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

A

about - Variable in class org.sbml.jsbml.Annotation
matches the about XML attribute of an annotation element in a SBML file.
about - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
abs(double, MathContainer) - Static method in class org.sbml.jsbml.ASTNode
Creates and returns an ASTNode that computes the absolute value of the given double value.
abs(int, MathContainer) - Static method in class org.sbml.jsbml.ASTNode
Creates and returns an ASTNode that computes the absolute value of the given integer value.
abs(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
The absolute value represented by the given ASTNode.
abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
AbstractMathContainer - Class in org.sbml.jsbml
Base class for all the SBML components which contain MathML nodes.
AbstractMathContainer() - Constructor for class org.sbml.jsbml.AbstractMathContainer
Creates a MathContainer instance.
AbstractMathContainer(AbstractMathContainer) - Constructor for class org.sbml.jsbml.AbstractMathContainer
Creates a MathContainer instance from a given MathContainer.
AbstractMathContainer(ASTNode, int, int) - Constructor for class org.sbml.jsbml.AbstractMathContainer
Creates a MathContainer instance from an ASTNode, level and version.
AbstractMathContainer(int, int) - Constructor for class org.sbml.jsbml.AbstractMathContainer
Creates a MathContainer instance from a level and version.
AbstractNamedSBase - Class in org.sbml.jsbml
The base class for each SBML element with an optional id and name.
AbstractNamedSBase() - Constructor for class org.sbml.jsbml.AbstractNamedSBase
Creates an AbstractNamedSBase.
AbstractNamedSBase(AbstractNamedSBase) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
Creates an AbstractNamedSBase from a given AbstractNamedSBase.
AbstractNamedSBase(int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
Creates an AbstractNamedSBase from a level and version.
AbstractNamedSBase(String) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
Creates an AbstractNamedSBase with the given identifier.
AbstractNamedSBase(String, int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
Creates an AbctractNamedSBase from an id, level and version.
AbstractNamedSBase(String, String, int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
Creates an AbctractNamedSBase from an id, name, level and version.
AbstractNamedSBaseWithUnit - Class in org.sbml.jsbml
This simple implementation of the interfaces NamedSBaseWithDerivedUnit and SBaseWithUnit defines elements that can be addressed by their identifier and are or can be associated with a defined Unit or UnitDefinition.
AbstractNamedSBaseWithUnit() - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
AbstractNamedSBaseWithUnit(AbstractNamedSBaseWithUnit) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
AbstractNamedSBaseWithUnit(int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
AbstractNamedSBaseWithUnit(String) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
AbstractNamedSBaseWithUnit(String, int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
AbstractNamedSBaseWithUnit(String, String, int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
AbstractSBase - Class in org.sbml.jsbml
The base class for each SBase component.
AbstractSBase() - Constructor for class org.sbml.jsbml.AbstractSBase
Creates an AbstractSBase instance.
AbstractSBase(int, int) - Constructor for class org.sbml.jsbml.AbstractSBase
Creates an AbstractSBase instance with the given Level and Version.
AbstractSBase(SBase) - Constructor for class org.sbml.jsbml.AbstractSBase
Creates an AbstractSBase instance from a given AbstractSBase.
AbstractSBase.NOTES_TYPE - Enum in org.sbml.jsbml
 
AbstractSBase.NOTES_TYPE() - Constructor for enum org.sbml.jsbml.AbstractSBase.NOTES_TYPE
 
AbstractTreeNode - Class in org.sbml.jsbml
A basic implementation of the TreeNode interface.
AbstractTreeNode() - Constructor for class org.sbml.jsbml.AbstractTreeNode
 
AbstractTreeNode(TreeNode) - Constructor for class org.sbml.jsbml.AbstractTreeNode
Constructor for cloning.
accepts(Object) - Method in class org.sbml.jsbml.util.filters.AndFilter
 
accepts(Object) - Method in class org.sbml.jsbml.util.filters.AssignmentVariableFilter
 
accepts(Object) - Method in class org.sbml.jsbml.util.filters.BoundaryConditionFilter
 
accepts(Object) - Method in class org.sbml.jsbml.util.filters.CVTermFilter
 
accepts(Object) - Method in interface org.sbml.jsbml.util.filters.Filter
This method checks whether the given object is of the correct type and has the desired properties set to be acceptable.
accepts(Object) - Method in class org.sbml.jsbml.util.filters.NameFilter
 
accepts(Object) - Method in class org.sbml.jsbml.util.filters.OrFilter
 
accepts(Object) - Method in class org.sbml.jsbml.util.filters.SBOFilter
 
accepts(Object) - Method in class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
 
add(int, T) - Method in class org.sbml.jsbml.ListOf
 
add(T) - Method in class org.sbml.jsbml.ListOf
 
add(Option) - Method in class org.sbml.jsbml.SBMLErrorLog
Adds an option.
add(SBMLError) - Method in class org.sbml.jsbml.SBMLErrorLog
Adds an error.
add(String, String, String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Adds an attribute (a name/value pair) to this XMLAttributes set optionally with a prefix and URI defining a namespace.
add(String, String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Adds an attribute (a name/value pair) to this XMLAttributes set optionally with a prefix and URI defining a namespace.
add(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Adds an attribute (a name/value pair) to this XMLAttributes set optionally with a prefix and URI defining a namespace.
add(XMLTriple, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Adds an attribute with the given XMLTriple/value pair to this XMLAttributes set.
add(String, String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Appends an XML namespace prefix and URI pair to this list of namespace declarations.
add(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Appends an XML namespace URI with an empty prefix to this list of namespace declarations.
add_escapes(String) - Static method in exception org.sbml.jsbml.text.parser.ParseException
Used to convert raw characters to their escaped version when these raw version cannot be used as part of an ASCII string literal.
addAll(Collection<? extends T>) - Method in class org.sbml.jsbml.ListOf
 
addAll(int, Collection<? extends T>) - Method in class org.sbml.jsbml.ListOf
 
addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in class org.sbml.jsbml.AbstractTreeNode
 
addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
Adds recursively all given TreeNodeChangeListener instances to this element.
addAnnotationNamespace(String, String, String) - Method in class org.sbml.jsbml.Annotation
Adds a namespace to the map annotationNamespace of this object.
addAnnotationParsers(StartElement) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Associates any unknown namespaces with the AnnotationParser.
addAttr(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
Adds an attribute to the attribute set in this XMLToken optionally with a prefix and URI defining a namespace.
addAttr(String, String, String) - Method in class org.sbml.jsbml.xml.XMLToken
Adds an attribute to the attribute set in this XMLToken optionally with a prefix and URI defining a namespace.
addAttr(String, String, String, String) - Method in class org.sbml.jsbml.xml.XMLToken
Adds an attribute to the attribute set in this XMLToken optionally with a prefix and URI defining a namespace.
addAttr(XMLTriple, String) - Method in class org.sbml.jsbml.xml.XMLToken
Adds an attribute with the given XMLTriple/value pair to the attribute set in this XMLToken.
addAttributes(Map<String, String>) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
Adds an attribute to this attributes HashMap.
addChild(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Adds a child to this node.
addChild(XMLNode) - Method in class org.sbml.jsbml.xml.XMLNode
Adds a child to this XMLNode.
addCompartment(Compartment) - Method in class org.sbml.jsbml.Model
Adds a Compartment instance to the listOfCompartments of this Model.
addCompartmentType(CompartmentType) - Method in class org.sbml.jsbml.Model
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
addConstraint(Constraint) - Method in class org.sbml.jsbml.Model
Adds a Constraint instance to the listOfConstraints of this Model.
addCreator(Creator) - Method in class org.sbml.jsbml.History
Adds a Creator instance to this History.
addCVTerm(CVTerm) - Method in class org.sbml.jsbml.AbstractSBase
 
addCVTerm(CVTerm) - Method in class org.sbml.jsbml.Annotation
Adds a CVTerm and checks whether the required name spaces have already been added to the Annotation.rdfAnnotationNamespaces.
addCVTerm(CVTerm) - Method in interface org.sbml.jsbml.SBase
 
addCVTerm - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
addDeclaredNamespace(String, String) - Method in class org.sbml.jsbml.AbstractSBase
Adds an additional name space to the set of declared namespaces of this SBase.
addDeclaredNamespace(String, String) - Method in interface org.sbml.jsbml.SBase
Adds an additional name space to the set of declared namespaces of this SBase.
addDeclaredNamespace - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
addEscapes(String) - Static method in error org.sbml.jsbml.text.parser.TokenMgrError
Replaces unprintable characters by their escaped (or unicode escaped) equivalents in the given string
addEvent(Event) - Method in class org.sbml.jsbml.Model
Adds an Event instance to the listOfEvents of this Model.
addEventAssignment(EventAssignment) - Method in class org.sbml.jsbml.Event
Adds an EventAssignment instance to the list of EventAssignments of this Event.
addExtension(String, Annotation) - Method in class org.sbml.jsbml.Annotation
Adds an Annotation extension object to the extensions map of this object.
addExtension - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
addFilter(Filter) - Method in class org.sbml.jsbml.util.filters.AndFilter
 
addFunctionDefinition(FunctionDefinition) - Method in class org.sbml.jsbml.Model
Adds a FunctionDefinition instance to the listOfFunctionDefinitions of this Model.
addInitialAssignment(InitialAssignment) - Method in class org.sbml.jsbml.Model
Adds an InitialAssignment instance to the listOfInitialAssignments of this Model.
addIOProgressListener(IOProgressListener) - Method in interface org.sbml.jsbml.SBMLInputConverter
 
addIOProgressListener(IOProgressListener) - Method in interface org.sbml.jsbml.SBMLOutputConverter
Allows this class to fire events through this event Listener.
addLocalParameter(LocalParameter) - Method in class org.sbml.jsbml.KineticLaw
Adds a copy of the given Parameter object to the list of local parameters in this KineticLaw.
addModifiedDate(Date) - Method in class org.sbml.jsbml.History
Adds a Date of modification to this History.
addModifier(ModifierSpeciesReference) - Method in class org.sbml.jsbml.Reaction
Adds a ModifierSpeciesReference instance to this Reaction.
addNamespace(String) - Method in class org.sbml.jsbml.AbstractSBase
Adds an additional namespace to the set of namespaces of this SBase if the given namespace is not yet present within this SortedSet.
addNamespace(String) - Method in interface org.sbml.jsbml.SBase
Adds an additional name space to the set of name spaces of this SBase if the given name space is not yet present within this SortedSet.
addNamespace(String, String, String) - Method in class org.sbml.jsbml.SBMLDocument
Adds a name space to the SBMLNamespaces of this SBMLDocument.
addNamespace - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
addNamespace(String) - Method in class org.sbml.jsbml.xml.XMLToken
Appends an XML namespace prefix and URI pair to this XMLToken.
addNamespace(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
Appends an XML namespace prefix and URI pair to this XMLToken.
addNode(OverdeterminationValidator.Node<T>) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
 
addNode(OverdeterminationValidator.Node<S>) - Method in interface org.sbml.jsbml.validator.OverdeterminationValidator.Node
Adds a node to the list of nodes (creates an edge from this node to another one)
addNode(OverdeterminationValidator.Node<T>) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
 
addNode(OverdeterminationValidator.Node<T>) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
 
addParameter(LocalParameter) - Method in class org.sbml.jsbml.KineticLaw
addParameter(Parameter) - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
A KineticLaw can only contain instances of LocalParameters. Please use KineticLaw.addLocalParameter(LocalParameter) and create an instance of LocalParameter for your purposes.
addParameter(Parameter) - Method in class org.sbml.jsbml.Model
Adds a Parameter instance to the listOfParameters of this Model.
addPredefinedUnits() - Method in class org.sbml.jsbml.Model
Adds all the possible unit kinds as UnitDefinition, so that the method Model.getUnitDefinition(String) would be able to return a valid UnitDefinition even if one of these kinds is passed as parameter.
addProduct(SpeciesReference) - Method in class org.sbml.jsbml.Reaction
Adds a SpeciesReference instance to the listOfProducts of this Reaction.
addRDFAnnotationNamespace(String, String, String) - Method in class org.sbml.jsbml.Annotation
Adds a name space to the rdfAnnotationNamespaces Map of this object.
addReactant(SpeciesReference) - Method in class org.sbml.jsbml.Reaction
Adds a SpeciesReference instance to the listOfReactants of this Reaction.
addReaction(Reaction) - Method in class org.sbml.jsbml.Model
Adds a Reaction instance to the listOfReactions of this Model.
addResource(String) - Method in class org.sbml.jsbml.CVTerm
Adds a resource to the CVTerm.
addResources(String...) - Method in class org.sbml.jsbml.CVTerm
Adds list of resources to the CVTerm.
addResourceURI(String) - Method in class org.sbml.jsbml.CVTerm
Adds a resource to the CVTerm.
addRule(Rule) - Method in class org.sbml.jsbml.Model
Adds a Rule instance to the listOfRules of this Model.
addSpecies(Species) - Method in class org.sbml.jsbml.Model
Adds a Species instance to the listOfSpecies of this Model.
addSpeciesType(SpeciesType) - Method in class org.sbml.jsbml.Model
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
addTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.AbstractTreeNode
 
addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
 
addTreeNodeChangeListener(TreeNodeChangeListener) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
Adds recursively a listener to the TreeNodeWithChangeSupport object and all of its sub-elements.
addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
Adds a listener to this TreeNodeWithChangeSupport object and optionally also to all of its child nodes.
addUnit(String) - Method in class org.sbml.jsbml.UnitDefinition
 
addUnit(Unit) - Method in class org.sbml.jsbml.UnitDefinition
Adds an Unit to this UnitDefinition.
addUnit(Unit.Kind) - Method in class org.sbml.jsbml.UnitDefinition
Convenient method to add a new unit object with the given kind that will have the same level/version combination than this UnitDefinition object.
addUnitDefinition(UnitDefinition) - Method in class org.sbml.jsbml.Model
Adds an UnitDefinition instance to the listOfUnitDefinitions of this Model.
addUnitDefinitionIfNotContained(Model, UnitDefinition) - Static method in class org.sbml.jsbml.JSBML
Adds the given UnitDefinition to the given model or returns the identifier of an equivalent UnitDefinition that is already part of the model.
addUnitDefinitionOrReturnIdenticalUnit(UnitDefinition) - Method in class org.sbml.jsbml.Model
Checks whether an identical UnitDefinition like the given UnitDefinition is already in this Model's Model.listOfUnitDefinitions.
addWritingParser(List<WritingParser>, WritingParser, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Adds a WritingParser to the given list of WritingParser
adjustBeginLineColumn(int, int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Method to adjust line and column numbers for the start of a token.
AlgebraicRule - Class in org.sbml.jsbml
Represents the algebraicRule XML element of a SBML file.
AlgebraicRule() - Constructor for class org.sbml.jsbml.AlgebraicRule
Creates an AlgebraicRule instance.
AlgebraicRule(AlgebraicRule) - Constructor for class org.sbml.jsbml.AlgebraicRule
Creates an AlgebraicRule instance from a given AlgebraicRule instance.
AlgebraicRule(ASTNode, int, int) - Constructor for class org.sbml.jsbml.AlgebraicRule
Creates an AlgebraicRule instance from math, level and version.
AlgebraicRule(int, int) - Constructor for class org.sbml.jsbml.AlgebraicRule
Creates an AlgebraicRule instance from level and version.
alias2sbo - Static variable in class org.sbml.jsbml.SBO
 
amount - Variable in class org.sbml.jsbml.Species
True means initial amount is set.
AND - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
and(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
AndFilter - Class in org.sbml.jsbml.util.filters
A Filter that accepts an item only if all of its internal filters also accept the given item.
AndFilter() - Constructor for class org.sbml.jsbml.util.filters.AndFilter
 
AndFilter(Filter...) - Constructor for class org.sbml.jsbml.util.filters.AndFilter
 
andReplacement - Variable in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
 
annotation - Variable in class org.sbml.jsbml.AbstractSBase
annotations of the SBML component.
Annotation - Class in org.sbml.jsbml
An Annotation represents the annotations of an SBase element.
Annotation() - Constructor for class org.sbml.jsbml.Annotation
Creates an Annotation instance.
Annotation(Annotation) - Constructor for class org.sbml.jsbml.Annotation
Creates a new Annotation instance by cloning the given Annotation.
Annotation(List<CVTerm>) - Constructor for class org.sbml.jsbml.Annotation
Creates an Annotation instance from a list of CVTerm objects.
Annotation(Map<String, String>) - Constructor for class org.sbml.jsbml.Annotation
Creates an Annotation instance from a given Map of annotations.
Annotation(String) - Constructor for class org.sbml.jsbml.Annotation
Creates an Annotation instance from a String containing non RDF annotation.
Annotation(String, List<CVTerm>) - Constructor for class org.sbml.jsbml.Annotation
Creates an Annotation instance from a String containing non RDF annotation and a list of CVTerm.
annotation - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
AnnotationElement - Class in org.sbml.jsbml
A common super class for all those elements that can be part of an Annotation.
AnnotationElement() - Constructor for class org.sbml.jsbml.AnnotationElement
 
