Overview
Package
Class
Tree
Deprecated
Index
Help
PREV NEXT
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
J
K
M
N
O
P
R
S
T
U
A
actionPerformed(ActionEvent)
- Method in class jp.sbi.celldesigner.plugin.
PluginAction
The action when the plug-in menu is clicked on CellDesigner.
actionPerformed(ActionEvent)
- Method in class jp.sbi.celldesigner.plugin.
PluginCloneModelDoSthAction
actionPerformed(ActionEvent)
- Method in class jp.sbi.celldesigner.plugin.
PluginCreateModelDoSthAction
actionPerformed(ActionEvent)
- Method in class jp.sbi.celldesigner.plugin.
PluginMassShowerAction
actionPerformed(ActionEvent)
- Method in class jp.sbi.celldesigner.plugin.
PluginOpenFileAndDoSomethingAction
add(PluginAction)
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
Adds a PluginAction to this PluginMenu.
add(PluginMenu)
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
Adds a PluginMenu to this PluginMenu.
add(PluginMenuItem)
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
Adds a PluginMenuItem to this PluginMenu.
ADD_PRODUCT
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
ADD_PRODUCT
ADD_REACTANT
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
ADD_REACTANT
addCellDesignerPluginMenu(PluginMenu)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Adds the menu for this plug-in to CellDesigner.
addCompartment(PluginCompartment)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Adds a PluginCompartment to the list.
addCompartmentPopupMenu(PluginMenu)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Adds the compartment popup menu to CellDesigner.
addCompartmentPopupMenuSeparator()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Adds the boundary to the compartment popup menu of CellDesigner.
addCompartmentType(PluginCompartmentType)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
addConstraint(PluginConstraint)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
addCVTerm(CVTerm)
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
addEvent(PluginEvent)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Adds the PluginEvent to the list.
addEventAssignment(PluginEventAssignment)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
Adds a PluginEventAssignment to the list.
addFunctionDefinition(PluginFunctionDefinition)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Adds a PluginFunctionDefinition to the list.
addGLogicGate(PluginGLogicGate)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
addInitialAssignment(PluginInitialAssignment)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
addMember(InformationDisplayerAbst)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
addMember(InformationDisplayerAbst)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
addModifier(PluginModifierSpeciesReference)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Adds a PluginModifierSpeciesReference to this PluginReaction.
addModifiers(PluginModifierSpeciesReference)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
addParameter(PluginParameter)
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Adds a PluginParameter to the list of PluginParameter of this PluginKineticLaw.
addParameter(PluginParameter)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Adds the PluginParameter to the list.
addPluginBindingRegion(PluginBindingRegion)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Adds a PluginBindingRegion to the list.
addPluginMenu()
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Adds the PluginMenu to CellDesigner.
addPluginModificationRegion(PluginModificationRegion)
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
Adds PluginModificationRegion
addPluginModificationRegion(PluginModificationRegion)
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
Adds a PluginModificationRegion to the list.
addPluginModificationRegion(PluginModificationRegion)
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
Adds a PluginModificationRegion to this PluginRNA.
addPluginModificationResidue(PluginModificationResidue)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Adds a PluginModificationResidue to the list.
addProduct(PluginSpeciesReference)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Adds Product (PluginSpeciesReference) to this PluginReaction.
addReactant(PluginSpeciesReference)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Adds the given Reactant (PluginSpeciesReference) to this PluginReaction.
addReaction(PluginReaction)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Adds a PluginReaction to the list.
addReactionPopupMenu(PluginMenu)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Adds the reaction popup menu to CellDesigner.
addReactionPopupMenuSeparator()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Adds the boundary to the reaction popup menu of CellDesigner.
addRule(PluginRule)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Adds a PluginRule to the list.
addSeparator()
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
Adds the separator of this PluginMenu.
addSpecies(PluginSpecies)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
addSpecies(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
addSpecies(PluginSpecies)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Adds a PluginSpecies to the list in this PluginModel.
addSpeciesAlias(PluginSpeciesAlias)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
addSpeciesAlias(PluginSpeciesAlias)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Adds the PluginSpeciesAlias to this Species.
addSpeciesPopupMenu(PluginMenu)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Adds the species popup menu to CellDesigner.
addSpeciesPopupMenuSeparator()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Adds the boundary to the species popup menu of CellDesigner.
addSpeciesType(PluginSpeciesType)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
addUnit(PluginUnit)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
Sets the PluginUnit of this PluginUnitDefinition.
addUnitDefinition(PluginUnitDefinition)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Adds a PluginUnitDefinition to the list.
ANNOTATION
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
ANTISENSE_RNA
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
ANTISENSE_RNA
append(PluginSBase)
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
Adds a PluginSBase to this PluginListOf
appendProtein(PluginProtein)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Adds the PluginProtein to the list.
B
BOOLEAN_LOGIC_GATE_AND
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
BOOLEAN_LOGIC_GATE_AND
BOOLEAN_LOGIC_GATE_NOT
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
BOOLEAN_LOGIC_GATE_OR
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
BOOLEAN_LOGIC_GATE_OR
BOOLEAN_LOGIC_GATE_UNKNOWN
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
BOOLEAN_LOGIC_GATE_UNKNOWN
C
calcArrayPtrFromPercent(String[][], int)
- Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
CATALYSIS
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
CATALYSIS
CellDesignerPlug
- Interface in
jp.sbi.celldesigner.plugin
Interface class of CellDesignerPlugin.
CellDesignerPlugin
- Class in
jp.sbi.celldesigner.plugin
Interface class of CellDesignerPlugin.
CellDesignerPlugin()
- Constructor for class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
ChangeCVTermToMiriamDefinition(List)
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
clear()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Clears all PluginParameter of this PluginKineticLaw.
clear()
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
Clears this PluginListOf
clone(Modification)
- Method in class jp.sbi.celldesigner.plugin.
PluginModification
Clones this PluginModification
clone(StructuralState)
- Method in class jp.sbi.celldesigner.plugin.
PluginStructuralState
cloneCurrModel()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
CLOSEUP_NORTHEAST
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
CLOSEUP_NORTHEAST
CLOSEUP_NORTHWEST
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
CLOSEUP_NORTHWEST
CLOSEUP_SOUTHEAST
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
CLOSEUP_SOUTHEAST
CLOSEUP_SOUTHWEST
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
CLOSEUP_SOUTHWEST
colorDefaultMax
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
colorDefaultMid
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
colorDefaultMin
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
colorSystemDefaultEnd
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
colorSystemDefaultMid
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
colorSystemDefaultStart
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
COMPLEX
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
COMPLEX
contains(PluginSBase)
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
convertToPluginAntiSenseRNA(AntiSenseRNA)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Converts AntiSenseRNA to PluginAntiSenseRNA
convertToPluginAntiSenseRNA(AntiSenseRNA)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts AntiSenseRNA to PluginAntiSenseRNA
convertToPluginCompartment(Compartment, CompartmentAnnotation)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Converts Compartment to PluginCompartment
convertToPluginCompartment(Compartment, CompartmentAnnotation)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Compartment to PluginCompartment
convertToPluginCompartmentType(CompartmentType)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
convertToPluginConstraint(Constraint)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
convertToPluginEvent(Event)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Event to PluginEvent
convertToPluginEventAssignment(EventAssignment, PluginEvent)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts EventAssignment to PluginEventAssignment
convertToPluginFunctionDefinition(FunctionDefinition)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts FunctionDefinition to PluginFunctionDefinition
convertToPluginGene(Gene)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Converts Gene to PluginGene
convertToPluginGene(Gene)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Gene to PluginGene
convertToPluginInitialAssignment(InitialAssignment)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
convertToPluginKineticLaw(KineticLaw, PluginReaction)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Converts KineticLaw to PluginKineticLaw
convertToPluginKineticLaw(KineticLaw, PluginReaction)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts KineticLaw to PluginKineticLaw
convertToPluginModel(Model)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Converts Model to PluginModel
convertToPluginModel(Model, SBModel)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Converts Model to PluginModel
convertToPluginModel(Model)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Model to PluginModel
convertToPluginModel(Model, SBModel)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Model to PluginModel
convertToPluginModifierSpeciesReference(ModifierSpeciesReference, PluginReaction, ReactionLink, SpeciesReferenceAnnotation, PluginSpecies)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Convers ModifierSpeciesReference to PluginModifierSpeciesReference
convertToPluginParameter(Parameter, PluginKineticLaw)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Parameter to PluginParameter
convertToPluginParameter(Parameter, PluginModel)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Parameter to PluginParameter
convertToPluginProtein(Protein)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Protein to PluginProtein
convertToPluginReaction(Reaction, ReactionAnnotation)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Converts Reaction to PluginReaction
convertToPluginReaction(Reaction, ReactionAnnotation)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Reaction to PluginReaction
convertToPluginRNA(RNA)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Converts RNA to PluginRNA
convertToPluginRNA(RNA)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts RNA to PluginRNA
convertToPluginRule(Rule, PluginModel)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Rule to PluginRule
convertToPluginSBase(SBase)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Converts SBase to PluginSBase
convertToPluginSBase(SBase)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts SBase to PluginSBase
convertToPluginSpecies(Species, SpeciesAnnotation)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Converts Species to PluginSpecies
convertToPluginSpecies(Species, SpeciesAnnotation)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Species to PluginSpecies
convertToPluginSpeciesAlias(SpeciesAlias, PluginSpecies)
- Method in class jp.sbi.celldesigner.plugin.
