIC_GATE_AND
BOOLEAN_LOGIC_GATE_NOT - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
BOOLEAN_LOGIC_GATE_OR - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  BOOLEAN_LOGIC_GATE_OR
BOOLEAN_LOGIC_GATE_UNKNOWN - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  BOOLEAN_LOGIC_GATE_UNKNOWN

## C

calcArrayPtrFromPercent(String[][], int) - Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
CATALYSIS - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  CATALYSIS
CellDesignerPlug - Interface in jp.sbi.celldesigner.plugin
  Interface class of CellDesignerPlugin.
CellDesignerPlugin - Class in jp.sbi.celldesigner.plugin
  Interface class of CellDesignerPlugin.
CellDesignerPlugin() - Constructor for class jp.sbi.celldesigner.plugin.CellDesignerPlugin
ChangeCVTermToMiriamDefinition(List) - Method in class jp.sbi.celldesigner.plugin.PluginSBase
clear() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Clears all PluginParameter of this PluginKineticLaw.
clear() - Method in class jp.sbi.celldesigner.plugin.PluginListOf
  Clears this PluginListOf
clone(Modification) - Method in class jp.sbi.celldesigner.plugin.PluginModification
  Clones this PluginModification
clone(StructuralState) - Method in class jp.sbi.celldesigner.plugin.PluginStructuralState
cloneCurrModel() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
CLOSEUP_NORTHEAST - Static variable in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  CLOSEUP_NORTHEAST
CLOSEUP_NORTHWEST - Static variable in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  CLOSEUP_NORTHWEST
CLOSEUP_SOUTHEAST - Static variable in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  CLOSEUP_SOUTHEAST
CLOSEUP_SOUTHWEST - Static variable in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  CLOSEUP_SOUTHWEST
colorDefaultMax - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
colorDefaultMid - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
colorDefaultMin - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
colorSystemDefaultEnd - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
colorSystemDefaultMid - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
colorSystemDefaultStart - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
COMPLEX - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  COMPLEX
contains(PluginSBase) - Method in class jp.sbi.celldesigner.plugin.PluginListOf
convertToPluginAntiSenseRNA(AntiSenseRNA) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Converts AntiSenseRNA to PluginAntiSenseRNA
convertToPluginAntiSenseRNA(AntiSenseRNA) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts AntiSenseRNA to PluginAntiSenseRNA
convertToPluginCompartment(Compartment, CompartmentAnnotation) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Converts Compartment to PluginCompartment
convertToPluginCompartment(Compartment, CompartmentAnnotation) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Compartment to PluginCompartment
convertToPluginCompartmentType(CompartmentType) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
convertToPluginConstraint(Constraint) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
convertToPluginEvent(Event) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Event to PluginEvent
convertToPluginEventAssignment(EventAssignment, PluginEvent) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts EventAssignment to PluginEventAssignment
convertToPluginFunctionDefinition(FunctionDefinition) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts FunctionDefinition to PluginFunctionDefinition
convertToPluginGene(Gene) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Converts Gene to PluginGene
convertToPluginGene(Gene) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Gene to PluginGene
convertToPluginInitialAssignment(InitialAssignment) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
convertToPluginKineticLaw(KineticLaw, PluginReaction) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Converts KineticLaw to PluginKineticLaw
convertToPluginKineticLaw(KineticLaw, PluginReaction) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts KineticLaw to PluginKineticLaw
convertToPluginModel(Model) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Converts Model to PluginModel
convertToPluginModel(Model, SBModel) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Converts Model to PluginModel
convertToPluginModel(Model) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Model to PluginModel
convertToPluginModel(Model, SBModel) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Model to PluginModel
convertToPluginModifierSpeciesReference(ModifierSpeciesReference, PluginReaction, ReactionLink, SpeciesReferenceAnnotation, PluginSpecies) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Convers ModifierSpeciesReference to PluginModifierSpeciesReference
convertToPluginParameter(Parameter, PluginKineticLaw) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Parameter to PluginParameter
convertToPluginParameter(Parameter, PluginModel) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Parameter to PluginParameter
convertToPluginProtein(Protein) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Protein to PluginProtein
convertToPluginReaction(Reaction, ReactionAnnotation) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Converts Reaction to PluginReaction
convertToPluginReaction(Reaction, ReactionAnnotation) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Reaction to PluginReaction
convertToPluginRNA(RNA) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Converts RNA to PluginRNA
convertToPluginRNA(RNA) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts RNA to PluginRNA
convertToPluginRule(Rule, PluginModel) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Rule to PluginRule
convertToPluginSBase(SBase) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Converts SBase to PluginSBase
convertToPluginSBase(SBase) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts SBase to PluginSBase
convertToPluginSpecies(Species, SpeciesAnnotation) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Converts Species to PluginSpecies
convertToPluginSpecies(Species, SpeciesAnnotation) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Species to PluginSpecies
convertToPluginSpeciesAlias(SpeciesAlias, PluginSpecies) - Method in class jp.sbi.celldesigner.plugin.PluginModelBuilder
  Convers SpeciesAlias to PluginSpeciesAlias
convertToPluginSpeciesAlias(SpeciesAlias, PluginSpecies) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Convers SpeciesAlias to PluginSpeciesAlias
convertToPluginSpeciesReference(SpeciesReference, PluginReaction, SpeciesReferenceAnnotation, PluginSpecies) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts SpeciesReference to PluginSpeciesReference
convertToPluginSpeciesType(SpeciesType) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
convertToPluginUnit(Unit, PluginUnitDefinition) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts Unit to PluginUnit
convertToPluginUnitDefinition(UnitDefinition) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
  Converts UnitDefinition to PluginUnitDefinition
converttoReactionLinkSTRAIGHTCURVELineType(int) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSystemOutUtils
createCopy() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
createNewAliasId() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Create NewAliasId
createNewCompartmentId() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Creates NewCompartmentId
createNewReactionId() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Creates NewReactionId
createNewSpeciesId() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Creates NewSpeciesId

## D

DEGRADATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  DEGRADATION
DEGRADED - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  DEGRADED
deleteMember(InformationDisplayerAbst) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
DISSOCIATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  DISSOCIATION
doCircularLayout() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
doMyTask(ProcessBarFrm) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassOutputAnimationTask
doStateChanged() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
dosthAfterMyTask() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassOutputAnimationTask
dropDisplayers() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
DRUG - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType

## E

equals(PluginModification) - Method in class jp.sbi.celldesigner.plugin.PluginModification
  Compares the given PluginModification to this PluginModification
equals(StructuralState) - Method in class jp.sbi.celldesigner.plugin.PluginStructuralState
exportDrawAreaToImageFile(String, String, String) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin

## F

firstRun - Variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
formatPoint2DDoubleOutputString(Object) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSystemOutUtils

## G

GENE - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  GENE
generateGif() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
generateMovie() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
get(int) - Method in class jp.sbi.celldesigner.plugin.PluginListOf
  Gets PluginSBase with the given index from this PluginListOf.
getAction() - Method in class jp.sbi.celldesigner.plugin.PluginMenu
getAction() - Method in class jp.sbi.celldesigner.plugin.PluginMenuItem
getActive() - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  Gets a state for transcriptional starting site.
getAlias() - Method in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
getAliasID() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getAllIncludedSpeciesAliases() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getAllModels() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Deprecated.
getAllMyPostionInfomations() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getAllMyPostionInfomations(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getAllPointsInLineOfReactionLink(ReactionLink, Vector<Vector>) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSystemOutUtils
getAllSpeciesNodes() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getAngle() - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
getAngle() - Method in class jp.sbi.celldesigner.plugin.PluginInformationBox
getAngle() - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
getAngle() - Method in class jp.sbi.celldesigner.plugin.PluginStructuralState
getAnnotation() - Method in class jp.sbi.celldesigner.plugin.PluginSBase
getAnnotationString() - Method in class jp.sbi.celldesigner.plugin.PluginSBase
getAntiSenseRNA(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginAntiSenseRNA with the given id.
getAntiSenseRNA() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getArray() - Method in class jp.sbi.celldesigner.plugin.PluginListOf
getAuxDatas() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getBoundaryCondition() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getCharge() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getColor() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
getColor() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getCompartment(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginCompartment with the given index.
getCompartment(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginCompartment with the given id.
getCompartment() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getCompartmentType() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getCompartmentType(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getCompartmentType(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getCompartmentTypeOfPanel() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getComponents() - Method in class jp.sbi.celldesigner.plugin.PluginMenu
getConstant() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getConstant() - Method in class jp.sbi.celldesigner.plugin.PluginParameter
getConstant() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getConstraint(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getConstraint(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getCurrentModelRadioButton() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
getCVTerm(int) - Method in class jp.sbi.celldesigner.plugin.PluginSBase
getDatasOfAllSheet() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getDatasOfCurrentSheet() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getDataType() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getDefaultColor(String) - Static method in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  Gets the default color of the given compartmentType.
getDefaultColor(String) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  Gets the default color of the given speciesType.
getDefaultLineWidth(String) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  Gets the default linewidth of the given speciesType.
getDefaultSize(String) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  Gets the default size of the given speciesType.
getDelay() - Method in class jp.sbi.celldesigner.plugin.PluginEvent
getEndTime() - Method in class jp.sbi.celldesigner.plugin.simulation.PluginSimulation
getEvent(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginEvent with the given index.
getEvent(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginEvent with the given id.
getEventAssignment(int) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
  Gets the PluginEventAssignment with the given index
getExponent() - Method in class jp.sbi.celldesigner.plugin.PluginUnit
getExtensionId() - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
getExtensionId() - Method in class jp.sbi.celldesigner.plugin.PluginGene
getExtensionId() - Method in class jp.sbi.celldesigner.plugin.PluginProtein
getExtensionId() - Method in class jp.sbi.celldesigner.plugin.PluginRNA
getExtensionId() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getExtensionType() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getFast() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getFile() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getFormula() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
getFormula() - Method in class jp.sbi.celldesigner.plugin.PluginRule
getFrameLineWidth() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getFrmController() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
getFunctionDefinition(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginFunctionDefinition with the given index.
getFunctionDefinition(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginFunctionDefinition with the given id.
getGateLink() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
getGateType() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getGene(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginGene with the given id.
getGene() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getGLogicGateType() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
getHasOnlySubstanceUnits() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getHeight() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getHeight() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getHomodimer() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getHypothetical() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getId() - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
getId() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getId() - Method in class jp.sbi.celldesigner.plugin.PluginCompartmentType
getId() - Method in class jp.sbi.celldesigner.plugin.PluginEvent
getId() - Method in class jp.sbi.celldesigner.plugin.PluginFunctionDefinition
getId() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getId() - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
getId() - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
getId() - Method in class jp.sbi.celldesigner.plugin.PluginParameter
getId() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getId() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getId() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesType
getId() - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
getInformationShowerName() - Method in interface jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerImpl
getInformationShowerName() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
getInformationShowerReadOnlyPK() - Method in interface jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerImpl
getInformationShowerReadOnlyPK() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
getInitialAmount() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getInitialAssignment(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getInitialAssignment(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getInitialConcentration() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getInnerWidth() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getJCheckBoxAutoResizeGif() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassAnimOutputOptionFrm
  This method initializes jCheckBoxAutoResizeGif
getJCheckBoxAutoResizeMov() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassAnimOutputOptionFrm
  This method initializes jCheckBoxAutoResizeMov
getJCheckBoxGifOut() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassAnimOutputOptionFrm
  This method initializes jCheckBoxGifOut
getJCheckBoxMovOut() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassAnimOutputOptionFrm
  This method initializes jCheckBoxMovOut
getJMenu() - Method in class jp.sbi.celldesigner.plugin.PluginMenu
getJMenuItem() - Method in class jp.sbi.celldesigner.plugin.PluginMenuItem
getJTextFieldGifFileName() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassAnimOutputOptionFrm
  This method initializes jTextFieldGifFileName
getJTextFieldMovFileName() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassAnimOutputOptionFrm
  This method initializes jTextFieldMovFileName
getKind() - Method in class jp.sbi.celldesigner.plugin.PluginUnit
getKindString() - Method in class jp.sbi.celldesigner.plugin.PluginUnit
getKineticLaw() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getL1TypeCode() - Method in class jp.sbi.celldesigner.plugin.PluginAssignmentRule
getLabel() - Method in class jp.sbi.celldesigner.plugin.PluginModification
  Gets the text of label for the state
getLabel1String() - Method in class jp.sbi.celldesigner.plugin.PluginInformationBox
getLabel2String() - Method in class jp.sbi.celldesigner.plugin.PluginInformationBox
getLineColor() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getLineColor() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getLineWidth() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
getLineWidth() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getListOfAllSpeciesAlias() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfAllSpeciesAlias(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfAntiSenseRNAs() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfCompartments() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfCompartmentTypes() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfConstraints() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfDisplayers() - Method in interface jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerImpl
getListOfDisplayers() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
getListOfEventAssignments() - Method in class jp.sbi.celldesigner.plugin.PluginEvent
getListOfEvents() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfFunctionDefinitions() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfGenes() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfGLogicGates() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getListOfInitialAssignments() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfModifiers() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getListOfParameters() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
getListOfParameters() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfPluginBindingRegion() - Method in class jp.sbi.celldesigner.plugin.PluginProtein
getListOfPluginRegion() - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
getListOfPluginRegion() - Method in class jp.sbi.celldesigner.plugin.PluginGene
getListOfPluginRegion() - Method in class jp.sbi.celldesigner.plugin.PluginRNA
getListOfPluginResidue() - Method in class jp.sbi.celldesigner.plugin.PluginProtein
getListOfProducts() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getListOfProteins() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfReactants() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getListOfReactions() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfRNAs() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfRules() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfSpecies() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfSpecies(PluginAntiSenseRNA) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfSpecies(PluginGene) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfSpecies(PluginProtein) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the list of PluginProtein added the given PluginProtein to.
getListOfSpecies(PluginRNA) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfSpeciesAlias() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getListOfSpeciesTypes() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfUnitDefinitions() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getListOfUnits() - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
getMappingArrayMassShowerConfigWinFrm() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getMappingArrayMassShowerMainWinFrmInstanceInCurrentGStructure() - Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getMappingKeyComboBox() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getMassDatas() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getMath() - Method in class jp.sbi.celldesigner.plugin.PluginConstraint
getMath() - Method in class jp.sbi.celldesigner.plugin.PluginEventAssignment
getMath() - Method in class jp.sbi.celldesigner.plugin.PluginFunctionDefinition
getMath() - Method in class jp.sbi.celldesigner.plugin.PluginInitialAssignment
getMath() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
getMath() - Method in class jp.sbi.celldesigner.plugin.PluginRule
getMaxVaule() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
getMaxVaule() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getMaxVauleColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
getMaxVauleColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getMembers() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
getMenuComponent(int) - Method in class jp.sbi.celldesigner.plugin.PluginMenu
getMenuComponentCount() - Method in class jp.sbi.celldesigner.plugin.PluginMenu
getMessage() - Method in class jp.sbi.celldesigner.plugin.PluginConstraint
getmicroArrayRadioButton() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
getMidPointInLine() - Method in class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
  Get the junction information of three linked lines if this link is three-linked line.
getMidVaule() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
getMidVaule() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getMidVauleColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
getMidVauleColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getMinVaule() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
getMinVaule() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getMinVauleColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
getMinVauleColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getMiriamDatas() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getModel(String) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getModelType() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getModifications() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getModificationType() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
getModificationType() - Method in class jp.sbi.celldesigner.plugin.PluginModifierSpeciesReference
getModifier(int) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Gets the PluginModifierSpeciesReference with the given index of this PluginReaction.
getModifiers() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
getMultiplier() - Method in class jp.sbi.celldesigner.plugin.PluginUnit
getName() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
getName() - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
getName() - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
getName() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getName() - Method in class jp.sbi.celldesigner.plugin.PluginCompartmentType
getName() - Method in class jp.sbi.celldesigner.plugin.PluginEvent
getName() - Method in class jp.sbi.celldesigner.plugin.PluginFunctionDefinition
getName() - Method in class jp.sbi.celldesigner.plugin.PluginGene
getName() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getName() - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
getName() - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
getName() - Method in class jp.sbi.celldesigner.plugin.PluginParameter
getName() - Method in class jp.sbi.celldesigner.plugin.PluginProtein
getName() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getName() - Method in class jp.sbi.celldesigner.plugin.PluginRNA
getName() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getName() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getName() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesType
getName() - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
getNamePositionX() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getNamePositionY() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getNewModelRadioButton() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
getNotes() - Method in class jp.sbi.celldesigner.plugin.PluginSBase
getNotes() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getNotesString() - Method in class jp.sbi.celldesigner.plugin.PluginSBase
getNotesString() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getNumBindingRegions() - Method in class jp.sbi.celldesigner.plugin.PluginProtein
getNumCompartments() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumCompartmentTypes() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumConstraints() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumCVTerms() - Method in class jp.sbi.celldesigner.plugin.PluginSBase
getNumEventAssignments() - Method in class jp.sbi.celldesigner.plugin.PluginEvent
getNumEvents() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumFunctionDefinitions() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumGLogicGates() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getNumInitialAssignments() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumItems() - Method in class jp.sbi.celldesigner.plugin.PluginListOf
  Deprecated. In libSBML 3, getNumItems has been renamed to size().
getNumModifiers() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getNumOfSteps() - Method in class jp.sbi.celldesigner.plugin.simulation.PluginSimulation
getNumParameters() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
getNumParameters() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumProducts() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getNumReactants() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getNumReactions() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumRegions() - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
getNumRegions() - Method in class jp.sbi.celldesigner.plugin.PluginGene
getNumRegions() - Method in class jp.sbi.celldesigner.plugin.PluginRNA
getNumResidues() - Method in class jp.sbi.celldesigner.plugin.PluginProtein
getNumRules() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumSpecies() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumSpeciesAlias() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getNumSpeciesTypes() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumUnitDefinitions() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getNumUnits() - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
getOffset() - Method in class jp.sbi.celldesigner.plugin.PluginUnit
getOldmiriamRelationIndex() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getOpenFilename() - Method in class jp.sbi.celldesigner.plugin.PluginOpenFileAndDoSomethingAction
getOpenXmlFileRadioButton() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
getOuterWidth() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getOutputFile() - Method in class jp.sbi.celldesigner.plugin.simulation.PluginSimulation
getOutputGifFileName() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getOutputMovFileName() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getOutside() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getParameter(int) - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Gets the PluginParameter with the given index from the list.
getParameter(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginParameter with the given index.
getParameter(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginParameter with the given id.
getParent() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
getParentEvent() - Method in class jp.sbi.celldesigner.plugin.PluginEventAssignment
getParentExtensionSBase() - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
getParentID() - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
getParentID() - Method in class jp.sbi.celldesigner.plugin.PluginEventAssignment
getParentID() - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
getParentID() - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
getParentID() - Method in class jp.sbi.celldesigner.plugin.PluginUnit
getParentModel() - Method in class jp.sbi.celldesigner.plugin.PluginRule
getParentProtein() - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
getParentProtein() - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
getParentReaction() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
getParentReaction() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
getParentReaction() - Method in class jp.sbi.celldesigner.plugin.PluginParameter
getParentReaction() - Method in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
getParentReactionID() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
getParentReactionID() - Method in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
getParentSBase() - Method in class jp.sbi.celldesigner.plugin.PluginListOf
getParentSBase() - Method in class jp.sbi.celldesigner.plugin.PluginSBase
getParentSBaseID() - Method in class jp.sbi.celldesigner.plugin.PluginParameter
getParentUnitDefinition() - Method in class jp.sbi.celldesigner.plugin.PluginUnit
getPluginBindingRegion(int) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Gets the PluginBindingRegion with the given index.
getPluginInformationBox() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getPluginInformationBox() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getPluginListOfStructuralStates() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Gets a list of PluginStructuralStates
getPluginModificationRegion(int) - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
  Gets the PluginModificationRegion with the given index.
getPluginModificationRegion(int) - Method in class jp.sbi.celldesigner.plugin.PluginGene
  Gets the PluginModificationRegion with the given index.
getPluginModificationRegion(int) - Method in class jp.sbi.celldesigner.plugin.PluginRNA
  Gets the PluginModificationRegion with the given index.
getPluginModificationResidue(int) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Gets the PluginModificationResidue with the given index.
getPluginSpeciesAlias(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets PluginSpeciesAlias with the given id.
getPointsInLine() - Method in class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
  Get all the key points information in the line of the link.
getPos() - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
getPositionToCompartment() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getProcessNodeIdx() - Method in class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
  Get the process node index which rely on the index of the subline included process node in BaseReactionLink if this link have process node.
getProduct(int) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Gets the Product (PluginSpeciesReference) of this PluginReaction with the given index.
getProtein(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginProtein with the given id.
getProtein() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getproteomicsRadioButton() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
getPureSBMLString() - Method in class jp.sbi.celldesigner.plugin.PluginModel
getReactant(int) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Gets the Reactant (PluginSpeciesReference) with the given index from this PluginReaction.
getReaction(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginReaction with the given index.
getReaction(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginReaction with the given id.
getReactionLinkMembers() - Method in class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
  Get the members of this link, for instance the members will be Add_reactant, Add_product, modification link, gate link information, if this link is BaseReactionLink.
getReactionType() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getReferenceGStructure() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getReferenceType() - Method in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
getRefsOfGateInReaction() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
getRelationFromCVTerm(CVTerm) - Static method in class jp.sbi.celldesigner.plugin.PluginSBase
getRelationsAndIDCols() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getRepaintBounds() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
getResidue() - Method in class jp.sbi.celldesigner.plugin.PluginModification
getReversible() - Method in class jp.sbi.celldesigner.plugin.PluginReaction
getRNA(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginRNA with the given id.
getRNA() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getRsltDtBindingFrm() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
getRule(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginRule with the given index from the list.
getScale() - Method in class jp.sbi.celldesigner.plugin.PluginUnit
getSelectedAllNode() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getSelectedAllNode(PluginModel) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getSelectedCompartmentNode() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getSelectedCompartmentNode(PluginModel) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getSelectedModel() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getSelectedReactionNode() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getSelectedReactionNode(PluginModel) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getSelectedSpeciesNode() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getSelectedSpeciesNode(PluginModel) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
getSide() - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
getSimpleColorSettingWinFrm() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
getSize() - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
  get size
getSize() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getSize() - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
getSize() - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  gets size
getSpatialDimensions() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getSpatialSizeUnits() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getSpecies(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginSpecies with the given index.
getSpecies(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginSpecies with the given id.
getSpecies() - Method in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
getSpecies() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getSpeciesAlias(int) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getSpeciesAlias(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getSpeciesAliases() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
getSpeciesInstance() - Method in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
getSpeciesType(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getSpeciesType(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
getSpeciesType() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getSpeciesTypeComboBox() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
getState() - Method in class jp.sbi.celldesigner.plugin.PluginModification
getState() - Method in class jp.sbi.celldesigner.plugin.PluginStructuralState
getStateString() - Method in class jp.sbi.celldesigner.plugin.PluginInformationBox
getStoichiometry() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesReference
getStoichiometryMath() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesReference
getSubstanceUnits() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
getSubstanceUnits() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getSymbol() - Method in class jp.sbi.celldesigner.plugin.PluginInitialAssignment
getText() - Method in class jp.sbi.celldesigner.plugin.PluginMenu
getText() - Method in class jp.sbi.celldesigner.plugin.PluginMenuItem
getThickness() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getTimeUnits() - Method in class jp.sbi.celldesigner.plugin.PluginEvent
getTimeUnits() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
getTrigger() - Method in class jp.sbi.celldesigner.plugin.PluginEvent
getType() - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
getType() - Method in class jp.sbi.celldesigner.plugin.PluginAssignmentRule
getType() - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
  get type
getType() - Method in class jp.sbi.celldesigner.plugin.PluginGene
getType() - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
getType() - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  gets type
getType() - Method in class jp.sbi.celldesigner.plugin.PluginProtein
getType() - Method in class jp.sbi.celldesigner.plugin.PluginRNA
getType() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getTypeOfLine() - Method in class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
  Get the type of the Link, only Add_reactant and Add_product has this type, which is Curve or Straight based on the property of the link.
getUnit(int) - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
  Gets the PluginUnit with the given index.
getUnitDefinition(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginUnitDefinition with the given index.
getUnitDefinition(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Gets the PluginUnitDefinition with the given id.
getUnits() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getUnits() - Method in class jp.sbi.celldesigner.plugin.PluginParameter
getUnits() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
getUserDefaultEndColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
getUserDefaultMidColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
getUserDefaultStartColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
getUseValuesFromTriggerTime() - Method in class jp.sbi.celldesigner.plugin.PluginEvent
getValue() - Method in class jp.sbi.celldesigner.plugin.PluginParameter
getVariable() - Method in class jp.sbi.celldesigner.plugin.PluginAssignmentRule
getVariable() - Method in class jp.sbi.celldesigner.plugin.PluginEventAssignment
getVariable() - Method in class jp.sbi.celldesigner.plugin.PluginRateRule
getVolume() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getWidth() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getWidth() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getX() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getX() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
getY() - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
getY() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
giveMeNewID() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
giveMeOutputFileName(String, String) - Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm

## H

havehadAMappingArrayMassShowerMainWinFrmInstanceInCurrentGStructure(boolean) - Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
haveInputedData() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
havePhenotypeInSrouce(PluginSBase) - Static method in class jp.sbi.celldesigner.plugin.PluginReaction
HETERODIMER_ASSOCIATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  HETERODIMER_ASSOCIATION
HOMODIMER_FORMATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  HOMODIMER_FORMATION

## I

iCmpColNum - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
iCurrentModel - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
iMappingArrayMassMarginBetweenRect3DAndMsg - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
iMappingArrayMassRect3DDisplayerHeight - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
iMappingArrayMassRect3DDisplayerWidth - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
iMcsColNum - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
iMicroArrayDataType - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
iMpkColNum - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
iNewModel - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
InformationDisplayerAbst - Class in jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer
InformationDisplayerAbst() - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
InformationElementImpl - Interface in jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer
InformationShowerImpl - Interface in jp.sbi.celldesigner.plugin.InfoCenter.InfoShower
InformationShowerMappingArrayMass - Class in jp.sbi.celldesigner.plugin.InfoCenter.InfoShower
InformationShowerMappingArrayMass(SBModelFrame) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
InformationShowerMappingArrayMass(SBModelFrame, JFrame) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
InformationShowerMappingArrayMass(SBModelFrame, JFrame, String[][], String[][], double, double) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
InformationShowerMappingArrayMass(SBModelFrame, JFrame, String[][], String[][], int, double, double) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
InformationShowerMappingArrayMass(SBModelFrame, JFrame, String[][], String[][], int, int, double, double) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
InformationShowerMappingArrayMass(SBModelFrame, JFrame, String[][], String[][], int, int, Color, Color, Color, double, double) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
INHIBITION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  INHIBITION
initDialog() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassAnimOutputOptionFrm
initDialog(boolean, int, int, boolean) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
initDialogUsing(MappingArrayMassShowerMainWinFrm) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassAnimOutputOptionFrm
initMappingArrayMassShowerConfigWinFrm(Color, Color, Color, double, double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
inShape(double, double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
iNSpColNum - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
intersects(Rectangle2D.Double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
ION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  ION
iOpenXmlFile - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
iProteomicsDataType - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
isActive() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
isCanceled() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassAnimOutputOptionFrm
isCanceled() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
isCanceled() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
isHighlighted() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
isOutputGif() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
isOutputMovie() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
iSpIColNum - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
iSpNColNum - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
iSptColNum - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
isReferenceSameModel(PluginSBase) - Method in class jp.sbi.celldesigner.plugin.PluginModel
isSameModel(Model) - Method in class jp.sbi.celldesigner.plugin.PluginModel
isScaleOutputGif() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
isScaleOutputMovie() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
isSetInitialAmount() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
isSetInitialConcentration() - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
isShowGuideMsg() - Method in class jp.sbi.celldesigner.plugin.PluginMassShowerAction
isShowGuideMsg() - Method in class jp.sbi.celldesigner.plugin.PluginOpenFileAndDoSomethingAction
isStarted() - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
isStarted() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
isValidCompartmentType(PluginCompartment) - Static method in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
isValidModifierType(PluginSimpleSpeciesReference) - Static method in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
isValidProteinsType(PluginProtein) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
isValidReaction(PluginReaction) - Static method in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
isValidReactionType(PluginReaction) - Static method in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
isValidSpeciesAliasType(PluginSpeciesAlias) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
isValidSpeciesType(PluginSpecies) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
isVisible(SBModelFrame, GStructure) - Method in interface jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerImpl
isVisible(SBModelFrame, GStructure) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
IsWinBeenUsing() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm

## J

jp.sbi.celldesigner.plugin - package jp.sbi.celldesigner.plugin
jp.sbi.celldesigner.plugin.DataObject - package jp.sbi.celldesigner.plugin.DataObject
jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer - package jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer
jp.sbi.celldesigner.plugin.InfoCenter.InfoShower - package jp.sbi.celldesigner.plugin.InfoCenter.InfoShower
jp.sbi.celldesigner.plugin.InfoCenter.InfoUI - package jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
jp.sbi.celldesigner.plugin.simulation - package jp.sbi.celldesigner.plugin.simulation
jp.sbi.celldesigner.plugin.util - package jp.sbi.celldesigner.plugin.util