AnnotationElement(AnnotationElement) - Constructor for class org.sbml.jsbml.AnnotationElement
 
annotationNamespaces - Variable in class org.sbml.jsbml.Annotation
contains all the name spaces of the matching XML annotation node
annotationNameSpaces - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
AnnotationParser - Class in org.sbml.jsbml.xml.parsers
The AnnotationParser is used when some subelements of an annotation XML node have a namespace URI/prefix which doesn't match any ReadingParser class and so can't be parsed with another ReadingParser than this one.
AnnotationParser() - Constructor for class org.sbml.jsbml.xml.parsers.AnnotationParser
 
append(T) - Method in class org.sbml.jsbml.ListOf
Adds item to the end of this ListOf.
append(StringBuffer, Object...) - Static method in class org.sbml.jsbml.util.StringTools
Takes the given StringBuffer as input and appends every further Object to it.
append(StringBuilder, Object...) - Static method in class org.sbml.jsbml.util.StringTools
 
append(String) - Method in class org.sbml.jsbml.xml.XMLToken
Appends characters to this XML text content.
appendNoRDFAnnotation(String) - Method in class org.sbml.jsbml.Annotation
Appends some'annotation' to the non RDF annotation StringBuilder of this object.
appendNotes(String) - Method in class org.sbml.jsbml.AbstractSBase
 
appendNotes(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase
Appends notes to the existing notes.
appendNotes(String) - Method in interface org.sbml.jsbml.SBase
Appends 'notes' to the notes String of this object.
appendNotes(XMLNode) - Method in interface org.sbml.jsbml.SBase
Appends 'notes' to the notes of this object.
arccos(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arccosh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arccosh(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the arccosh of n
arccot(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arccot(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the arcus-cotangens of a double value.
arccoth(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arccoth(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the arccoth of n
arccsc(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arccsc(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the arccosecant of a double value
arccsch(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arccsch(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the arccsch of n
arcsec(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arcsec(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the arcsecant of a double value
arcsech(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arcsech(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the arcsech of n
arcsin(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arcsinh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arcsinh(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the arcsinh of n
arctan(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arctanh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
arctanh(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the arctanh of n
AREA - Static variable in class org.sbml.jsbml.UnitDefinition
Identifier of the (for SBML Level 2) predefined UnitDefinition area.
area(int, int) - Static method in class org.sbml.jsbml.UnitDefinition
Predefined unit for area.
areaUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
areaUnitsID - Variable in class org.sbml.jsbml.Model
Represents the 'areaUnits' XML attribute of a model element.
areCompatible(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
Predicate returning true or false depending on whether two UnitDefinition objects are compatible.
areEquivalent(Unit, String) - Static method in class org.sbml.jsbml.Unit
Checks whether the given Unit and the Unit represented by the given String are equivalent.
areEquivalent(Unit, Unit) - Static method in class org.sbml.jsbml.Unit
Predicate returning true or false depending on whether Unit objects are equivalent.
areEquivalent(Unit.Kind, Unit.Kind) - Static method in enum org.sbml.jsbml.Unit.Kind
Tests whether the both given unit kinds are equivalent, i.e., it also considers METRE and METER and LITRE and LITER.
areEquivalent(UnitDefinition, String) - Static method in class org.sbml.jsbml.UnitDefinition
Checks whether the given UnitDefinition and the UnitDefinition or Unit represented by the given String are equivalent.
areEquivalent(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
Predicate returning true or false depending on whether two UnitDefinition objects are equivalent.
areIdentical(Unit, Unit) - Static method in class org.sbml.jsbml.Unit
Predicate returning true or false depending on whether two Unit objects are identical.
areIdentical(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
Predicate returning true or false depending on whether two UnitDefinition objects are identical.
arg - Variable in class org.sbml.jsbml.text.parser.FormulaParser.JJCalls
 
arith(char, Object...) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Basic method which links several elements with a mathematical operator.
arith(Object, Object...) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula
Basic method which links several elements with a mathematical operator.
arithmethicOperation(ASTNode.Type, ASTNode...) - Static method in class org.sbml.jsbml.ASTNode
Creates a new ASTNode of type operator and adds the given nodes as children.
arithmeticOperation(ASTNode.Type, ASTNode) - Method in class org.sbml.jsbml.ASTNode
Creates a new node with the type of this node, moves all children of this node to this new node, sets the type of this node to the given operator, adds the new node as left child of this node and the given astnode as the right child of this node.
Assignment - Interface in org.sbml.jsbml
An Assignment can be seen as a mathematical equation with a Variable on the left hand side and an equation on the right hand side that assigns a value to the Variable.
AssignmentRule - Class in org.sbml.jsbml
Represents the assignmentRule XML element of a SBML file.
AssignmentRule() - Constructor for class org.sbml.jsbml.AssignmentRule
Creates an AssignmentRule instance.
AssignmentRule(AssignmentRule) - Constructor for class org.sbml.jsbml.AssignmentRule
Creates a cloned AssignmentRule instance from a given AssignmentRule.
AssignmentRule(ExplicitRule) - Constructor for class org.sbml.jsbml.AssignmentRule
Creates a cloned AssignmentRule instance from a given ExplicitRule.
AssignmentRule(ASTNode, int, int) - Constructor for class org.sbml.jsbml.AssignmentRule
Creates an AssignmentRule instance from a given math, level and version.
AssignmentRule(ASTNode, Parameter) - Constructor for class org.sbml.jsbml.AssignmentRule
Creates an AssignmentRule instance from a given math and Parameter.
AssignmentRule(ASTNode, Variable) - Constructor for class org.sbml.jsbml.AssignmentRule
Creates an AssignmentRule instance from a given math and Variable.
AssignmentRule(int, int) - Constructor for class org.sbml.jsbml.AssignmentRule
Creates an AssignmentRule instance with the given level and version.
AssignmentRule(Parameter) - Constructor for class org.sbml.jsbml.AssignmentRule
Creates an AssignmentRule instance from a given Parameter.
AssignmentRule(Parameter, ASTNode) - Constructor for class org.sbml.jsbml.AssignmentRule
Creates an AssignmentRule instance from a given math and Parameter.
AssignmentRule(Variable) - Constructor for class org.sbml.jsbml.AssignmentRule
Creates an AssignmentRule instance from a given variable.
AssignmentRule(Variable, ASTNode) - Constructor for class org.sbml.jsbml.AssignmentRule
Creates an AssignmentRule instance from a given variable and math.
AssignmentVariableFilter - Class in org.sbml.jsbml.util.filters
This filter only accepts instances of Assignment with the variable as given in the constructor of this object.
AssignmentVariableFilter() - Constructor for class org.sbml.jsbml.util.filters.AssignmentVariableFilter
 
AssignmentVariableFilter(String) - Constructor for class org.sbml.jsbml.util.filters.AssignmentVariableFilter
 
ASTNode - Class in org.sbml.jsbml
A node in the Abstract Syntax Tree (AST) representation of a mathematical expression.
ASTNode() - Constructor for class org.sbml.jsbml.ASTNode
Creates a new ASTNode of unspecified type and without a pointer to its containing MathContainer.
ASTNode(ASTNode) - Constructor for class org.sbml.jsbml.ASTNode
Copy constructor; Creates a deep copy of the given ASTNode.
ASTNode(CallableSBase) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode referring to the given CallableSBase.
ASTNode(CallableSBase, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode referring to the given CallableSBase.
ASTNode(char) - Constructor for class org.sbml.jsbml.ASTNode
Creates a new ASTNode representing an operator, i.e., an internal node.
ASTNode(char, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
Creates a new ASTNode representing an operator, i.e., an internal node.
ASTNode(double) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode.
ASTNode(double, int) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode.
ASTNode(double, int, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode.
ASTNode(double, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode.
ASTNode(int) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode with the given integer value.
ASTNode(int, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode with the given integer value for the given MathContainer as its parent SBML object.
ASTNode(int, String, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode with the given integer value with the given associated ASTNode.unitId for the given MathContainer as its parent SBML object.
ASTNode(MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode.
ASTNode(String) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode with the given name.
ASTNode(String, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode with the given name.
ASTNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.ASTNode
Creates a new ASTNode of the given ASTNode.Type but without a pointer to its MathContainer.
ASTNode(ASTNode.Type, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
Creates and returns a new ASTNode.
ASTNode.Type - Enum in org.sbml.jsbml
An enumeration of all possible types that can be represented by an abstract syntax tree node.
ASTNode.Type() - Constructor for enum org.sbml.jsbml.ASTNode.Type
 
ASTNodeCompiler - Interface in org.sbml.jsbml.util.compilers
A compiler for abstract syntax trees.
ASTNodeValue - Class in org.sbml.jsbml.util.compilers
When interpreting ASTNodes, the ASTNodeCompiler takes elements of this class as arguments and performs its operations on it.
ASTNodeValue(ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(boolean, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(double, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(float, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(long, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(int, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(CallableSBase, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(Node, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(Number, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(String, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(ASTNode.Type, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ASTNodeValue(UnitDefinition, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
 
attributeNames - Variable in class org.sbml.jsbml.xml.XMLAttributes
 
attributes - Variable in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
Contains the XML attributes of a SBML component to write.
attributes - Variable in class org.sbml.jsbml.xml.XMLToken
 
attributeValues - Variable in class org.sbml.jsbml.xml.XMLAttributes
 
augmentMatching() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
Improves the matching as far as possible with augmenting paths
augmentPath(int) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
Tries augment every path found in the graph to a new path of the given length + 2 (a new node at the beginning and the end of the path)
available - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
AVOGADRO_L3V1 - Static variable in class org.sbml.jsbml.util.Maths
Avogadro's constant of 6.02214179 ⋅ 1023 mol-1.

B

backup(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Backup a number of characters.
baseListType - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
beginColumn - Variable in class org.sbml.jsbml.text.parser.Token
The column number of the first character of this Token.
beginLine - Variable in class org.sbml.jsbml.text.parser.Token
The line number of the first character of this Token.
BeginToken() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Start.
biologicalQualifierMap - Variable in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
The map containing all the relationships Miriam qualifier String <=> Miriam qualifier Qualifier.
BiologicalQualifierParser - Class in org.sbml.jsbml.xml.parsers
A BiologicalQualifierParser is used to parse the XML elements and attributes which have this namespace URI : http://biomodels.net/biology-qualifiers/.
BiologicalQualifierParser() - Constructor for class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
Creates a BiologicalQualifierParser instance and initialises the biologicalQualifierMap.
bipartiteGraph - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
The source node of the bipartite graph, respectively the bipartite graph
BOOLEAN_LOGIC - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
bottomrule - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Requires LaTeX package booktabs.
boundary - Variable in class org.sbml.jsbml.validator.MultipartPost
 
boundaryCondition - Variable in class org.sbml.jsbml.Species
Represents the 'boundaryCondition' attribute of a Species element.
boundaryCondition - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
BoundaryConditionFilter - Class in org.sbml.jsbml.util.filters
This filter accepts species whose boundary condition is set to true.
BoundaryConditionFilter() - Constructor for class org.sbml.jsbml.util.filters.BoundaryConditionFilter
Constructs a new boundary condition filter.
brackets(Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
brackets(Object) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula
 
brackets(Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Encloses the given formula in brackets.
bufcolumn - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
buffer - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
bufline - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
bufpos - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
Position in buffer.
bufsize - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
buildGraph() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
Build the bipartite graph by reference to SBML specification level 3 version 1 Core
buildMatching() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
Build the maximum matching with the greedy algorithm from the Hopcroft and Karp paper.

C

C_DOT - Static variable in class org.sbml.jsbml.util.compilers.HTMLFormula
Multiplication symbol “⋅”.
CallableSBase - Interface in org.sbml.jsbml
The interface CallableSBase represents an SBase that can be called in mathematical expressions, i.e., ASTNode, via its identifier.
canConvert(Class) - Method in class org.sbml.jsbml.xml.xstream.converter.MessageConverter
 
category - Variable in exception org.sbml.jsbml.SBMLError
 
category - Variable in exception org.sbml.jsbml.SBMLException
The category of this exception.
category - Variable in class org.sbml.jsbml.util.Detail
 
ceiling(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
ceiling(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
characters - Variable in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
Represents the text of a SBML component to write.
characters - Variable in class org.sbml.jsbml.xml.XMLToken
 
charge - Variable in class org.sbml.jsbml.Species
Deprecated.
charge - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
checkAndSetVariable(String) - Method in class org.sbml.jsbml.EventAssignment
Sets the variableID of this EventAssignment to 'variable'.
checkAndSetVariable(String) - Method in class org.sbml.jsbml.InitialAssignment
Sets the variableID of this InitialAssignment to 'variable'.
checkBrackets(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Creates brackets if needed.
checkBrackets(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Creates brackets if needed.
checkConsistency() - Method in class org.sbml.jsbml.SBMLDocument
Validates the SBMLDocument using the SBML.org online validator (http://sbml.org/validator/).
checkConsistency(String, HashMap<String, String>) - Static method in class org.sbml.jsbml.validator.SBMLValidator
Validates an SBML model using the SBML.org online validator (http://sbml.org/validator/).
checkConsistency(String) - Static method in class org.sbml.jsbml.validator.SBMLValidator
Parses the XML String returned by the libSBML online validator or web services.
checkConsistencyParameters - Variable in class org.sbml.jsbml.SBMLDocument
Contains all the parameter to validate the SBML document
checkContainsNumbersReferingToUnits(Node) - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
Recursively checks whether the given Node contains any numbers that refer to unit declarations.
checkDenominatorBrackets(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Creates brackets if needed.
checkForDimensionlessOrInvalidUnits(UnitDefinition) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
Throws an IllegalArgumentException if the given units do not represent a dimensionless or invalid unit.
checkIdentifier(String) - Method in class org.sbml.jsbml.AbstractNamedSBase
Checks if the sID is a valid identifier.
checkIdentifier(String) - Method in class org.sbml.jsbml.FunctionDefinition
Checks if the sID is a valid identifier.
checkLevelAndVersionCompatibility(SBase) - Method in class org.sbml.jsbml.AbstractSBase
Checks whether or not the given SBase has the same level and version configuration than this element.
checkMetaId(String) - Method in class org.sbml.jsbml.SBMLDocument
Checks if the given meta identifier can be added in this SBMLDocument 's SBMLDocument.mappingFromMetaId2SBase.
checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
checkTerm(int) - Static method in class org.sbml.jsbml.SBO
Checks the format of the given SBO integer portion.
checkTerm(String) - Static method in class org.sbml.jsbml.SBO
Checks the format of the given SBO string.
childNode - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
children() - Method in class org.sbml.jsbml.AbstractTreeNode
 
childrenElements - Variable in class org.sbml.jsbml.xml.XMLNode
 
className - Variable in class org.sbml.jsbml.ASTNode
Possible attributes for a MathML element
className - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
clear() - Method in class org.sbml.jsbml.ListOf
 
clear() - Method in class org.sbml.jsbml.UnitDefinition
Removes all Unit elements from the list of Units in this object.
clear() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
Sets all the variable of this object to null.
clear() - Method in class org.sbml.jsbml.xml.XMLAttributes
Clears (deletes) all attributes in this XMLAttributes object.
clear() - Method in class org.sbml.jsbml.xml.XMLNamespaces
Clears (deletes) all XML namespace declarations in this XMLNamespaces object.
clearAttributes() - Method in class org.sbml.jsbml.xml.XMLToken
Clears (deletes) all attributes in this XMLToken.
clearListOfEventAssignments() - Method in class org.sbml.jsbml.Event
Remove all the EventAssignments of the listOfEventAssignments of this Event.
clearLog() - Method in class org.sbml.jsbml.SBMLErrorLog
Clears the log.
clearNamespaces() - Method in class org.sbml.jsbml.xml.XMLToken
Clears (deletes) all XML namespace declarations in the XMLNamespaces of this XMLToken.
clone() - Method in class org.sbml.jsbml.AbstractMathContainer
 
clone() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
clone() - Method in class org.sbml.jsbml.AbstractSBase
 
clone() - Method in class org.sbml.jsbml.AbstractTreeNode
 
clone() - Method in class org.sbml.jsbml.AlgebraicRule
 
clone() - Method in class org.sbml.jsbml.Annotation
 
clone() - Method in class org.sbml.jsbml.AssignmentRule
 
clone() - Method in class org.sbml.jsbml.ASTNode
 
clone() - Method in class org.sbml.jsbml.Compartment
 
clone() - Method in class org.sbml.jsbml.CompartmentType
Deprecated.
clone() - Method in class org.sbml.jsbml.Constraint
 
clone() - Method in class org.sbml.jsbml.Creator
 
clone() - Method in class org.sbml.jsbml.CVTerm
 
clone() - Method in class org.sbml.jsbml.Delay
 
clone() - Method in class org.sbml.jsbml.Event
 
clone() - Method in class org.sbml.jsbml.EventAssignment
 
clone() - Method in class org.sbml.jsbml.ExplicitRule
 
clone() - Method in class org.sbml.jsbml.FunctionDefinition
 
clone() - Method in class org.sbml.jsbml.History
 
clone() - Method in class org.sbml.jsbml.InitialAssignment
 
clone() - Method in class org.sbml.jsbml.KineticLaw
 
clone() - Method in class org.sbml.jsbml.ListOf
 
clone() - Method in class org.sbml.jsbml.LocalParameter
 
clone() - Method in class org.sbml.jsbml.Model
 
clone() - Method in class org.sbml.jsbml.ModifierSpeciesReference
 
clone() - Method in class org.sbml.jsbml.Parameter
 
clone() - Method in class org.sbml.jsbml.Priority
 
clone() - Method in class org.sbml.jsbml.QuantityWithUnit
 
clone() - Method in class org.sbml.jsbml.RateRule
 
clone() - Method in class org.sbml.jsbml.Reaction
 
clone() - Method in class org.sbml.jsbml.Rule
 
clone() - Method in interface org.sbml.jsbml.SBase
Creates a copy of this object, i.e., e new SBase with the same properties like this one and returns a pointer to it.
clone() - Method in class org.sbml.jsbml.SBMLDocument
 
clone() - Method in class org.sbml.jsbml.SBMLReader
 
clone() - Method in class org.sbml.jsbml.SBMLWriter
 
clone() - Method in class org.sbml.jsbml.SBO.Term
 
clone() - Method in class org.sbml.jsbml.SBO.Triple
 
clone() - Method in class org.sbml.jsbml.Species
 
clone() - Method in class org.sbml.jsbml.SpeciesReference
 
clone() - Method in class org.sbml.jsbml.SpeciesType
Deprecated.
clone() - Method in class org.sbml.jsbml.StoichiometryMath
Deprecated.
clone() - Method in class org.sbml.jsbml.Symbol
 
clone() - Method in class org.sbml.jsbml.Trigger
 
clone() - Method in class org.sbml.jsbml.Unit
 
clone() - Method in class org.sbml.jsbml.UnitDefinition
 
clone() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
 
clone() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
clone() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent
 
clone() - Method in class org.sbml.jsbml.util.ValuePair
 
clone() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
Clones this Graph without terminal node
clone() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
 
clone() - Method in class org.sbml.jsbml.xml.XMLAttributes
Creates and returns a deep copy of this XMLAttributes set.
clone() - Method in class org.sbml.jsbml.xml.XMLNamespaces
Creates and returns a deep copy of this XMLNamespaces list.
clone() - Method in class org.sbml.jsbml.xml.XMLNode
 
clone() - Method in class org.sbml.jsbml.xml.XMLToken
 
clone() - Method in class org.sbml.jsbml.xml.XMLTriple
Creates and returns a deep copy of this XMLTriple set.
cloneAsAssignmentRule() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
 
cloneAsRateRule() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
 
CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
code - Variable in exception org.sbml.jsbml.SBMLError
 
code - Variable in exception org.sbml.jsbml.SBMLException
 
collectMetaIds(Map<String, SBase>, SBase, boolean, boolean) - Method in class org.sbml.jsbml.SBMLDocument
Collects all meta identifiers of this AbstractSBase and all of its sub-elements if recursively is true.
colorbox(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
column - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
column - Variable in class org.sbml.jsbml.util.Location
 
column - Variable in class org.sbml.jsbml.xml.XMLToken
 
command(String, Object) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
command(String, Object, Object) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
compareTo(SBO.Term) - Method in class org.sbml.jsbml.SBO.Term
 
compareTo(SBO.Triple) - Method in class org.sbml.jsbml.SBO.Triple
 
compareTo(L, V) - Method in class org.sbml.jsbml.util.ValuePair
Convenient method to compare two values to this ValuePair.
compareTo(ValuePair<L, V>) - Method in class org.sbml.jsbml.util.ValuePair
 
COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
Compartment - Class in org.sbml.jsbml
Represents the compartment in a model, i.e., a variable element with name, identifier, unit, and value that may change during a simulation.
Compartment() - Constructor for class org.sbml.jsbml.Compartment
Creates a Compartment instance.
Compartment(Compartment) - Constructor for class org.sbml.jsbml.Compartment
Creates a Compartment instance from a given compartment.
Compartment(int, int) - Constructor for class org.sbml.jsbml.Compartment
Creates a Compartment instance from a level and version.
Compartment(String) - Constructor for class org.sbml.jsbml.Compartment
Creates a Compartment instance with the given id.
Compartment(String, int, int) - Constructor for class org.sbml.jsbml.Compartment
Creates a Compartment instance from an id, level and version.
Compartment(String, String, int, int) - Constructor for class org.sbml.jsbml.Compartment
Creates a Compartment instance from an id, name, level and version.
compartment - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
compartmentID - Variable in class org.sbml.jsbml.Reaction
Represents the 'compartment' XML attribute of a reaction element.
compartmentID - Variable in class org.sbml.jsbml.Species
Represents the 'compartment' attribute of a Species element.
CompartmentType - Class in org.sbml.jsbml
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
CompartmentType() - Constructor for class org.sbml.jsbml.CompartmentType
Deprecated.
CompartmentType(CompartmentType) - Constructor for class org.sbml.jsbml.CompartmentType
Deprecated.
CompartmentType(int, int) - Constructor for class org.sbml.jsbml.CompartmentType
Deprecated.
CompartmentType(String) - Constructor for class org.sbml.jsbml.CompartmentType
Deprecated. 
CompartmentType(String, int, int) - Constructor for class org.sbml.jsbml.CompartmentType
Deprecated.
CompartmentType(String, String, int, int) - Constructor for class org.sbml.jsbml.CompartmentType
Deprecated.
compartmentType - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
compartmentTypeID - Variable in class org.sbml.jsbml.Compartment
Deprecated.
compile(ASTNodeCompiler) - Method in class org.sbml.jsbml.ASTNode
Compiles this ASTNode and returns the result.
compile(Compartment) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
compile(double, int, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Creates an ASTNodeValue that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.
compile(double, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
compile(int, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
compile(CallableSBase) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
compile(String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
A compiler will also have to deal with a name.
compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
compile(double, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
compile(int, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
compile(String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
compile(double, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
compile(int, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
compile(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
This method returns the correct LaTeX expression for a function which returns the size of a compartment.
compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
compile(double, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
compile(int, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
compile(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
compile(double, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
compile(int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
compile(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
compile(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
Compiles this ASTNode and produce an XMLStreamWriter representing this node in mathML.
compile(boolean) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
Compile boolean values
compile(Compartment) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
compile(double, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
compile(int, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
compile(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
compileBvar(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileCi(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileConstantElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileCSymbol(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileElement(String, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileExponentiale(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileFunctionElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileInteger(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileLambda(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileLog(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileLogicalOperator(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileNegativeInfinity(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileNotANumber(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compilePi(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compilePiecewise(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compilePositiveInfinity(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compiler - Variable in class org.sbml.jsbml.util.compilers.ASTNodeValue
An ASTNodeCompiler that is needed in the case that this ASTNodeValue contains a derivative of CallableSBase as value to translate this value into a double.
compileRational(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileReal(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileReal_e(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileRelationalOperator(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileRootElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
compileUserFunction(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
concat(Object...) - Static method in class org.sbml.jsbml.util.StringTools
This method concatenates two or more object strings into a new StringBuffer.
connection - Variable in class org.sbml.jsbml.validator.MultipartPost
 
constant - Variable in class org.sbml.jsbml.SpeciesReference
Represents the 'constant' XML attribute of this SpeciesReference.
constant - Variable in class org.sbml.jsbml.Symbol
The constant attribute of this variable.
constant - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
CONSTANT_E - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
CONSTANT_FALSE - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
CONSTANT_PI - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
The constant pi
CONSTANT_TRUE - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
Constraint - Class in org.sbml.jsbml
Represents the constraint XML element of a SBML file.
Constraint() - Constructor for class org.sbml.jsbml.Constraint
Creates a Constraint instance.
Constraint(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Constraint
Creates a Constraint instance from an ASTNode, a level and a version.
Constraint(Constraint) - Constructor for class org.sbml.jsbml.Constraint
Creates a Constraint instance from a given Constraint.
Constraint(int, int) - Constructor for class org.sbml.jsbml.Constraint
Creates a Constraint instance from a level and a version.
contains(Object) - Method in class org.sbml.jsbml.ListOf
 
contains(ListOf<? extends SimpleSpeciesReference>, Species) - Static method in class org.sbml.jsbml.util.SubModel
 
containsAll(Collection<?>) - Method in class org.sbml.jsbml.ListOf
 
containsArith(Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Tests whether the String representation of the given object contains any arithmetic symbols and if the given object is already sorrounded by brackets.
containsCompartment(String) - Method in class org.sbml.jsbml.Model
Returns true if this model contains a reference to a Compartment with the given identifier.
containsFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
Returns true if this model contains a reference to a FunctionDefinition with the given identifier.
containsMetaId(String) - Method in class org.sbml.jsbml.SBMLDocument
A check to see whether elements have been registered to this SBMLDocument with the given meta identifier.
containsParameter(String) - Method in class org.sbml.jsbml.Model
Returns true if this model contains a reference to a Parameter with the given identifier.
containsQuantity(Quantity) - Method in class org.sbml.jsbml.Model
Returns true if this Model contains a reference to the given Quantity.
containsSpecies(String) - Method in class org.sbml.jsbml.Model
Returns true if this Model contains a reference to the given Species.
containsUndeclaredUnits() - Method in class org.sbml.jsbml.AbstractMathContainer
 
containsUndeclaredUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
containsUndeclaredUnits() - Method in class org.sbml.jsbml.ASTNode
Returns true or false depending on whether this ASTNode refers to elements such as parameters or numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.jsbml.Event
Deprecated.
containsUndeclaredUnits() - Method in class org.sbml.jsbml.Reaction
 
containsUndeclaredUnits() - Method in interface org.sbml.jsbml.SBaseWithDerivedUnit
Returns true or false depending on whether this SBaseWithDerivedUnit refers to elements such as parameters or numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.jsbml.SpeciesReference
 
containsUndeclaredUnits() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
Flag to indicate whether or not units have been fully declared for this value.
containsUniqueNamedSBase(String) - Method in class org.sbml.jsbml.Model
Returns true if this Model contains a reference to the given UniqueNamedSBase.
containsUnitDefinition(String) - Method in class org.sbml.jsbml.Model
Returns true if this Model contains a reference to the given UnitDefinition.
conversionFactor - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
conversionFactorID - Variable in class org.sbml.jsbml.Model
Represents the 'conversionFactor' XML attribute of a model element.
conversionFactorID - Variable in class org.sbml.jsbml.Species
Represents the 'conversionFactor' attribute of a Species element.
convertAlias2SBO(String) - Static method in class org.sbml.jsbml.SBO
Returns an SBO id corresponding to the given alias.
convertModel(Object) - Method in interface org.sbml.jsbml.SBMLInputConverter
 
convertSBO2Alias(int) - Static method in class org.sbml.jsbml.SBO
Returns an alias corresponding to the given SBO id.
convertStringToXMLNode(String) - Static method in class org.sbml.jsbml.xml.XMLNode
Returns an XMLNode which is derived from a string containing XML content.
convertStringToXMLNode(String, XMLNamespaces) - Static method in class org.sbml.jsbml.xml.XMLNode
Returns an XMLNode which is derived from a string containing XML content.
convertToGMT(Date) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
Convert timezone of datetime string to GMT.
convertToGMT(String) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
Convert timezone of datetime string to GMT.
convertToGMT(Timestamp) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
Convert timezone of datetime string to GMT.
convertToSI(Unit) - Static method in class org.sbml.jsbml.Unit
Returns a UnitDefinition object which contains the argument Unit converted to the appropriate SI unit.
convertToSIUnits() - Method in class org.sbml.jsbml.UnitDefinition
This method converts this unit definition to a
convertXMLNodeToString(XMLNode) - Static method in class org.sbml.jsbml.xml.XMLNode
Returns a string representation of a given XMLNode.
copy(Map<String, String>, Map<String, String>) - Static method in class org.sbml.jsbml.Annotation
Copies one Map instance into another.
copy(InputStream, OutputStream) - Method in class org.sbml.jsbml.validator.MultipartPost
 
cos(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
cosh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
cot(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
cot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
cot(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the cot of n
coth(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
coth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
coth(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the coth of n
COULD_NOT_CREATE_ELEMENT_MSG - Static variable in class org.sbml.jsbml.Model
Error message to indicate that an element could not be created.
create(InputStream, boolean) - Method in interface org.sbml.jsbml.util.DocumentFactory
Creates an XML DOM document by parsing the content of the specified byte stream as XML, using a nonvalidating parser.
create(InputStream, Object[], ErrorHandler) - Method in interface org.sbml.jsbml.util.DocumentFactory
Creates an XML DOM document by parsing the content of the specified byte stream as XML, using a validating parser.
create(Reader, boolean) - Method in interface org.sbml.jsbml.util.DocumentFactory
Creates an XML DOM document by parsing the content of the specified character stream as XML, using a nonvalidating parser.
create(Reader, Object[], ErrorHandler) - Method in interface org.sbml.jsbml.util.DocumentFactory
Creates an XML DOM document by parsing the content of the specified character stream as XML, using a validating parser.
create(InputStream, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
Creates an XML DOM document by parsing the content of the specified byte stream as XML, using a nonvalidating parser.
create(InputStream, Object[], ErrorHandler) - Method in class org.sbml.jsbml.util.JAXPFacade
Creates an XML DOM document by parsing the content of the specified byte stream as XML, using a validating parser.
create(Reader, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
Creates an XML DOM document by parsing the content of the specified character stream as XML, using a nonvalidating parser.
create(Reader, Object[], ErrorHandler) - Method in class org.sbml.jsbml.util.JAXPFacade
Creates an XML DOM document by parsing the content of the specified character stream as XML, using a validating parser.
createAlgebraicRule() - Method in class org.sbml.jsbml.Model
Creates a new AlgebraicRule inside this Model and returns it.
createApplyNode(Node, ASTNodeValue...) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
createApplyNode(Node, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
Creates an apply Node with the given tag Node as its child and ASTNodeValues on the same level as the tag Node .
createApplyNode(String, ASTNode...) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
createApplyNode(String, ASTNodeValue...) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
createApplyNode(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
Creates a Node with the tag "apply" and adds the given Node as its child.
createAssignmentRule() - Method in class org.sbml.jsbml.Model
Creates a new AssignmentRule inside this Model and returns it.
createCiElement(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
createCnElement(double, int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
createCnElement(Number, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
createCompartment() - Method in class org.sbml.jsbml.Model
Creates a new Compartment inside this Model and returns it.
createCompartment(String) - Method in class org.sbml.jsbml.Model
Creates a new Compartment inside this Model and returns it.
createCompartmentType() - Method in class org.sbml.jsbml.Model
Deprecated.
CompartmentTypes should no longer be used.
createCompartmentType(String) - Method in class org.sbml.jsbml.Model
Deprecated.
CompartmentTypes should no longer be used.
createConstant(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
Creates an ASTNodeValue with the single node as defined by the tagName.
createConstraint() - Method in class org.sbml.jsbml.Model
Creates a new Constraint inside this Model and returns it.
createCSymbol(String, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
created - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
createDelay() - Method in class org.sbml.jsbml.Event
 
createDelay(ASTNode) - Method in class org.sbml.jsbml.Event
 
createDelay() - Method in class org.sbml.jsbml.Model
Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.
createEMAILElement(String, StringBuffer) - Method in class org.sbml.jsbml.Creator
Writes the EMAIL element of the Creator in 'buffer'
createEvent() - Method in class org.sbml.jsbml.Model
Creates a new Event inside this Model and returns it.
createEvent(String) - Method in class org.sbml.jsbml.Model
Creates a new Event inside this Model and returns it.
createEventAssignment() - Method in class org.sbml.jsbml.Event
 
createEventAssignment(String, ASTNode) - Method in class org.sbml.jsbml.Event
 
createEventAssignment(Variable, ASTNode) - Method in class org.sbml.jsbml.Event
 
createEventAssignment() - Method in class org.sbml.jsbml.Model
Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.
createFunctionDefinition() - Method in class org.sbml.jsbml.Model
Creates a new FunctionDefinition inside this Model and returns it.
createFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
Creates a new FunctionDefinition inside this Model and returns it.
createHistory() - Method in class org.sbml.jsbml.AbstractSBase
 
createHistory() - Method in class org.sbml.jsbml.Annotation
 
createIndentationString(int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
This method creates the necessary number of white spaces at the beginning of an entry in the SBML file.
createInitialAssignment() - Method in class org.sbml.jsbml.Model
Creates a new InitialAssignment inside this Model and returns it.
createKineticLaw() - Method in class org.sbml.jsbml.Model
Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.
createKineticLaw() - Method in class org.sbml.jsbml.Reaction
Creates a new KineticLaw object, installs it as this Reaction's 'kineticLaw' sub-element, and returns it.
createKineticLawParameter() - Method in class org.sbml.jsbml.Model
Creates a new local LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
createKineticParameter(String) - Method in class org.sbml.jsbml.Model
Creates a new local LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
createLocalParameter() - Method in class org.sbml.jsbml.KineticLaw
 
createLocalParameter(String) - Method in class org.sbml.jsbml.KineticLaw
 
createMathMLDocumentFor(Node, int) - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
createMessage(String, String, SBase) - Static method in exception org.sbml.jsbml.PropertyException
Creates an error message pointing out that the property of the given name is not defined in the Level/Version combination of the given SBase.
createModel() - Method in class org.sbml.jsbml.SBMLDocument
Deprecated.
If not working with SBML Level 2 use SBMLDocument.createModel(String) instead.
createModel(String) - Method in class org.sbml.jsbml.SBMLDocument
Creates a new instance of Model from id and the level and version of this SBMLDocument.
createModifier() - Method in class org.sbml.jsbml.Model
Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it.
createModifier(String) - Method in class org.sbml.jsbml.Model
Creates a new ModifierSpeciesReference with the specified 'id'.
createModifier() - Method in class org.sbml.jsbml.Reaction
Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it.
createModifier(Species) - Method in class org.sbml.jsbml.Reaction
Creates a new ModifierSpeciesReference, which points to the given Species, adds it to this Reaction's Reaction.listOfModifiers, and returns a pointer to it.
createModifier(String) - Method in class org.sbml.jsbml.Reaction
 
createModifier(String, Species) - Method in class org.sbml.jsbml.Reaction
Creates a new ModifierSpeciesReference with the given id as its identifier, which points to the given Species, adds it to this Reaction's Reaction.listOfModifiers, and returns a pointer to it.
createModifier(String, String) - Method in class org.sbml.jsbml.Reaction
Creates a new ModifierSpeciesReference with the given id as its identifier, which points to the Species with the given id, adds it to this Reaction's Reaction.listOfModifiers, and returns a pointer to it.
createNElement(String, StringBuffer) - Method in class org.sbml.jsbml.Creator
Writes the N element of the Creator in 'buffer'
createOrGElement(String, StringBuffer) - Method in class org.sbml.jsbml.Creator
Writes the ORG element of the Creator in 'buffer'
createParameter() - Method in class org.sbml.jsbml.Model
Creates a new Parameter inside this Model and returns it.
createParameter(String) - Method in class org.sbml.jsbml.Model
Creates a new Parameter.
createPriority() - Method in class org.sbml.jsbml.Event
Creates a new, empty Priority, adds it to this Event and returns the Priority.
createPriority(ASTNode) - Method in class org.sbml.jsbml.Event
 
createProduct() - Method in class org.sbml.jsbml.Model
Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.
createProduct(String) - Method in class org.sbml.jsbml.Model
 
createProduct() - Method in class org.sbml.jsbml.Reaction
Creates a new SpeciesReference, adds it to this Reaction's Reaction.listOfProducts and returns it.
createProduct(Species) - Method in class org.sbml.jsbml.Reaction
Creates a new SpeciesReference, which points to the given Species, adds it to this Reaction's Reaction.listOfProducts and returns a pointer to it.
createProduct(String) - Method in class org.sbml.jsbml.Reaction
 
createProduct(String, Species) - Method in class org.sbml.jsbml.Reaction
Creates a new SpeciesReference with the given id as its identifier, which points to the given Species, adds it to this Reaction's Reaction.listOfProducts and returns a pointer to it.
createProduct(String, String) - Method in class org.sbml.jsbml.Reaction
 
createRateRule() - Method in class org.sbml.jsbml.Model
Creates a new RateRule inside this Model and returns it.
createReactant() - Method in class org.sbml.jsbml.Model
Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
createReactant(String) - Method in class org.sbml.jsbml.Model
Creates a new SpeciesReference object, with the specified 'id', for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
createReactant() - Method in class org.sbml.jsbml.Reaction
Creates a new SpeciesReference, adds it to this Reaction's Reaction.listOfReactants and returns it.
createReactant(Species) - Method in class org.sbml.jsbml.Reaction
Creates a new SpeciesReference to the given Species and adds it to the Reaction.listOfReactants.
createReactant(String) - Method in class org.sbml.jsbml.Reaction
 
createReactant(String, Species) - Method in class org.sbml.jsbml.Reaction
Creates a new SpeciesReference with the given id as identifier, which points to the given Species and adds it to the Reaction.listOfReactants.
createReactant(String, String) - Method in class org.sbml.jsbml.Reaction
 
createReaction() - Method in class org.sbml.jsbml.Model
Creates a new Reaction inside this Model and returns it.
createReaction(String) - Method in class org.sbml.jsbml.Model
Creates a new Reaction inside this Model and returns it.
createSpecies() - Method in class org.sbml.jsbml.Model
Creates a new Species inside this Model and returns it.
createSpecies(String) - Method in class org.sbml.jsbml.Model
Creates a new Species inside this Model and returns it.
createSpecies(String, Compartment) - Method in class org.sbml.jsbml.Model
Creates a new Species inside this Model and returns it.
createSpeciesType() - Method in class org.sbml.jsbml.Model
Deprecated.
createSpeciesType(String) - Method in class org.sbml.jsbml.Model
Deprecated.
createTrigger() - Method in class org.sbml.jsbml.Event
 
createTrigger(boolean, boolean) - Method in class org.sbml.jsbml.Event
 
createTrigger(boolean, boolean, ASTNode) - Method in class org.sbml.jsbml.Event
 
createTrigger() - Method in class org.sbml.jsbml.Model
Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it.
createUnit() - Method in class org.sbml.jsbml.Model
Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.
createUnit(Unit.Kind) - Method in class org.sbml.jsbml.Model
Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.
createUnit() - Method in class org.sbml.jsbml.UnitDefinition
 
createUnit(Unit.Kind) - Method in class org.sbml.jsbml.UnitDefinition
 
createUnitDefinition() - Method in class org.sbml.jsbml.Model
Creates a new UnitDefinition inside this Model and returns it.
createUnitDefinition(String) - Method in class org.sbml.jsbml.Model
Creates a new UnitDefinition inside this Model and returns it.
creation - Variable in class org.sbml.jsbml.History
Date of creation
Creator - Class in org.sbml.jsbml
Contains all the information about a creator of a Model (or other SBase in level 3).
Creator() - Constructor for class org.sbml.jsbml.Creator
Creates a Creator instance.
Creator(Creator) - Constructor for class org.sbml.jsbml.Creator
Creates a Creator instance from a given Creator.
Creator(String, String, String, String) - Constructor for class org.sbml.jsbml.Creator
Creates a Creator instance.
creator - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
CreatorParser - Class in org.sbml.jsbml.xml.parsers
A CreatorParser is used to parser the subelements of an annotation element which have this namespaceURI : http://purl.org/dc/elements/1.1/.
CreatorParser() - Constructor for class org.sbml.jsbml.xml.parsers.CreatorParser
 
csc(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
csc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
csc(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the csc of n
csch(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
csch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
csch(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the csch of n
curChar - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
curLexState - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
currentList - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
currentToken - Variable in exception org.sbml.jsbml.text.parser.ParseException
This is the last token that has been consumed successfully.
CVTerm - Class in org.sbml.jsbml
Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element of a SBML component.
CVTerm() - Constructor for class org.sbml.jsbml.CVTerm
Creates a CVTerm instance.
CVTerm(CVTerm) - Constructor for class org.sbml.jsbml.CVTerm
Creates a CVTerm instance from a given CVTerm.
CVTerm(CVTerm.Qualifier, String...) - Constructor for class org.sbml.jsbml.CVTerm
Guesses the CVTerm.Type argument and sets the CVTerm.Qualifier attribute appropriately.
CVTerm(CVTerm.Type, CVTerm.Qualifier, String...) - Constructor for class org.sbml.jsbml.CVTerm
Creates a new CVTerm with the given CVTerm.Type and CVTerm.Qualifier pointing to all given resources.
CVTerm.Qualifier - Enum in org.sbml.jsbml
This enum list all the possible MIRIAM qualifiers.
CVTerm.Qualifier() - Constructor for enum org.sbml.jsbml.CVTerm.Qualifier
 
