All Methods
Removals
Additions
Changes
Bold is New, strike is deleted


A  C D E F G H I L M P Q R S T U V W TOP
add
  type  (SBMLError) in org.sbml.jsbml.SBMLErrorLog
  type  (Option) in org.sbml.jsbml.SBMLErrorLog
addExtension (String, ASTNodePlugin)
addPlugin (String, ASTNodePlugin)
addResource (int, String)
addSemanticsAnnotation (XMLNode)

C  A D E F G H I L M P Q R S T U V W TOP
checkAttribute (String)
checkConsistencyOffline ()
compileSemanticAnnotations (ASTNode)
createInvalidUnit ()
createPlugin (String)
createPluginFor (ASTNode)

D  A C E F G H I L M P Q R S T U V W TOP
disablePackage (String)

E  A C D F G H I L M P Q R S T U V W TOP
enablePackage
  type  (String) in org.sbml.jsbml.ASTNode
  type  (String, boolean) in org.sbml.jsbml.ASTNode
equals
  type  (Object) in org.sbml.jsbml.AbstractNamedSBase
  type  (Object) in org.sbml.jsbml.FunctionDefinition

F  A C D E G H I L M P Q R S T U V W TOP
findUniqueSBase (String)

G  A C D E F H I L M P Q R S T U V W TOP
getAllostericActivator ()
getAllostericInhibitor ()
getAssignmentRuleByVariable (String)
getBiochemicalReaction ()
getCompetetiveInhibitor ()
getCompetitiveInhibitor ()
getComplexAssembly ()
getConversion ()
getDegradation ()
getDNA ()
getDNASegment ()
getElementByMetaId
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
getElementBySId
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.Model
  type  (String) in org.sbml.jsbml.SBase
getEnthalpyChange ()
getEntropyChange ()
getEquilibriumConstant ()
getExtension (String)
getExtensionCount ()
getExtensionPackages ()
getGeneticInteraction ()
getGibbsFreeEnergyChange ()
getId
  type  () in org.sbml.jsbml.AbstractNamedSBase
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.FunctionDefinition
  type  () in org.sbml.jsbml.SBase
getInitialAssignment (String)
getInitialAssignmentById (String)
getInitialAssignmentBySymbol (String)
getIonicStrength ()
getIrreversibleInhibitor ()
getListOfSemanticsAnnotations ()
getLogger ()
getModifierUnknownActivity ()
getMolecularInteraction ()
getName
  type  () in org.sbml.jsbml.AbstractNamedSBase
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.FunctionDefinition
  type  () in org.sbml.jsbml.SBase
getNonAllostericActivator ()
getNonCompetetiveInhibitor ()
getNonCompetitiveInhibitor ()
getNumberOfNonEmptyChildElement (XMLNode)
getNumPlugins ()
getNumSemanticsAnnotations ()
getOtherListName ()
getpH ()
getPlugin (String)
getPMg ()
getPotentiator ()
getRateOf
  type  (String) in org.sbml.jsbml.util.compilers.ASTNodeCompiler
  type  (String) in org.sbml.jsbml.util.compilers.FindUnitsCompiler
  type  (String) in org.sbml.jsbml.util.compilers.FormulaCompiler
  type  (String) in org.sbml.jsbml.util.compilers.LaTeXCompiler
  type  (String) in org.sbml.jsbml.util.compilers.MathMLCompiler
  type  (String) in org.sbml.jsbml.util.compilers.UnitsCompiler
getRateRuleByVariable (String)
getResource (int)
getRNASegment ()
getRule (String)
getRuleById (String)
getRuleByVariable (String)
getSBaseById (String)
getSemanticsAnnotation (int)
getSmallMolecule ()
getTemplateReaction ()
getTemplateReactionRegulation ()
getTerm ()
getThermodynamicTemperature ()
getTransportWithBiochemicalReaction ()
getTriple ()
getUncompetitiveInhibitor ()
getUnitDefinitionById (String)
getUnknownQualifierName ()

H  A C D E F G I L M P Q R S T U V W TOP
hashCode
  type  () in org.sbml.jsbml.AbstractNamedSBase
  type  () in org.sbml.jsbml.FunctionDefinition
hasTerm
  type  (int) in org.sbml.jsbml.SBO
  type  (String) in org.sbml.jsbml.SBO