## K

KNOWN_TRANSITION_OMITTED - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  KNOWN_TRANSITION_OMITTED

## M

main(String[]) - Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
MappingArrayMassShowerConfigWinFrm - Class in jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
MappingArrayMassShowerConfigWinFrm() - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
MappingArrayMassShowerConfigWinFrm(Color, Color, Color, double, double) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
MappingArrayMassShowerMainWinFrm - Class in jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
MappingArrayMassShowerMainWinFrm(RsltDtTpMdlSelectFrm, RsltDtBindingFrm, boolean) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
MappingArrayMassShowerMainWinFrm(Color, Color, Color) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
MassAnimOutputOptionFrm - Class in jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
MassAnimOutputOptionFrm(JFrame) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassAnimOutputOptionFrm
  This method initializes
MassOutputAnimationTask - Class in jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
MassOutputAnimationTask(JFrame, JFrame, ProcessBarFrm, MappingArrayMassShowerMainWinFrm.restoreUI) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MassOutputAnimationTask
MINIMUM_SIZE_ANY - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  constants for minimum size
MINIMUM_SIZE_DNAMETYLATION - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  constants for minimum size
MINIMUM_SIZE_EMPTY - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  constants for minimum size
modelBase - Variable in class jp.sbi.celldesigner.plugin.PluginModel
modelClosed(PluginSBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when Model is closed on CellDesigner.
modelClosed(SBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when Model is closed on CellDesigner.
modelClosed(SBase) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
modelOpened(PluginSBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when Model is opened on CellDesigner.
modelOpened(SBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when Model is opened on CellDesigner.
modelOpened(SBase) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
modelSelectChanged(PluginSBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when the selected Model is changed on CellDesigner.
modelSelectChanged(SBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when the selected Model is changed on CellDesigner.
modelSelectChanged(SBase) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
MODIFIER - Static variable in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
  ReferenceType "MODIFIER"
MODULATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
MShowerMain - Class in jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
MShowerMain(RsltDtTpMdlSelectFrm, RsltDtBindingFrm, boolean) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MShowerMain
myActionPerformed(ActionEvent) - Method in interface jp.sbi.celldesigner.plugin.PluginActionListener
  Called when the plug-in menu is clicked on CellDesigner.

## N

NEGATIVE_INFLUENCE - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
notifySBaseAdded(PluginSBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Notifies CellDesigner when SBase is added.
notifySBaseAdded(PluginSBase) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  notifySBaseAdded
notifySBaseChanged(PluginSBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Notifies CellDesigner when some properties of SBase are changed.
notifySBaseChanged(PluginSBase) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  notifySBaseChanged
notifySBaseDeleted(PluginSBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Notifies CellDesigner when SBase is deleted.
notifySBaseDeleted(PluginSBase) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  notifySBaseDeleted

## O

onEdge(double, double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
openXlsFile(Component) - Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
OpenXlsFileErrorMsg - Static variable in class jp.sbi.celldesigner.plugin.PluginMassShowerAction
OVAL - Static variable in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  OVAL

## P

PHENOTYPE - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  PHENOTYPE
PHYSICAL_STIMULATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
PluginAction - Class in jp.sbi.celldesigner.plugin
  Interface of the action class of the plug-in menu.
PluginAction() - Constructor for class jp.sbi.celldesigner.plugin.PluginAction
PluginActionListener - Interface in jp.sbi.celldesigner.plugin
  PluginActionListener
PluginAlgebraicRule - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.AlgebraicRule for the plug-in.
PluginAlgebraicRule(PluginModel) - Constructor for class jp.sbi.celldesigner.plugin.PluginAlgebraicRule
  Constructor
PluginAntiSenseRNA - Class in jp.sbi.celldesigner.plugin
  This class represents anti sense RNA.
PluginAntiSenseRNA() - Constructor for class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
  Constructor
PluginAntiSenseRNA(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
  Constructor
PluginAssignmentRule - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.AssignmentRule for the plug-in.
PluginAssignmentRule(PluginModel) - Constructor for class jp.sbi.celldesigner.plugin.PluginAssignmentRule
  Constructor
PluginBindingRegion - Class in jp.sbi.celldesigner.plugin
  Class for modification bindingRegion.
PluginBindingRegion(PluginProtein) - Constructor for class jp.sbi.celldesigner.plugin.PluginBindingRegion
  Constructor
PluginCloneModelDoSthAction - Class in jp.sbi.celldesigner.plugin
PluginCloneModelDoSthAction() - Constructor for class jp.sbi.celldesigner.plugin.PluginCloneModelDoSthAction
PluginCompartment - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.Compartment for the plug-in.
PluginCompartment(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginCompartment
  Constructor
PluginCompartment(String, String) - Constructor for class jp.sbi.celldesigner.plugin.PluginCompartment
  Constructor
PluginCompartmentSymbolType - Class in jp.sbi.celldesigner.plugin.util
  This class defines CompartmentType for PluginCompartment.
PluginCompartmentSymbolType() - Constructor for class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
PluginCompartmentType - Class in jp.sbi.celldesigner.plugin
PluginCompartmentType(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginCompartmentType
PluginConstraint - Class in jp.sbi.celldesigner.plugin
PluginConstraint(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginConstraint
PluginCreateModelDoSthAction - Class in jp.sbi.celldesigner.plugin
PluginCreateModelDoSthAction() - Constructor for class jp.sbi.celldesigner.plugin.PluginCreateModelDoSthAction
PluginDoSthAbstractAction - Class in jp.sbi.celldesigner.plugin
PluginDoSthAbstractAction() - Constructor for class jp.sbi.celldesigner.plugin.PluginDoSthAbstractAction
PluginEvent - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.Event for the plug-in.
PluginEvent(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginEvent
  Constructor
PluginEventAssignment - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.EventAssignment for the plug-in.
PluginEventAssignment(PluginEvent) - Constructor for class jp.sbi.celldesigner.plugin.PluginEventAssignment
  Constructor
PluginFunctionDefinition - Class in jp.sbi.celldesigner.plugin
PluginFunctionDefinition(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginFunctionDefinition
  Constructor
PluginGene - Class in jp.sbi.celldesigner.plugin
  This class represents gene.
PluginGene() - Constructor for class jp.sbi.celldesigner.plugin.PluginGene
  Constructor
PluginGene(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginGene
  Constructor
PluginGLogicGate - Class in jp.sbi.celldesigner.plugin
PluginGLogicGate(PluginReaction, Vector) - Constructor for class jp.sbi.celldesigner.plugin.PluginGLogicGate
PluginGLogicGate(PluginReaction, Vector, String) - Constructor for class jp.sbi.celldesigner.plugin.PluginGLogicGate
PluginGLogicGate(PluginReaction, Vector, String, String) - Constructor for class jp.sbi.celldesigner.plugin.PluginGLogicGate
PluginInformationBox - Class in jp.sbi.celldesigner.plugin
PluginInformationBox() - Constructor for class jp.sbi.celldesigner.plugin.PluginInformationBox
PluginInitialAssignment - Class in jp.sbi.celldesigner.plugin
PluginInitialAssignment(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginInitialAssignment
PluginKineticLaw - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.KineticLaw for the plug-in.
PluginKineticLaw(PluginReaction) - Constructor for class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Constructor
PluginListOf - Class in jp.sbi.celldesigner.plugin
  This class wraps ListOf for the plug-in.
PluginListOf() - Constructor for class jp.sbi.celldesigner.plugin.PluginListOf
  Constructor
PluginListOf(PluginSBase) - Constructor for class jp.sbi.celldesigner.plugin.PluginListOf
  Constructor
PluginMassShowerAction - Class in jp.sbi.celldesigner.plugin
PluginMassShowerAction() - Constructor for class jp.sbi.celldesigner.plugin.PluginMassShowerAction
PluginMenu - Class in jp.sbi.celldesigner.plugin
  This class wraps JMenu for the plug-in.
PluginMenu() - Constructor for class jp.sbi.celldesigner.plugin.PluginMenu
  Constructor
PluginMenu(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginMenu
  Constructor
PluginMenu(PluginAction) - Constructor for class jp.sbi.celldesigner.plugin.PluginMenu
  Constructor
PluginMenu(String, PluginAction) - Constructor for class jp.sbi.celldesigner.plugin.PluginMenu
  Constructor
PluginMenu(String, PluginOpenFileAndDoSomethingAction) - Constructor for class jp.sbi.celldesigner.plugin.PluginMenu
PluginMenuItem - Class in jp.sbi.celldesigner.plugin
  This class wraps JMenuItem for the plug-in.
PluginMenuItem(String, PluginAction) - Constructor for class jp.sbi.celldesigner.plugin.PluginMenuItem
  Constructor
PluginMenuItem(String, PluginDoSthAbstractAction) - Constructor for class jp.sbi.celldesigner.plugin.PluginMenuItem
PluginModel - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.Model for the plug-in.
PluginModel(Model) - Constructor for class jp.sbi.celldesigner.plugin.PluginModel
  Constructor
PluginModelBuilder - Class in jp.sbi.celldesigner.plugin
PluginModelBuilder(SBModel) - Constructor for class jp.sbi.celldesigner.plugin.PluginModelBuilder
PluginModification - Class in jp.sbi.celldesigner.plugin
  ProteinModification An instance represents <modification> tag.
PluginModification() - Constructor for class jp.sbi.celldesigner.plugin.PluginModification
  Constructor
PluginModification(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginModification
  Constructor
PluginModification(String, String) - Constructor for class jp.sbi.celldesigner.plugin.PluginModification
  Constructor
PluginModificationRegion - Class in jp.sbi.celldesigner.plugin
  Class for region.
PluginModificationRegion(PluginGene) - Constructor for class jp.sbi.celldesigner.plugin.PluginModificationRegion
  Constructor
PluginModificationRegion(PluginRNA) - Constructor for class jp.sbi.celldesigner.plugin.PluginModificationRegion
  Constructor
PluginModificationRegion(PluginAntiSenseRNA) - Constructor for class jp.sbi.celldesigner.plugin.PluginModificationRegion
  Constructor
PluginModificationResidue - Class in jp.sbi.celldesigner.plugin
  Class for modification residue.
PluginModificationResidue(PluginProtein) - Constructor for class jp.sbi.celldesigner.plugin.PluginModificationResidue
  Constructor
PluginModifierSpeciesReference - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.ModifierSpeciesReference for the plug-in.
PluginModifierSpeciesReference(PluginReaction, PluginSpeciesAlias) - Constructor for class jp.sbi.celldesigner.plugin.PluginModifierSpeciesReference
  Constructor
PluginOpenFileAndDoSomethingAction - Class in jp.sbi.celldesigner.plugin
PluginOpenFileAndDoSomethingAction() - Constructor for class jp.sbi.celldesigner.plugin.PluginOpenFileAndDoSomethingAction
PluginParameter - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.Parameter for the plug-in.
PluginParameter(PluginKineticLaw) - Constructor for class jp.sbi.celldesigner.plugin.PluginParameter
  Constructor case of local parameter
PluginParameter(PluginModel) - Constructor for class jp.sbi.celldesigner.plugin.PluginParameter
  Constructor case of global parameter
PluginParameter(String, PluginKineticLaw) - Constructor for class jp.sbi.celldesigner.plugin.PluginParameter
  Constructor case of local parameter
PluginParameter(String, PluginModel) - Constructor for class jp.sbi.celldesigner.plugin.PluginParameter
  Constructor case of global parameter
PluginProtein - Class in jp.sbi.celldesigner.plugin
  This class represents Protein.
PluginProtein() - Constructor for class jp.sbi.celldesigner.plugin.PluginProtein
  Constructor
PluginProtein(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginProtein
  Constructor
PluginRateRule - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.RateRule for the plug-in.
PluginRateRule(PluginModel) - Constructor for class jp.sbi.celldesigner.plugin.PluginRateRule
  Constructor
PluginReaction - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.Reaction for the plug-in.
PluginReaction() - Constructor for class jp.sbi.celldesigner.plugin.PluginReaction
  Constructor
PluginReaction(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginReaction
  Constructor
PluginReactionSymbolType - Class in jp.sbi.celldesigner.plugin.util
  This class defines ReactionType for PluginReaction.
PluginReactionSymbolType() - Constructor for class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
PluginRealLineInformationDataObjOfReactionLink - Class in jp.sbi.celldesigner.plugin.DataObject
  ReactionLink Line information Class
PluginRealLineInformationDataObjOfReactionLink() - Constructor for class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
PluginRNA - Class in jp.sbi.celldesigner.plugin
  This class represents RNA.
PluginRNA() - Constructor for class jp.sbi.celldesigner.plugin.PluginRNA
  Constructor
PluginRNA(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginRNA
  Constructor
PluginRule - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.Rule for the plug-in.
PluginRule() - Constructor for class jp.sbi.celldesigner.plugin.PluginRule
PluginSBase - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.SBase for the plug-in.
PluginSBase() - Constructor for class jp.sbi.celldesigner.plugin.PluginSBase
  Constructor
PluginSBaseConverter - Class in jp.sbi.celldesigner.plugin
  PluginSBaseConverter
PluginSBaseConverter() - Constructor for class jp.sbi.celldesigner.plugin.PluginSBaseConverter
PluginSimpleSpeciesReference - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.SimpleSpeciesReference for the plug-in.
PluginSimpleSpeciesReference(PluginSpeciesAlias) - Constructor for class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
  Constructor
PluginSimulation - Class in jp.sbi.celldesigner.plugin.simulation
PluginSimulation(PluginModel) - Constructor for class jp.sbi.celldesigner.plugin.simulation.PluginSimulation
PluginSimulation(PluginModel, double, long) - Constructor for class jp.sbi.celldesigner.plugin.simulation.PluginSimulation
PluginSpecies - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.Species for the plug-in.
PluginSpecies(String, String) - Constructor for class jp.sbi.celldesigner.plugin.PluginSpecies
  Constructor
PluginSpecies() - Constructor for class jp.sbi.celldesigner.plugin.PluginSpecies
  Constructor
PluginSpeciesAlias - Class in jp.sbi.celldesigner.plugin
  PluginSpeciesAlias has drawing information such as position, color, name and type.
PluginSpeciesAlias(PluginSpecies, String) - Constructor for class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Constructor
PluginSpeciesAlias(SpeciesAlias, PluginSpecies) - Constructor for class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Constructor
PluginSpeciesReference - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.SpeciesReference for the plug-in.
PluginSpeciesReference(PluginReaction, PluginSpeciesAlias) - Constructor for class jp.sbi.celldesigner.plugin.PluginSpeciesReference
  Constructor
PluginSpeciesSymbolType - Class in jp.sbi.celldesigner.plugin.util
  This class defines ReactionType for PluginReaction.
PluginSpeciesSymbolType() - Constructor for class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
PluginSpeciesType - Class in jp.sbi.celldesigner.plugin
PluginSpeciesType(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginSpeciesType
PluginStructuralState - Class in jp.sbi.celldesigner.plugin
PluginStructuralState() - Constructor for class jp.sbi.celldesigner.plugin.PluginStructuralState
PluginSystemOutUtils - Class in jp.sbi.celldesigner.plugin.util
PluginSystemOutUtils() - Constructor for class jp.sbi.celldesigner.plugin.util.PluginSystemOutUtils
PluginUnit - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.Unit for the plug-in.
PluginUnit(PluginUnitDefinition) - Constructor for class jp.sbi.celldesigner.plugin.PluginUnit
  Constructor
PluginUnitDefinition - Class in jp.sbi.celldesigner.plugin
  This class wraps org.sbml.libsbml.UnitDefinition for the plug-in.
PluginUnitDefinition(String) - Constructor for class jp.sbi.celldesigner.plugin.PluginUnitDefinition
  Constructor
popupAvailable() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
POSITIVE_INFLUENCE - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
printDebugInfoOfRealLineInformationOfReactionLink(PluginRealLineInformationDataObjOfReactionLink, int) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSystemOutUtils
processMyAction(ActionEvent) - Method in class jp.sbi.celldesigner.plugin.PluginDoSthAbstractAction
processWindowEvent(WindowEvent) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
processWindowEvent(WindowEvent) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
PRODUCT - Static variable in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
  ReferenceType "PRODUCT"
PROTEIN - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  PROTEIN
PROTEIN_GENERIC - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  GENERIC
PROTEIN_ION_CHANNEL - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  ION_CHANNEL
PROTEIN_RECEPTOR - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  RECEPTOR
PROTEIN_TRUNCATED - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  TRUNCATED