CVTerm.Type - Enum in org.sbml.jsbml
This enum list all the possible MIRIAM qualifiers type.
CVTerm.Type() - Constructor for enum org.sbml.jsbml.CVTerm.Type
 
CVTermFilter - Class in org.sbml.jsbml.util.filters
This filter accepts only instances of CVTerm with a certain content or instances of SBase that are annotated with appropriate CVTerm objects.
CVTermFilter() - Constructor for class org.sbml.jsbml.util.filters.CVTermFilter
 
CVTermFilter(CVTerm.Qualifier) - Constructor for class org.sbml.jsbml.util.filters.CVTermFilter
 
CVTermFilter(CVTerm.Qualifier, String) - Constructor for class org.sbml.jsbml.util.filters.CVTermFilter
 

D

datePattern - Variable in class org.sbml.jsbml.xml.stax.DateProcessor
 
datePatternWithMilitaryTimezone - Variable in class org.sbml.jsbml.xml.stax.DateProcessor
 
datePatternWithoutTimezoneInfo - Variable in class org.sbml.jsbml.xml.stax.DateProcessor
 
DateProcessor - Class in org.sbml.jsbml.xml.stax
Format time to W3DTF
DateProcessor() - Constructor for class org.sbml.jsbml.xml.stax.DateProcessor
 
DatesParser - Class in org.sbml.jsbml.xml.parsers
A DatesParser is used to parse the subNodes of an annotation which have this namespace URI : http://purl.org/dc/terms/.
DatesParser() - Constructor for class org.sbml.jsbml.xml.parsers.DatesParser
 
debug(String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger
 
DEBUG_MODE - Static variable in class org.sbml.jsbml.ListOf
Switches the behavior of the ListOf.toString() method from displaying the ListOf.Type (default) to the complete content of all instances of ListOf
debugStream - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
Debug output.
DECIMAL_FORMAT - Static variable in class org.sbml.jsbml.util.StringTools
 
declaredNamespaces - Variable in class org.sbml.jsbml.AbstractSBase
Contains all the namespaces declared on the XML node with their prefixes.
def - Variable in class org.sbml.jsbml.SBO.Term
The base properties of this SBO.Term.
DEFAULT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
Lexical state.
defaultLexState - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
definitionURL - Variable in class org.sbml.jsbml.ASTNode
The value of the definitionURL for csymbol element.
definitionURL - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
Delay - Class in org.sbml.jsbml
Represents the delay subnode of an event element.
Delay() - Constructor for class org.sbml.jsbml.Delay
Creates a Delay instance.
Delay(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Delay
Creates a Delay instance from an ASTNode, level and version.
Delay(Delay) - Constructor for class org.sbml.jsbml.Delay
Creates a Delay instance from a given Delay.
Delay(int, int) - Constructor for class org.sbml.jsbml.Delay
Creates a Delay instance from a level and version.
delay - Variable in class org.sbml.jsbml.Event
Represents the delay sub-element of an event element.
delay(String, ASTNode, ASTNode, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Evaluates delay functions.
delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
deleteNode(OverdeterminationValidator.Node<T>) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
 
deleteNode(OverdeterminationValidator.Node<S>) - Method in interface org.sbml.jsbml.validator.OverdeterminationValidator.Node
Deletes node from the list of adjacent nodes
deleteNode(OverdeterminationValidator.Node<T>) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
 
deleteNode(OverdeterminationValidator.Node<T>) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
 
denominator - Variable in class org.sbml.jsbml.ASTNode
 
denominator - Variable in class org.sbml.jsbml.SpeciesReference
Represents the 'denominator' XML attribute of this SpeciesReference.
denominator - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
deriveUnit() - Method in class org.sbml.jsbml.ASTNode
Evaluates recursively this ASTNode and creates a new UnitDefinition with respect of all referenced elements.
descriptionBegin - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Surrounded by new line symbols.
descriptionEnd - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Surrounded by new line symbols.
descriptionItem(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
This method simplifies the process of creating descriptions.
detail - Variable in exception org.sbml.jsbml.SBMLError
 
Detail - Class in org.sbml.jsbml.util
 
Detail() - Constructor for class org.sbml.jsbml.util.Detail
 
diff(ASTNode...) - Static method in class org.sbml.jsbml.ASTNode
Creates a new ASTNode of type MINUS and adds the given nodes as children
diff(Object...) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Returns the difference of the given elements as StringBuffer.
digit - Static variable in class org.sbml.jsbml.AbstractNamedSBase
 
DIGIT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
dimensionless() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
Creates a dimensionless unit definition object encapsulated in an ASTNodeValue.
disable_tracing() - Method in class org.sbml.jsbml.text.parser.FormulaParser
Disable tracing.
DIVIDE - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
divideBy(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Divides this node by the given node
divideBy(CallableSBase) - Method in class org.sbml.jsbml.ASTNode
Divides this node by the given SBML element.
divideBy(UnitDefinition) - Method in class org.sbml.jsbml.UnitDefinition
Divides this unit definition by the second unit definition.
document - Variable in class org.sbml.jsbml.util.compilers.MathMLCompiler
XML document for the output.
DocumentFactory - Interface in org.sbml.jsbml.util
An interface for XML DOM document factories.
Done() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Reset buffer when finished.
done() - Method in class org.sbml.jsbml.validator.MultipartPost
 
dummyValue - Variable in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
DUPLICATE_IDENTIFIER_MSG - Static variable in exception org.sbml.jsbml.IdentifierException
 
DUPLICATE_OBJECT_ID - Static variable in class org.sbml.jsbml.JSBML
 

E

elementName - Variable in class org.sbml.jsbml.xml.xstream.converter.MessageConverter
 
email - Variable in class org.sbml.jsbml.Creator
email of the creator
email - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
EMPTY_SET - Static variable in class org.sbml.jsbml.util.compilers.HTMLFormula
HTML code for the empty set symbol “∅”.
enable_tracing() - Method in class org.sbml.jsbml.text.parser.FormulaParser
Enable tracing.
encodeForHTML(String) - Static method in class org.sbml.jsbml.util.StringTools
 
encoding - Variable in class org.sbml.jsbml.ASTNode
Possible attributes for a MathML element
encoding - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
endColumn - Variable in class org.sbml.jsbml.text.parser.Token
The column number of the last character of this Token.
endLine - Variable in class org.sbml.jsbml.text.parser.Token
The line number of the last character of this Token.
EOF - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
End of File.
EOL - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
eol - Variable in exception org.sbml.jsbml.text.parser.ParseException
The end of line string for this machine.
eq(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates a new ASTNode of type RELATIONAL_EQ.
eq(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Equal.
eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
eq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
eqBegin - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Surrounded by new line symbols.
eqEnd - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
End equation; cf.
equals(Object) - Method in class org.sbml.jsbml.AbstractNamedSBase
 
equals(Object) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
equals(Object) - Method in class org.sbml.jsbml.AbstractSBase
 
equals(Object) - Method in class org.sbml.jsbml.AbstractTreeNode
 
equals(Object) - Method in class org.sbml.jsbml.Annotation
 
equals(Object) - Method in class org.sbml.jsbml.ASTNode
 
equals(Object) - Method in class org.sbml.jsbml.Compartment
 
equals(Object) - Method in class org.sbml.jsbml.Creator
 
equals(Object) - Method in class org.sbml.jsbml.CVTerm
 
equals(Object) - Method in class org.sbml.jsbml.Event
 
equals(Object) - Method in class org.sbml.jsbml.EventAssignment
 
equals(Object) - Method in class org.sbml.jsbml.ExplicitRule
 
equals(Object) - Method in class org.sbml.jsbml.FunctionDefinition
 
equals(Object) - Method in class org.sbml.jsbml.History
 
equals(Object) - Method in class org.sbml.jsbml.InitialAssignment
 
equals(Object) - Method in class org.sbml.jsbml.KineticLaw
 
equals(Object) - Method in class org.sbml.jsbml.ListOf
 
equals(Object) - Method in class org.sbml.jsbml.LocalParameter
 
equals(Object) - Method in class org.sbml.jsbml.Model
 
equals(Object) - Method in class org.sbml.jsbml.QuantityWithUnit
 
equals(Object) - Method in class org.sbml.jsbml.Reaction
 
equals(Object) - Method in interface org.sbml.jsbml.SBase
Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
equals(Object) - Method in class org.sbml.jsbml.SBMLDocument
 
equals(Object) - Method in class org.sbml.jsbml.SBMLReader
 
equals(Object) - Method in class org.sbml.jsbml.SBMLWriter
 
equals(Object) - Method in class org.sbml.jsbml.SBO.Term
 
equals(Object) - Method in class org.sbml.jsbml.SBO.Triple
 
equals(Object) - Method in class org.sbml.jsbml.SimpleSpeciesReference
 
equals(Object) - Method in class org.sbml.jsbml.Species
 
equals(Object) - Method in class org.sbml.jsbml.SpeciesReference
 
equals(Object) - Method in class org.sbml.jsbml.Symbol
 
equals(Object) - Method in class org.sbml.jsbml.Trigger
 
equals(Object) - Method in class org.sbml.jsbml.Unit
 
equals(Object) - Method in class org.sbml.jsbml.util.TreeNodeAdapter
 
equals(Object) - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
equals(Object) - Method in class org.sbml.jsbml.util.ValuePair
 
equals(Object) - Method in class org.sbml.jsbml.xml.XMLAttributes
Equality comparison method for XMLAttributes.
equals(Object) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Equality comparison method for XMLNamespaces.
equals(Object) - Method in class org.sbml.jsbml.xml.XMLToken
 
equals(Object) - Method in class org.sbml.jsbml.xml.XMLTriple
Equality comparison method for XMLTriple.
equationHash - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
HashMap with id -> node for equations
equations - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
List with nodes representing an equation in the model
error(String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger
 
ERROR_MESSAGE_INVALID_DIM - Static variable in class org.sbml.jsbml.Compartment
This message will be displayed if the user tries to set the spatial dimensions of this element to a value other than 0, 1, 2, or 3.
ERROR_MESSAGE_ZERO_DIM - Static variable in class org.sbml.jsbml.Compartment
This is the error message to be displayed if an application tries to set units or size attribute for this compartment but the spatial dimensions have been set to zero.
errorCode - Variable in error org.sbml.jsbml.text.parser.TokenMgrError
Indicates the reason why the exception is thrown.
Event - Class in org.sbml.jsbml
Represents the event XML element of a SBML file.
Event() - Constructor for class org.sbml.jsbml.Event
Creates an Event instance.
Event(Event) - Constructor for class org.sbml.jsbml.Event
Creates an Event instance from a given event.
Event(int, int) - Constructor for class org.sbml.jsbml.Event
Creates an Event from a level and version.
Event(String) - Constructor for class org.sbml.jsbml.Event
 
Event(String, int, int) - Constructor for class org.sbml.jsbml.Event
Creates an Event instance from an id, level and version.
Event(String, String, int, int) - Constructor for class org.sbml.jsbml.Event
Creates an Event instance from an id, name, level and version.
EventAssignment - Class in org.sbml.jsbml
Represents the eventAssignment XML element of a SBML file.
EventAssignment() - Constructor for class org.sbml.jsbml.EventAssignment
Creates an EventAssignment instance.
EventAssignment(EventAssignment) - Constructor for class org.sbml.jsbml.EventAssignment
Creates an EventAssignment instance from a given EventAssignment.
EventAssignment(int, int) - Constructor for class org.sbml.jsbml.EventAssignment
Creates an EventAssignment instance from a level and version.
excerpt - Variable in exception org.sbml.jsbml.SBMLError
 
exp(ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Returns a new ASTNode that represents Euler's constant raised by the power of the given exponent.
exp(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
exp(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
exp(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
exp(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
exp(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
exp(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
ExpandBuff(boolean) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
 
expectedTokenSequences - Variable in exception org.sbml.jsbml.text.parser.ParseException
Each entry in this array is an array of integers.
ExplicitRule - Class in org.sbml.jsbml
An explicit Rule is a rule that explicitly declares its variable element.
ExplicitRule() - Constructor for class org.sbml.jsbml.ExplicitRule
Creates a new ExplicitRule.
ExplicitRule(ASTNode, int, int) - Constructor for class org.sbml.jsbml.ExplicitRule
Creates a new ExplicitRule
ExplicitRule(ASTNode, Variable) - Constructor for class org.sbml.jsbml.ExplicitRule
Creates a new ExplicitRule with the given ASTNode element for the assignment to the given Variable or the derivative of the Variable.
ExplicitRule(ExplicitRule) - Constructor for class org.sbml.jsbml.ExplicitRule
Creates a new ExplicitRule
ExplicitRule(int, int) - Constructor for class org.sbml.jsbml.ExplicitRule
Creates a new ExplicitRule
ExplicitRule(Parameter) - Constructor for class org.sbml.jsbml.ExplicitRule
Creates a new ExplicitRule
ExplicitRule(Parameter, ASTNode) - Constructor for class org.sbml.jsbml.ExplicitRule
Creates a new ExplicitRule
ExplicitRule(Variable) - Constructor for class org.sbml.jsbml.ExplicitRule
Creates an ExplicitRule instance from a given Variable.
ExplicitRule(Variable, ASTNode) - Constructor for class org.sbml.jsbml.ExplicitRule
Creates a new ExplicitRule
EXPNUMBER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
exponent - Variable in class org.sbml.jsbml.ASTNode
 
exponent - Variable in class org.sbml.jsbml.Unit
Represents the 'exponent' XML attribute of an unit element.
exponent - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
Expression() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
extensions - Variable in class org.sbml.jsbml.Annotation
contains all the annotation extension objects with the name space of their package.
extentUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
extentUnitsID - Variable in class org.sbml.jsbml.Model
Represents the 'extentUnits' XML attribute of a model element.

F

FACTORIAL - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
factorial(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
factorial(int) - Static method in class org.sbml.jsbml.util.Maths
This method computes the factorial! function.
familyName - Variable in class org.sbml.jsbml.Creator
Family name of the creator
familyName - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
fast - Variable in class org.sbml.jsbml.Reaction
Represents the 'fast' XML attribute of a reaction element.
fast - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
fatal(String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger
 
file - Variable in class org.sbml.jsbml.SBMLErrorLog
 
FillBuff() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
 
Filter - Interface in org.sbml.jsbml.util.filters
A filter is a general interface that allows to check an object for a certain property.
filterCVTerms(CVTerm.Qualifier) - Method in class org.sbml.jsbml.AbstractSBase
 
filterCVTerms(CVTerm.Qualifier, String) - Method in class org.sbml.jsbml.AbstractSBase
 