PluginModelBuilder
Convers SpeciesAlias to PluginSpeciesAlias
convertToPluginSpeciesAlias(SpeciesAlias, PluginSpecies)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Convers SpeciesAlias to PluginSpeciesAlias
convertToPluginSpeciesReference(SpeciesReference, PluginReaction, SpeciesReferenceAnnotation, PluginSpecies)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts SpeciesReference to PluginSpeciesReference
convertToPluginSpeciesType(SpeciesType)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
convertToPluginUnit(Unit, PluginUnitDefinition)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts Unit to PluginUnit
convertToPluginUnitDefinition(UnitDefinition)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
Converts UnitDefinition to PluginUnitDefinition
converttoReactionLinkSTRAIGHTCURVELineType(int)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSystemOutUtils
createCopy()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
createNewAliasId()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Create NewAliasId
createNewCompartmentId()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Creates NewCompartmentId
createNewReactionId()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Creates NewReactionId
createNewSpeciesId()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Creates NewSpeciesId
D
DEGRADATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
DEGRADATION
DEGRADED
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
DEGRADED
deleteMember(InformationDisplayerAbst)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
DISSOCIATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
DISSOCIATION
doCircularLayout()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
doMyTask(ProcessBarFrm)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassOutputAnimationTask
doStateChanged()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
dosthAfterMyTask()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassOutputAnimationTask
dropDisplayers()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
DRUG
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
E
equals(PluginModification)
- Method in class jp.sbi.celldesigner.plugin.
PluginModification
Compares the given PluginModification to this PluginModification
equals(StructuralState)
- Method in class jp.sbi.celldesigner.plugin.
PluginStructuralState
exportDrawAreaToImageFile(String, String, String)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
F
firstRun
- Variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
formatPoint2DDoubleOutputString(Object)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSystemOutUtils
G
GENE
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
GENE
generateGif()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
generateMovie()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
get(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
Gets PluginSBase with the given index from this PluginListOf.
getAction()
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
getAction()
- Method in class jp.sbi.celldesigner.plugin.
PluginMenuItem
getActive()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
Gets a state for transcriptional starting site.
getAlias()
- Method in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
getAliasID()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getAllIncludedSpeciesAliases()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getAllModels()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Deprecated.
getAllMyPostionInfomations()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getAllMyPostionInfomations(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getAllPointsInLineOfReactionLink(ReactionLink, Vector<Vector>)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSystemOutUtils
getAllSpeciesNodes()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getAngle()
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
getAngle()
- Method in class jp.sbi.celldesigner.plugin.
PluginInformationBox
getAngle()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
getAngle()
- Method in class jp.sbi.celldesigner.plugin.
PluginStructuralState
getAnnotation()
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
getAnnotationString()
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
getAntiSenseRNA(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginAntiSenseRNA with the given id.
getAntiSenseRNA()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getArray()
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
getAuxDatas()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getBoundaryCondition()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getCharge()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getColor()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
getColor()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getCompartment(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginCompartment with the given index.
getCompartment(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginCompartment with the given id.
getCompartment()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getCompartmentType()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getCompartmentType(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getCompartmentType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getCompartmentTypeOfPanel()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getComponents()
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
getConstant()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getConstant()
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
getConstant()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getConstraint(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getConstraint(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getCurrentModelRadioButton()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
getCVTerm(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
getDatasOfAllSheet()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getDatasOfCurrentSheet()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getDataType()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getDefaultColor(String)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
Gets the default color of the given compartmentType.
getDefaultColor(String)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
Gets the default color of the given speciesType.
getDefaultLineWidth(String)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
Gets the default linewidth of the given speciesType.
getDefaultSize(String)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
Gets the default size of the given speciesType.
getDelay()
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
getEndTime()
- Method in class jp.sbi.celldesigner.plugin.simulation.
PluginSimulation
getEvent(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginEvent with the given index.
getEvent(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginEvent with the given id.
getEventAssignment(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
Gets the PluginEventAssignment with the given index
getExponent()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
getExtensionId()
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
getExtensionId()
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
getExtensionId()
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
getExtensionId()
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
getExtensionId()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getExtensionType()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getFast()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getFile()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getFormula()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
getFormula()
- Method in class jp.sbi.celldesigner.plugin.
PluginRule
getFrameLineWidth()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getFrmController()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
getFunctionDefinition(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginFunctionDefinition with the given index.
getFunctionDefinition(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginFunctionDefinition with the given id.
getGateLink()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
getGateType()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getGene(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginGene with the given id.
getGene()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getGLogicGateType()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
getHasOnlySubstanceUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getHeight()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getHeight()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getHomodimer()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getHypothetical()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartmentType
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginFunctionDefinition
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesType
getId()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
getInformationShowerName()
- Method in interface jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerImpl
getInformationShowerName()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
getInformationShowerReadOnlyPK()
- Method in interface jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerImpl
getInformationShowerReadOnlyPK()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
getInitialAmount()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getInitialAssignment(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getInitialAssignment(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getInitialConcentration()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getInnerWidth()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getJCheckBoxAutoResizeGif()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassAnimOutputOptionFrm
This method initializes jCheckBoxAutoResizeGif
getJCheckBoxAutoResizeMov()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassAnimOutputOptionFrm
This method initializes jCheckBoxAutoResizeMov
getJCheckBoxGifOut()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassAnimOutputOptionFrm
This method initializes jCheckBoxGifOut
getJCheckBoxMovOut()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassAnimOutputOptionFrm
This method initializes jCheckBoxMovOut
getJMenu()
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
getJMenuItem()
- Method in class jp.sbi.celldesigner.plugin.
PluginMenuItem
getJTextFieldGifFileName()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassAnimOutputOptionFrm
This method initializes jTextFieldGifFileName
getJTextFieldMovFileName()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassAnimOutputOptionFrm
This method initializes jTextFieldMovFileName
getKind()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
getKindString()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
getKineticLaw()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getL1TypeCode()
- Method in class jp.sbi.celldesigner.plugin.
PluginAssignmentRule
getLabel()
- Method in class jp.sbi.celldesigner.plugin.
PluginModification
Gets the text of label for the state
getLabel1String()
- Method in class jp.sbi.celldesigner.plugin.
PluginInformationBox
getLabel2String()
- Method in class jp.sbi.celldesigner.plugin.
PluginInformationBox
getLineColor()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getLineColor()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getLineWidth()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
getLineWidth()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getListOfAllSpeciesAlias()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfAllSpeciesAlias(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfAntiSenseRNAs()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfCompartments()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfCompartmentTypes()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfConstraints()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfDisplayers()
- Method in interface jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerImpl
getListOfDisplayers()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
getListOfEventAssignments()
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
getListOfEvents()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfFunctionDefinitions()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfGenes()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfGLogicGates()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getListOfInitialAssignments()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfModifiers()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getListOfParameters()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
getListOfParameters()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfPluginBindingRegion()
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
getListOfPluginRegion()
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
getListOfPluginRegion()
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
getListOfPluginRegion()
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
getListOfPluginResidue()
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
getListOfProducts()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getListOfProteins()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfReactants()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getListOfReactions()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfRNAs()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfRules()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfSpecies()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfSpecies(PluginAntiSenseRNA)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfSpecies(PluginGene)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfSpecies(PluginProtein)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the list of PluginProtein added the given PluginProtein to.
getListOfSpecies(PluginRNA)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfSpeciesAlias()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getListOfSpeciesTypes()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfUnitDefinitions()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getListOfUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
getMappingArrayMassShowerConfigWinFrm()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getMappingArrayMassShowerMainWinFrmInstanceInCurrentGStructure()
- Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getMappingKeyComboBox()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getMassDatas()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getMath()
- Method in class jp.sbi.celldesigner.plugin.
PluginConstraint
getMath()
- Method in class jp.sbi.celldesigner.plugin.
PluginEventAssignment
getMath()
- Method in class jp.sbi.celldesigner.plugin.
PluginFunctionDefinition
getMath()
- Method in class jp.sbi.celldesigner.plugin.
PluginInitialAssignment
getMath()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
getMath()
- Method in class jp.sbi.celldesigner.plugin.
PluginRule
getMaxVaule()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
getMaxVaule()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getMaxVauleColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
getMaxVauleColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getMembers()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
getMenuComponent(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
getMenuComponentCount()
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
getMessage()
- Method in class jp.sbi.celldesigner.plugin.
PluginConstraint
getmicroArrayRadioButton()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
getMidPointInLine()
- Method in class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
Get the junction information of three linked lines if this link is three-linked line.
getMidVaule()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
getMidVaule()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getMidVauleColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
getMidVauleColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getMinVaule()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
getMinVaule()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getMinVauleColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
getMinVauleColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getMiriamDatas()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getModel(String)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getModelType()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getModifications()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getModificationType()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
getModificationType()
- Method in class jp.sbi.celldesigner.plugin.
