All Methods

Removals

Additions

Changes

Bold is New, strike is deleted

A  C D E F G H I L M O P R S T U V W TOP
accept
  type  (SBase) in org.sbml.jsbml.KineticLaw
  type  (SBase) in org.sbml.jsbml.Model
addAll
  type  (int, Collection<? extends T>) in org.sbml.jsbml.ListOf
  type  (Collection<? extends T>) in org.sbml.jsbml.ListOf
addAllChangeListeners
  type  (Collection<TreeNodeChangeListener>, boolean) in org.sbml.jsbml.AbstractTreeNode
  type  (Collection<TreeNodeChangeListener>, boolean) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
addAnnotationNamespace (String, String, String)
addDeclaredNamespace (String, String)
addExtension
  type  (String, SBasePlugin) in org.sbml.jsbml.AbstractSBase
  type  (String, Annotation) in org.sbml.jsbml.Annotation
  type  (String, SBasePlugin) in org.sbml.jsbml.SBase
addIOProgressListener
  type  (IOProgressListener) in org.sbml.jsbml.SBMLInputConverter
  type  (IOProgressListener) in org.sbml.jsbml.SBMLOutputConverter
addNamespace
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String, String, String) in org.sbml.jsbml.SBMLDocument
  type  (String) in org.sbml.jsbml.SBase
addPlugin
  type  (String, SBasePlugin) in org.sbml.jsbml.AbstractSBase
  type  (String, SBasePlugin) in org.sbml.jsbml.SBase
addRDFAnnotationNamespace (String, String, String)
append (SBase)
appendNoRDFAnnotation (String)
appendNotes
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase

C  A D E F G H I L M O P R S T U V W TOP
checkBrackets (ASTNode)
checkDenominatorBrackets (ASTNode)
clearUserObjects
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.util.TreeNodeWithChangeSupport
clone ()
concatStringBuilder (Object[])
containsReaction (String)
containsUndeclaredUnits
  type  () in org.sbml.jsbml.Compartment
  type  () in org.sbml.jsbml.Species
containsUserObjectKey
  type  (Object) in org.sbml.jsbml.AbstractTreeNode
  type  (Object) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
convertModel (T)
convertSBMLDocument
  type  (File) in org.sbml.jsbml.SBMLInputConverter
  type  (String) in org.sbml.jsbml.SBMLInputConverter
convertStringToXMLNode (String)
convertXMLNodeToString (XMLNode)
createHistory ()
createModel ()
createPlugin
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
createSpecies (String, String, Compartment)
createSpeciesType
  type  () in org.sbml.jsbml.Model
  type  (String) in org.sbml.jsbml.Model

D  A C E F G H I L M O P R S T U V W TOP
disablePackage
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBMLDocument
  type  (String) in org.sbml.jsbml.SBase

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

F  A C D E G H I L M O P R S T U V W TOP
fill
  type  (int, char) in org.sbml.jsbml.util.StringTools
  type  (int, char, String) in org.sbml.jsbml.util.StringTools
filter
  type  (Filter) in org.sbml.jsbml.AbstractTreeNode
  type  (Filter, boolean) in org.sbml.jsbml.AbstractTreeNode
  type  (Filter, boolean, boolean) in org.sbml.jsbml.AbstractTreeNode
  type  (Filter) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
  type  (Filter, boolean) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
  type  (Filter, boolean, boolean) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
filterCVTerms
  type  (Qualifier, boolean, String[]) in org.sbml.jsbml.AbstractSBase
  type  (Qualifier, String, boolean) in org.sbml.jsbml.AbstractSBase
  type  (Qualifier, boolean, String[]) in org.sbml.jsbml.SBase
  type  (Qualifier, String, boolean) in org.sbml.jsbml.SBase
filterList (Filter)
filterResources
  type  (String) in org.sbml.jsbml.CVTerm
  type  (String[]) in org.sbml.jsbml.CVTerm
  type  (Pattern[]) in org.sbml.jsbml.CVTerm
findIdentical (UnitDefinition)
firePropertyChange (String, Object, Object)
formulaToString (ASTNode, FormulaCompiler)