filterCVTerms(CVTerm.Qualifier) - Method in class org.sbml.jsbml.Annotation
Returns a list of CVTerm having the given qualifier.
filterCVTerms(CVTerm.Qualifier, String) - Method in class org.sbml.jsbml.Annotation
Returns a list of CVTerm having the given qualifier and where the URI contains the given pattern.
filterCVTerms(CVTerm.Qualifier) - Method in interface org.sbml.jsbml.SBase
This method returns a list of all qualifiers of the given type.
filterCVTerms(CVTerm.Qualifier, String) - Method in interface org.sbml.jsbml.SBase
Queries the list of controlled vocabulary terms for those terms whose qualifier is of the given type and selects only those resources from these terms that contain the given pattern.
filterForSpecies - Variable in class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
Decides whether to filter for the identifier of the referenced Species or if to use id and name to filter for the instance of SimpleSpeciesReference itself.
filterList(Filter) - Method in class org.sbml.jsbml.ListOf
Returns a new ListOf that contains only those elements that satisfy a certain filter criterion.
filterResources(String) - Method in class org.sbml.jsbml.CVTerm
Returns a list of resources that contain the given pattern.
filters - Variable in class org.sbml.jsbml.util.filters.AndFilter
A set of filters whose conditions have to be satisfied to accept an item.
findCallableSBase(String) - Method in class org.sbml.jsbml.Model
Returns a CallableSBase element of the Model that has the given 'id' as identifier or null if no element is found.
findLocalParameters(String) - Method in class org.sbml.jsbml.Model
Finds all instances of LocalParameter in this Model and adds them to a List.
findModifierSpeciesReference(String) - Method in class org.sbml.jsbml.Model
Returns the ModifierSpeciesReference with all Reactions of this Model that has 'id' as id.
findNamedSBase(String) - Method in class org.sbml.jsbml.Model
Returns a NamedSBase element of the model that has the given 'id' as id or null if no element is found.
findNamedSBaseWithDerivedUnit(String) - Method in class org.sbml.jsbml.Model
Returns a NamedSBaseWithDerivedUnit element of the Model that has the given 'id' as id or null if no element is found.
findQuantity(String) - Method in class org.sbml.jsbml.Model
Searches for an instance of Quantity within all of this Model's components that has the given identifier or name attribute and returns it.
findQuantityWithUnit(String) - Method in class org.sbml.jsbml.Model
Searches for an instance of QuantityWithUnit within all of this Model's components that has the given identifier or name attribute and returns it.
findReactionsForLocalParameter(String) - Method in class org.sbml.jsbml.Model
Returns a SortedSet of identifiers of all Reaction elements within this Model whose KineticLaws contain a LocalParameter that has the given 'id' or null if no element cannot be found.
findReferencedGlobalParameters() - Method in class org.sbml.jsbml.ASTNode
Goes through the formula and identifies all global parameters that are referenced by this rate equation.
findSBase(String) - Method in class org.sbml.jsbml.SBMLDocument
Looks up the SBase registered in this SBMLDocument for the given metaId.
findShortestPath(int, OverdeterminationValidator.Node<SBase>, List<OverdeterminationValidator.Node<SBase>>) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
Finds all paths of the length i whose nodes are part of the matching.
findSimpleSpeciesReference(String) - Method in class org.sbml.jsbml.Model
Returns the SimpleSpeciesReference within all Reactions of this Model that has 'id' as id.
findSpeciesReference(String) - Method in class org.sbml.jsbml.Model
Returns the SpeciesReference with all Reactions of this Model that has 'id' as id.
findSymbol(String) - Method in class org.sbml.jsbml.Model
Searches in the list of Compartments, Species, and Parameters for the element with the given identifier.
findUniqueNamedSBase(String) - Method in class org.sbml.jsbml.Model
Returns a UniqueNamedSBase element that has the given 'id' within this Model or null if no such element can be found.
findUnitDefinition(String) - Method in class org.sbml.jsbml.Model
Returns a UnitDefinition element that has the given 'id' within this Model or null if no such element can be found.
FindUnitsCompiler - Class in org.sbml.jsbml.util.compilers
Finds if an ASTNode is using any units attribute.
FindUnitsCompiler() - Constructor for class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
findUnitsCompiler - Variable in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
findVariable(String) - Method in class org.sbml.jsbml.Model
Searches the Variable with the given identifier in this model.
fireNodeAddedEvent() - Method in class org.sbml.jsbml.AbstractTreeNode
 
fireNodeAddedEvent() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
All TreeNodeChangeListener instances linked to this TreeNode are informed about the adding of this Object to an owning parent Object.
fireNodeRemovedEvent() - Method in class org.sbml.jsbml.AbstractSBase
 
fireNodeRemovedEvent() - Method in class org.sbml.jsbml.AbstractTreeNode
 
fireNodeRemovedEvent() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
All TreeNodeChangeListener instances linked to this TreeNode are informed about the deletion of this TreeNode from a parent Object.
firePropertyChange(String, Object, Object) - Method in class org.sbml.jsbml.AbstractTreeNode
 
firePropertyChange(String, Object, Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
All TreeNodeChangeListeners are informed about the change in this AbstractTreeNode.
first - Variable in class org.sbml.jsbml.text.parser.FormulaParser.JJCalls
 
firstHit(Filter) - Method in class org.sbml.jsbml.ListOf
Returns the first element in this list that satisfies a certain filter criterion.
firstLetterLowerCase(String) - Static method in class org.sbml.jsbml.util.StringTools
Returns a String whose first letter is now in lower case.
firstLetterUpperCase(String) - Static method in class org.sbml.jsbml.util.StringTools
Returns a String who's first letter is now in upper case.
floor(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
format(double) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
This method returns a StringBuffer representing a properly LaTeX formatted number.
formatToW3CDTF(Date) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
Format date to W3CDTF.
formatToW3CDTF(String) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
Format datetime string to W3CDTF.
formatToW3CDTF(Timestamp) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
Format datetime to W3CDTF.
formula - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
FormulaCompiler - Class in org.sbml.jsbml.util.compilers
This class creates C-like infix formula Strings that represent the content of ASTNodes.
FormulaCompiler() - Constructor for class org.sbml.jsbml.util.compilers.FormulaCompiler
 
FormulaCompilerNoPiecewise - Class in org.sbml.jsbml.util.compilers
Produces an infix formula like FormulaCompiler but removes all the piecewise functions.
FormulaCompilerNoPiecewise() - Constructor for class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
 
FormulaParser - Class in org.sbml.jsbml.text.parser
 
FormulaParser(InputStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser
Constructor with InputStream.
FormulaParser(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser
Constructor with InputStream and supplied encoding
FormulaParser(Reader) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser
Constructor.
FormulaParser(FormulaParserTokenManager) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser
Constructor with generated Token Manager.
FormulaParser.JJCalls - Class in org.sbml.jsbml.text.parser
 
FormulaParser.JJCalls() - Constructor for class org.sbml.jsbml.text.parser.FormulaParser.JJCalls
 
FormulaParser.LookaheadSuccess - Error in org.sbml.jsbml.text.parser
 
FormulaParser.LookaheadSuccess() - Constructor for error org.sbml.jsbml.text.parser.FormulaParser.LookaheadSuccess
 
FormulaParserConstants - Interface in org.sbml.jsbml.text.parser
Token literal values and constants.
FormulaParserTokenManager - Class in org.sbml.jsbml.text.parser
Token Manager.
FormulaParserTokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserTokenManager
Constructor.
FormulaParserTokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserTokenManager
Constructor.
formulaToString(ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Returns the formula from the given ASTNode as an SBML Level 1 text-string mathematical formula.
formulaToString(ASTNode) - Static method in class org.sbml.jsbml.JSBML
Converts an ASTNode formula to a text string using a specific syntax for mathematical formulas.
frac(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates a new ASTNode of type DIVIDE with the given nodes as children.
frac(int, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates a new ASTNode that of type DIVIDE with the given numerator and denominator.
frac(MathContainer, CallableSBase, CallableSBase) - Static method in class org.sbml.jsbml.ASTNode
Creates a new ASTNode that divides two named sbase objects.
frac(MathContainer, String, String) - Static method in class org.sbml.jsbml.ASTNode
Returns a new ASTNode that of type DIVIDE with the two entities as numerator and denominator.
frac(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Fraction of two ASTNodes
frac(int, int) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
A fraction of two int values.
frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
frac(int, int) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
frac(Object, Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Returns a fraction with the given elements as numerator and denominator.
frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
frac(int, int) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
frac(int, int) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
frac(Object, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
frac(int, int) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
frac(int, int) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
function(FunctionDefinition, List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
function(String, List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
function(FunctionDefinition, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
function(FunctionDefinition, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
function(String, ASTNode...) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
function(FunctionDefinition, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
function(String, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Decides whether to produce brackets.
function(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Without brackets.
function(FunctionDefinition, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
function(String, ASTNode...) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
function(FunctionDefinition, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
FunctionDefinition - Class in org.sbml.jsbml
Represents the functionDefinition XML element of a SBML file.
FunctionDefinition() - Constructor for class org.sbml.jsbml.FunctionDefinition
Creates a FunctionDefinition instance.
FunctionDefinition(FunctionDefinition) - Constructor for class org.sbml.jsbml.FunctionDefinition
Creates a FunctionDefinition instance from a given FunctionDefinition.
FunctionDefinition(int, int) - Constructor for class org.sbml.jsbml.FunctionDefinition
Creates a FunctionDefinition instance from a level and version.
FunctionDefinition(String, ASTNode, int, int) - Constructor for class org.sbml.jsbml.FunctionDefinition
Creates a FunctionDefinition instance from an id, ASTNode, level and version.
FunctionDefinition(String, int, int) - Constructor for class org.sbml.jsbml.FunctionDefinition
Creates a FunctionDefinition instance from an id, level and version.

G

gen - Variable in class org.sbml.jsbml.text.parser.FormulaParser.JJCalls
 
generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParser
Generate ParseException.
generateSubModel(Model, String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
Generates a sub-model containing the elements passed as argument and all the necessary dependencies.
generateSubModel(Model, String[], String[], String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
Generates a sub-model containing the elements passed as argument and all the necessary dependencies.
generateSubModel(Model, String[], String[], String[], String[], String[], boolean, boolean, boolean, boolean, boolean) - Static method in class org.sbml.jsbml.util.SubModel
Creates a sub-model with the option to ignore certain items.
geq(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates an ASTNode representing greater or equal for the two given nodes.
geq(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Greater equal.
geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
get(int) - Method in class org.sbml.jsbml.ListOf
Returns the element at the specified position in this list or null if the index is negative or too big.
get(String) - Method in class org.sbml.jsbml.ListOf
Gets the list element which has the id 'id'.
getAbout() - Method in class org.sbml.jsbml.Annotation
Returns the about String of this object.
getAllowsChildren() - Method in class org.sbml.jsbml.AbstractMathContainer
 
getAllowsChildren() - Method in class org.sbml.jsbml.AbstractSBase
 
getAllowsChildren() - Method in class org.sbml.jsbml.Annotation
 
getAllowsChildren() - Method in class org.sbml.jsbml.ASTNode
 
getAllowsChildren() - Method in class org.sbml.jsbml.Creator
 
getAllowsChildren() - Method in class org.sbml.jsbml.CVTerm
 
getAllowsChildren() - Method in class org.sbml.jsbml.Event
 
getAllowsChildren() - Method in class org.sbml.jsbml.History
 
getAllowsChildren() - Method in class org.sbml.jsbml.ListOf
 
getAllowsChildren() - Method in class org.sbml.jsbml.Model
 
getAllowsChildren() - Method in class org.sbml.jsbml.Reaction
 
getAllowsChildren() - Method in class org.sbml.jsbml.SBMLDocument
 
getAllowsChildren() - Method in class org.sbml.jsbml.SpeciesReference
 
getAllowsChildren() - Method in class org.sbml.jsbml.UnitDefinition
 
getAllowsChildren() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
 
getAllowsChildren() - Method in class org.sbml.jsbml.xml.XMLNode
 
getAndReplacement() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
Gets the String that will be used to replace ' and ' (the mathML <and> element) in the boolean expressions.
getAnnotation() - Method in class org.sbml.jsbml.AbstractSBase
 
getAnnotation() - Method in interface org.sbml.jsbml.SBase
Returns the content of the 'annotation' sub-element of this object as an Annotation instance.
getAnnotationBuilder() - Method in class org.sbml.jsbml.Annotation
Returns the StringBuilder representing non RDF annotations.
getAnnotationNamespaces() - Method in class org.sbml.jsbml.Annotation
Returns the annotationNamespace map of this object.
getAnnotationString() - Method in class org.sbml.jsbml.AbstractSBase
Returns the Annotation of this SBML object as a String.
getAnnotationString() - Method in interface org.sbml.jsbml.SBase
Returns the content of the 'annotation' sub-element of this object as a String.
getAntisenseRNA() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id for antisense RNA.
getAreaUnits() - Method in class org.sbml.jsbml.Model
Returns the area units ID of this Model.
getAreaUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns the UnitDefinition instance which has the area units ID of this Model as id.
getArgument(int) - Method in class org.sbml.jsbml.FunctionDefinition
Get the nth argument to this function.
getArgument(String) - Method in class org.sbml.jsbml.FunctionDefinition
Get the argument named name to this FunctionDefinition.
getAttributes() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
getAttributes() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the attributes of this element.
getAttributesLength() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the number of attributes in the attributes set.
getAttrIndex(String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the index of an attribute with the given local name.
getAttrIndex(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the index of an attribute with the given local name and namespace URI.
getAttrIndex(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the index of an attribute with the given XMLTriple.
getAttrName(int) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the local name of an attribute in the attributes set in this XMLToken (by position).
getAttrPrefix(int) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the prefix of an attribute in the attribute set in this XMLToken (by position).
getAttrPrefixedName(int) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the prefixed name of an attribute in the attribute set in this XMLToken (by position).
getAttrURI(int) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the namespace URI of an attribute in the attribute set in this XMLToken (by position).
getAttrValue(int) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the value of an attribute in the attribute set in this XMLToken (by position).
getAttrValue(String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns a value of an attribute with the given local name.
getAttrValue(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns a value of an attribute with the given local name and namespace URI.
getAttrValue(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLToken
Returns a value of an attribute with the given XMLTriple.
getBeginColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Get token beginning column number.
getBeginLine() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Get token beginning line number.
getBindingActivator() - Static method in class org.sbml.jsbml.SBO
 
getBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm
Returns the Biological QualifierType code for this CVTerm.
getBody() - Method in class org.sbml.jsbml.FunctionDefinition
Get the mathematical expression that is the body of this FunctionDefinition object.
getBoundaryCondition() - Method in class org.sbml.jsbml.Species
 
getBytesFromResourceLocation(String) - Method in class org.sbml.jsbml.resources.Resource
Gets the byte data from a file at the given resource location.
getBytesFromStream(InputStream) - Method in class org.sbml.jsbml.resources.Resource
Gets the byte data from a file.
getCalculatedStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference
This method computes the fraction of the stoichiometry and the denominator.
getCatalysis() - Static method in class org.sbml.jsbml.SBO
 
getCatalyst() - Static method in class org.sbml.jsbml.SBO
 
getCatalyticActivator() - Static method in class org.sbml.jsbml.SBO
 
getCategory() - Method in exception org.sbml.jsbml.SBMLError
Returns the category of the SBMLError
getCategory() - Method in exception org.sbml.jsbml.SBMLException
 
getCategory() - Method in class org.sbml.jsbml.util.Detail
 
getCharacter() - Method in class org.sbml.jsbml.ASTNode
Gets the value of this node as a single character.
getCharacters() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
getCharacters() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the text of this element.
getCharge() - Method in class org.sbml.jsbml.Species
Deprecated.
getChild(int) - Method in class org.sbml.jsbml.ASTNode
Gets a child of this node according to an index number.
getChild(int) - Method in class org.sbml.jsbml.xml.XMLNode
Deprecated.
getChildAt(int) - Method in class org.sbml.jsbml.AbstractMathContainer
 
getChildAt(int) - Method in class org.sbml.jsbml.AbstractSBase
 
getChildAt(int) - Method in class org.sbml.jsbml.Annotation
 
getChildAt(int) - Method in class org.sbml.jsbml.ASTNode
 
getChildAt(int) - Method in class org.sbml.jsbml.Constraint
 
getChildAt(int) - Method in class org.sbml.jsbml.Creator
 
getChildAt(int) - Method in class org.sbml.jsbml.CVTerm
 
getChildAt(int) - Method in class org.sbml.jsbml.Event
 
getChildAt(int) - Method in class org.sbml.jsbml.History
 
getChildAt(int) - Method in class org.sbml.jsbml.KineticLaw
 
getChildAt(int) - Method in class org.sbml.jsbml.ListOf
 
getChildAt(int) - Method in class org.sbml.jsbml.Model
 
getChildAt(int) - Method in class org.sbml.jsbml.Reaction
 
getChildAt(int) - Method in class org.sbml.jsbml.SBMLDocument
 
getChildAt(int) - Method in class org.sbml.jsbml.SpeciesReference
 
getChildAt(int) - Method in class org.sbml.jsbml.UnitDefinition
 
getChildAt(int) - Method in class org.sbml.jsbml.util.TreeNodeAdapter
 
getChildAt(int) - Method in class org.sbml.jsbml.xml.XMLNode
 
getChildCount() - Method in class org.sbml.jsbml.AbstractMathContainer
 
getChildCount() - Method in class org.sbml.jsbml.AbstractSBase
 
getChildCount() - Method in class org.sbml.jsbml.Annotation
 
getChildCount() - Method in class org.sbml.jsbml.ASTNode
 
getChildCount() - Method in class org.sbml.jsbml.Constraint
 
getChildCount() - Method in class org.sbml.jsbml.Creator
 
getChildCount() - Method in class org.sbml.jsbml.CVTerm
 
getChildCount() - Method in class org.sbml.jsbml.Event
 
getChildCount() - Method in class org.sbml.jsbml.History
 
getChildCount() - Method in class org.sbml.jsbml.KineticLaw
 
getChildCount() - Method in class org.sbml.jsbml.ListOf
 
getChildCount() - Method in class org.sbml.jsbml.Model
 
getChildCount() - Method in class org.sbml.jsbml.Reaction
 
getChildCount() - Method in class org.sbml.jsbml.SBMLDocument
 
getChildCount() - Method in class org.sbml.jsbml.SpeciesReference
 
getChildCount() - Method in class org.sbml.jsbml.UnitDefinition
 
getChildCount() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
 
getChildCount() - Method in class org.sbml.jsbml.xml.XMLNode
 
getChildren() - Method in class org.sbml.jsbml.ASTNode
Returns the list of children of the current ASTNode.
getChildren() - Method in class org.sbml.jsbml.SBO.Term
Returns a set of all the children Term.
getClassName() - Method in class org.sbml.jsbml.ASTNode
Returns the class name of the mathML element represented by this ASTNode.
getCode() - Method in exception org.sbml.jsbml.SBMLError
Returns the code of this SBMLError.
getCode() - Method in exception org.sbml.jsbml.SBMLException
 
getColumn() - Method in exception org.sbml.jsbml.SBMLError
Returns the column where this SBMLError happened.
getColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Deprecated.
getColumn() - Method in class org.sbml.jsbml.util.Location
 
getColumn() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the column at which this XMLToken occurred in the input document or data stream.
getCompartment(int) - Method in class org.sbml.jsbml.Model
Gets the nth Compartment instance of the listOfCompartments.
getCompartment(String) - Method in class org.sbml.jsbml.Model
Gets the Compartment of the listOfCompartments which has 'id' as id.
getCompartment() - Method in class org.sbml.jsbml.Reaction
Only available if Level >= 3.
getCompartment() - Method in class org.sbml.jsbml.Species
 
getCompartmentInstance() - Method in class org.sbml.jsbml.Reaction
 
getCompartmentInstance() - Method in class org.sbml.jsbml.Species
 
getCompartmentType() - Method in class org.sbml.jsbml.Compartment
Deprecated.
Only defined in SBML Level 2 Versions 2 through 4.
getCompartmentType(int) - Method in class org.sbml.jsbml.Model
Deprecated.
getCompartmentType(String) - Method in class org.sbml.jsbml.Model
Deprecated.
getCompartmentTypeInstance() - Method in class org.sbml.jsbml.Compartment
Deprecated.
getCompetetiveInhibitor() - Static method in class org.sbml.jsbml.SBO
 
getCompleteInhibitor() - Static method in class org.sbml.jsbml.SBO
 
getComplex() - Static method in class org.sbml.jsbml.SBO
 
getConservationLaw() - Static method in class org.sbml.jsbml.SBO
 
getConstant() - Method in class org.sbml.jsbml.SpeciesReference
 
getConstant() - Method in class org.sbml.jsbml.Symbol
 
getConstant() - Method in interface org.sbml.jsbml.Variable
 
getConstantAvogadro(String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Creates an ASTNodeValue that represent's Avogadro's number.
getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
getConstantE() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
getConstantE() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
getConstantE() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
getConstantE() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
getConstantE() - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
getConstantE() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
getConstantE() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
getConstantFalse() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
getConstantPi() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
getConstantPi() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
getConstantPi() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
getConstantPi() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
getConstantPi() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
getConstantPi() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
getConstantTrue() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
getConstraint(int) - Method in class org.sbml.jsbml.Model
Gets the nth Constraint object in this Model.
getContinuousFramework() - Static method in class org.sbml.jsbml.SBO
 