## R

REACTANT - Static variable in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
  ReferenceType "REACTANT"
ReadDataErrorMsg - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
recreateMappingArrayMassDisplayers(String[][], String[][], int, int, Color, Color, Color, double, double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
REDUCED_MODULATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
REDUCED_PHYSICAL_STIMULATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
REDUCED_TRIGGER - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
remove(int) - Method in class jp.sbi.celldesigner.plugin.PluginListOf
  Removes PluginSBase with the given index from this PluginListOf.
remove(PluginSBase) - Method in class jp.sbi.celldesigner.plugin.PluginListOf
  Removes the PluginSBase from this PluginListOf.
removeAntiSenseRNA(PluginAntiSenseRNA) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the given PluginAntiSenseRNA from the list.
removeAntiSenseRNA(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginAntiSenseRNA with the given index from the list.
removeCompartment(PluginCompartment) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the given PluginCompartment from the list.
removeCompartment(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginCompartment with the given id from the list.
removeCompartment(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginCompartment with the given index from the list.
removeCompartmentType(PluginCompartmentType) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeCompartmentType(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeCompartmentType(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeConstraint(PluginConstraint) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeConstraint(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeConstraint(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeEvent(PluginEvent) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the given PluginEvent from the list.
removeEvent(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Remove the PluginEvent with the given id.
removeEvent(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginEvent with the given index.
removeEventAssignment(PluginEventAssignment) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
  Removes a PluginEventAssignment from the list.
removeEventAssignment(int) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
  Removes the PluginAssignment with the given index from the list.
removeFunctionDefinition(PluginFunctionDefinition) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the given PluginFunctionDefinition from the list.
removeFunctionDefinition(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginFunctionDefinition with the given id from the list.
removeFunctionDefinition(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginFunctionDefinition with the given index from the list.
removeGene(PluginGene) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the given PluginGene from the list.
removeGene(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginGene with the given index from the list.
removeGLogicGate(int) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
removeGLogicGate(PluginGLogicGate) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
removeInitialAssignment(PluginInitialAssignment) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeInitialAssignment(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeInitialAssignment(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeModifier(PluginModifierSpeciesReference) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Removes a PluginModifierSpeciesReference from this PluginReaction.
removeModifier(int) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Removes the PluginModifierSpeciesReference from this PluginReaction.
removeParameter(PluginParameter) - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Removes the PluginParameter from the list of PluginParameter of this PluginKineticLaw.
removeParameter(int) - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Remove the PluginParameter with the given index from the list.
removeParameter(PluginParameter) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Remove the given PluginParameter from the list.
removeParameter(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Remove the PluginParameter with the given id.
removeParameter(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginParameter with the given index to the list.
removePluginBindingRegion(PluginBindingRegion) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Removes the given PluginBindingRegion from the list.
removePluginBindingRegion(int) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Removes the PluginBindingRegion with the given index from the list.
removePluginModificationRegion(PluginModificationRegion) - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
  Removes the given PluginModificationRegion.
removePluginModificationRegion(int) - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
  Remove the PluginModificationRegion with the given index.
removePluginModificationRegion(PluginModificationRegion) - Method in class jp.sbi.celldesigner.plugin.PluginGene
  Removes the given PluginModificationRegion from the list.
removePluginModificationRegion(int) - Method in class jp.sbi.celldesigner.plugin.PluginGene
  Removes the PluginModificationRegion with the given index from the list.
removePluginModificationRegion(PluginModificationRegion) - Method in class jp.sbi.celldesigner.plugin.PluginRNA
  Removes the given PluginModificationRegion from this PluginRNA.
removePluginModificationRegion(int) - Method in class jp.sbi.celldesigner.plugin.PluginRNA
  Removes the PluginModificationRegion with the given index from this PluginRNA.
removePluginModificationResidue(PluginModificationResidue) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Removes the given PluginModificationResidue from the list.
removePluginModificationResidue(int) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Removes the PluginModificationResidue with the given index from the list.
removeProduct(PluginSpeciesReference) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Removes the given Product (PluginSpeciesReference) from this PluginReaction.
removeProduct(int) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Removes the Product (PluginSpeciesReference) with the given index from this PluginReaction.
removeProtein(PluginProtein) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the given PluginProtein from the list.
removeProtein(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginProtein with the given index.
removeReactant(PluginSpeciesReference) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Removes the given Reactant (PluginSpeciesReference) from this PluginReaction.
removeReactant(int) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Removes the Reactant with the given index from this PluginReaction.
removeReaction(PluginReaction) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the given PluginReaction from the list.
removeReaction(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginReaction with the given id from the list.
removeReaction(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginReaction with the given index from the list.
removeRNA(PluginRNA) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Adds a PluginRNA to the list
removeRNA(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginRNA with the given index from the list.
removeRule(PluginRule) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the given PluginRule from the list.
removeRule(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginRule with the given index from the list.
removeSpecies(String) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
removeSpecies(PluginSpecies) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
removeSpecies(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginSpecies with the given id from the list
removeSpecies(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginSpecies with the given index from the list.
removeSpeciesAlias(int) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
removeSpeciesAlias(int) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Removes PluginSpeciesAlias from this Species.
removeSpeciesAlias(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Removes PluginSpeciesAlias from this Species.
removeSpeciesType(PluginSpeciesType) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeSpeciesType(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeSpeciesType(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
removeUnit(PluginUnit) - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
  Removes the PluginUnit from this PluginUnitDefinition.
removeUnit(int) - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
  Removes the PluginUnit with the given index from this PluginUnitDefinition.
removeUnitDefinition(PluginUnitDefinition) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Remove the given PluginUnitDefinition from the list.
removeUnitDefinition(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Removes the PluginUnitDefinition with the given id from the list.
removeUnitDefinition(int) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Remove the PluginUnitDefinition with the given index from the list.
renewDisplayersArray() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
repaintPreviewColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
repaintPreviewColor() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
resetAllIncludedPluginSpeciesAliases(PluginModel, PluginSpeciesAlias) - Static method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
resetDataAndCompentsInThisWinFrm() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
resetStateString() - Method in class jp.sbi.celldesigner.plugin.PluginInformationBox
restoreUIafterAnimOut(MappingArrayMassShowerMainWinFrm.restoreUI) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
RNA - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  RNA
RsltDtBindingFrm - Class in jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
RsltDtBindingFrm(Frame, File, List, int, int) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
RsltDtTpMdlSelectFrm - Class in jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
RsltDtTpMdlSelectFrm(Frame) - Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtTpMdlSelectFrm
runSimulation() - Method in class jp.sbi.celldesigner.plugin.simulation.PluginSimulation