G  A C D E F H I L M O P R S T U V W TOP
getActivator ()
getAnnotationBuilder ()
getAnnotationNamespaces ()
getAnnotationString
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.SBase
getArgumentCount ()
getAssociation ()
getAttributes ()
getBiologicalQualifierFor (String)
getChild (int)
getChildElement (String, String)
getChildElements (String, String)
getCompartment ()
getCompartmentCount ()
getCompartmentType
  type  (int) in org.sbml.jsbml.Model
  type  (String) in org.sbml.jsbml.Model
getCompartmentTypeCount ()
getConstraintCount ()
getConsumption ()
getCreatorCount ()
getCVTermCount
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.Annotation
  type  () in org.sbml.jsbml.SBase
getDeclaredNamespaces ()
getDelayCount ()
getDissociation ()
getElementByMetaId (String)
getErrorCount
  type  () in org.sbml.jsbml.SBMLDocument
  type  () in org.sbml.jsbml.SBMLErrorLog
getEventAssignment (String)
getEventAssignmentCount
  type  () in org.sbml.jsbml.Event
  type  () in org.sbml.jsbml.Model
getEventCount ()
getExtension
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.Annotation
  type  (String) in org.sbml.jsbml.SBase
getExtensionCount
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.SBase
getExtensionPackages
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.SBase
getFullAnnotation ()
getFullAnnotationString ()
getFunctionDefinitionCount ()
getIdManager (SBase)
getInhibition ()
getInitialAssignmentCount ()
getKineticLawCount ()
getListOfCount ()
getListOfSBMLElementsToWrite (Object)
getLocalParameterCount ()
getLocation ()
getMacromolecule ()
getMathContainerCount ()
getMessageString ()
getModelQualifierFor (String)
getModifiedDateCount ()
getModifierCount ()
getModifierSpeciesReferenceCount ()
getModifierSpeciesReferences ()
getModulation ()
getNamedSBaseCount ()
getNamedSBaseWithDerivedUnitCount ()
getNamespace
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.SBase
getNamespaces
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.Annotation
  type  () in org.sbml.jsbml.SBase
  type  () in org.sbml.jsbml.xml.parsers.MathMLParser
  type  () in org.sbml.jsbml.xml.parsers.MathMLStaxParser
  type  () in org.sbml.jsbml.xml.parsers.ReadingParser
  type  () in org.sbml.jsbml.xml.parsers.SBMLCoreParser
  type  () in org.sbml.jsbml.xml.parsers.WritingParser
getNecessaryStimulation ()
getNonCovalentComplex ()
getNonRDFannotation ()
getNonRDFannotationAsString ()
getNotesString
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.SBase
getNumChildren
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.xml.XMLNode
getNumErrors
  type  () in org.sbml.jsbml.SBMLInputConverter
  type  (Object) in org.sbml.jsbml.SBMLOutputConverter
getNumPlugins
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.SBase
getOriginalModel ()
getOtherAttribute (String)
getOtherAttributes ()
getPackage ()
getPackageRequired (String)
getParameterCount ()
getParent ()
getPertubingAgent ()
getPkgRequired (String)
getPlugin
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
getProcess ()
getProductCount ()
getProduction ()
getQualifier ()
getQuantityCount ()
getQuantityWithUnitCount ()
getRDFAnnotationNamespaces ()
getReactantCount ()
getReactionCount ()
getReadingParsers (String)
getResourceCount ()
getRoot
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.util.TreeNodeWithChangeSupport
getRuleCount ()
getSBaseCount ()
getSBaseWithDerivedUnitCount ()
getSBMLDocumentNamespaces ()
getSideProduct ()
getSideSubstrate ()
getSpatialSizeUnits ()
getSpatialSizeUnitsInstance ()
getSpeciesCount ()
getSpeciesReferenceCount ()
getSpeciesType
  type  (int) in org.sbml.jsbml.Model
  type  (String) in org.sbml.jsbml.Model
getSpeciesTypeCount ()
getSpeciesWithBoundaryConditionCount ()
getStimulation ()
getStoichiometryMathCount ()
getSymbolCount ()
getTerm
  type  () in org.sbml.jsbml.SBO.Term
  type  () in org.sbml.jsbml.util.filters.SBOFilter
getTerms ()
getTriggerCount ()
getTriple ()
getUnitCount
  type  () in org.sbml.jsbml.Model
  type  () in org.sbml.jsbml.UnitDefinition
getUnitDefinitionCount ()
getUnits ()
getUnitsInstance ()
getUserObject
  type  (Object) in org.sbml.jsbml.ASTNode
  type  (Object) in org.sbml.jsbml.AbstractTreeNode
  type  (Object) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
getVariableCount ()
getWriteWarnings (T)
getWritingParsers (String)