getConversionFactor() - Method in class org.sbml.jsbml.Model
Returns the conversionFactor ID of this Model.
getConversionFactor() - Method in class org.sbml.jsbml.Species
 
getConversionFactorInstance() - Method in class org.sbml.jsbml.Model
Returns the Parameter instance which has the conversionFactorID of this Model as id.
getConversionFactorInstance() - Method in class org.sbml.jsbml.Species
 
getCreatedDate() - Method in class org.sbml.jsbml.History
Returns the createdDate from the History.
getCreator(int) - Method in class org.sbml.jsbml.History
Get the nth Creator object in this History.
getCVTerm(int) - Method in class org.sbml.jsbml.AbstractSBase
 
getCVTerm(int) - Method in class org.sbml.jsbml.Annotation
Returns the CVTerm at the ith position in the list of CVTerms.
getCVTerm(int) - Method in interface org.sbml.jsbml.SBase
 
getCVTerms() - Method in class org.sbml.jsbml.AbstractSBase
 
getCVTerms() - Method in interface org.sbml.jsbml.SBase
 
getDeclaredNamespaces() - Method in class org.sbml.jsbml.AbstractSBase
 
getDeclaredNamespaces() - Method in interface org.sbml.jsbml.SBase
Returns all the namespaces declared on this object.
getDefaultIndentChar() - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
getDefaultIndentCount() - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
getDefaultLevel() - Method in class org.sbml.jsbml.SBMLDocument
The default SBML Level of new SBMLDocument objects.
getDefaultPossibleEnzymes() - Static method in class org.sbml.jsbml.SBO
Creates and returns a list of molecule types accepted as an enzyme by default.
getDefaultVersion() - Method in class org.sbml.jsbml.SBMLDocument
The default Version of new SBMLDocument objects.
getDefinition() - Method in class org.sbml.jsbml.SBO.Term
Returns the definition of this SBO.Term, which is stored in the corresponding OBO file under the key def.
getDefinitionURIavogadro() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
getDefinitionURIdelay() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
getDefinitionURItime() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
getDefinitionURL() - Method in class org.sbml.jsbml.ASTNode
Returns the definitionURL
getDelay() - Method in class org.sbml.jsbml.Event
 
getDenominator() - Method in class org.sbml.jsbml.ASTNode
Gets the value of the denominator of this node.
getDenominator() - Method in class org.sbml.jsbml.SpeciesReference
Deprecated.
Use for Level 1 only.
getDerivedUnitDefinition() - Method in class org.sbml.jsbml.AbstractMathContainer
 
getDerivedUnitDefinition() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Compartment
 
getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Event
Deprecated.
getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Reaction
 
getDerivedUnitDefinition() - Method in interface org.sbml.jsbml.SBaseWithDerivedUnit
This method derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model.
getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Species
 
getDerivedUnitDefinition() - Method in class org.sbml.jsbml.SpeciesReference
 
getDerivedUnits() - Method in class org.sbml.jsbml.AbstractMathContainer
 
getDerivedUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
getDerivedUnits() - Method in class org.sbml.jsbml.Event
Deprecated.
getDerivedUnits() - Method in class org.sbml.jsbml.Reaction
 
getDerivedUnits() - Method in interface org.sbml.jsbml.SBaseWithDerivedUnit
This method derives the unit of this quantity.
getDerivedUnits() - Method in class org.sbml.jsbml.SpeciesReference
 
getDerivedVariable() - Method in class org.sbml.jsbml.AlgebraicRule
Provides a convenient way to obtain the variable whose amount is determined by this rule.
getDetail() - Method in exception org.sbml.jsbml.SBMLError
 
getDiscreteFramework() - Static method in class org.sbml.jsbml.SBO
 
getDocument() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
getDrug() - Static method in class org.sbml.jsbml.SBO
 
getElementName() - Method in class org.sbml.jsbml.AbstractSBase
 
getElementName() - Method in class org.sbml.jsbml.AssignmentRule
 
getElementName() - Method in class org.sbml.jsbml.ListOf
 
getElementName() - Method in class org.sbml.jsbml.LocalParameter
 
getElementName() - Method in interface org.sbml.jsbml.SBase
 
getElementName() - Method in class org.sbml.jsbml.SBMLDocument
 
getElementName() - Method in class org.sbml.jsbml.Species
 
getElementName() - Method in class org.sbml.jsbml.SpeciesReference
 
getElementNameEquivalent() - Method in enum org.sbml.jsbml.CVTerm.Qualifier
Returns a name corresponding to this Qualifier Object.
getElementNameEquivalent() - Method in enum org.sbml.jsbml.CVTerm.Type
Returns a name corresponding to this Type of qualifier Object.
getElementNameEquivalentToQualifier(CVTerm.Qualifier) - Static method in class org.sbml.jsbml.Annotation
Returns a String which represents the given CVTerm.Qualifier.
getEmail() - Method in class org.sbml.jsbml.Creator
Returns the email from the Creator.
getEmptySet() - Static method in class org.sbml.jsbml.SBO
 
getEncoding() - Method in class org.sbml.jsbml.ASTNode
Returns the encoding of the mathML element represented by this ASTNode.
getEndColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Get token end column number.
getEndLine() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Get token end line number.
getEntity() - Static method in class org.sbml.jsbml.SBO
 
getEnzymaticCatalysis() - Static method in class org.sbml.jsbml.SBO
 
getError(int) - Method in class org.sbml.jsbml.SBMLDocument
 
getError(long) - Method in class org.sbml.jsbml.SBMLErrorLog
Returns the nth SBMLError object in this log.
getErrorId() - Method in exception org.sbml.jsbml.xml.XMLException
 
getErrorLog() - Method in class org.sbml.jsbml.SBMLDocument
This method returns a collection of all SBMLErrors reflecting problems in the overall data structure of this SBMLDocument.
getEssentialActivator() - Static method in class org.sbml.jsbml.SBO
 
getEvent(int) - Method in class org.sbml.jsbml.Model
Gets the nth Event object in this Model.
getEvent(String) - Method in class org.sbml.jsbml.Model
Gets the Event which as the given id as id.
getEvent() - Static method in class org.sbml.jsbml.SBO
 
getEventAssignment(int) - Method in class org.sbml.jsbml.Event
 
getExcerpt() - Method in exception org.sbml.jsbml.SBMLError
Returns a fragment of the original XML file that induced the error.
getExponent() - Method in class org.sbml.jsbml.ASTNode
Gets the exponent value of this ASTNode.
getExponent() - Method in class org.sbml.jsbml.Unit
 
getExponentAsDouble() - Method in class org.sbml.jsbml.Unit
Deprecated.
getExtension(String) - Method in class org.sbml.jsbml.Annotation
Returns the Annotation extension object matching 'namespace'.
getExtentUnits() - Method in class org.sbml.jsbml.Model
Returns the extent units ID of this Model.
getExtentUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns the UnitDefinition instance which has the extent units ID of this Model as id.
getFamilyName() - Method in class org.sbml.jsbml.Creator
Returns the familyName from the Creator.
getFast() - Method in class org.sbml.jsbml.Reaction
 
getFile() - Method in class org.sbml.jsbml.SBMLErrorLog
Returns the file containing the xml error log representation.
getFilters() - Method in class org.sbml.jsbml.util.filters.AndFilter
 
getFirst() - Method in class org.sbml.jsbml.ListOf
The first element in this list.
getFormula() - Method in class org.sbml.jsbml.AbstractMathContainer
Deprecated.
getFormula() - Method in interface org.sbml.jsbml.MathContainer
Deprecated.
As this is part of SBML Level 1, it is strongly recommended not to work with the String representation of a formula, but to deal with a more flexible ASTNode.
getFunctionalCompartment() - Static method in class org.sbml.jsbml.SBO
 
getFunctionalEntity() - Static method in class org.sbml.jsbml.SBO
 
getFunctionDefinition(int) - Method in class org.sbml.jsbml.Model
Gets the nth FunctionDefinition instance of the listOfFunstionDefinitions.
getFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
Returns the FunctionDefinition of the Model.listOfFunctionDefinitions which has 'id' as id.
getGene() - Static method in class org.sbml.jsbml.SBO
 
getGeneCodingRegion() - Static method in class org.sbml.jsbml.SBO
 
getGeneric() - Static method in class org.sbml.jsbml.SBO
 
getGivenName() - Method in class org.sbml.jsbml.Creator
Returns the givenName from the Creator.
getHasOnlySubstanceUnits() - Method in class org.sbml.jsbml.Species
 
getHillEquation() - Static method in class org.sbml.jsbml.SBO
 
getHistory() - Method in class org.sbml.jsbml.AbstractSBase
 
getHistory() - Method in class org.sbml.jsbml.Annotation
Returns the History of the Annotation.
getHistory() - Method in interface org.sbml.jsbml.SBase
 
getId() - Method in class org.sbml.jsbml.AbstractNamedSBase
 
getId() - Method in class org.sbml.jsbml.ASTNode
Returns the id of the mathML element represented by this ASTNode.
getId() - Method in class org.sbml.jsbml.FunctionDefinition
 
getId() - Method in interface org.sbml.jsbml.NamedSBase
 
getId() - Method in class org.sbml.jsbml.SBO.Term
Returns the SBO identifier of this SBO.Term, for instance: SBO:0000031.
getId() - Method in class org.sbml.jsbml.util.filters.AssignmentVariableFilter
 
getId() - Method in class org.sbml.jsbml.util.filters.NameFilter
 
GetImage() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Get token literal value.
getIndent() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
getIndent() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
getIndentationChar() - Method in class org.sbml.jsbml.SBMLWriter
Gives the symbol that is used to indent the SBML output for a better structure and to improve human-readability.
getIndentationChar() - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Gives the symbol that is used to indent the SBML output for a better structure and to improve human-readability.
getIndentationCount() - Method in class org.sbml.jsbml.SBMLWriter
Gives the number of indent symbols that are inserted in a line to better structure the SBML output.
getIndentationCount() - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Gives the number of indent symbols that are inserted in a line to better structure the SBML output.
getIndenting() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
getIndenting() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
getIndex(TreeNode) - Method in class org.sbml.jsbml.AbstractTreeNode
 
getIndex(String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns the index of an attribute with the given name.
getIndex(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns the index of an attribute with the given local name and namespace URI.
getIndex(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns the index of an attribute with the given XMLTriple.
getIndex(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Gets the index of an XML namespace declaration by URI.
getIndexByPrefix(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Gets the index of an XML namespace declaration by prefix.
getInhibitor() - Static method in class org.sbml.jsbml.SBO
 
getInitialAmount() - Method in class org.sbml.jsbml.Species
 
getInitialAssignment(int) - Method in class org.sbml.jsbml.Model
Gets the nth InitialAssignment object in this Model.
getInitialAssignment(String) - Method in class org.sbml.jsbml.Model
Returns the InitialAssignment of the Model.listOfInitialAssignments whose symbol attribute, i.e., whose Variable has the given variable as identifier.
getInitialConcentration() - Method in class org.sbml.jsbml.Species
 
getInitialValue() - Method in class org.sbml.jsbml.Trigger
 
getInstance() - Static method in class org.sbml.jsbml.resources.Resource
 
getInstance() - Static method in class org.sbml.jsbml.util.JAXPFacade
Creates and returns a new JAXPFacade.
getInteger() - Method in class org.sbml.jsbml.ASTNode
Gets the value of this node as an integer.
getInteger(ASTNode) - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
getInteraction() - Static method in class org.sbml.jsbml.SBO
 
getIon() - Static method in class org.sbml.jsbml.SBO
 
getIonChannel() - Static method in class org.sbml.jsbml.SBO
 
getJSBMLDottedVersion() - Static method in class org.sbml.jsbml.JSBML
Returns the JSBML version as a string of the form '1.2.3'.
getJSBMLVersion() - Static method in class org.sbml.jsbml.JSBML
Returns the JSBML version as an integer: version 1.2.3 becomes 123.
getJSBMLVersionString() - Static method in class org.sbml.jsbml.JSBML
Returns the JSBML version as a string: version 1.2.3 becomes '123'.
getKind() - Method in class org.sbml.jsbml.Unit
 
getKineticConstant() - Static method in class org.sbml.jsbml.SBO
 
getKineticLaw() - Method in class org.sbml.jsbml.Reaction
 
getL() - Method in class org.sbml.jsbml.util.ValuePair
 
getLang() - Method in class org.sbml.jsbml.util.Message
 
getLast() - Method in class org.sbml.jsbml.ListOf
Returns the last element in this list.
getLastElementOf(ListOf<? extends T>) - Method in class org.sbml.jsbml.Model
Returns the last element added in the given list.
getLeftChild() - Method in class org.sbml.jsbml.ASTNode
Gets the left child of this node.
getLength() - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns the number of attributes in the set.
getLength() - Method in class org.sbml.jsbml.xml.XMLNamespaces
Returns the total number of URI-and-prefix pairs stored in this particular XMLNamespaces instance.
getLengthUnits() - Method in class org.sbml.jsbml.Model
Returns the length units ID of this Model.
getLengthUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns the length units of this Model as a UnitDefinition.
getLevel() - Method in class org.sbml.jsbml.AbstractSBase
 
getLevel() - Method in interface org.sbml.jsbml.SBase
Returns the SBML Level of the overall SBML document.
getLevel() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
Returns the level of the SBML document that was the basis to create this ASTNodeValue.
getLevel() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
getLevelAndVersion() - Method in class org.sbml.jsbml.AbstractSBase
 
getLevelAndVersion() - Method in interface org.sbml.jsbml.SBase
Returns the Level and Version combination of this SBase.
getLine() - Method in exception org.sbml.jsbml.SBMLError
Returns the line where this SBMLError happened.
getLine() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Deprecated.
getLine() - Method in class org.sbml.jsbml.util.Location
 
getLine() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the line at which this XMLToken occurred in the input document or data stream.
getListOfCompartments() - Method in class org.sbml.jsbml.Model
Returns the listOfCompartments of this Model.
getListOfCompartmentTypes() - Method in class org.sbml.jsbml.Model
Deprecated. 
getListOfConstraints() - Method in class org.sbml.jsbml.Model
Returns the listOfConstraints of this Model.
getListOfCreators() - Method in class org.sbml.jsbml.History
Get the list of Creator objects in this History.
getListOfCVTerms() - Method in class org.sbml.jsbml.Annotation
Returns the list of CVTerms.
getListOfErrors() - Method in class org.sbml.jsbml.SBMLDocument
This method returns a collection of all SBMLErrors reflecting problems in the overall data structure of this SBMLDocument.
getListOfEventAssignments() - Method in class org.sbml.jsbml.Event
 
getListOfEvents() - Method in class org.sbml.jsbml.Model
Returns the listOfEvents of this Model.
getListOfFunctionDefinitions() - Method in class org.sbml.jsbml.Model
Returns the listOfFunctionDefinitions of this Model.
getListOfInitialAssignments() - Method in class org.sbml.jsbml.Model
Returns the listOfInitialAssignments of this Model.
getListOfLocalParameters() - Method in class org.sbml.jsbml.KineticLaw
 
getListOfModifiedDates() - Method in class org.sbml.jsbml.History
Get the list of ModifiedDate objects in this History.
getListOfModifiers() - Method in class org.sbml.jsbml.Reaction
 
getListOfNodes() - Method in class org.sbml.jsbml.ASTNode
Returns the list of children of the current ASTNode.
getListOfNodes(Filter) - Method in class org.sbml.jsbml.ASTNode
Returns the list of children of the current ASTNode that satisfy the given filter.
getListOfParameters() - Method in class org.sbml.jsbml.KineticLaw
getListOfParameters() - Method in class org.sbml.jsbml.Model
Returns the listOfParameters of this Model.
getListOfPredefinedUnitDefinitions() - Method in class org.sbml.jsbml.Model
 
getListOfProducts() - Method in class org.sbml.jsbml.Reaction
 
getListOfReactants() - Method in class org.sbml.jsbml.Reaction
 
getListOfReactions() - Method in class org.sbml.jsbml.Model
Returns the listOfReactions of this Model.
getListOfRules() - Method in class org.sbml.jsbml.Model
Returns the listOfRules of this Model.
getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
getListOfSBMLElementsToWrite(Object) - Method in interface org.sbml.jsbml.xml.parsers.WritingParser
Returns the list of children of the objectToWrite.
getListOfSpecies() - Method in class org.sbml.jsbml.Model
Returns the listOfSpecies of this Model.
getListOfSpeciesTypes() - Method in class org.sbml.jsbml.Model
Deprecated. 
getListOfTreeNodeChangeListeners() - Method in class org.sbml.jsbml.AbstractTreeNode
 
getListOfTreeNodeChangeListeners() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
Returns all TreeNodeChangeListeners that are assigned to this element.
getListOfUnitDefinitions() - Method in class org.sbml.jsbml.Model
Returns the listOfUnitDefinitions of this Model.
getListOfUnits() - Method in class org.sbml.jsbml.UnitDefinition
 
getLocalParameter(int) - Method in class org.sbml.jsbml.KineticLaw
 
getLocalParameter(String) - Method in class org.sbml.jsbml.KineticLaw
 
getLocalParameterCount() - Method in class org.sbml.jsbml.KineticLaw
 
getLocation() - Method in exception org.sbml.jsbml.SBMLError
Returns the location where this SBMLError happened.
getLogger() - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
 
getLogger() - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
getLogicalFramework() - Static method in class org.sbml.jsbml.SBO
 
getMantissa() - Method in class org.sbml.jsbml.ASTNode
Gets the mantissa value of this node.
getMatching() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
Returns the determined matching
getMaterialEntity() - Static method in class org.sbml.jsbml.SBO
 
getMath() - Method in class org.sbml.jsbml.AbstractMathContainer
 
getMath() - Method in interface org.sbml.jsbml.MathContainer
If MathContainer.isSetMath() returns true, this method returns the ASTNode belonging to this MathContainer.
getMathematicalExpression() - Static method in class org.sbml.jsbml.SBO
 
getMathMLString() - Method in class org.sbml.jsbml.AbstractMathContainer
 
getMathMLString() - Method in interface org.sbml.jsbml.MathContainer
If MathContainer.isSetMath() returns true, this method returns the corresponding MathML String, otherwise an empty String will be returned.
getMessage() - Method in class org.sbml.jsbml.Constraint
Returns the message of this Constraint.
getMessage() - Method in exception org.sbml.jsbml.SBMLError
Returns the message of the SBMLError
getMessage() - Method in error org.sbml.jsbml.text.parser.TokenMgrError
You can also modify the body of this method to customize your error messages.
getMessage() - Method in class org.sbml.jsbml.util.Message
 