I  A C D E F G H L M P Q R S T U V W TOP
implies
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.ASTNodeCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FindUnitsCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FormulaCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.LaTeXCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.MathMLCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.UnitsCompiler
initDefaults
  type  (int, int, boolean) in org.sbml.jsbml.Compartment
  type  (int, int, boolean) in org.sbml.jsbml.Parameter
  type  (int, int, boolean) in org.sbml.jsbml.Reaction
  type  (int, int, boolean) in org.sbml.jsbml.Species
  type  (int, int, boolean) in org.sbml.jsbml.SpeciesReference
isExtendedByOtherPackages ()
isIdMandatory
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.SBase
isListOfCompartmentsEmpty ()
isListOfCompartmentTypesEmpty ()
isListOfConstraintsEmpty ()
isListOfEventAssignmentEmpty ()
isListOfEventsEmpty ()
isListOfFunctionDefinitionsEmpty ()
isListOfInitialAssignmentsEmpty ()
isListOfLocalParametersEmpty ()
isListOfModifiersEmpty ()
isListOfParametersEmpty ()
isListOfProductsEmpty ()
isListOfReactantsEmpty ()
isListOfReactionsEmpty ()
isListOfRulesEmpty ()
isListOfSpeciesEmpty ()
isListOfSpeciesTypesEmpty ()
isListOfUnitDefinitionEmpty ()
isListOfUnitsEmpty ()
isLiteral ()
isPackageEnabled (String)
isPackageURIEnabled (String)
isReadingInProgress ()
isSemantics ()
isSetId
  type  () in org.sbml.jsbml.AbstractNamedSBase
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.FunctionDefinition
  type  () in org.sbml.jsbml.SBase
isSetName
  type  () in org.sbml.jsbml.AbstractNamedSBase
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.FunctionDefinition
  type  () in org.sbml.jsbml.SBase
isSetPlugin (String)
isVariantOfDimensionless ()

L  A C D E F G H I M P Q R S T U V W TOP
logicalOperationFunction (String, List<ASTNode>)

M  A C D E F G H I L P Q R S T U V W TOP
max
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.ASTNodeCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FindUnitsCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FormulaCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.LaTeXCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.MathMLCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.UnitsCompiler
min
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.ASTNodeCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FindUnitsCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FormulaCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.LaTeXCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.MathMLCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.UnitsCompiler

P  A C D E F G H I L M Q R S T U V W TOP
parseMathML (String)
printASTNode ()
printCreator ()
printCVTerm ()
printSpeciesReference
  type  () in org.sbml.jsbml.SimpleSpeciesReference
  type  () in org.sbml.jsbml.SpeciesReference
printUnit ()
processAttribute
  type  (String, String, String, String, String, boolean, Object) in org.sbml.jsbml.xml.parsers.AbstractReaderWriter
  type  (String, String, String, String, String, boolean, Object) in org.sbml.jsbml.xml.parsers.MathMLParser
  type  (String, String, String, String, String, boolean, Object) in org.sbml.jsbml.xml.parsers.MathMLStaxParser
  type  (String, String, String, String, String, boolean, Object) in org.sbml.jsbml.xml.parsers.ReadingParser
  type  (String, String, String, String, String, boolean, Object) in org.sbml.jsbml.xml.parsers.SBMLCoreParser
  type  (String, String, String, String, String, boolean, Object) in org.sbml.jsbml.xml.parsers.XMLNodeReader
processUnknownAttribute (String, String, String, String, Object)
processUnknownElement (String, String, String, Object)

Q  A C D E F G H I L M P R S T U V W TOP
quotient
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.ASTNodeCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FindUnitsCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FormulaCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.LaTeXCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.MathMLCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.UnitsCompiler

R  A C D E F G H I L M P Q S T U V W TOP
readAttribute
  type  (String, String, String) in org.sbml.jsbml.AbstractNamedSBase
  type  (String, String, String) in org.sbml.jsbml.FunctionDefinition
  type  (String, String, String) in org.sbml.jsbml.ListOf
rem
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.ASTNodeCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FindUnitsCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FormulaCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.LaTeXCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.MathMLCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.UnitsCompiler
remove (String)
removeResourceURI (int)