## S

sbase - Variable in class jp.sbi.celldesigner.plugin.PluginSBase
  sbase
SBaseAdded(PluginSBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when a PluginSBase is added on CellDesigner.
SBaseAdded(SBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when SBase is added on CellDesigner.
SBaseAdded(SpeciesAlias, Species) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when SBase is added on CellDesigner.
SBaseAdded(SBase) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
SBaseAdded(SpeciesAlias, Species) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
SBaseChanged(PluginSBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when some properties of PluginSBase are changed on CellDesigner.
SBaseChanged(SBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when some properties of SBase are changed on CellDesigner.
SBaseChanged(SpeciesAlias, Species) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when some properties of SBase are changed on CellDesigner.
SBaseChanged(SBase) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
SBaseChanged(SpeciesAlias, Species) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
SBaseDeleted(PluginSBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when PluginSBase is deleted on CellDesigner.
SBaseDeleted(SBase) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when SBase is deleted on CellDesigner.
SBaseDeleted(SpeciesAlias, Species) - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
  Called when SBase is deleted on CellDesigner.
SBaseDeleted(SBase) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
SBaseDeleted(SpeciesAlias, Species) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
SBaseSelected() - Method in interface jp.sbi.celldesigner.plugin.CellDesignerPlug
SBaseSelected() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
setActive(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  Sets a state for transcriptional starting site.
setAlias(PluginSpeciesAlias) - Method in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
  Sets the PluginSpeciesAlias of this PluginSimpleSpeciesReference
setAllIncludedSpeciesAliases(Vector) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
setAngle(double) - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
  Sets the angle of this PluginBindingRegion.
setAngle(double) - Method in class jp.sbi.celldesigner.plugin.PluginInformationBox
setAngle(double) - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  Sets the angle of this PluginModificationResidue.
setAngle(double) - Method in class jp.sbi.celldesigner.plugin.PluginStructuralState
setAnnotation(XMLNode) - Method in class jp.sbi.celldesigner.plugin.PluginSBase
setAnnotationString(String) - Method in class jp.sbi.celldesigner.plugin.PluginSBase
setAntiSenseRNA(PluginAntiSenseRNA) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the PluginAntiSenseRNA of this PluginSpeciesAlias.
setAuxDatas(String[][]) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
setBoundaryCondition(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the boundaryCondition of this PluginSpecies.
setCharge(int) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the charge of this PluginSpecies.
setColor(String, Color, Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
setColor(Color) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
  Sets the color of this GLogicGate.
setColor(Color) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the color of this PluginSpeciesAlias.
setCompartment(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the compartment of this PluginSpecies.
setCompartmentType(String) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the type of this PluginCompartment.
setCompartmentTypeOfPanel(String) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
setConstant(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets true if this PluginCompartment is constant
setConstant(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginParameter
  Sets the constant of this PluginParameter.
setConstant(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the constant of this PluginSpecies.
setCursorBySpecification(Cursor) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
setCVTerm(XMLNode) - Method in class jp.sbi.celldesigner.plugin.PluginSBase
setDatasOfAllSheet(List) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
setDataType(int) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
setDelay(ASTNode) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
  Sets the delay of this PluginEvent to the given ASTNode.
setDelay(Delay) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
setEnable(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginMenu
  Sets the enable status of this PluginMenu to true if this PluginMenu is enabled.
setEnable(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginMenuItem
  Sets true if this PluginMenuItem is enabled
setEndTime(double) - Method in class jp.sbi.celldesigner.plugin.simulation.PluginSimulation
setExponent(int) - Method in class jp.sbi.celldesigner.plugin.PluginUnit
  Sets the exponent of this PluginUnit.
setFast(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Sets the fast status of this PluginReaction to the given value (boolean)
setFile(File) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
setFirstRun(boolean) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
setFormula(String) - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Sets the formula of this PluginKineticLaw.
setFormula(String) - Method in class jp.sbi.celldesigner.plugin.PluginRule
  Sets the Formula of this PluginRule.
setFormulaFromMath() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Deprecated. setFormulaFromMath is removed in libSBML 3.x
setFrameLineWidth(double) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the FrameLineWidth of this PluginSpeciesAlias.
setFramePosition(double, double) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the position for this PluginSpeciesAlias.
setFrameSize(double, double) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the FrameSize (width & height) for this PluginSpeciesAlias
setFrmController(JFrame) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
setGateLink(ReactionLink) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
setGateSpeciesAliasesAndModificationType() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
setGateType(String) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
setGene(PluginGene) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the PluginGene of this PluginSpeciesAlias.
setGLogicGateType(String) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
setGraphicDisplayerFromInputData(String[][], String[][], boolean) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
setGraphicDisplayerFromInputData(String[][], String[][], int, Color, Color, Color, boolean) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
setHasOnlySubstanceUnits(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the HasOnlySubstanceUnits of this PluginSpecies.
setHeight(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the height of this PluginCompartment.
setHighlighted(boolean) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
setHomodimer(int) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the homodimer of this PluginSpeciesAlias.
setHypothetical(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the hypothetical of this PluginSpeciesAlias.
setId(String) - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
  Sets the id of this PluginBindingRegion.
setId(String) - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  Sets the id of this PluginModificationRegion.
setId(String) - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  Sets the id of this PluginModificationResidue.
setId(String) - Method in class jp.sbi.celldesigner.plugin.PluginParameter
  Sets the id of this PluginParameter.
setId(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the id of this PluginSpecies.
setInfoAll(String, String, String) - Method in class jp.sbi.celldesigner.plugin.PluginInformationBox
setInitialAmount(double) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the InitialAmount of this PluginSpecies.
setInitialConcentration(double) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the initialConcentration of this PluginSpecies.
setInnerPaintColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
setInnerPaintMode(String) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
setInnerWidth(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the InnerWidth of this PluginCompartment.
setIsActive(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets activity
setIsWinBeenUsing(boolean) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
setKind(int) - Method in class jp.sbi.celldesigner.plugin.PluginUnit
  Sets the kind of this PluginUnit.
setKind(String) - Method in class jp.sbi.celldesigner.plugin.PluginUnit
setKineticLaw(PluginKineticLaw) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Sets the PluginKineticLaw of this PluginReaction.
setL1TypeCode(int) - Method in class jp.sbi.celldesigner.plugin.PluginAssignmentRule
  Sets the type of this PluginAssignmentRule.
setLineColor(Color) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets a lineColor of this PluginCompartment.
setLineColor(Color) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Sets the lineColor of this PluginReaction.
setLineWidth(double) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
  Sets the line width of this GLogicGate.
setLineWidth(double) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Sets the line width of this PluginReaction.
setListOfAntiSenseRNAs(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginAntiSenseRNA of this PluginModel.
setListOfCompartments(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginCompartment of this PluginModel
setListOfCompartmentTypes(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
setListOfConstraints(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
setListOfEventAssignments(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
  Sets the list of PluginEventAssignment of this PluginEvent.
setListOfEvents(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginEvent of this PluginModel.
setListOfFunctionDefinitions(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginFunctionDefinition of this PluginModel.
setListOfGenes(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginGene of this PluginModel.
setListOfGLogicGates(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
setListOfInitialAssignments(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
setListOfModifiers(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Sets the list of PluginModifierSpeciesReference of this PluginReaction.
setListOfParameters(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Sets the list of PluginParameter of this PluginKineticLaw.
setListOfParameters(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginParameter of this PluginModel.
setListOfPluginBindingRegion(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Sets the list of PluginBindingRegion of this PluginProtein.
setListOfPluginRegion(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
  Sets the list of PluginModificationRegion
setListOfPluginRegion(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginGene
  Sets the list of PluginModificationRegion of this PluginGene.
setListOfPluginRegion(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginRNA
  Sets the list of PluginModificationRegion of this PluginRNA.
setListOfPluginResidue(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Sets the list of PluginModificationResidue of this PluginProtein.
setListOfProducts(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Sets the list of Products (PluginSpeciesReference) of this PluginReaction.
setListOfProteins(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginProtein of this PluginModel.
setListOfReactants(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Sets the list of Reactants (PluginSpeciesReference) of this PluginReaction.
setListOfReactions(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the PluginReaction of this PluginModel.
setListOfRNAs(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginRNA of this PluginModel.
setListOfRules(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginRule of this PluginModel.
setListOfSpecies(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginSpecies of this PluginModel.
setListOfSpeciesAlias(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets listOfPluginSpeciesAlias of this PluginSpecies.
setListOfSpeciesTypes(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
setListOfUnitDefinitions(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the list of PluginUnitDefinition of this PluginModel
setListOfUnits(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
  Sets the list of PluginUnit of this PluginUnitDefinition
setMassDatas(String[][]) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
setMath(ASTNode) - Method in class jp.sbi.celldesigner.plugin.PluginEventAssignment
  Sets the Math of this PluginEventAssignment to the given ASTNode
setMath(ASTNode) - Method in class jp.sbi.celldesigner.plugin.PluginFunctionDefinition
  Sets the Math of this PluginFunctionDefinition to the given ASTNode.
setMath(String) - Method in class jp.sbi.celldesigner.plugin.PluginInitialAssignment
setMath(ASTNode) - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Sets the Math of this PluginKineticLaw to the given ASTNode.
setMath(ASTNode) - Method in class jp.sbi.celldesigner.plugin.PluginRule
  Sets the Math of this PluginRule.
setMathFromFormula() - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Deprecated. setFormulaFromMath is removed in libSBML 3.x
setMaxVaule(double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
setMaxVaule(double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
setMaxVauleColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
setMaxVauleColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
setMaxVauleColorDirectly(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
setMessage(String) - Method in class jp.sbi.celldesigner.plugin.PluginConstraint
setMidPointInLine(Point2D.Double) - Method in class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
  Set the junction information of three linked lines if this link is three-linked line.
setMidVauleColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
setMidVauleColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
setMidVauleColorDirectly(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
setMinVaule(double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
setMinVaule(double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
setMinVauleColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
setMinVauleColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
setMinVauleColorDirectly(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
setMiriamDatas(Vector[]) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
setModelType(int) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
setModifications(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the list of PluginModification of this PluginSpeciesAlias.
setModificationType(String) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
setModificationType(String) - Method in class jp.sbi.celldesigner.plugin.PluginModifierSpeciesReference
  Sets the modificationType of this PluginModifierSpeciesReference.