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

I  A C D E F G H L M O P R S T U V W TOP
initDefaults (int, int, boolean)
initializeAnnotationParsers ()
initializePackageParserNamespaces
  type  () in org.sbml.jsbml.xml.stax.SBMLReader
  type  () in org.sbml.jsbml.xml.stax.SBMLWriter
insertNoRDFAnnotation (String, int)
isAssociation (int)
isDissociation (int)
isExtendedByOtherPackages
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.SBase
isIgnoredPackage (String)
isIgnoredPkg (String)
isPackageEnabled
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBMLDocument
  type  (String) in org.sbml.jsbml.SBase
isPackageEnabledOrDisabled (String)
isPackageURIEnabled
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
isPkgEnabled
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
isPkgURIEnabled
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
isPredefined (UnitDefinition)
isProcess (int)
isSetOtherAttributes ()
isSetPackageRequired (String)
isSetPkgRequired (String)
isSetPlugin
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
isSetQualifier ()
isSetSpatialSizeUnitsInstance ()
isSetTypeQualifier ()
isSetUserObject ()
isSetUserObjects
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.util.TreeNodeWithChangeSupport
isValidMetaId (String)
isVector ()

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

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

O  A C D E F G H I L M P R S T U V W TOP
of (Comparable<? super L>, Comparable<? super V>)

P  A C D E F G H I L M O R S T U V W TOP
parseFormula (String, IFormulaParser)
parseSBMLShort (String)
printErrors ()
processAttribute
  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
processStartElement
  type  (String, String, String, boolean, boolean, Object) in org.sbml.jsbml.xml.parsers.MathMLParser
  type  (String, String, String, boolean, boolean, Object) in org.sbml.jsbml.xml.parsers.MathMLStaxParser
  type  (String, String, String, boolean, boolean, Object) in org.sbml.jsbml.xml.parsers.ReadingParser
  type  (String, String, String, boolean, boolean, Object) in org.sbml.jsbml.xml.parsers.SBMLCoreParser
putUserObject
  type  (Object, Object) in org.sbml.jsbml.AbstractTreeNode
  type  (Object, Object) in org.sbml.jsbml.util.TreeNodeWithChangeSupport

R  A C D E F G H I L M O P S T U V W TOP
readMathML (String, TreeNodeChangeListener, MathContainer)
register
  type  (SBase) in org.sbml.jsbml.KineticLaw
  type  (SBase) in org.sbml.jsbml.Model
relation (ASTNode, String, ASTNode)
remove (String)
removeAllTreeNodeChangeListeners
  type  (boolean) in org.sbml.jsbml.AbstractTreeNode
  type  (boolean) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
removeChild
  type  (long) in org.sbml.jsbml.xml.XMLNode
  type  (XMLNode) in org.sbml.jsbml.xml.XMLNode
  type  (int) in org.sbml.jsbml.xml.XMLNode
removeCompartmentType
  type  (int) in org.sbml.jsbml.Model
  type  (String) in org.sbml.jsbml.Model
removeCVTerm
  type  (CVTerm) in org.sbml.jsbml.AbstractSBase
  type  (int) in org.sbml.jsbml.AbstractSBase
  type  (CVTerm) in org.sbml.jsbml.Annotation
  type  (int) in org.sbml.jsbml.Annotation
  type  (CVTerm) in org.sbml.jsbml.SBase
  type  (int) in org.sbml.jsbml.SBase
removeEventAssignment (EventAssignment)
removeFromParent
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.CVTerm
  type  () in org.sbml.jsbml.util.TreeNodeWithChangeSupport
removeMultiplier ()
removeNamespace (String)
removeOffset ()
removeResource (int)
removeRule (Rule)
removeSpeciesType
  type  (int) in org.sbml.jsbml.Model
  type  (String) in org.sbml.jsbml.Model
removeUnneccessaryElements (Model, Object)
removeUserObject
  type  (Object) in org.sbml.jsbml.AbstractTreeNode
  type  (Object) in org.sbml.jsbml.util.TreeNodeWithChangeSupport

