All Differences

Removals

Additions

Changes

Bold is New, strike is deleted

A  B C D E F G I L M N O P R S T U V W X TOP
AbstractReaderWriter
accept
  type  (SBase) in org.sbml.jsbml.KineticLaw
  type  (SBase) in org.sbml.jsbml.Model
addAllChangeListeners
  type  (Collection<TreeNodeChangeListener>, boolean) in org.sbml.jsbml.AbstractTreeNode
  type  (Collection<TreeNodeChangeListener>, boolean) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
addDeclaredNamespace (String, String)
addExtension
  type  (String, SBasePlugin) in org.sbml.jsbml.AbstractSBase
  type  (String, SBasePlugin) in org.sbml.jsbml.SBase
addPlugin
  type  (String, SBasePlugin) in org.sbml.jsbml.AbstractSBase
  type  (String, SBasePlugin) in org.sbml.jsbml.SBase
AnnotationReader
AnnotationWriter

B  A C D E F G I L M N O P R S T U V W X TOP
base
BASE_UNIT_SUFFIX

C  A B D E F G I L M N O P R S T U V W X TOP
checkBrackets (ASTNode)
checkDenominatorBrackets (ASTNode)
clearUserObjects
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.util.TreeNodeWithChangeSupport
concatStringBuilder (Object[])
containsReaction (String)
containsUserObjectKey
  type  (Object) in org.sbml.jsbml.AbstractTreeNode
  type  (Object) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
convertSBMLDocument
  type  (File) in org.sbml.jsbml.SBMLInputConverter
  type  (String) in org.sbml.jsbml.SBMLInputConverter
createdDate
createHistory ()
createPlugin
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
createSpecies (String, String, Compartment)

D  A B C E F G I L M N O P R S T U V W X 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 B C D F G I L M N O P R S T U V W X 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
extension

F  A B C D E G I L M N O P R S T U V W X 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
filterResources
  type  (String[]) in org.sbml.jsbml.CVTerm
  type  (Pattern[]) in org.sbml.jsbml.CVTerm
findIdentical (UnitDefinition)
FormulaCompilerLibSBML
FormulaParserLL3
FormulaParserLL3Constants
FormulaParserLL3TokenManager
formulaToString (ASTNode, FormulaCompiler)

G  A B C D E F I L M N O P R S T U V W X TOP
getActivator ()
getArgumentCount ()
getAssociation ()
getBiologicalQualifierFor (String)
getChildElement (String, String)
getChildElements (String, String)
getCompartment ()
getCompartmentCount ()
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.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 ()
getLocalParameterCount ()
getMacromolecule ()
getMathContainerCount ()
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.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 ()
getNonRDFannotationAsString ()
getNumPlugins
  type  () in org.sbml.jsbml.AbstractSBase
  type  () in org.sbml.jsbml.SBase
getOtherAttribute (String)
getOtherAttributes ()
getPackage ()
getPackageRequired (String)
getParameterCount ()
getPertubingAgent ()
getPkgRequired (String)
getPlugin
  type  (String) in org.sbml.jsbml.AbstractSBase
  type  (String) in org.sbml.jsbml.SBase
getProcess ()
getProductCount ()
getProduction ()
getQualifier ()
getQuantityCount ()
getQuantityWithUnitCount ()
getReactantCount ()
getReactionCount ()
getResourceCount ()
getRoot
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.util.TreeNodeWithChangeSupport
getRuleCount ()
getSBaseCount ()
getSBaseWithDerivedUnitCount ()
getSideProduct ()
getSideSubstrate ()
getSpeciesCount ()
getSpeciesReferenceCount ()
getSpeciesTypeCount ()
getSpeciesWithBoundaryConditionCount ()
getStimulation ()
getStoichiometryMathCount ()
getSymbolCount ()
getTerms ()
getTriggerCount ()
getUnitCount
  type  () in org.sbml.jsbml.Model
  type  () in org.sbml.jsbml.UnitDefinition
getUnitDefinitionCount ()
getUserObject
  type  (Object) in org.sbml.jsbml.AbstractTreeNode
  type  (Object) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
getVariableCount ()