PluginModifierSpeciesReference
getModifier(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Gets the PluginModifierSpeciesReference with the given index of this PluginReaction.
getModifiers()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
getMultiplier()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
getName()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartmentType
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginFunctionDefinition
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesType
getName()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
getNamePositionX()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getNamePositionY()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getNewModelRadioButton()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
getNotes()
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
getNotes()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getNotesString()
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
getNotesString()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getNumBindingRegions()
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
getNumCompartments()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumCompartmentTypes()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumConstraints()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumCVTerms()
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
getNumEventAssignments()
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
getNumEvents()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumFunctionDefinitions()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumGLogicGates()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getNumInitialAssignments()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumItems()
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
Deprecated.
In libSBML 3, getNumItems has been renamed to size().
getNumModifiers()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getNumOfSteps()
- Method in class jp.sbi.celldesigner.plugin.simulation.
PluginSimulation
getNumParameters()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
getNumParameters()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumProducts()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getNumReactants()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getNumReactions()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumRegions()
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
getNumRegions()
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
getNumRegions()
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
getNumResidues()
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
getNumRules()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumSpecies()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumSpeciesAlias()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getNumSpeciesTypes()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumUnitDefinitions()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getNumUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
getOffset()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
getOldmiriamRelationIndex()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getOpenFilename()
- Method in class jp.sbi.celldesigner.plugin.
PluginOpenFileAndDoSomethingAction
getOpenXmlFileRadioButton()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
getOuterWidth()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getOutputFile()
- Method in class jp.sbi.celldesigner.plugin.simulation.
PluginSimulation
getOutputGifFileName()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getOutputMovFileName()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getOutside()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getParameter(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Gets the PluginParameter with the given index from the list.
getParameter(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginParameter with the given index.
getParameter(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginParameter with the given id.
getParent()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
getParentEvent()
- Method in class jp.sbi.celldesigner.plugin.
PluginEventAssignment
getParentExtensionSBase()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
getParentID()
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
getParentID()
- Method in class jp.sbi.celldesigner.plugin.
PluginEventAssignment
getParentID()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
getParentID()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
getParentID()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
getParentModel()
- Method in class jp.sbi.celldesigner.plugin.
PluginRule
getParentProtein()
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
getParentProtein()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
getParentReaction()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
getParentReaction()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
getParentReaction()
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
getParentReaction()
- Method in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
getParentReactionID()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
getParentReactionID()
- Method in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
getParentSBase()
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
getParentSBase()
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
getParentSBaseID()
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
getParentUnitDefinition()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
getPluginBindingRegion(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Gets the PluginBindingRegion with the given index.
getPluginInformationBox()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getPluginInformationBox()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getPluginListOfStructuralStates()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Gets a list of PluginStructuralStates
getPluginModificationRegion(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
Gets the PluginModificationRegion with the given index.
getPluginModificationRegion(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
Gets the PluginModificationRegion with the given index.
getPluginModificationRegion(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
Gets the PluginModificationRegion with the given index.
getPluginModificationResidue(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Gets the PluginModificationResidue with the given index.
getPluginSpeciesAlias(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets PluginSpeciesAlias with the given id.
getPointsInLine()
- Method in class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
Get all the key points information in the line of the link.
getPos()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
getPositionToCompartment()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getProcessNodeIdx()
- Method in class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
Get the process node index which rely on the index of the subline included process node in BaseReactionLink if this link have process node.
getProduct(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Gets the Product (PluginSpeciesReference) of this PluginReaction with the given index.
getProtein(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginProtein with the given id.
getProtein()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getproteomicsRadioButton()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
getPureSBMLString()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getReactant(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Gets the Reactant (PluginSpeciesReference) with the given index from this PluginReaction.
getReaction(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginReaction with the given index.
getReaction(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginReaction with the given id.
getReactionLinkMembers()
- Method in class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
Get the members of this link, for instance the members will be Add_reactant, Add_product, modification link, gate link information, if this link is BaseReactionLink.
getReactionType()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getReferenceGStructure()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getReferenceType()
- Method in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
getRefsOfGateInReaction()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
getRelationFromCVTerm(CVTerm)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSBase
getRelationsAndIDCols()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getRepaintBounds()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
getResidue()
- Method in class jp.sbi.celldesigner.plugin.
PluginModification
getReversible()
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
getRNA(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginRNA with the given id.
getRNA()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getRsltDtBindingFrm()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
getRule(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginRule with the given index from the list.
getScale()
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
getSelectedAllNode()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getSelectedAllNode(PluginModel)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getSelectedCompartmentNode()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getSelectedCompartmentNode(PluginModel)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getSelectedModel()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getSelectedReactionNode()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getSelectedReactionNode(PluginModel)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getSelectedSpeciesNode()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getSelectedSpeciesNode(PluginModel)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
getSide()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
getSimpleColorSettingWinFrm()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
getSize()
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
get size
getSize()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getSize()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
getSize()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
gets size
getSpatialDimensions()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getSpatialSizeUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getSpecies(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginSpecies with the given index.
getSpecies(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginSpecies with the given id.
getSpecies()
- Method in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
getSpecies()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getSpeciesAlias(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getSpeciesAlias(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getSpeciesAliases()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
getSpeciesInstance()
- Method in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
getSpeciesType(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getSpeciesType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
getSpeciesType()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getSpeciesTypeComboBox()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
getState()
- Method in class jp.sbi.celldesigner.plugin.
PluginModification
getState()
- Method in class jp.sbi.celldesigner.plugin.
PluginStructuralState
getStateString()
- Method in class jp.sbi.celldesigner.plugin.
PluginInformationBox
getStoichiometry()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesReference
getStoichiometryMath()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesReference
getSubstanceUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
getSubstanceUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getSymbol()
- Method in class jp.sbi.celldesigner.plugin.
PluginInitialAssignment
getText()
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
getText()
- Method in class jp.sbi.celldesigner.plugin.
PluginMenuItem
getThickness()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getTimeUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
getTimeUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
getTrigger()
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
getType()
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
getType()
- Method in class jp.sbi.celldesigner.plugin.
PluginAssignmentRule
getType()
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
get type
getType()
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
getType()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
getType()
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
gets type
getType()
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
getType()
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
getType()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getTypeOfLine()
- Method in class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
Get the type of the Link, only Add_reactant and Add_product has this type, which is Curve or Straight based on the property of the link.
getUnit(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
Gets the PluginUnit with the given index.
getUnitDefinition(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginUnitDefinition with the given index.
getUnitDefinition(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Gets the PluginUnitDefinition with the given id.
getUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
getUnits()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
getUserDefaultEndColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
getUserDefaultMidColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
getUserDefaultStartColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
getUseValuesFromTriggerTime()
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
getValue()
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
getVariable()
- Method in class jp.sbi.celldesigner.plugin.
PluginAssignmentRule
getVariable()
- Method in class jp.sbi.celldesigner.plugin.
PluginEventAssignment
getVariable()
- Method in class jp.sbi.celldesigner.plugin.
PluginRateRule
getVolume()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getWidth()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getWidth()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getX()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getX()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
getY()
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
getY()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
giveMeNewID()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
giveMeOutputFileName(String, String)
- Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
H
havehadAMappingArrayMassShowerMainWinFrmInstanceInCurrentGStructure(boolean)
- Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
haveInputedData()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
havePhenotypeInSrouce(PluginSBase)
- Static method in class jp.sbi.celldesigner.plugin.
PluginReaction
HETERODIMER_ASSOCIATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
HETERODIMER_ASSOCIATION
HOMODIMER_FORMATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
HOMODIMER_FORMATION
I
iCmpColNum
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
iCurrentModel
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
iMappingArrayMassMarginBetweenRect3DAndMsg
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
iMappingArrayMassRect3DDisplayerHeight
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
iMappingArrayMassRect3DDisplayerWidth
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
iMcsColNum
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
iMicroArrayDataType
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
iMpkColNum
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
iNewModel
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
InformationDisplayerAbst
- Class in
jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer
InformationDisplayerAbst()
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
InformationElementImpl
- Interface in
jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer
InformationShowerImpl
- Interface in
jp.sbi.celldesigner.plugin.InfoCenter.InfoShower
InformationShowerMappingArrayMass
- Class in
jp.sbi.celldesigner.plugin.InfoCenter.InfoShower
InformationShowerMappingArrayMass(SBModelFrame)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
InformationShowerMappingArrayMass(SBModelFrame, JFrame)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
InformationShowerMappingArrayMass(SBModelFrame, JFrame, String[][], String[][], double, double)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
InformationShowerMappingArrayMass(SBModelFrame, JFrame, String[][], String[][], int, double, double)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
InformationShowerMappingArrayMass(SBModelFrame, JFrame, String[][], String[][], int, int, double, double)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
InformationShowerMappingArrayMass(SBModelFrame, JFrame, String[][], String[][], int, int, Color, Color, Color, double, double)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
INHIBITION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
INHIBITION
initDialog()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassAnimOutputOptionFrm
initDialog(boolean, int, int, boolean)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
initDialogUsing(MappingArrayMassShowerMainWinFrm)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassAnimOutputOptionFrm
initMappingArrayMassShowerConfigWinFrm(Color, Color, Color, double, double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
inShape(double, double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
iNSpColNum
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
intersects(Rectangle2D.Double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
ION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
ION
iOpenXmlFile
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
iProteomicsDataType
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
isActive()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
isCanceled()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassAnimOutputOptionFrm
isCanceled()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
isCanceled()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
isHighlighted()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
isOutputGif()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
isOutputMovie()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
iSpIColNum
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
iSpNColNum
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
iSptColNum
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
isReferenceSameModel(PluginSBase)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
isSameModel(Model)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
isScaleOutputGif()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
isScaleOutputMovie()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
isSetInitialAmount()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
isSetInitialConcentration()
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
isShowGuideMsg()
- Method in class jp.sbi.celldesigner.plugin.