getMessageInstance() - Method in exception org.sbml.jsbml.SBMLError
 
getMessageString() - Method in class org.sbml.jsbml.Constraint
Returns the message of this Constraint as an XML String.
getMessengerRNA() - Static method in class org.sbml.jsbml.SBO
 
getMetaId() - Method in class org.sbml.jsbml.AbstractSBase
 
getMetaId() - Method in interface org.sbml.jsbml.SBase
 
getModel() - Method in class org.sbml.jsbml.AbstractSBase
 
getModel() - Method in interface org.sbml.jsbml.SBase
Returns the Model object in which the current SBase is located.
getModel() - Method in class org.sbml.jsbml.SBMLDocument
Returns the model of this SBMLDocument.
getModelHistory() - Method in class org.sbml.jsbml.Model
Deprecated.
getModellingFramework() - Static method in class org.sbml.jsbml.SBO
 
getModelQualifierType() - Method in class org.sbml.jsbml.CVTerm
Returns the Model QualifierType code for this CVTerm.
getModifiedDate() - Method in class org.sbml.jsbml.History
Returns the modifiedDate from the History.
getModifiedDate(int) - Method in class org.sbml.jsbml.History
Get the nth Date object in the list of ModifiedDates in this History.
getModifier(int) - Method in class org.sbml.jsbml.Reaction
 
getModifier(String) - Method in class org.sbml.jsbml.Reaction
Searches the first ModifierSpeciesReference in the Reaction.listOfModifiers of this Reaction with the given identifier.
getModifier() - Static method in class org.sbml.jsbml.SBO
 
getModifierForSpecies(String) - Method in class org.sbml.jsbml.Reaction
Returns the first ModifierSpeciesReference in the Reaction.listOfModifiers of this Reaction whose 'species' attribute points to a Species with the given identifier.
getMultiplier() - Method in class org.sbml.jsbml.Unit
 
getName() - Method in class org.sbml.jsbml.AbstractNamedSBase
 
getName() - Method in class org.sbml.jsbml.ASTNode
Gets the name of this node.
getName() - Method in class org.sbml.jsbml.FunctionDefinition
 
getName() - Method in interface org.sbml.jsbml.NamedSBase
 
getName() - Method in class org.sbml.jsbml.SBO.Term
Returns the name of this SBO.Term, i.e., a very short characterization.
getName() - Method in enum org.sbml.jsbml.Unit.Kind
Returns the name of this unit kind.
getName() - Method in class org.sbml.jsbml.util.filters.NameFilter
 
getName() - Method in class org.sbml.jsbml.util.Option
 
getName() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
getName(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns the local name of an attribute in this XMLAttributes set (by position).
getName() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the (unqualified) name of this XML element.
getName() - Method in class org.sbml.jsbml.xml.XMLTriple
Returns the name portion of this XMLTriple.
getNameOrID(NamedSBase) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
If the field printNameIfAvailable is false this method returns a the id of the given SBase.
getNamespace() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
getNamespaceFrom(int, int) - Static method in class org.sbml.jsbml.JSBML
 
getNamespaceIndex(String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the index of an XML namespace declaration by URI.
getNamespaceIndexByPrefix(String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the index of an XML namespace declaration by prefix.
getNamespacePrefix(int) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the prefix of an XML namespace declaration by position.
getNamespacePrefix(String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the prefix of an XML namespace declaration by its URI.
getNamespaces() - Method in class org.sbml.jsbml.AbstractSBase
 
getNamespaces() - Method in class org.sbml.jsbml.Annotation
Returns the list of all the namespaces of all the packages which extend this object.
getNamespaces() - Method in interface org.sbml.jsbml.SBase
Returns all the namespaces of all the packages which are currently extending this object.
getNamespaces() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the XML namespace declarations for this XML element.
getNamespacesLength() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the number of XML namespaces stored in the XMLNamespaces of this XMLToken.
getNamespaceURI() - Method in enum org.sbml.jsbml.CVTerm.Type
Returns the name space associated to this CVTerm.Type.
getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
 
getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.CreatorParser
 
getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.DatesParser
 
getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
 
getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
 
getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.VCardParser
 
getNamespaceURI() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the URI of an XML namespace declaration for the empty prefix.
getNamespaceURI(int) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the URI of an XML namespace declaration by its position.
getNamespaceURI(String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns the URI of an XML namespace declaration by its prefix.
getNegativeInfinity() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
getNextNode() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
 
getNextNode() - Method in interface org.sbml.jsbml.validator.OverdeterminationValidator.Node
Returns the next node in the list of nodes
getNextNode() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
 
getNextNode() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
 
getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParser
Get the next Token.
getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
Get the next Token.
getNode(int) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
 
getNode(int) - Method in interface org.sbml.jsbml.validator.OverdeterminationValidator.Node
Returns the i-th node in the list of nodes
getNode(int) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
 
getNode(int) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
 
getNodes() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
 
getNodes() - Method in interface org.sbml.jsbml.validator.OverdeterminationValidator.Node
Returns the list of adjacent nodes
getNodes() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
 
getNodes() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
 
getNonCompetetiveInhibitor() - Static method in class org.sbml.jsbml.SBO
 
getNonEssentialActivator() - Static method in class org.sbml.jsbml.SBO
 
getNonRDFannotation() - Method in class org.sbml.jsbml.Annotation
Returns the String containing annotations other than RDF annotation.
getNotes() - Method in class org.sbml.jsbml.AbstractSBase
Returns an XMLNode object that represent the notes of this element.
getNotes() - Method in interface org.sbml.jsbml.SBase
Returns the XMLNode containing the notes sub-element of this object.
getNotesString() - Method in class org.sbml.jsbml.AbstractSBase
 
getNotesString() - Method in interface org.sbml.jsbml.SBase
 
getNumArguments() - Method in class org.sbml.jsbml.FunctionDefinition
Get the number of arguments (bound variables) taken by this FunctionDefinition.
getNumbering(long) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
getNumChildren() - Method in class org.sbml.jsbml.AbstractTreeNode
Deprecated.
use TreeNode.getChildCount()
getNumChildren() - Method in class org.sbml.jsbml.xml.XMLNode
Deprecated.
getNumCompartments() - Method in class org.sbml.jsbml.Model
Returns the number of Compartments of this Model.
getNumCompartmentTypes() - Method in class org.sbml.jsbml.Model
Deprecated.
getNumConstraints() - Method in class org.sbml.jsbml.Model
Returns the number of Constraints of this Model.
getNumCreators() - Method in class org.sbml.jsbml.History
Get the number of Creator objects in this History.
getNumCVTerms() - Method in class org.sbml.jsbml.AbstractSBase
 
getNumCVTerms() - Method in class org.sbml.jsbml.Annotation
Gives the number of CVTerms in this Annotation.
getNumCVTerms() - Method in interface org.sbml.jsbml.SBase
 
getNumDelays() - Method in class org.sbml.jsbml.Model
Returns the number of Delays of this Model.
getNumerator() - Method in class org.sbml.jsbml.ASTNode
Gets the value of the numerator of this node.
getNumErrors() - Method in class org.sbml.jsbml.SBMLDocument
 
getNumErrors() - Method in class org.sbml.jsbml.SBMLErrorLog
Returns the number of errors that have been logged.
getNumErrors() - Method in interface org.sbml.jsbml.SBMLInputConverter
 
getNumErrors(Object) - Method in interface org.sbml.jsbml.SBMLOutputConverter
 
getNumEventAssignments() - Method in class org.sbml.jsbml.Event
 
getNumEventAssignments() - Method in class org.sbml.jsbml.Model
Returns the number of EventAssignments of this Model.
getNumEvents() - Method in class org.sbml.jsbml.Model
Returns the number of Events of this Model.
getNumFailsWithSeverity(SBMLError.SEVERITY) - Method in class org.sbml.jsbml.SBMLErrorLog
Returns the number of errors that have been logged with the given severity code.
getNumFunctionDefinitions() - Method in class org.sbml.jsbml.Model
Returns the number of FunctionDefinitions of this Model.
getNumInitialAssignments() - Method in class org.sbml.jsbml.Model
Returns the number of InitialAssignments of this Model.
getNumKineticLaws() - Method in class org.sbml.jsbml.Model
Returns the number of KineticLaws of this Model.
getNumListsOf() - Method in class org.sbml.jsbml.Model
Returns the number of ListOfs of this Model.
getNumLocalParameters() - Method in class org.sbml.jsbml.KineticLaw
getNumLocalParameters() - Method in class org.sbml.jsbml.Model
Returns the number of parameters that are contained within kineticLaws in the reactions of this model.
getNumMathContainers() - Method in class org.sbml.jsbml.Model
Returns the number of elements that can contain math in the Model .
getNumModifiedDates() - Method in class org.sbml.jsbml.History
Get the number of ModifiedDate objects in this History.
getNumModifiers() - Method in class org.sbml.jsbml.Reaction
 
getNumModifierSpeciesReferences() - Method in class org.sbml.jsbml.Model
Returns the number of ModifierSpeciesReferences in the Model.
getNumNamedSBases() - Method in class org.sbml.jsbml.Model
Returns the number of NamedSBases in the Model, so elements that can have a name.
getNumNamedSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.Model
Returns the number of NamedSBaseWithDerivedUnits in the Model, so elements that can have a name and a unit that can be derived.
getNumParameters() - Method in class org.sbml.jsbml.KineticLaw
getNumParameters() - Method in class org.sbml.jsbml.Model
Returns the number of Parameters of this Model.
getNumProducts() - Method in class org.sbml.jsbml.Reaction
 
getNumQuantities() - Method in class org.sbml.jsbml.Model
Returns the number of Quantitys of this Model.
getNumQuantitiesWithUnit() - Method in class org.sbml.jsbml.Model
Returns the number of QuantityWithUnits of this Model.
getNumReactants() - Method in class org.sbml.jsbml.Reaction
 
getNumReactions() - Method in class org.sbml.jsbml.Model
Returns the number of Reactions of this Model.
getNumResources() - Method in class org.sbml.jsbml.CVTerm
Returns the number of resources for this CVTerm.
getNumRules() - Method in class org.sbml.jsbml.Model
Returns the number of Rules of this model.
getNumSBases() - Method in class org.sbml.jsbml.Model
Returns the number of SBases of this model.
getNumSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.Model
Returns the number of SBaseWithDerivedUnits of this model.
getNumSpecies() - Method in class org.sbml.jsbml.Model
Returns the number of Species of this Model.
getNumSpeciesReferences() - Method in class org.sbml.jsbml.Model
Returns the number of SpeciesReferencess of this Model.
getNumSpeciesTypes() - Method in class org.sbml.jsbml.Model
Deprecated.
getNumSpeciesWithBoundaryCondition() - Method in class org.sbml.jsbml.Model
Returns the number of Species whose boundary condition is set to true.
getNumStoichiometryMath() - Method in class org.sbml.jsbml.Model
Returns the number of StoichiometryMath in the Model.
getNumSymbols() - Method in class org.sbml.jsbml.Model
Returns the number of all instances of Symbol referenced within the model.
getNumTriggers() - Method in class org.sbml.jsbml.Model
Returns the number of Trigger of this Model.
getNumUnitDefinitions() - Method in class org.sbml.jsbml.Model
Returns the number of UnitDefinitions of this Model.
getNumUnits() - Method in class org.sbml.jsbml.Model
Returns the number of Units of this Model.
getNumUnits() - Method in class org.sbml.jsbml.UnitDefinition
 
getNumVariables() - Method in class org.sbml.jsbml.Model
Returns the number of Variables of this Model.
getObject() - Method in class org.sbml.jsbml.SBO.Triple
Returns the object of this SBO.Triple.
getOffset() - Method in class org.sbml.jsbml.Unit
Deprecated. 
getOmitXMLDeclaration() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
getOmitXMLDeclaration() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
getOntology() - Static method in class org.sbml.jsbml.SBO
Grants access to the underlying Ontology form BioJava.
getOptions() - Method in class org.sbml.jsbml.SBMLErrorLog
Returns the list of options.
getOrganisation() - Method in class org.sbml.jsbml.Creator
Returns the organisation from the Creator.
getOrganization() - Method in class org.sbml.jsbml.Creator
Returns the organisation from the Creator.
getOriginalModel() - Method in interface org.sbml.jsbml.SBMLInputConverter
 
getOrReplacement() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
Gets the String that will be used to replace ' or ' (the mathML <or> element) in the boolean expressions.
getOutside() - Method in class org.sbml.jsbml.Compartment
Returns the outside id of this compartment.
getOutsideInstance() - Method in class org.sbml.jsbml.Compartment
Returns the compartment instance which matches the outside id in Model.
getParameter(int) - Method in class org.sbml.jsbml.KineticLaw
getParameter(String) - Method in class org.sbml.jsbml.KineticLaw
getParameter(int) - Method in class org.sbml.jsbml.Model
Gets the nth Parameter object in this Model.
getParameter(String) - Method in class org.sbml.jsbml.Model
Returns the Parameter of the listOfParameters which has 'id' as id
getParent() - Method in class org.sbml.jsbml.AbstractSBase
This is equivalent to calling AbstractSBase.getParentSBMLObject(), but this method is needed for TreeNode.
getParent() - Method in class org.sbml.jsbml.AbstractTreeNode
 
getParent() - Method in class org.sbml.jsbml.ASTNode
 
getParent() - Method in class org.sbml.jsbml.CompartmentType
Deprecated.
getParent() - Method in class org.sbml.jsbml.Constraint
 
getParent() - Method in class org.sbml.jsbml.Delay
 
getParent() - Method in class org.sbml.jsbml.Event
 
getParent() - Method in class org.sbml.jsbml.EventAssignment
 
getParent() - Method in class org.sbml.jsbml.FunctionDefinition
 
getParent() - Method in class org.sbml.jsbml.InitialAssignment
 
getParent() - Method in class org.sbml.jsbml.KineticLaw
 
getParent() - Method in class org.sbml.jsbml.LocalParameter
 
getParent() - Method in class org.sbml.jsbml.Model
 
getParent() - Method in class org.sbml.jsbml.Priority
 
getParent() - Method in class org.sbml.jsbml.Reaction
 
getParent() - Method in class org.sbml.jsbml.Rule
 
getParent() - Method in class org.sbml.jsbml.SpeciesType
Deprecated.
getParent() - Method in class org.sbml.jsbml.StoichiometryMath
Deprecated.
getParent() - Method in class org.sbml.jsbml.Trigger
 
getParent() - Method in class org.sbml.jsbml.Unit
 
getParent() - Method in class org.sbml.jsbml.UnitDefinition
 
getParentSBMLObject() - Method in class org.sbml.jsbml.AbstractSBase
 
getParentSBMLObject() - Method in class org.sbml.jsbml.ASTNode
This method is convenient when holding an object nested inside other objects in an SBML model.
getParentSBMLObject() - Method in class org.sbml.jsbml.KineticLaw
This method is convenient when holding an object nested inside other objects in an SBML model.
getParentSBMLObject() - Method in class org.sbml.jsbml.LocalParameter
 
getParentSBMLObject() - Method in interface org.sbml.jsbml.SBase
This method is convenient when holding an object nested inside other objects in an SBML model.
getParentTerms() - Method in class org.sbml.jsbml.SBO.Term
Returns the parent Terms.
getParserNamespace() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
getPartialInhibitor() - Static method in class org.sbml.jsbml.SBO
 
getParticipant() - Static method in class org.sbml.jsbml.SBO
 
getParticipantRole() - Static method in class org.sbml.jsbml.SBO
 
getPattern() - Method in class org.sbml.jsbml.util.filters.CVTermFilter
 
getPersistent() - Method in class org.sbml.jsbml.Trigger
 
getPhenotype() - Static method in class org.sbml.jsbml.SBO
 
getPhysicalCompartment() - Static method in class org.sbml.jsbml.SBO
 
getPhysicalParticipant() - Static method in class org.sbml.jsbml.SBO
 
getPiecewiseMap() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
Gets a Map of the piecewise expressions that have been transformed.
getPositiveInfinity() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
getPossibleEnzymes(String...) - Static method in class org.sbml.jsbml.SBO
Creates and returns a list of molecule types that are accepted as an enzyme for the given type names.
getPredefinedUnit(String, int, int) - Static method in class org.sbml.jsbml.UnitDefinition
This method returns the predefined unit with the given identifier for the specified level and version combination or null if either for the given combination of level and version there is no such predefined unit or the identifier is not one of those belonging to the group of predefined unit definitions.
getPredefinedUnitDefinition(String) - Method in class org.sbml.jsbml.Model
Returns a UnitDefinition representing one of the predefined units of SBML, returns null if the given unit kind is not a valid one for the SBML level and version of this Model.
getPredefinedUnitID() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
Returns the predefined unit identifier for this data type with the current level/version combination.
getPredefinedUnitID() - Method in class org.sbml.jsbml.Compartment
 
getPredefinedUnitID() - Method in class org.sbml.jsbml.Event
 
getPredefinedUnitID() - Method in class org.sbml.jsbml.LocalParameter
 
getPredefinedUnitID() - Method in class org.sbml.jsbml.Parameter
 
getPredefinedUnitID() - Method in class org.sbml.jsbml.Species
 
getPredicate() - Method in class org.sbml.jsbml.SBO.Triple
Returns the predicate of this SBO.Triple.
getPrefix() - Method in class org.sbml.jsbml.Unit
 
getPrefix() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
getPrefix(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns the prefix of an attribute in this XMLAttributes set (by position).
getPrefix(int) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Gets the prefix of an XML namespace declaration by its position.
getPrefix(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Gets the prefix of an XML namespace declaration by its URI.
getPrefix() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the namespace prefix of this XML element.
getPrefix() - Method in class org.sbml.jsbml.xml.XMLTriple
Returns the prefix portion of this XMLTriple.
getPrefixAsWord() - Method in class org.sbml.jsbml.Unit
 
getPrefixedName(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns the prefixed name of an attribute in this XMLAttributes set (by position).
getPrefixedName() - Method in class org.sbml.jsbml.xml.XMLTriple
Returns the prefixed name from this XMLTriple.
getPreviousParent() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent
Access the pointer to the previous parent node of the removed node, may be null.
getPriority() - Method in class org.sbml.jsbml.Event
 
getProduct(int) - Method in class org.sbml.jsbml.Reaction
 
getProduct(String) - Method in class org.sbml.jsbml.Reaction
Searches the first SpeciesReference in the listOfProducts of this Reaction with the given identifier.
getProduct() - Static method in class org.sbml.jsbml.SBO
 
getProductForSpecies(String) - Method in class org.sbml.jsbml.Reaction
Returns the first SpeciesReference in the Reaction.listOfProducts of this Reaction whose 'species' attribute points to a Species with the given identifier.
getProgramName() - Method in class org.sbml.jsbml.SBMLWriter
 