setMultiplier(double) - Method in class jp.sbi.celldesigner.plugin.PluginUnit
  Sets the multiplier of this PluginUnit.
setMyPostionInfomations(GStructure, ReactionLink) - Static method in class jp.sbi.celldesigner.plugin.util.PluginSystemOutUtils
setName(String) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
  Sets the name of this PluginAntiSenseRNA
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
  Sets the name of this PluginBindingRegion.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the name of this PluginCompartment
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginCompartmentType
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
  Sets the name of this PluginEvent.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginFunctionDefinition
  Sets the name of this PluginFunctionDefinition.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginGene
  Sets the name of this PluginGene.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Sets the name of this PluginModel.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  Sets the name of this PluginModificationRegion
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  Sets the name of this PluginModificationResidue.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginParameter
  Sets the name of this PluginParameter.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Sets the name of this PluginProtein.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Sets the name of this PluginReaction.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginRNA
  Sets the name of this PluginRNA.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the name of this PluginSpecies.
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the name of this PluginSpeciesAlias
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesType
setName(String) - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
  Sets the name of this PluginUnitDefinition.
setNamePositionX(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets x position of this PluginCompartment name
setNamePositionY(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets y positon of this PluginCompartment name
setNotes(String) - Method in class jp.sbi.celldesigner.plugin.PluginSBase
  Sets the Notes of this PluginSBase.
setNotes(XMLNode) - Method in class jp.sbi.celldesigner.plugin.PluginSBase
setNumOfSteps(long) - Method in class jp.sbi.celldesigner.plugin.simulation.PluginSimulation
setOffset(double) - Method in class jp.sbi.celldesigner.plugin.PluginUnit
  Sets the offset of this PluginUnit.
setOldmiriamRelationIndex(int) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
setOpenFilename(String) - Method in class jp.sbi.celldesigner.plugin.PluginOpenFileAndDoSomethingAction
setOuterWidth(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the outerWidth of this PluginCompartment.
setOutputFile(String) - Method in class jp.sbi.celldesigner.plugin.simulation.PluginSimulation
setOutside(String) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the outside of this PluginCompartment
setOutterLineColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
setParent(Object) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
setParentReaction(PluginReaction) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
setParentSBase(PluginSBase) - Method in class jp.sbi.celldesigner.plugin.PluginSBase
  Sets the ParentSBase of this PluginSBase.
setPluginGLogicGateEventEnd() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
  If setPluginGLogicGateEventStart() method has been called, called after last notifySBaseXXX method.
setPluginGLogicGateEventStart() - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
  Must be called before first notifySBaseXXX method.
setPluginInformationBox(PluginInformationBox) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
setPluginInformationBox(PluginInformationBox) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
setPluginListOfStructuralStates(PluginListOf) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets a list of PluginStructuralStates
setPointsInLine(Vector) - Method in class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
  Set all the key points information in the line of the link.
setPos(double) - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  Sets the position of this PluginModificationRegion.
setPosition(double, double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
setPositionToCompartment(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the position of this PluginSpecies
setProcessNodeIdx(int) - Method in class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
  Set the process node index which rely on the index of the subline included processNode in BaseReactionLink if this link have process node.
setProtein(PluginProtein) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the PluginProtein of this PluginSpeciesAlias.
setReactionLinkMembers(Vector) - Method in class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
  Set the members of this link, for instance the members will be Add_reactant, Add_product, modification link, gate information.
setReactionType(String) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Sets the type of this PluginReaction.
setReferenceType(String) - Method in class jp.sbi.celldesigner.plugin.PluginSimpleSpeciesReference
  Sets the ReferenceType of this PluginSimpleSpeciesReference.
setRefsOfGateInReaction(SBModel, PluginGLogicGate) - Method in class jp.sbi.celldesigner.plugin.PluginGLogicGate
  Sets the references of the GLogicGate.
setResidue(String) - Method in class jp.sbi.celldesigner.plugin.PluginModification
  Sets the id of residue of this PluginModification.
setReversible(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Sets the reversible status of this PluginReaction to the given value (boolean).
setRNA(PluginRNA) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the PluginRNA of this PluginSpeciesAlias.
setSBModelFrameController(SBModelFrame) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
setScale(int) - Method in class jp.sbi.celldesigner.plugin.PluginUnit
  Sets the scale of this PluginUnit
setShowGuideMsgFlg(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginMassShowerAction
setShowGuideMsgFlg(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginOpenFileAndDoSomethingAction
setSide(String) - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  Sets the type of side of this PluginModificationResidue
setSize(double, double) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
setSize(double) - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
  set size
setSize(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the size of this PluginCompartment
setSize(double) - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  Sets the size of this PluginModificationRegion
setSize(double) - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  sets size
setSpatialDimensions(long) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets SpatialDimensions of this PluginCompartment If value is not one of [0, 1, 2, 3] the function will have no effect (i.e.
setSpatialSizeUnits(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the spatialSizeUnits of this PluginSpecies.
setSpecies(PluginSpecies) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the PluginSpecies of this PluginSpeciesAlias.
setSpeciesType(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
setStarted(boolean) - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
  Sets the start flag
  Note: Set true if a plugin is invoked.
setState(String) - Method in class jp.sbi.celldesigner.plugin.PluginModification
  Sets the state of this PluginModification to the given string.
setState(String) - Method in class jp.sbi.celldesigner.plugin.PluginStructuralState
setStoichiometry(double) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesReference
  Sets the stoichiometry of this PluginSpeciesReference.
setStoichiometryMath(StoichiometryMath) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesReference
  Sets the stoichiometryMath of this PluginSpeciesReference.
setStoichiometryMath(ASTNode) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesReference
setSubstanceUnits(String) - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Sets the substanceUnits of this PluginKineticLaw.
setSubstanceUnits(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the hasOnlySubstanceUnits field of this PluginSpecies.
setTargetGStructure() - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
setThickness(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets a thickness of this PluginCompartment.
setTimeUnits(String) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
  Sets the timeUnits of this PluginEvent to the given string.
setTimeUnits(String) - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Sets the timeUnits of this PluginKineticLaw.
setToolTipText(String) - Method in class jp.sbi.celldesigner.plugin.PluginMenu
  Sets the ToolTipText of this PluginMenu.
setToolTipText(String) - Method in class jp.sbi.celldesigner.plugin.PluginMenuItem
  Sets the ToolTipText of this PluginMenuItem.
setTrigger(ASTNode) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
  Sets the trigger of this PluginEvent to the given ASTNode.
setTrigger(Trigger) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
setType(String) - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
  Sets the type of this PluginAntiSenseRNA
setType(String) - Method in class jp.sbi.celldesigner.plugin.PluginBindingRegion
  set type
setType(String) - Method in class jp.sbi.celldesigner.plugin.PluginGene
  Sets the type of this PluginGene.
setType(String) - Method in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  Sets type of this PluginModificationRegion
setType(String) - Method in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  sets type
setType(String) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Sets the type of this PluginProtein.
setType(String) - Method in class jp.sbi.celldesigner.plugin.PluginRNA
  Sets the type of this PluginRNA.
setType(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Sets the type of this PluginSpeciesAlias.
setTypeOfLine(String) - Method in class jp.sbi.celldesigner.plugin.DataObject.PluginRealLineInformationDataObjOfReactionLink
  Set the type of the Link, only Add_reactant and Add_product has this type, which is Curve or Straight based on the property of the link.
setUnits(String) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the units of this PluginCompartment.
setUnits(String) - Method in class jp.sbi.celldesigner.plugin.PluginParameter
  Sets the unit of this PluginParameter.
setUnits(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Sets the units of this PluginSpecies
setUserDefaultEndColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
setUserDefaultMidColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
setUserDefaultStartColor(Color) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.InformationShowerMappingArrayMass
setUseValuesFromTriggerTime(boolean) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
setValue(double) - Method in class jp.sbi.celldesigner.plugin.PluginParameter
  Sets the value of this PluginParameter.
setVariable(String) - Method in class jp.sbi.celldesigner.plugin.PluginAssignmentRule
  Sets the variable of this PluginAssginmentRule
setVariable(String) - Method in class jp.sbi.celldesigner.plugin.PluginEventAssignment
  Sets the variable of this PluginEventAssignment to the given string.
setVariable(String) - Method in class jp.sbi.celldesigner.plugin.PluginRateRule
  Sets the variable of this PluginRateRule.
setVolume(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the volume of this PluginCompartment.
setWidth(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the width of this PluginCompartment.
setX(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the x position of this PluginCompartment.
setY(double) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Sets the y position of this PluginCompartment.
showNoticeMsg(String, int) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerConfigWinFrm
showPopup(MouseEvent, double, double, GStructure) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.InformationDisplayerAbst
SIDE_INSIDE - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  constants for side field
SIDE_NONE - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  constants for side field
SIDE_OUTSIDE - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  constants for side field
SIMPLE_MOLECULE - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  SIMPLE_MOLECULE
size() - Method in class jp.sbi.celldesigner.plugin.PluginListOf
SQUARE - Static variable in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  SQUARE
SQUARE_CLOSEUP_NORTHEAST - Static variable in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  SQUARE_CLOSEUP_NORTHEAST
SQUARE_CLOSEUP_NORTHWEST - Static variable in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  SQUARE_CLOSEUP_NORTHWEST
SQUARE_CLOSEUP_SOUTHEAST - Static variable in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  SQUARE_CLOSEUP_SOUTHEAST
SQUARE_CLOSEUP_SOUTHWEST - Static variable in class jp.sbi.celldesigner.plugin.util.PluginCompartmentSymbolType
  SQUARE_CLOSEUP_SOUTHWEST
STATE_ACETYLATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  for state field
STATE_DONT_CARE - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  for state field
STATE_EMPTY - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  for state field
STATE_GLYCOSYLATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  stateフィールド用の定数
STATE_HISTON1 - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  for state field
STATE_HISTON2 - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  for state field
STATE_HYDROXYLATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  for state field
STATE_METHYLATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  for state field
STATE_MYRISTOYLATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  stateフィールド用の定数
STATE_PALMYTOYLATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  stateフィールド用の定数
STATE_PHOSPHORYLATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  for state field
STATE_PRENYLATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  stateフィールド用の定数
STATE_PROTONATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  stateフィールド用の定数
STATE_SULFATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  stateフィールド用の定数
STATE_TRANSITION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  STATE_TRANSITION
STATE_UBIQUITINATED - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  for state field
STATE_UNKNOWN - Static variable in class jp.sbi.celldesigner.plugin.PluginModification
  for state field
stateChangedToPercent(int, boolean) - Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.MappingArrayMassShowerMainWinFrm
STR_CLOSED - Static variable in class jp.sbi.celldesigner.plugin.PluginStructuralState
STR_EMPTY - Static variable in class jp.sbi.celldesigner.plugin.PluginStructuralState
STR_EMPTY_STATE - Static variable in class jp.sbi.celldesigner.plugin.PluginInformationBox
STR_OPEN - Static variable in class jp.sbi.celldesigner.plugin.PluginStructuralState
STR_OPEN_STATE - Static variable in class jp.sbi.celldesigner.plugin.PluginInformationBox
STR_USER_DEFINED - Static variable in class jp.sbi.celldesigner.plugin.PluginStructuralState
strID - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm
strName - Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.RsltDtBindingFrm