PluginMassShowerAction
isShowGuideMsg()
- Method in class jp.sbi.celldesigner.plugin.
PluginOpenFileAndDoSomethingAction
isStarted()
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
isStarted()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
isValidCompartmentType(PluginCompartment)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
isValidModifierType(PluginSimpleSpeciesReference)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
isValidProteinsType(PluginProtein)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
isValidReaction(PluginReaction)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
isValidReactionType(PluginReaction)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
isValidSpeciesAliasType(PluginSpeciesAlias)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
isValidSpeciesType(PluginSpecies)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
isVisible(SBModelFrame, GStructure)
- Method in interface jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerImpl
isVisible(SBModelFrame, GStructure)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
IsWinBeenUsing()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
J
jp.sbi.celldesigner.plugin
- package jp.sbi.celldesigner.plugin
jp.sbi.celldesigner.plugin.DataObject
- package jp.sbi.celldesigner.plugin.DataObject
jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer
- package jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer
jp.sbi.celldesigner.plugin.InfoCenter.InfoShower
- package jp.sbi.celldesigner.plugin.InfoCenter.InfoShower
jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
- package jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
jp.sbi.celldesigner.plugin.simulation
- package jp.sbi.celldesigner.plugin.simulation
jp.sbi.celldesigner.plugin.util
- package jp.sbi.celldesigner.plugin.util
K
KNOWN_TRANSITION_OMITTED
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
KNOWN_TRANSITION_OMITTED
M
main(String[])
- Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
MappingArrayMassShowerConfigWinFrm
- Class in
jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
MappingArrayMassShowerConfigWinFrm()
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
MappingArrayMassShowerConfigWinFrm(Color, Color, Color, double, double)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
MappingArrayMassShowerMainWinFrm
- Class in
jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
MappingArrayMassShowerMainWinFrm(RsltDtTpMdlSelectFrm, RsltDtBindingFrm, boolean)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
MappingArrayMassShowerMainWinFrm(Color, Color, Color)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
MassAnimOutputOptionFrm
- Class in
jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
MassAnimOutputOptionFrm(JFrame)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassAnimOutputOptionFrm
This method initializes
MassOutputAnimationTask
- Class in
jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
MassOutputAnimationTask(JFrame, JFrame, ProcessBarFrm, MappingArrayMassShowerMainWinFrm.restoreUI)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MassOutputAnimationTask
MINIMUM_SIZE_ANY
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
constants for minimum size
MINIMUM_SIZE_DNAMETYLATION
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
constants for minimum size
MINIMUM_SIZE_EMPTY
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
constants for minimum size
modelBase
- Variable in class jp.sbi.celldesigner.plugin.
PluginModel
modelClosed(PluginSBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when Model is closed on CellDesigner.
modelClosed(SBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when Model is closed on CellDesigner.
modelClosed(SBase)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
modelOpened(PluginSBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when Model is opened on CellDesigner.
modelOpened(SBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when Model is opened on CellDesigner.
modelOpened(SBase)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
modelSelectChanged(PluginSBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when the selected Model is changed on CellDesigner.
modelSelectChanged(SBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when the selected Model is changed on CellDesigner.
modelSelectChanged(SBase)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
MODIFIER
- Static variable in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
ReferenceType "MODIFIER"
MODULATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
MShowerMain
- Class in
jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
MShowerMain(RsltDtTpMdlSelectFrm, RsltDtBindingFrm, boolean)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MShowerMain
myActionPerformed(ActionEvent)
- Method in interface jp.sbi.celldesigner.plugin.
PluginActionListener
Called when the plug-in menu is clicked on CellDesigner.
N
NEGATIVE_INFLUENCE
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
notifySBaseAdded(PluginSBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Notifies CellDesigner when SBase is added.
notifySBaseAdded(PluginSBase)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
notifySBaseAdded
notifySBaseChanged(PluginSBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Notifies CellDesigner when some properties of SBase are changed.
notifySBaseChanged(PluginSBase)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
notifySBaseChanged
notifySBaseDeleted(PluginSBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Notifies CellDesigner when SBase is deleted.
notifySBaseDeleted(PluginSBase)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
notifySBaseDeleted
O
onEdge(double, double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
openXlsFile(Component)
- Static method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
OpenXlsFileErrorMsg
- Static variable in class jp.sbi.celldesigner.plugin.
PluginMassShowerAction
OVAL
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
OVAL
P
PHENOTYPE
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
PHENOTYPE
PHYSICAL_STIMULATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
PluginAction
- Class in
jp.sbi.celldesigner.plugin
Interface of the action class of the plug-in menu.
PluginAction()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginAction
PluginActionListener
- Interface in
jp.sbi.celldesigner.plugin
PluginActionListener
PluginAlgebraicRule
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.AlgebraicRule for the plug-in.
PluginAlgebraicRule(PluginModel)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginAlgebraicRule
Constructor
PluginAntiSenseRNA
- Class in
jp.sbi.celldesigner.plugin
This class represents anti sense RNA.
PluginAntiSenseRNA()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
Constructor
PluginAntiSenseRNA(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
Constructor
PluginAssignmentRule
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.AssignmentRule for the plug-in.
PluginAssignmentRule(PluginModel)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginAssignmentRule
Constructor
PluginBindingRegion
- Class in
jp.sbi.celldesigner.plugin
Class for modification bindingRegion.
PluginBindingRegion(PluginProtein)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginBindingRegion
Constructor
PluginCloneModelDoSthAction
- Class in
jp.sbi.celldesigner.plugin
PluginCloneModelDoSthAction()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginCloneModelDoSthAction
PluginCompartment
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.Compartment for the plug-in.
PluginCompartment(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginCompartment
Constructor
PluginCompartment(String, String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginCompartment
Constructor
PluginCompartmentSymbolType
- Class in
jp.sbi.celldesigner.plugin.util
This class defines CompartmentType for PluginCompartment.
PluginCompartmentSymbolType()
- Constructor for class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
PluginCompartmentType
- Class in
jp.sbi.celldesigner.plugin
PluginCompartmentType(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginCompartmentType
PluginConstraint
- Class in
jp.sbi.celldesigner.plugin
PluginConstraint(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginConstraint
PluginCreateModelDoSthAction
- Class in
jp.sbi.celldesigner.plugin
PluginCreateModelDoSthAction()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginCreateModelDoSthAction
PluginDoSthAbstractAction
- Class in
jp.sbi.celldesigner.plugin
PluginDoSthAbstractAction()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginDoSthAbstractAction
PluginEvent
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.Event for the plug-in.
PluginEvent(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginEvent
Constructor
PluginEventAssignment
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.EventAssignment for the plug-in.
PluginEventAssignment(PluginEvent)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginEventAssignment
Constructor
PluginFunctionDefinition
- Class in
jp.sbi.celldesigner.plugin
PluginFunctionDefinition(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginFunctionDefinition
Constructor
PluginGene
- Class in
jp.sbi.celldesigner.plugin
This class represents gene.
PluginGene()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginGene
Constructor
PluginGene(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginGene
Constructor
PluginGLogicGate
- Class in
jp.sbi.celldesigner.plugin
PluginGLogicGate(PluginReaction, Vector)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginGLogicGate
PluginGLogicGate(PluginReaction, Vector, String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginGLogicGate
PluginGLogicGate(PluginReaction, Vector, String, String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginGLogicGate
PluginInformationBox
- Class in
jp.sbi.celldesigner.plugin
PluginInformationBox()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginInformationBox
PluginInitialAssignment
- Class in
jp.sbi.celldesigner.plugin
PluginInitialAssignment(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginInitialAssignment
PluginKineticLaw
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.KineticLaw for the plug-in.
PluginKineticLaw(PluginReaction)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Constructor
PluginListOf
- Class in
jp.sbi.celldesigner.plugin
This class wraps ListOf for the plug-in.
PluginListOf()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginListOf
Constructor
PluginListOf(PluginSBase)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginListOf
Constructor
PluginMassShowerAction
- Class in
jp.sbi.celldesigner.plugin
PluginMassShowerAction()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginMassShowerAction
PluginMenu
- Class in
jp.sbi.celldesigner.plugin
This class wraps JMenu for the plug-in.
PluginMenu()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginMenu
Constructor
PluginMenu(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginMenu
Constructor
PluginMenu(PluginAction)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginMenu
Constructor
PluginMenu(String, PluginAction)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginMenu
Constructor
PluginMenu(String, PluginOpenFileAndDoSomethingAction)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginMenu
PluginMenuItem
- Class in
jp.sbi.celldesigner.plugin
This class wraps JMenuItem for the plug-in.
