- 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
-
- 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
-
- 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
- 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.
- 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
-
- 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
-
- 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
-