S  A C D E F G H I L M P Q R T U V W TOP
setId
  type  (String) in org.sbml.jsbml.AbstractNamedSBase
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.FunctionDefinition
  type  (String) in org.sbml.jsbml.SBase
setLogger (XMLLogger)
setName
  type  (String) in org.sbml.jsbml.AbstractNamedSBase
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.FunctionDefinition
  type  (String) in org.sbml.jsbml.SBase
setOtherListName (String)
setUnknownQualifierName (String)
storeElementsOrder (String, Object)

T  A C D E F G H I L M P Q R S U V W TOP
times (T[])
toFormula ()
toString
  type  () in org.sbml.jsbml.AbstractMathContainer
  type  () in org.sbml.jsbml.AbstractNamedSBase
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.CVTerm
  type  () in org.sbml.jsbml.Creator
  type  () in org.sbml.jsbml.EventAssignment
  type  () in org.sbml.jsbml.FunctionDefinition
  type  () in org.sbml.jsbml.KineticLaw
  type  () in org.sbml.jsbml.ListOf
  type  () in org.sbml.jsbml.SimpleSpeciesReference
  type  () in org.sbml.jsbml.SpeciesReference
  type  () in org.sbml.jsbml.Unit
  type  () in org.sbml.jsbml.math.ASTArithmeticOperatorNode
  type  () in org.sbml.jsbml.math.ASTBinaryFunctionNode
  type  () in org.sbml.jsbml.math.ASTBoolean
  type  () in org.sbml.jsbml.math.ASTCSymbolAvogadroNode
  type  () in org.sbml.jsbml.math.ASTCSymbolDelayNode
  type  () in org.sbml.jsbml.math.ASTCSymbolTimeNode
  type  () in org.sbml.jsbml.math.ASTCiFunctionNode
  type  () in org.sbml.jsbml.math.ASTCiNumberNode
  type  () in org.sbml.jsbml.math.ASTCnExponentialNode
  type  () in org.sbml.jsbml.math.ASTCnIntegerNode
  type  () in org.sbml.jsbml.math.ASTCnNumberNode
  type  () in org.sbml.jsbml.math.ASTCnRationalNode
  type  () in org.sbml.jsbml.math.ASTCnRealNode
  type  () in org.sbml.jsbml.math.ASTConstantNumber
  type  () in org.sbml.jsbml.math.ASTDivideNode
  type  () in org.sbml.jsbml.math.ASTFunction
  type  () in org.sbml.jsbml.math.ASTHyperbolicNode
  type  () in org.sbml.jsbml.math.ASTLambdaFunctionNode
  type  () in org.sbml.jsbml.math.ASTLogarithmNode
  type  () in org.sbml.jsbml.math.ASTLogicalOperatorNode
  type  () in org.sbml.jsbml.math.ASTMinusNode
  type  () in org.sbml.jsbml.math.ASTNumber
  type  () in org.sbml.jsbml.math.ASTPiecewiseFunctionNode
  type  () in org.sbml.jsbml.math.ASTPlusNode
  type  () in org.sbml.jsbml.math.ASTPowerNode
  type  () in org.sbml.jsbml.math.ASTQualifierNode
  type  () in org.sbml.jsbml.math.ASTRelationalOperatorNode
  type  () in org.sbml.jsbml.math.ASTRootNode
  type  () in org.sbml.jsbml.math.ASTTimesNode
  type  () in org.sbml.jsbml.math.ASTTrigonometricNode
  type  () in org.sbml.jsbml.math.ASTUnaryFunctionNode
  type  () in org.sbml.jsbml.math.AbstractASTNode
  type  () in org.sbml.jsbml.xml.XMLToken

U  A C D E F G H I L M P Q R S T V W TOP
unsetExtension (String)
unsetId
  type  () in org.sbml.jsbml.AbstractNamedSBase
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.FunctionDefinition
  type  () in org.sbml.jsbml.SBase
unsetName
  type  () in org.sbml.jsbml.AbstractNamedSBase
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.FunctionDefinition
  type  () in org.sbml.jsbml.SBase
unsetPlugin (String)

V  A C D E F G H I L M P Q R S T U W TOP
vector (T[])

W  A C D E F G H I L M P Q R S T U V TOP
writeXMLAttributes
  type  () in org.sbml.jsbml.AbstractNamedSBase
  type  () in org.sbml.jsbml.FunctionDefinition