PluginMenuItem(String, PluginAction)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginMenuItem
Constructor
PluginMenuItem(String, PluginDoSthAbstractAction)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginMenuItem
PluginModel
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.Model for the plug-in.
PluginModel(Model)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginModel
Constructor
PluginModelBuilder
- Class in
jp.sbi.celldesigner.plugin
PluginModelBuilder(SBModel)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginModelBuilder
PluginModification
- Class in
jp.sbi.celldesigner.plugin
ProteinModification An instance represents <modification> tag.
PluginModification()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginModification
Constructor
PluginModification(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginModification
Constructor
PluginModification(String, String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginModification
Constructor
PluginModificationRegion
- Class in
jp.sbi.celldesigner.plugin
Class for region.
PluginModificationRegion(PluginGene)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginModificationRegion
Constructor
PluginModificationRegion(PluginRNA)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginModificationRegion
Constructor
PluginModificationRegion(PluginAntiSenseRNA)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginModificationRegion
Constructor
PluginModificationResidue
- Class in
jp.sbi.celldesigner.plugin
Class for modification residue.
PluginModificationResidue(PluginProtein)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginModificationResidue
Constructor
PluginModifierSpeciesReference
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.ModifierSpeciesReference for the plug-in.
PluginModifierSpeciesReference(PluginReaction, PluginSpeciesAlias)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginModifierSpeciesReference
Constructor
PluginOpenFileAndDoSomethingAction
- Class in
jp.sbi.celldesigner.plugin
PluginOpenFileAndDoSomethingAction()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginOpenFileAndDoSomethingAction
PluginParameter
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.Parameter for the plug-in.
PluginParameter(PluginKineticLaw)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginParameter
Constructor case of local parameter
PluginParameter(PluginModel)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginParameter
Constructor case of global parameter
PluginParameter(String, PluginKineticLaw)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginParameter
Constructor case of local parameter
PluginParameter(String, PluginModel)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginParameter
Constructor case of global parameter
PluginProtein
- Class in
jp.sbi.celldesigner.plugin
This class represents Protein.
PluginProtein()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginProtein
Constructor
PluginProtein(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginProtein
Constructor
PluginRateRule
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.RateRule for the plug-in.
PluginRateRule(PluginModel)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginRateRule
Constructor
PluginReaction
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.Reaction for the plug-in.
PluginReaction()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginReaction
Constructor
PluginReaction(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginReaction
Constructor
PluginReactionSymbolType
- Class in
jp.sbi.celldesigner.plugin.util
This class defines ReactionType for PluginReaction.
PluginReactionSymbolType()
- Constructor for class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
PluginRealLineInformationDataObjOfReactionLink
- Class in
jp.sbi.celldesigner.plugin.DataObject
ReactionLink Line information Class
PluginRealLineInformationDataObjOfReactionLink()
- Constructor for class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
PluginRNA
- Class in
jp.sbi.celldesigner.plugin
This class represents RNA.
PluginRNA()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginRNA
Constructor
PluginRNA(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginRNA
Constructor
PluginRule
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.Rule for the plug-in.
PluginRule()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginRule
PluginSBase
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.SBase for the plug-in.
PluginSBase()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginSBase
Constructor
PluginSBaseConverter
- Class in
jp.sbi.celldesigner.plugin
PluginSBaseConverter
PluginSBaseConverter()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginSBaseConverter
PluginSimpleSpeciesReference
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.SimpleSpeciesReference for the plug-in.
PluginSimpleSpeciesReference(PluginSpeciesAlias)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
Constructor
PluginSimulation
- Class in
jp.sbi.celldesigner.plugin.simulation
PluginSimulation(PluginModel)
- Constructor for class jp.sbi.celldesigner.plugin.simulation.
PluginSimulation
PluginSimulation(PluginModel, double, long)
- Constructor for class jp.sbi.celldesigner.plugin.simulation.
PluginSimulation
PluginSpecies
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.Species for the plug-in.
PluginSpecies(String, String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginSpecies
Constructor
PluginSpecies()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginSpecies
Constructor
PluginSpeciesAlias
- Class in
jp.sbi.celldesigner.plugin
PluginSpeciesAlias has drawing information such as position, color, name and type.
PluginSpeciesAlias(PluginSpecies, String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Constructor
PluginSpeciesAlias(SpeciesAlias, PluginSpecies)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Constructor
PluginSpeciesReference
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.SpeciesReference for the plug-in.
PluginSpeciesReference(PluginReaction, PluginSpeciesAlias)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginSpeciesReference
Constructor
PluginSpeciesSymbolType
- Class in
jp.sbi.celldesigner.plugin.util
This class defines ReactionType for PluginReaction.
PluginSpeciesSymbolType()
- Constructor for class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
PluginSpeciesType
- Class in
jp.sbi.celldesigner.plugin
PluginSpeciesType(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginSpeciesType
PluginStructuralState
- Class in
jp.sbi.celldesigner.plugin
PluginStructuralState()
- Constructor for class jp.sbi.celldesigner.plugin.
PluginStructuralState
PluginSystemOutUtils
- Class in
jp.sbi.celldesigner.plugin.util
PluginSystemOutUtils()
- Constructor for class jp.sbi.celldesigner.plugin.util.
PluginSystemOutUtils
PluginUnit
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.Unit for the plug-in.
PluginUnit(PluginUnitDefinition)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginUnit
Constructor
PluginUnitDefinition
- Class in
jp.sbi.celldesigner.plugin
This class wraps org.sbml.libsbml.UnitDefinition for the plug-in.
PluginUnitDefinition(String)
- Constructor for class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
Constructor
popupAvailable()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
POSITIVE_INFLUENCE
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
printDebugInfoOfRealLineInformationOfReactionLink(PluginRealLineInformationDataObjOfReactionLink, int)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSystemOutUtils
processMyAction(ActionEvent)
- Method in class jp.sbi.celldesigner.plugin.
PluginDoSthAbstractAction
processWindowEvent(WindowEvent)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
processWindowEvent(WindowEvent)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
PRODUCT
- Static variable in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
ReferenceType "PRODUCT"
PROTEIN
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
PROTEIN
PROTEIN_GENERIC
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
GENERIC
PROTEIN_ION_CHANNEL
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
ION_CHANNEL
PROTEIN_RECEPTOR
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
RECEPTOR
PROTEIN_TRUNCATED
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
TRUNCATED
R
REACTANT
- Static variable in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
ReferenceType "REACTANT"
ReadDataErrorMsg
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
recreateMappingArrayMassDisplayers(String[][], String[][], int, int, Color, Color, Color, double, double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
REDUCED_MODULATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
REDUCED_PHYSICAL_STIMULATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
REDUCED_TRIGGER
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
remove(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
Removes PluginSBase with the given index from this PluginListOf.
remove(PluginSBase)
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
Removes the PluginSBase from this PluginListOf.
removeAntiSenseRNA(PluginAntiSenseRNA)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the given PluginAntiSenseRNA from the list.
removeAntiSenseRNA(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginAntiSenseRNA with the given index from the list.
removeCompartment(PluginCompartment)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the given PluginCompartment from the list.
removeCompartment(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginCompartment with the given id from the list.
removeCompartment(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginCompartment with the given index from the list.
removeCompartmentType(PluginCompartmentType)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeCompartmentType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeCompartmentType(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeConstraint(PluginConstraint)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeConstraint(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeConstraint(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeEvent(PluginEvent)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the given PluginEvent from the list.
removeEvent(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Remove the PluginEvent with the given id.
removeEvent(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginEvent with the given index.
removeEventAssignment(PluginEventAssignment)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
Removes a PluginEventAssignment from the list.
removeEventAssignment(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
Removes the PluginAssignment with the given index from the list.
removeFunctionDefinition(PluginFunctionDefinition)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the given PluginFunctionDefinition from the list.
removeFunctionDefinition(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginFunctionDefinition with the given id from the list.
removeFunctionDefinition(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginFunctionDefinition with the given index from the list.
removeGene(PluginGene)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the given PluginGene from the list.
removeGene(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginGene with the given index from the list.
removeGLogicGate(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
removeGLogicGate(PluginGLogicGate)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
removeInitialAssignment(PluginInitialAssignment)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeInitialAssignment(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeInitialAssignment(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeModifier(PluginModifierSpeciesReference)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Removes a PluginModifierSpeciesReference from this PluginReaction.
removeModifier(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Removes the PluginModifierSpeciesReference from this PluginReaction.
removeParameter(PluginParameter)
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Removes the PluginParameter from the list of PluginParameter of this PluginKineticLaw.
removeParameter(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Remove the PluginParameter with the given index from the list.
removeParameter(PluginParameter)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Remove the given PluginParameter from the list.
removeParameter(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Remove the PluginParameter with the given id.
removeParameter(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginParameter with the given index to the list.
removePluginBindingRegion(PluginBindingRegion)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Removes the given PluginBindingRegion from the list.
removePluginBindingRegion(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Removes the PluginBindingRegion with the given index from the list.
removePluginModificationRegion(PluginModificationRegion)
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
Removes the given PluginModificationRegion.
removePluginModificationRegion(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
Remove the PluginModificationRegion with the given index.