S  A C D E F G H I L M O P R T U V W TOP
saveChanges
  type  (Model, Object) in org.sbml.jsbml.SBMLOutputConverter
  type  (Reaction, Object) in org.sbml.jsbml.SBMLOutputConverter
selector
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.ASTNodeCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FindUnitsCompiler
  type  (Object[]) in org.sbml.jsbml.util.compilers.FormulaCompiler
  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
set (int, SBase)
setAnnotationAttributes (NamedNodeMap)
setAnnotationNamespaces (Map<String, String>)
setAreaUnits (Kind)
setColumn (int)
setExtentUnits (Kind)
setFormula (String)
setId (String)
setLengthUnits (Kind)
setLine (int)
setListener (ProgressListener)
setLocation (Location)
setMessage (String)
setNamespace (String)
setNonRDFAnnotation
  type  (XMLNode) in org.sbml.jsbml.Annotation
  type  (String) in org.sbml.jsbml.Annotation
setNotes
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
setOtherAttribute (String, String)
setPackage (String)
setPackageRequired (String, boolean)
setParent (TreeNode)
setPkgRequired (String, boolean)
setQualifier (Qualifier)
setRdfAnnotationNamespaces (Map<String, String>)
setSpatialSizeUnits
  type  (String) in org.sbml.jsbml.Species
  type  (UnitDefinition) in org.sbml.jsbml.Species
setSubstanceUnits (Kind)
setTerm (int)
setTerms (int[])
setThisAsParentSBMLObject (SBase)
setTimeUnits (Kind)
setUnits
  type  (Kind) in org.sbml.jsbml.ASTNode
  type  (UnitDefinition) in org.sbml.jsbml.ASTNode
setUserObject (Object)
setVolumeUnits (Kind)

T  A C D E F G H I L M O P R S U V W TOP
toFormula (FormulaCompiler)
toString
  type  () in org.sbml.jsbml.SpeciesReference
  type  () in org.sbml.jsbml.util.ValuePair
  type  () in org.sbml.jsbml.xml.XMLAttributes
  type  () in org.sbml.jsbml.xml.XMLNode
  type  () in org.sbml.jsbml.xml.XMLTriple
toXML
  type  (String, StringBuffer) in org.sbml.jsbml.Creator
  type  (XMLNode) in org.sbml.jsbml.xml.parsers.XMLNodeWriter
toXMLAnnotationString (String)
toXMLString ()

U  A C D E F G H I L M O P R S T V W TOP
unregister
  type  (SBase) in org.sbml.jsbml.AbstractSBase
  type  (SBase) in org.sbml.jsbml.KineticLaw
  type  (SBase) in org.sbml.jsbml.Model
  type  (SBase) in org.sbml.jsbml.SBase
unregisterChild
  type  (SBase) in org.sbml.jsbml.AbstractSBase
  type  (SBase) in org.sbml.jsbml.SBase
unsetExtension
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
unsetNamespace ()
unsetPlugin
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
unsetQualifier ()
unsetUserObject ()
userObjectKeySet
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.util.TreeNodeWithChangeSupport

V  A C D E F G H I L M O P R S T U W TOP
valuePairOf (Comparable<? super L>, Comparable<? super V>)
vector
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.ASTNodeCompiler
  type  (List<ASTNode>) in org.sbml.jsbml.util.compilers.FindUnitsCompiler
  type  (Object[]) in org.sbml.jsbml.util.compilers.FormulaCompiler
  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

W  A C D E F G H I L M O P R S T U V TOP
write
  type  (SBMLDocument, String) in org.sbml.jsbml.xml.stax.SBMLWriter
  type  (SBMLDocument, String, String, String) in org.sbml.jsbml.xml.stax.SBMLWriter
writeAnnotation (SBase)
writeModel (Model)
writeSBML
  type  (SBMLDocument, String) in org.sbml.jsbml.JSBML
  type  (Object, String) in org.sbml.jsbml.SBMLOutputConverter
  type  (Object, String, String, String) in org.sbml.jsbml.SBMLOutputConverter
  type  (T, String) in org.sbml.jsbml.SBMLOutputConverter
  type  (T, String, String, String) in org.sbml.jsbml.SBMLOutputConverter