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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
Converts CompartmentType to PluginCompartmentType
convertToPluginConstraint(Constraint) - Static method in class jp.sbi.celldesigner.plugin.PluginSBaseConverter
Converts Constraint to PluginConstraint
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
Converts InitialAssignment to PluginInitialAssignment
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
Converts SpeciesType to PluginSpeciesType
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
Runs circular layout.
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
 
export() - Method in class jp.sbi.celldesigner.plugin.sbgnml.PluginSBGNML
Convert PluginModel which has CelLDesigner annotation to SBGN object model and then export as SBGN-ML.
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
Get the annotation of this PluginSBase.
getAnnotationString() - Method in class jp.sbi.celldesigner.plugin.PluginSBase
Get the annotation of this 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
Returns endTime.
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
Gets the kind of this PluginUnit as String.
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
Returns numOfSteps.
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
Returns outputFilename
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
Gets PluginInformationBox
getPluginListOfStructuralStates() - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesAlias
Gets a list of PluginStructuralStates
getPluginMenu() - Method in class jp.sbi.celldesigner.plugin.CellDesignerPlugin
 
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.
getSbgnFile() - Method in class jp.sbi.celldesigner.plugin.sbgnml.PluginSBGNML
Returns sbgnFile object.
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
 
havePhenotypeInSource(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.sbgnml - package jp.sbi.celldesigner.plugin.sbgnml
 
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
 
PluginSBGNML - Class in jp.sbi.celldesigner.plugin.sbgnml
Plugin class for exporting Graphical Notation to SBGN-ML.
PluginSBGNML(PluginModel) - Constructor for class jp.sbi.celldesigner.plugin.sbgnml.PluginSBGNML
Class constructor specifying pluginModel
PluginSBGNML(PluginModel, File) - Constructor for class jp.sbi.celldesigner.plugin.sbgnml.PluginSBGNML
Class constructor specifying pluginModel and sbgnFile
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
Plugin class for executing simulation with given PluginModel.
PluginSimulation(PluginModel) - Constructor for class jp.sbi.celldesigner.plugin.simulation.PluginSimulation
Class constructor specifying pluginModel
PluginSimulation(PluginModel, double, long) - Constructor for class jp.sbi.celldesigner.plugin.simulation.PluginSimulation
Class constructor specifying pluginModel, endtime and numstep
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
Run a simulation with given pluginModel, endtime and numsteps.

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
Notifies CelLDesigner when SBase is selected.
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
Set the annotation of this PluginSBase.
setAnnotationString(String) - Method in class jp.sbi.celldesigner.plugin.PluginSBase
Set the annotation of this 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
Sets endTime.
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
Sets the kind of this PluginUnit with String.
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 position 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
Sets numOfSteps
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
Sets outpuFilename
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.
setSbgnFile(File) - Method in class jp.sbi.celldesigner.plugin.sbgnml.PluginSBGNML
Sets sbgnFile
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
Sets the SpeciesType of this 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
Sets the stoichiometry of this PluginSpeciesReference.
setStoichiometryMath(String) - Method in class jp.sbi.celldesigner.plugin.PluginSpeciesReference
Sets the stoichiometryMath of this 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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