removePluginModificationRegion(PluginModificationRegion)
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
Removes the given PluginModificationRegion from the list.
removePluginModificationRegion(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
Removes the PluginModificationRegion with the given index from the list.
removePluginModificationRegion(PluginModificationRegion)
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
Removes the given PluginModificationRegion from this PluginRNA.
removePluginModificationRegion(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
Removes the PluginModificationRegion with the given index from this PluginRNA.
removePluginModificationResidue(PluginModificationResidue)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Removes the given PluginModificationResidue from the list.
removePluginModificationResidue(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Removes the PluginModificationResidue with the given index from the list.
removeProduct(PluginSpeciesReference)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Removes the given Product (PluginSpeciesReference) from this PluginReaction.
removeProduct(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Removes the Product (PluginSpeciesReference) with the given index from this PluginReaction.
removeProtein(PluginProtein)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the given PluginProtein from the list.
removeProtein(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginProtein with the given index.
removeReactant(PluginSpeciesReference)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Removes the given Reactant (PluginSpeciesReference) from this PluginReaction.
removeReactant(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Removes the Reactant with the given index from this PluginReaction.
removeReaction(PluginReaction)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the given PluginReaction from the list.
removeReaction(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginReaction with the given id from the list.
removeReaction(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginReaction with the given index from the list.
removeRNA(PluginRNA)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Adds a PluginRNA to the list
removeRNA(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginRNA with the given index from the list.
removeRule(PluginRule)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the given PluginRule from the list.
removeRule(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginRule with the given index from the list.
removeSpecies(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
removeSpecies(PluginSpecies)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
removeSpecies(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginSpecies with the given id from the list
removeSpecies(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginSpecies with the given index from the list.
removeSpeciesAlias(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
removeSpeciesAlias(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Removes PluginSpeciesAlias from this Species.
removeSpeciesAlias(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Removes PluginSpeciesAlias from this Species.
removeSpeciesType(PluginSpeciesType)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeSpeciesType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeSpeciesType(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
removeUnit(PluginUnit)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
Removes the PluginUnit from this PluginUnitDefinition.
removeUnit(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
Removes the PluginUnit with the given index from this PluginUnitDefinition.
removeUnitDefinition(PluginUnitDefinition)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Remove the given PluginUnitDefinition from the list.
removeUnitDefinition(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Removes the PluginUnitDefinition with the given id from the list.
removeUnitDefinition(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Remove the PluginUnitDefinition with the given index from the list.
renewDisplayersArray()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
repaintPreviewColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
repaintPreviewColor()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
resetAllIncludedPluginSpeciesAliases(PluginModel, PluginSpeciesAlias)
- Static method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
resetDataAndCompentsInThisWinFrm()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
resetStateString()
- Method in class jp.sbi.celldesigner.plugin.
PluginInformationBox
restoreUIafterAnimOut(MappingArrayMassShowerMainWinFrm.restoreUI)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
RNA
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
RNA
RsltDtBindingFrm
- Class in
jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
RsltDtBindingFrm(Frame, File, List, int, int)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
RsltDtTpMdlSelectFrm
- Class in
jp.sbi.celldesigner.plugin.InfoCenter.InfoUI
RsltDtTpMdlSelectFrm(Frame)
- Constructor for class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtTpMdlSelectFrm
runSimulation()
- Method in class jp.sbi.celldesigner.plugin.simulation.
PluginSimulation
S
sbase
- Variable in class jp.sbi.celldesigner.plugin.
PluginSBase
sbase
SBaseAdded(PluginSBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when a PluginSBase is added on CellDesigner.
SBaseAdded(SBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when SBase is added on CellDesigner.
SBaseAdded(SpeciesAlias, Species)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when SBase is added on CellDesigner.
SBaseAdded(SBase)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
SBaseAdded(SpeciesAlias, Species)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
SBaseChanged(PluginSBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when some properties of PluginSBase are changed on CellDesigner.
SBaseChanged(SBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when some properties of SBase are changed on CellDesigner.
SBaseChanged(SpeciesAlias, Species)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when some properties of SBase are changed on CellDesigner.
SBaseChanged(SBase)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
SBaseChanged(SpeciesAlias, Species)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
SBaseDeleted(PluginSBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when PluginSBase is deleted on CellDesigner.
SBaseDeleted(SBase)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when SBase is deleted on CellDesigner.
SBaseDeleted(SpeciesAlias, Species)
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
Called when SBase is deleted on CellDesigner.
SBaseDeleted(SBase)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
SBaseDeleted(SpeciesAlias, Species)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
SBaseSelected()
- Method in interface jp.sbi.celldesigner.plugin.
CellDesignerPlug
SBaseSelected()
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
setActive(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
Sets a state for transcriptional starting site.
setAlias(PluginSpeciesAlias)
- Method in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
Sets the PluginSpeciesAlias of this PluginSimpleSpeciesReference
setAllIncludedSpeciesAliases(Vector)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
setAngle(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
Sets the angle of this PluginBindingRegion.
setAngle(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginInformationBox
setAngle(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
Sets the angle of this PluginModificationResidue.
setAngle(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginStructuralState
setAnnotation(XMLNode)
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
setAnnotationString(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
setAntiSenseRNA(PluginAntiSenseRNA)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the PluginAntiSenseRNA of this PluginSpeciesAlias.
setAuxDatas(String[][])
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
setBoundaryCondition(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the boundaryCondition of this PluginSpecies.
setCharge(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the charge of this PluginSpecies.
setColor(String, Color, Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
setColor(Color)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
Sets the color of this GLogicGate.
setColor(Color)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the color of this PluginSpeciesAlias.
setCompartment(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the compartment of this PluginSpecies.
setCompartmentType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the type of this PluginCompartment.
setCompartmentTypeOfPanel(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
setConstant(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets true if this PluginCompartment is constant
setConstant(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
Sets the constant of this PluginParameter.
setConstant(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the constant of this PluginSpecies.
setCursorBySpecification(Cursor)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
setCVTerm(XMLNode)
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
setDatasOfAllSheet(List)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
setDataType(int)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
setDelay(ASTNode)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
Sets the delay of this PluginEvent to the given ASTNode.
setDelay(Delay)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
setEnable(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
Sets the enable status of this PluginMenu to true if this PluginMenu is enabled.
setEnable(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginMenuItem
Sets true if this PluginMenuItem is enabled
setEndTime(double)
- Method in class jp.sbi.celldesigner.plugin.simulation.
PluginSimulation
setExponent(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
Sets the exponent of this PluginUnit.
setFast(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Sets the fast status of this PluginReaction to the given value (boolean)
setFile(File)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
setFirstRun(boolean)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
setFormula(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Sets the formula of this PluginKineticLaw.
setFormula(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginRule
Sets the Formula of this PluginRule.
setFormulaFromMath()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Deprecated.
setFormulaFromMath is removed in libSBML 3.x
setFrameLineWidth(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the FrameLineWidth of this PluginSpeciesAlias.
setFramePosition(double, double)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the position for this PluginSpeciesAlias.
setFrameSize(double, double)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the FrameSize (width & height) for this PluginSpeciesAlias
setFrmController(JFrame)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
setGateLink(ReactionLink)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
setGateSpeciesAliasesAndModificationType()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
setGateType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
setGene(PluginGene)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the PluginGene of this PluginSpeciesAlias.
setGLogicGateType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
setGraphicDisplayerFromInputData(String[][], String[][], boolean)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
setGraphicDisplayerFromInputData(String[][], String[][], int, Color, Color, Color, boolean)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
setHasOnlySubstanceUnits(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the HasOnlySubstanceUnits of this PluginSpecies.
setHeight(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the height of this PluginCompartment.
setHighlighted(boolean)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
setHomodimer(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the homodimer of this PluginSpeciesAlias.
setHypothetical(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the hypothetical of this PluginSpeciesAlias.
setId(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
Sets the id of this PluginBindingRegion.
setId(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
Sets the id of this PluginModificationRegion.
setId(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
Sets the id of this PluginModificationResidue.
setId(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
Sets the id of this PluginParameter.
setId(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the id of this PluginSpecies.
setInfoAll(String, String, String)
- Method in class jp.sbi.celldesigner.plugin.
