All Differences Index

All Differences

Removals

Additions

Changes

Bold is New, ~~strike~~ is deleted

A C D E F G H I J K L M O P Q R S T U V W X TOP
AbstractASTNode
AbstractASTNodePlugin
AbstractMathContainer
  org.sbml.jsbml
  AbstractMathContainer (String, int, int) constructor
AbstractNamedSBase
AbstractReaderWriter
AbstractSBase
  org.sbml.jsbml
  AbstractSBase (String) constructor
  AbstractSBase (String, int, int) constructor
  AbstractSBase (String, String, int, int) constructor
AbstractTreeNode
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)
Assignment
ASTArithmeticOperatorNode
ASTBinaryFunctionNode
ASTBoolean
ASTCiFunctionNode
ASTCiNumberNode
ASTCnExponentialNode
ASTCnIntegerNode
ASTCnNumberNode
ASTCnRationalNode
ASTCnRealNode
ASTConstantNumber
ASTCSymbolAvogadroNode
ASTCSymbolDelayNode
ASTCSymbolTimeNode
ASTDivideNode
ASTFunction
ASTHyperbolicNode
ASTLambdaFunctionNode
ASTLogarithmNode
ASTLogicalOperatorNode
ASTMinusNode
ASTNode
ASTNodeCompiler
ASTNodePlugin
ASTNumber
ASTPiecewiseFunctionNode
ASTPlusNode
ASTPowerNode
ASTQualifierNode
ASTRelationalOperatorNode
ASTRootNode
ASTTimesNode
ASTTrigonometricNode
ASTUnaryFunctionNode

C A D E F G H I J K L M O P Q R S T U V W X TOP
checkAttribute (String)
checkConsistencyOffline ()
CHILD_ELEMENT_NAMES
Compartment
compileSemanticAnnotations (ASTNode)
Constraint
createInvalidUnit ()
createPlugin (String)
createPluginFor (ASTNode)
Creator
CVTerm

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

E A C D F G H I J K L M O P Q R S T U V W X 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
Event
EventAssignment
EXPONENTIALE

F A C D E G H I J K L M O P Q R S T U V W X TOP
findUniqueSBase (String)
FindUnitsCompiler
FORMULA_ARGUMENT_SEPARATOR
FormulaCompiler
  org.sbml.jsbml.math.compiler
  org.sbml.jsbml.util.compilers
FunctionDefinition

G A C D E F H I J K L M O P Q R S T U V W X 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 J K L M O P Q R S T U V W X 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 J K L M O P Q R S T U V W X TOP
IdFilter
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
in org.sbml.jsbml.util.compilers.LaTeXCompiler
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
INVERSE_TRIGONOMETRIC_PREFIX
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 ()

J A C D E F G H I K L M O P Q R S T U V W X TOP
JSBML
JSBML_MATH_COUNT
JSBML_WRONG_SBO_TERM

K A C D E F G H I J L M O P Q R S T U V W X TOP
KineticLaw

L A C D E F G H I J K M O P Q R S T U V W X TOP
LaTeXCompiler
ListOf
  org.sbml.jsbml
  ListOf (String) constructor
  ListOf (String, int, int) constructor
  ListOf (String, String, int, int) constructor
listOfListeners
ListOfWithName
logicalOperationFunction (String, List<ASTNode>)

M A C D E F G H I J K L O P Q R S T U V W X TOP
MathMLCompiler
MathMLParser
MathMLStaxParser
MathMLXMLStreamCompiler
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
MetaIdFilter
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
Model
org.sbml.jsbml
org.sbml.jsbml.ext
org.sbml.jsbml.math
org.sbml.jsbml.math.compiler
org.sbml.jsbml.ontology
org.sbml.jsbml.util
org.sbml.jsbml.util.compilers
org.sbml.jsbml.util.filters
org.sbml.jsbml.validator.offline
org.sbml.jsbml.validator.offline.constraints
org.sbml.jsbml.validator.offline.constraints.helper
org.sbml.jsbml.validator.offline.factory
org.sbml.jsbml.xml
org.sbml.jsbml.xml.parsers
otherListName

P A C D E F G H I J K L M O Q R S T U V W X TOP
PackageParser
Parameter
parseMathML (String)
PIECEWISE_ID
printASTNode ()
printCreator ()
printCVTerm ()
printSpeciesReference
  type () in org.sbml.jsbml.SimpleSpeciesReference
  type () in org.sbml.jsbml.SpeciesReference
printUnit ()
Priority
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 J K L M O P R S T U V W X 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 J K L M O P Q S T U V W X TOP
Reaction
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
READING_IN_PROGRESS
ReadingParser
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)
Rule

S A C D E F G H I J K L M O P Q R T U V W X TOP
SBase
SBMLCoreParser
SBMLDocument
SBMLErrorLog
SBMLRDFAnnotationParser
SBO
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)
SIdFilter
SimpleSpeciesReference
SimpleTreeNodeChangeListener
Species
SpeciesReference
storeElementsOrder (String, Object)

T A C D E F G H I J K L M O P Q R S U V W X TOP
Term
  org.sbml.jsbml.ontology
  Term (Term) constructor
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
Trigger
Triple
  org.sbml.jsbml.ontology
  Triple (Triple) constructor

U A C D E F G H I J K L M O P Q R S T V W X TOP
UniqueNamedSBase
UniqueSId
Unit
UnitDefinition
UnitsCompiler
~~UNKNOWN_ATTRIBUTES~~
~~UNKNOWN_ELEMENTS~~
UNKNOWN_XML
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)
URI_RATE_OF_DEFINITION

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

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

X A C D E F G H I J K L M O P Q R S T U V W TOP
XMLAttributes
XMLNamespaces
XMLNodeReader
XMLToken
XMLTriple