I  A B C D E F G L M N O P R S T U V W X TOP
IdenticalUnitDefinitionFilter
IdManager
IFormulaParser
ignoredExtensions
ignoredXMLElements
initDefaults (int, int, boolean)
initializeAnnotationParsers ()
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 ()
isSetUserObjects
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.util.TreeNodeWithChangeSupport
isValidMetaId (String)
isVector ()

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

M  A B C D E F G I L N O P R S T U V W X TOP
metaIds ()
ModelBuilder
modifiedDate

N  A B C D E F G I L M O P R S T U V W X TOP
numBvars
numPiece

O  A B C D E F G I L M N P R S T U V W X TOP
of (Comparable<? super L>, Comparable<? super V>)
org.sbml.jsbml.ext
org.sbml.jsbml.math
org.sbml.jsbml.math.compiler
organization

P  A B C D E F G I L M N O R S T U V W X TOP
PackageParser
Pair
ParseException (Throwable) constructor
parseFormula (String, IFormulaParser)
ParserManager
ProgressListener
PROPERTY_UNDEFINED_EXCEPTION_MSG_SBASE
PROPERTY_UNDEFINED_EXCEPTION_MSG_TREE_NODE
PropertyUndefinedError
  PropertyUndefinedError (String, TreeNode) constructor
  PropertyUndefinedError (String, SBasePlugin) constructor
putUserObject
  type  (Object, Object) in org.sbml.jsbml.AbstractTreeNode
  type  (Object, Object) in org.sbml.jsbml.util.TreeNodeWithChangeSupport

R  A B C D E F G I L M N O P S T U V W X 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  (XMLNode) in org.sbml.jsbml.xml.XMLNode
  type  (int) in org.sbml.jsbml.xml.XMLNode
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
 in  org.sbml.jsbml.util.TreeNodeChangeEvent
removeEventAssignment (EventAssignment)
removeFromParent
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.CVTerm
  type  () in org.sbml.jsbml.util.TreeNodeWithChangeSupport
removeMultiplier ()
removeOffset ()
removeResource (int)
removeRule (Rule)
removeUserObject
  type  (Object) in org.sbml.jsbml.AbstractTreeNode
  type  (Object) in org.sbml.jsbml.util.TreeNodeWithChangeSupport
ResourceManager
RIGHT_BRACES
RIGHT_BRACKET

S  A B C D E F G I L M N O P R T U V W X TOP
SBMLErrorConverter
SBMLRDFAnnotationParser
SBMLtools
SBMLTypeUndefinedException
SBOFilter (int[]) constructor
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
setAreaUnits (Kind)
setColumn (int)
setExtentUnits (Kind)
setLengthUnits (Kind)
setLine (int)
setListener (ProgressListener)
setNamespace (String)
setNonRDFAnnotation (XMLNode)
setOtherAttribute (String, String)
setPackage (String)
setPackageRequired (String, boolean)
setPkgRequired (String, boolean)
setQualifier (Qualifier)
setSubstanceUnits (Kind)
setTerms (int[])
setTimeUnits (Kind)
setUnits
  type  (Kind) in org.sbml.jsbml.ASTNode
  type  (UnitDefinition) in org.sbml.jsbml.ASTNode
setVolumeUnits (Kind)
stringToType

T  A B C D E F G I L M N O P R S U V W X TOP
toFormula (FormulaCompiler)
toString
  type  () in org.sbml.jsbml.xml.XMLAttributes
  type  () in org.sbml.jsbml.xml.XMLTriple
toXMLAnnotationString (String)

U  A B C D E F G I L M N O P R S T V W X TOP
UNKNOWN_ATTRIBUTES
UNKNOWN_ELEMENTS
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 ()
userObjectKeySet
  type  () in org.sbml.jsbml.AbstractTreeNode
  type  () in org.sbml.jsbml.util.TreeNodeWithChangeSupport

V  A B C D E F G I L M N O P R S T U W X 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 B C D E F G I L M N O P R S T U V X TOP
writeSBML
  type  (T, String) in org.sbml.jsbml.SBMLOutputConverter
  type  (T, String, String, String) in org.sbml.jsbml.SBMLOutputConverter

X  A B C D E F G I L M N O P R S T U V W TOP
XMLNodeFilter
XMLNodeReader
XMLResourceBundleControl