PluginInformationBox
setInitialAmount(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the InitialAmount of this PluginSpecies.
setInitialConcentration(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the initialConcentration of this PluginSpecies.
setInnerPaintColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
setInnerPaintMode(String)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
setInnerWidth(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the InnerWidth of this PluginCompartment.
setIsActive(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets activity
setIsWinBeenUsing(boolean)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
setKind(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
Sets the kind of this PluginUnit.
setKind(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
setKineticLaw(PluginKineticLaw)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Sets the PluginKineticLaw of this PluginReaction.
setL1TypeCode(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginAssignmentRule
Sets the type of this PluginAssignmentRule.
setLineColor(Color)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets a lineColor of this PluginCompartment.
setLineColor(Color)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Sets the lineColor of this PluginReaction.
setLineWidth(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
Sets the line width of this GLogicGate.
setLineWidth(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Sets the line width of this PluginReaction.
setListOfAntiSenseRNAs(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginAntiSenseRNA of this PluginModel.
setListOfCompartments(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginCompartment of this PluginModel
setListOfCompartmentTypes(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
setListOfConstraints(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
setListOfEventAssignments(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
Sets the list of PluginEventAssignment of this PluginEvent.
setListOfEvents(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginEvent of this PluginModel.
setListOfFunctionDefinitions(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginFunctionDefinition of this PluginModel.
setListOfGenes(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginGene of this PluginModel.
setListOfGLogicGates(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
setListOfInitialAssignments(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
setListOfModifiers(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Sets the list of PluginModifierSpeciesReference of this PluginReaction.
setListOfParameters(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Sets the list of PluginParameter of this PluginKineticLaw.
setListOfParameters(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginParameter of this PluginModel.
setListOfPluginBindingRegion(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Sets the list of PluginBindingRegion of this PluginProtein.
setListOfPluginRegion(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
Sets the list of PluginModificationRegion
setListOfPluginRegion(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
Sets the list of PluginModificationRegion of this PluginGene.
setListOfPluginRegion(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
Sets the list of PluginModificationRegion of this PluginRNA.
setListOfPluginResidue(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Sets the list of PluginModificationResidue of this PluginProtein.
setListOfProducts(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Sets the list of Products (PluginSpeciesReference) of this PluginReaction.
setListOfProteins(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginProtein of this PluginModel.
setListOfReactants(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Sets the list of Reactants (PluginSpeciesReference) of this PluginReaction.
setListOfReactions(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the PluginReaction of this PluginModel.
setListOfRNAs(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginRNA of this PluginModel.
setListOfRules(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginRule of this PluginModel.
setListOfSpecies(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginSpecies of this PluginModel.
setListOfSpeciesAlias(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets listOfPluginSpeciesAlias of this PluginSpecies.
setListOfSpeciesTypes(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
setListOfUnitDefinitions(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the list of PluginUnitDefinition of this PluginModel
setListOfUnits(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
Sets the list of PluginUnit of this PluginUnitDefinition
setMassDatas(String[][])
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
setMath(ASTNode)
- Method in class jp.sbi.celldesigner.plugin.
PluginEventAssignment
Sets the Math of this PluginEventAssignment to the given ASTNode
setMath(ASTNode)
- Method in class jp.sbi.celldesigner.plugin.
PluginFunctionDefinition
Sets the Math of this PluginFunctionDefinition to the given ASTNode.
setMath(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginInitialAssignment
setMath(ASTNode)
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Sets the Math of this PluginKineticLaw to the given ASTNode.
setMath(ASTNode)
- Method in class jp.sbi.celldesigner.plugin.
PluginRule
Sets the Math of this PluginRule.
setMathFromFormula()
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Deprecated.
setFormulaFromMath is removed in libSBML 3.x
setMaxVaule(double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
setMaxVaule(double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
setMaxVauleColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
setMaxVauleColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
setMaxVauleColorDirectly(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
setMessage(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginConstraint
setMidPointInLine(Point2D.Double)
- Method in class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
Set the junction information of three linked lines if this link is three-linked line.
setMidVauleColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
setMidVauleColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
setMidVauleColorDirectly(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
setMinVaule(double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
setMinVaule(double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
setMinVauleColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
setMinVauleColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
setMinVauleColorDirectly(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
setMiriamDatas(Vector[])
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
setModelType(int)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
setModifications(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the list of PluginModification of this PluginSpeciesAlias.
setModificationType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
setModificationType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModifierSpeciesReference
Sets the modificationType of this PluginModifierSpeciesReference.
setMultiplier(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
Sets the multiplier of this PluginUnit.
setMyPostionInfomations(GStructure, ReactionLink)
- Static method in class jp.sbi.celldesigner.plugin.util.
PluginSystemOutUtils
setName(String)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
Sets the name of this PluginAntiSenseRNA
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
Sets the name of this PluginBindingRegion.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the name of this PluginCompartment
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartmentType
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
Sets the name of this PluginEvent.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginFunctionDefinition
Sets the name of this PluginFunctionDefinition.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
Sets the name of this PluginGene.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Sets the name of this PluginModel.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
Sets the name of this PluginModificationRegion
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
Sets the name of this PluginModificationResidue.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
Sets the name of this PluginParameter.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Sets the name of this PluginProtein.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Sets the name of this PluginReaction.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
Sets the name of this PluginRNA.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the name of this PluginSpecies.
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the name of this PluginSpeciesAlias
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesType
setName(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
Sets the name of this PluginUnitDefinition.
setNamePositionX(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets x position of this PluginCompartment name
setNamePositionY(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets y positon of this PluginCompartment name
setNotes(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
Sets the Notes of this PluginSBase.
setNotes(XMLNode)
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
setNumOfSteps(long)
- Method in class jp.sbi.celldesigner.plugin.simulation.
PluginSimulation
setOffset(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
Sets the offset of this PluginUnit.
setOldmiriamRelationIndex(int)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
setOpenFilename(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginOpenFileAndDoSomethingAction
setOuterWidth(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the outerWidth of this PluginCompartment.
setOutputFile(String)
- Method in class jp.sbi.celldesigner.plugin.simulation.
PluginSimulation
setOutside(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the outside of this PluginCompartment
setOutterLineColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
setParent(Object)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
setParentReaction(PluginReaction)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
setParentSBase(PluginSBase)
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
Sets the ParentSBase of this PluginSBase.
setPluginGLogicGateEventEnd()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
If setPluginGLogicGateEventStart() method has been called, called after last notifySBaseXXX method.
setPluginGLogicGateEventStart()
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
Must be called before first notifySBaseXXX method.
setPluginInformationBox(PluginInformationBox)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
setPluginInformationBox(PluginInformationBox)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
setPluginListOfStructuralStates(PluginListOf)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets a list of PluginStructuralStates
setPointsInLine(Vector)
- Method in class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
Set all the key points information in the line of the link.
setPos(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
Sets the position of this PluginModificationRegion.
setPosition(double, double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
setPositionToCompartment(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the position of this PluginSpecies
setProcessNodeIdx(int)
- Method in class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
Set the process node index which rely on the index of the subline included processNode in BaseReactionLink if this link have process node.
setProtein(PluginProtein)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the PluginProtein of this PluginSpeciesAlias.
setReactionLinkMembers(Vector)
- Method in class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
Set the members of this link, for instance the members will be Add_reactant, Add_product, modification link, gate information.
setReactionType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Sets the type of this PluginReaction.
setReferenceType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSimpleSpeciesReference
Sets the ReferenceType of this PluginSimpleSpeciesReference.
setRefsOfGateInReaction(SBModel, PluginGLogicGate)
- Method in class jp.sbi.celldesigner.plugin.
PluginGLogicGate
Sets the references of the GLogicGate.
setResidue(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModification
Sets the id of residue of this PluginModification.
setReversible(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Sets the reversible status of this PluginReaction to the given value (boolean).
setRNA(PluginRNA)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the PluginRNA of this PluginSpeciesAlias.
setSBModelFrameController(SBModelFrame)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
setScale(int)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnit
Sets the scale of this PluginUnit
setShowGuideMsgFlg(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginMassShowerAction
setShowGuideMsgFlg(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginOpenFileAndDoSomethingAction
setSide(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
Sets the type of side of this PluginModificationResidue
setSize(double, double)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
setSize(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
set size
setSize(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the size of this PluginCompartment
setSize(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
Sets the size of this PluginModificationRegion
setSize(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
sets size
setSpatialDimensions(long)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets SpatialDimensions of this PluginCompartment If value is not one of [0, 1, 2, 3] the function will have no effect (i.e.
setSpatialSizeUnits(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the spatialSizeUnits of this PluginSpecies.
setSpecies(PluginSpecies)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the PluginSpecies of this PluginSpeciesAlias.
setSpeciesType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
setStarted(boolean)
- Method in class jp.sbi.celldesigner.plugin.
CellDesignerPlugin
Sets the start flag
Note:
Set true if a plugin is invoked.
setState(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModification
Sets the state of this PluginModification to the given string.
setState(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginStructuralState
setStoichiometry(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesReference
Sets the stoichiometry of this PluginSpeciesReference.
setStoichiometryMath(StoichiometryMath)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesReference
Sets the stoichiometryMath of this PluginSpeciesReference.
setStoichiometryMath(ASTNode)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesReference
setSubstanceUnits(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Sets the substanceUnits of this PluginKineticLaw.
setSubstanceUnits(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the hasOnlySubstanceUnits field of this PluginSpecies.
setTargetGStructure()
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
setThickness(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets a thickness of this PluginCompartment.
setTimeUnits(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
Sets the timeUnits of this PluginEvent to the given string.
setTimeUnits(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Sets the timeUnits of this PluginKineticLaw.
setToolTipText(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginMenu
Sets the ToolTipText of this PluginMenu.
setToolTipText(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginMenuItem
Sets the ToolTipText of this PluginMenuItem.
setTrigger(ASTNode)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
Sets the trigger of this PluginEvent to the given ASTNode.
setTrigger(Trigger)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
setType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
Sets the type of this PluginAntiSenseRNA
setType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginBindingRegion
set type
setType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
Sets the type of this PluginGene.
setType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
Sets type of this PluginModificationRegion
setType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
sets type
setType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Sets the type of this PluginProtein.
setType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
Sets the type of this PluginRNA.
setType(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Sets the type of this PluginSpeciesAlias.
setTypeOfLine(String)
- Method in class jp.sbi.celldesigner.plugin.DataObject.