## T

toArray() - Method in class jp.sbi.celldesigner.plugin.PluginListOf
  Convers this PluginListOf to array The elements in the array refer to the same elements of this PluginListOf
toSBML() - Method in class jp.sbi.celldesigner.plugin.PluginSBase
  toSBML
toSBMLString() - Method in class jp.sbi.celldesigner.plugin.PluginModel
TRANSCRIPTION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  TRANSCRIPTION
TRANSLATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  TRANSLATION
TRANSPORT - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  TRANSPORT
TRIGGER - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
TRUNCATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  TRUNCATION
TYPE_BINDINGREGION - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  constants for type field
TYPE_CODING_REGION - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationRegion
TYPE_MODIFICATION_SITE - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationRegion
TYPE_PROTEIN_BINDING_DOMAIN - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationRegion
  constants for type field
TYPE_REGULATORY_REGION - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationRegion
TYPE_RESIDUE - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationResidue
  constants for type field
TYPE_TRANSCRIPTION_STARTING_SITE_L - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationRegion
TYPE_TRANSCRIPTION_STARTING_SITE_R - Static variable in class jp.sbi.celldesigner.plugin.PluginModificationRegion

## U

UNKNOWN - Static variable in class jp.sbi.celldesigner.plugin.util.PluginSpeciesSymbolType
  UNKNOWN
UNKNOWN_CATALYSIS - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  UNKNOWN_CATALYSIS
UNKNOWN_INHIBITION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  UNKNOWN_INHIBITION
UNKNOWN_NEGATIVE_INFLUENCE - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
UNKNOWN_POSITIVE_INFLUENCE - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
UNKNOWN_REDUCED_MODULATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
UNKNOWN_REDUCED_PHYSICAL_STIMULATION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
UNKNOWN_REDUCED_TRIGGER - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
UNKNOWN_TRANSITION - Static variable in class jp.sbi.celldesigner.plugin.util.PluginReactionSymbolType
  UNKNOWN_TRANSITION
update(PluginAntiSenseRNA) - Method in class jp.sbi.celldesigner.plugin.PluginAntiSenseRNA
  Updates all properties to the same as the given PluginAntiSenseRNA.
update(PluginCompartment) - Method in class jp.sbi.celldesigner.plugin.PluginCompartment
  Updates all properties of this PluginCompartment to the same as the given PluginCompartment.
update(PluginCompartmentType) - Method in class jp.sbi.celldesigner.plugin.PluginCompartmentType
update(PluginConstraint) - Method in class jp.sbi.celldesigner.plugin.PluginConstraint
update(PluginEvent) - Method in class jp.sbi.celldesigner.plugin.PluginEvent
  Update all properties of this PluginEvent to the same as the given PluginEvent.
update(PluginEventAssignment) - Method in class jp.sbi.celldesigner.plugin.PluginEventAssignment
  Updates all properties of this PluginEventAssignement to the same as the given PluginEventAssignment.
update(PluginFunctionDefinition) - Method in class jp.sbi.celldesigner.plugin.PluginFunctionDefinition
  Updates all properties of this PluginFunctionDefinition to the same as the given PluginFunctionDefinition.
update(PluginGene) - Method in class jp.sbi.celldesigner.plugin.PluginGene
  Update all properties of this PluginGene to the same as the given PluginGene.
update(PluginInitialAssignment) - Method in class jp.sbi.celldesigner.plugin.PluginInitialAssignment
update(PluginKineticLaw) - Method in class jp.sbi.celldesigner.plugin.PluginKineticLaw
  Update all properties of this PluginKineticLaw same as the given PluginKineticLaw.
update(PluginModel) - Method in class jp.sbi.celldesigner.plugin.PluginModel
  Update all properties of this PluginModel to the same as the given PluginModel
update(PluginParameter) - Method in class jp.sbi.celldesigner.plugin.PluginParameter
  Update all properties of this PluginParameter to the same as the given PluginParameter
update(PluginProtein) - Method in class jp.sbi.celldesigner.plugin.PluginProtein
  Update all properties of this PluginProtein to the same as the given PluginProtein
update(PluginRateRule) - Method in class jp.sbi.celldesigner.plugin.PluginRateRule
  Update all properties of this PluginRateRule to the same as the given PluginRateRule.
update(PluginReaction) - Method in class jp.sbi.celldesigner.plugin.PluginReaction
  Update all properties of this PluginReaction to the same as the given PluginReaction.
update(PluginRNA) - Method in class jp.sbi.celldesigner.plugin.PluginRNA
  Update all properties of this PluginRNA to the same as the given PluginRNA.
update(PluginRule) - Method in class jp.sbi.celldesigner.plugin.PluginRule
  Update all properties of this PluginRule to the same as the given PluginRule.
update(PluginSpecies) - Method in class jp.sbi.celldesigner.plugin.PluginSpecies
  Update all properties of this PluginSpecies to the same as the given PluginSpecies.
update(PluginSpeciesAlias) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
  Update all properties of this PluginSpeciesAlias to the same as the given PluginSpeciesAlias.
update(PluginSpeciesType) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesType
update(PluginUnitDefinition) - Method in class jp.sbi.celldesigner.plugin.PluginUnitDefinition
  Update all properties of this PluginUnitDefinition to the same as the given PluginUnitDefinition.

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