PluginRealLineInformationDataObjOfReactionLink
Set the type of the Link, only Add_reactant and Add_product has this type, which is Curve or Straight based on the property of the link.
setUnits(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the units of this PluginCompartment.
setUnits(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
Sets the unit of this PluginParameter.
setUnits(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Sets the units of this PluginSpecies
setUserDefaultEndColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
setUserDefaultMidColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
setUserDefaultStartColor(Color)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoShower.
InformationShowerMappingArrayMass
setUseValuesFromTriggerTime(boolean)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
setValue(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
Sets the value of this PluginParameter.
setVariable(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginAssignmentRule
Sets the variable of this PluginAssginmentRule
setVariable(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginEventAssignment
Sets the variable of this PluginEventAssignment to the given string.
setVariable(String)
- Method in class jp.sbi.celldesigner.plugin.
PluginRateRule
Sets the variable of this PluginRateRule.
setVolume(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the volume of this PluginCompartment.
setWidth(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the width of this PluginCompartment.
setX(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the x position of this PluginCompartment.
setY(double)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Sets the y position of this PluginCompartment.
showNoticeMsg(String, int)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerConfigWinFrm
showPopup(MouseEvent, double, double, GStructure)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoDisplayer.
InformationDisplayerAbst
SIDE_INSIDE
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
constants for side field
SIDE_NONE
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
constants for side field
SIDE_OUTSIDE
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
constants for side field
SIMPLE_MOLECULE
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
SIMPLE_MOLECULE
size()
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
SQUARE
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
SQUARE
SQUARE_CLOSEUP_NORTHEAST
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
SQUARE_CLOSEUP_NORTHEAST
SQUARE_CLOSEUP_NORTHWEST
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
SQUARE_CLOSEUP_NORTHWEST
SQUARE_CLOSEUP_SOUTHEAST
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
SQUARE_CLOSEUP_SOUTHEAST
SQUARE_CLOSEUP_SOUTHWEST
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginCompartmentSymbolType
SQUARE_CLOSEUP_SOUTHWEST
STATE_ACETYLATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
for state field
STATE_DONT_CARE
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
for state field
STATE_EMPTY
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
for state field
STATE_GLYCOSYLATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
stateフィールド用の定数
STATE_HISTON1
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
for state field
STATE_HISTON2
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
for state field
STATE_HYDROXYLATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
for state field
STATE_METHYLATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
for state field
STATE_MYRISTOYLATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
stateフィールド用の定数
STATE_PALMYTOYLATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
stateフィールド用の定数
STATE_PHOSPHORYLATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
for state field
STATE_PRENYLATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
stateフィールド用の定数
STATE_PROTONATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
stateフィールド用の定数
STATE_SULFATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
stateフィールド用の定数
STATE_TRANSITION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
STATE_TRANSITION
STATE_UBIQUITINATED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
for state field
STATE_UNKNOWN
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModification
for state field
stateChangedToPercent(int, boolean)
- Method in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
MappingArrayMassShowerMainWinFrm
STR_CLOSED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginStructuralState
STR_EMPTY
- Static variable in class jp.sbi.celldesigner.plugin.
PluginStructuralState
STR_EMPTY_STATE
- Static variable in class jp.sbi.celldesigner.plugin.
PluginInformationBox
STR_OPEN
- Static variable in class jp.sbi.celldesigner.plugin.
PluginStructuralState
STR_OPEN_STATE
- Static variable in class jp.sbi.celldesigner.plugin.
PluginInformationBox
STR_USER_DEFINED
- Static variable in class jp.sbi.celldesigner.plugin.
PluginStructuralState
strID
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
strName
- Static variable in class jp.sbi.celldesigner.plugin.InfoCenter.InfoUI.
RsltDtBindingFrm
T
toArray()
- Method in class jp.sbi.celldesigner.plugin.
PluginListOf
Convers this PluginListOf to array The elements in the array refer to the same elements of this PluginListOf
toSBML()
- Method in class jp.sbi.celldesigner.plugin.
PluginSBase
toSBML
toSBMLString()
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
TRANSCRIPTION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
TRANSCRIPTION
TRANSLATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
TRANSLATION
TRANSPORT
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
TRANSPORT
TRIGGER
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
TRUNCATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
TRUNCATION
TYPE_BINDINGREGION
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
constants for type field
TYPE_CODING_REGION
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
TYPE_MODIFICATION_SITE
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
TYPE_PROTEIN_BINDING_DOMAIN
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
constants for type field
TYPE_REGULATORY_REGION
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
TYPE_RESIDUE
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationResidue
constants for type field
TYPE_TRANSCRIPTION_STARTING_SITE_L
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
TYPE_TRANSCRIPTION_STARTING_SITE_R
- Static variable in class jp.sbi.celldesigner.plugin.
PluginModificationRegion
U
UNKNOWN
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginSpeciesSymbolType
UNKNOWN
UNKNOWN_CATALYSIS
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
UNKNOWN_CATALYSIS
UNKNOWN_INHIBITION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
UNKNOWN_INHIBITION
UNKNOWN_NEGATIVE_INFLUENCE
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
UNKNOWN_POSITIVE_INFLUENCE
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
UNKNOWN_REDUCED_MODULATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
UNKNOWN_REDUCED_PHYSICAL_STIMULATION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
UNKNOWN_REDUCED_TRIGGER
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
UNKNOWN_TRANSITION
- Static variable in class jp.sbi.celldesigner.plugin.util.
PluginReactionSymbolType
UNKNOWN_TRANSITION
update(PluginAntiSenseRNA)
- Method in class jp.sbi.celldesigner.plugin.
PluginAntiSenseRNA
Updates all properties to the same as the given PluginAntiSenseRNA.
update(PluginCompartment)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartment
Updates all properties of this PluginCompartment to the same as the given PluginCompartment.
update(PluginCompartmentType)
- Method in class jp.sbi.celldesigner.plugin.
PluginCompartmentType
update(PluginConstraint)
- Method in class jp.sbi.celldesigner.plugin.
PluginConstraint
update(PluginEvent)
- Method in class jp.sbi.celldesigner.plugin.
PluginEvent
Update all properties of this PluginEvent to the same as the given PluginEvent.
update(PluginEventAssignment)
- Method in class jp.sbi.celldesigner.plugin.
PluginEventAssignment
Updates all properties of this PluginEventAssignement to the same as the given PluginEventAssignment.
update(PluginFunctionDefinition)
- Method in class jp.sbi.celldesigner.plugin.
PluginFunctionDefinition
Updates all properties of this PluginFunctionDefinition to the same as the given PluginFunctionDefinition.
update(PluginGene)
- Method in class jp.sbi.celldesigner.plugin.
PluginGene
Update all properties of this PluginGene to the same as the given PluginGene.
update(PluginInitialAssignment)
- Method in class jp.sbi.celldesigner.plugin.
PluginInitialAssignment
update(PluginKineticLaw)
- Method in class jp.sbi.celldesigner.plugin.
PluginKineticLaw
Update all properties of this PluginKineticLaw same as the given PluginKineticLaw.
update(PluginModel)
- Method in class jp.sbi.celldesigner.plugin.
PluginModel
Update all properties of this PluginModel to the same as the given PluginModel
update(PluginParameter)
- Method in class jp.sbi.celldesigner.plugin.
PluginParameter
Update all properties of this PluginParameter to the same as the given PluginParameter
update(PluginProtein)
- Method in class jp.sbi.celldesigner.plugin.
PluginProtein
Update all properties of this PluginProtein to the same as the given PluginProtein
update(PluginRateRule)
- Method in class jp.sbi.celldesigner.plugin.
PluginRateRule
Update all properties of this PluginRateRule to the same as the given PluginRateRule.
update(PluginReaction)
- Method in class jp.sbi.celldesigner.plugin.
PluginReaction
Update all properties of this PluginReaction to the same as the given PluginReaction.
update(PluginRNA)
- Method in class jp.sbi.celldesigner.plugin.
PluginRNA
Update all properties of this PluginRNA to the same as the given PluginRNA.
update(PluginRule)
- Method in class jp.sbi.celldesigner.plugin.
PluginRule
Update all properties of this PluginRule to the same as the given PluginRule.
update(PluginSpecies)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpecies
Update all properties of this PluginSpecies to the same as the given PluginSpecies.
update(PluginSpeciesAlias)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesAlias
Update all properties of this PluginSpeciesAlias to the same as the given PluginSpeciesAlias.
update(PluginSpeciesType)
- Method in class jp.sbi.celldesigner.plugin.
PluginSpeciesType
update(PluginUnitDefinition)
- Method in class jp.sbi.celldesigner.plugin.
PluginUnitDefinition
Update all properties of this PluginUnitDefinition to the same as the given PluginUnitDefinition.
A
B
C
D
E
F
G
H
I
J
K
M
N
O
P
R
S
T
U
Overview
Package
Class
Tree
Deprecated
Index
Help
PREV NEXT
FRAMES
NO FRAMES
All Classes