getProgramVersion() - Method in class org.sbml.jsbml.SBMLWriter
 
getProtein() - Static method in class org.sbml.jsbml.SBO
 
getQualifier() - Method in class org.sbml.jsbml.util.filters.CVTermFilter
 
getQualifierType() - Method in class org.sbml.jsbml.CVTerm
Returns the Qualifier Type code for this CVTerm.
getQuantitativeParameter() - Static method in class org.sbml.jsbml.SBO
 
getRateLaw() - Static method in class org.sbml.jsbml.SBO
 
getRDFAnnotationNamespaces() - Method in class org.sbml.jsbml.Annotation
Returns the rdfAnnotationNamespaces Map of this object.
getReactant(int) - Method in class org.sbml.jsbml.Reaction
 
getReactant(String) - Method in class org.sbml.jsbml.Reaction
Searches the first SpeciesReference in the listOfReactants of this Reaction with the given identifier.
getReactant() - Static method in class org.sbml.jsbml.SBO
 
getReactantForSpecies(String) - Method in class org.sbml.jsbml.Reaction
Returns the first SpeciesReference in the Reaction.listOfReactants of this Reaction whose 'species' attribute points to a Species with the given identifier.
getReaction(int) - Method in class org.sbml.jsbml.Model
Gets the n-th Reaction object in this Model.
getReaction(String) - Method in class org.sbml.jsbml.Model
Returns the Reaction of the Model.listOfReactions which has 'id' as id.
getReadingParsers(String) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Gets the ReadingParser class associated with 'namespace'.
getReal() - Method in class org.sbml.jsbml.ASTNode
Gets the real-numbered value of this node.
getReceptor() - Static method in class org.sbml.jsbml.SBO
 
getReferencedNamedSBases() - Method in class org.sbml.jsbml.ASTNode
Returns a set of all the NamedSBase referenced on this node and all his descendant.
getRelatedCompartments(Model, String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
 
getRelatedEvents(Model, String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
 
getRelatedFunctions(Set<String>, Set<String>, ASTNode) - Static method in class org.sbml.jsbml.util.SubModel
 
getRelatedFunctionsId(Set<String>, Set<String>, ASTNode) - Static method in class org.sbml.jsbml.util.SubModel
 
getRelatedReactions(Model, String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
Returns an array of reaction id related to the reactsIds or speciesIds.
getRelatedRules(Model, String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
 
getRelatedSpecies(Model, String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel
 
getResources() - Method in class org.sbml.jsbml.CVTerm
Returns the resources for this CVTerm.
getResourceURI(int) - Method in class org.sbml.jsbml.CVTerm
Returns the value of the nth resource for this CVTerm.
getReversible() - Method in class org.sbml.jsbml.Reaction
 
getRightChild() - Method in class org.sbml.jsbml.ASTNode
Returns the last child in the list of children of this node.
getRNA() - Static method in class org.sbml.jsbml.SBO
 
getRule(int) - Method in class org.sbml.jsbml.Model
Gets the nth Rule of the listOfRules.
getRule(String) - Method in class org.sbml.jsbml.Model
Searches for the first instance of ExplicitRule within this Model's Model.listOfRules, whose variable attribute is set to the value passed to this method.
getSBaseListType() - Method in class org.sbml.jsbml.ListOf
 
getSBMLDocument() - Method in class org.sbml.jsbml.AbstractSBase
 
getSBMLDocument() - Method in interface org.sbml.jsbml.SBase
Returns the parent SBMLDocument object.
getSBMLDocumentAttributes() - Method in class org.sbml.jsbml.SBMLDocument
 
getSBMLDocumentNamespaces() - Method in class org.sbml.jsbml.SBMLDocument
 
getSBMLNSAttribute() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
getSBMLUnitsAttribute() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
getSBORoot() - Static method in class org.sbml.jsbml.SBO
Returns the root element of the SBO Ontology (SBO:0000000).
getSBOTerm() - Method in class org.sbml.jsbml.AbstractSBase
 
getSBOTerm() - Method in interface org.sbml.jsbml.SBase
Grants access to the Systems Biology Ontology (SBO) term associated with this SBase.
getSBOTermID() - Method in class org.sbml.jsbml.AbstractSBase
 
getSBOTermID() - Method in interface org.sbml.jsbml.SBase
Grants access to the Systems Biology Ontology (SBO) term associated with this SBase.
getScale() - Method in class org.sbml.jsbml.Unit
 
getSeverity() - Method in exception org.sbml.jsbml.SBMLError
Returns the severity of the SBMLError
getSeverity() - Method in class org.sbml.jsbml.util.Detail
 
getShortMessage() - Method in exception org.sbml.jsbml.SBMLError
 
getShortMessage() - Method in exception org.sbml.jsbml.SBMLException
 
getSimpleMolecule() - Static method in class org.sbml.jsbml.SBO
 
getSize() - Method in class org.sbml.jsbml.Compartment
Returns the size of this compartment.
getSource() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
getSource() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent
 
getSpatialDimensions() - Method in class org.sbml.jsbml.Compartment
getSpatialDimensionsAsDouble() - Method in class org.sbml.jsbml.Compartment
getSpatialSizeUnits() - Method in class org.sbml.jsbml.Species
If determined, this method first checks the explicitly set spatial size units of this Species.
getSpatialSizeUnitsInstance() - Method in class org.sbml.jsbml.Species
Determines the spatial units of this Species.
getSpecies(int) - Method in class org.sbml.jsbml.Model
Gets the n-th Species object in this Model.
getSpecies(String) - Method in class org.sbml.jsbml.Model
Gets the Species of the listOfSpecies which has 'id' as id.
getSpecies() - Method in class org.sbml.jsbml.SimpleSpeciesReference
 
getSpecies(SpeciesReference) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Returns the id of a PluginSpeciesReference object's belonging species as an object of type StringBuffer.
getSpeciesInstance() - Method in class org.sbml.jsbml.SimpleSpeciesReference
 
getSpeciesType(int) - Method in class org.sbml.jsbml.Model
Deprecated.
getSpeciesType(String) - Method in class org.sbml.jsbml.Model
Deprecated.
getSpeciesType() - Method in class org.sbml.jsbml.Species
Deprecated.
Only valid for SBML Level 2 Versions 2, 3, and 4.
getSpeciesTypeInstance() - Method in class org.sbml.jsbml.Species
Deprecated.
Only valid for SBML Level 2 Versions 2, 3, and 4.
getSpecificActivator() - Static method in class org.sbml.jsbml.SBO
 
getStateTransition() - Static method in class org.sbml.jsbml.SBO
 
getStatus() - Method in class org.sbml.jsbml.SBMLErrorLog
Returns the status of the error log.
getStatus() - Method in class org.sbml.jsbml.util.Option
 
getSteadyStateExpression() - Static method in class org.sbml.jsbml.SBO
 
getStimulator() - Static method in class org.sbml.jsbml.SBO
 
getStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference
 
getStoichiometry(SpeciesReference) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Returns the value of a PluginSpeciesReference object's stoichiometry either as a double or, if the stoichiometry has an integer value, as an int object.
getStoichiometryMath() - Method in class org.sbml.jsbml.SpeciesReference
Deprecated.
since SBML Level 3 this should not be used anymore.
getStreamFromFile(String) - Method in class org.sbml.jsbml.resources.Resource
Gets the byte data from a file.
getStreamFromResourceLocation(String) - Method in class org.sbml.jsbml.resources.Resource
Gets the byte data from a file at the given resource location.
getStyle() - Method in class org.sbml.jsbml.ASTNode
Returns the style of the mathML element represented by this ASTNode.
getSubject() - Method in class org.sbml.jsbml.SBO.Triple
Returns the subject of this SBO.Triple.
getSubstanceUnits() - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
getSubstanceUnits() - Method in class org.sbml.jsbml.Model
Returns the substance units ID of this model.
getSubstanceUnits() - Method in class org.sbml.jsbml.Species
 
getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns the UnitDefinition which has the substance units ID of this Model as id.
getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Species
 
GetSuffix(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Get the suffix.
getSymbol() - Method in class org.sbml.jsbml.InitialAssignment
getSymbol() - Method in enum org.sbml.jsbml.Unit.Kind
 
getSynonyms() - Method in class org.sbml.jsbml.SBO.Term
Returns all Synonyms of this SBO.Term.
getTabSize(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
 
getTerm(int) - Static method in class org.sbml.jsbml.SBO
Gets the SBO term with the id 'sboTerm'.
getTerm(String) - Static method in class org.sbml.jsbml.SBO
Gets the SBO term with the id 'sboTerm'.
getTerm() - Method in class org.sbml.jsbml.SBO.Term
Grants access to the underlying BioJava org.biojava.ontology.Term.
getTerm() - Method in class org.sbml.jsbml.util.filters.SBOFilter
 
getTerms() - Static method in class org.sbml.jsbml.SBO
Return the set of terms of the SBO Ontology.
getTimeUnits() - Method in class org.sbml.jsbml.Event
Deprecated. 
getTimeUnits() - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
getTimeUnits() - Method in class org.sbml.jsbml.Model
Returns the time units ID of this Model.
getTimeUnitsID() - Method in class org.sbml.jsbml.Event
Deprecated. 
getTimeUnitsInstance() - Method in class org.sbml.jsbml.Event
Deprecated. 
getTimeUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
getTimeUnitsInstance() - Method in class org.sbml.jsbml.Model
Gets the UnitDefinition representing the time units of this Model.
getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
Get the specific Token.
getTranscription() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'TRANSCRIPTION'
getTranscriptionalActivation() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'TRANSCRIPTIONAL_ACTIVATION'
getTranscriptionalInhibitor() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'TRANSCRIPTIONAL_INHIBITION'
getTransitionOmitted() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'KNOWN_TRANSITION_OMITTED'
getTranslation() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'TRANSLATION'
getTranslationalActivation() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'TRANSLATIONAL_ACTIVATION'
getTranslationalInhibitor() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'TRANSLATIONAL_INHIBITION'
getTransport() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'TRANSPORT'
getTreeNodeChangeListenerCount() - Method in class org.sbml.jsbml.AbstractTreeNode
 
getTreeNodeChangeListenerCount() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
 
getTrigger() - Method in class org.sbml.jsbml.Event
 
getTrigger() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'TRIGGER'
getTriple() - Method in class org.sbml.jsbml.SBO.Triple
Grants access to the original BioJava org.biojava.ontology.Triple.
getTriples(SBO.Term, SBO.Term, SBO.Term) - Static method in class org.sbml.jsbml.SBO
Returns a set of Triple which match the supplied subject, predicate and object.
getTruncated() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'TRUNCATED'
getType() - Method in class org.sbml.jsbml.ASTNode
Returns the type of this node.
getType() - Method in exception org.sbml.jsbml.SBMLException
 
getType() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
getType() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
 
getTypeFor(String) - Static method in enum org.sbml.jsbml.ASTNode.Type
Returns the ASTNode.Type corresponding to the given String.
getTypeOfNotes() - Method in class org.sbml.jsbml.xml.parsers.StringParser
 
getUnit(int) - Method in class org.sbml.jsbml.UnitDefinition
Returns a specific Unit instance belonging to this UnitDefinition.
getUnitDefinition(int) - Method in class org.sbml.jsbml.Model
Gets the nth UnitDefinition object in this Model.
getUnitDefinition(String) - Method in class org.sbml.jsbml.Model
Returns the UnitDefinition of the listOfUnitDefinitions which has 'id' as id.
getUnitKindsDefinedIn(int, int) - Static method in enum org.sbml.jsbml.Unit.Kind
Returns a set of Unit.Kind objects for the given level/version combination of SBML.
getUnitOntologyIdentifier() - Method in enum org.sbml.jsbml.Unit.Kind
Creates a unit ontology identifier for this Unit.Kind if possible and returns it.
getUnitOntologyNumber() - Method in enum org.sbml.jsbml.Unit.Kind
Looks for the corresponding unit ontology resource for this Unit.Kind.
getUnitOntologyResource() - Method in enum org.sbml.jsbml.Unit.Kind
Creates a MIRIAM resource pointing to the entry in the unit ontology corresponding to this Unit.Kind.
getUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
getUnits() - Method in class org.sbml.jsbml.ASTNode
Returns the units attribute.
getUnits() - Method in class org.sbml.jsbml.Event
Deprecated.
getUnits() - Method in class org.sbml.jsbml.ExplicitRule
Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
getUnits() - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
getUnits() - Method in interface org.sbml.jsbml.SBaseWithUnit
 
getUnits() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
getUnitsInstance() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
getUnitsInstance() - Method in class org.sbml.jsbml.ASTNode
Creates or obtains a UnitDefinition corresponding to the unit that has been set for this ASTNode and returns a pointer to it.
getUnitsInstance() - Method in class org.sbml.jsbml.Event
Deprecated.
getUnitsInstance() - Method in class org.sbml.jsbml.ExplicitRule
Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
getUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
getUnitsInstance() - Method in interface org.sbml.jsbml.SBaseWithUnit
 
getUnknownMolecule() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'UNKNOWN'
getUnknownTransition() - Static method in class org.sbml.jsbml.SBO
Returns the SBO id corresponding to the alias 'UNKNOWN_TRANSITION'
getURI(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns the namespace URI of an attribute in this XMLAttributes set (by position).
getURI(int) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Gets the URI of an XML namespace declaration by its position.
getURI(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Gets the URI of an XML namespace declaration by its prefix.
getURI() - Method in class org.sbml.jsbml.xml.XMLNamespaces
Gets the URI of an XML namespace declaration by the empty prefix.
getURI() - Method in class org.sbml.jsbml.xml.XMLToken
Returns the namespace URI of this XML element.
getURI() - Method in class org.sbml.jsbml.xml.XMLTriple
Returns the URI portion of this XMLTriple.
getUserObject() - Method in class org.sbml.jsbml.ASTNode
 
getUserObject() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
 
getUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event
 
getV() - Method in class org.sbml.jsbml.util.ValuePair
 
getValidationErrors() - Method in class org.sbml.jsbml.SBMLErrorLog
Returns the list of SBMLError
getValue() - Method in interface org.sbml.jsbml.Quantity
Returns the value of this Quantity.
getValue() - Method in class org.sbml.jsbml.QuantityWithUnit
 
getValue() - Method in class org.sbml.jsbml.SpeciesReference
 
getValue() - Method in class org.sbml.jsbml.text.parser.Token
An optional attribute value of the Token.
getValue() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
getValue() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
 
getValue() - Method in interface org.sbml.jsbml.validator.OverdeterminationValidator.Node
Returns the value of this node
getValue() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
 
getValue() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
 
getValue(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns the value of an attribute in this XMLAttributes set (by position).
getValue(String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns an attribute's value by name.
getValue(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns a value of an attribute with the given local name and namespace URI.
getValue(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns a value of an attribute with the given XMLTriple.
getVariable() - Method in interface org.sbml.jsbml.Assignment
Returns the variableID of this Assignment.
getVariable() - Method in class org.sbml.jsbml.ASTNode
Returns the variable of this node.
getVariable() - Method in class org.sbml.jsbml.EventAssignment
 
getVariable() - Method in class org.sbml.jsbml.ExplicitRule
 
getVariable() - Method in class org.sbml.jsbml.InitialAssignment
 
getVariableInstance() - Method in interface org.sbml.jsbml.Assignment
Returns the Variable instance which has the variableID of this Assignment as id.
getVariableInstance() - Method in class org.sbml.jsbml.EventAssignment
 
getVariableInstance() - Method in class org.sbml.jsbml.ExplicitRule
 
getVariableInstance() - Method in class org.sbml.jsbml.InitialAssignment
 
getVariables(ListOf<LocalParameter>, ASTNode, List<SBase>, int) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
Returns the variables in a MathML object without local parameter
getVersion() - Method in class org.sbml.jsbml.AbstractSBase
 
getVersion() - Method in interface org.sbml.jsbml.SBase
Returns the Version within the SBML Level of the overall SBML document.
getVersion() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
getVolume() - Method in class org.sbml.jsbml.Compartment
Deprecated.
The volume attribute is only defined in SBML Level 1. Please use Compartment.getSize().
getVolumeUnits() - Method in class org.sbml.jsbml.Model
Returns the volume units ID of this Model.
getVolumeUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns the UnitDefinition instance which has the volume units ID of this Model as id.
getWarnings() - Method in interface org.sbml.jsbml.SBMLInputConverter
 
getWordForNumber(long) - Static method in class org.sbml.jsbml.util.StringTools
Returns the number as an English word.
getWriteWarnings(Object) - Method in interface org.sbml.jsbml.SBMLOutputConverter
 
getWritingParsers(Object, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Gets all the writing parsers necessary to write the given object.
getWritingParsers(String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
getXMLnamespaceSBML() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
The additional MathML name space for units to numbers.
givenName - Variable in class org.sbml.jsbml.Creator
Given name of the creator
givenName - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
gt(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates an ASTNode representing greater than for the two given left and right child.
gt(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Greater than.
gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 

H

hasAttr(int) - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether an attribute with the given index exists in the attribute set in this XMLToken.
hasAttr(String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether an attribute with the given local name exists in the attribute set in this XMLToken.
hasAttr(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether an attribute with the given local name and namespace URI exists in the attribute set in this XMLToken.
hasAttr(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether an attribute with the given XML triple exists in the attribute set in this XMLToken
hasAttribute(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns true or false depending on whether an attribute with the given index exists in this XMLAttributes.
hasAttribute(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns true or false depending on whether an attribute with the given local name and namespace URI exists in this XMLAttributes.
hasAttribute(String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns true or false depending on whether an attribute with the given local name exists in this XMLAttributes.
hasAttribute(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns true or false depending on whether an attribute with the given XML triple exists in this XMLAttributes.
hashCode() - Method in class org.sbml.jsbml.AbstractNamedSBase
 
hashCode() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
hashCode() - Method in class org.sbml.jsbml.AbstractSBase
 
hashCode() - Method in class org.sbml.jsbml.AbstractTreeNode
 
hashCode() - Method in class org.sbml.jsbml.Annotation
 
hashCode() - Method in class org.sbml.jsbml.ASTNode
 
hashCode() - Method in class org.sbml.jsbml.Compartment
 
hashCode() - Method in class org.sbml.jsbml.Creator
 
hashCode() - Method in class org.sbml.jsbml.CVTerm
 
hashCode() - Method in class org.sbml.jsbml.Event
 
hashCode() - Method in class org.sbml.jsbml.EventAssignment
 
hashCode() - Method in class org.sbml.jsbml.ExplicitRule
 
hashCode() - Method in class org.sbml.jsbml.FunctionDefinition
 
hashCode() - Method in class org.sbml.jsbml.History
 
hashCode() - Method in class org.sbml.jsbml.InitialAssignment
 
hashCode() - Method in class org.sbml.jsbml.KineticLaw
 
hashCode() - Method in class org.sbml.jsbml.LocalParameter
 
hashCode() - Method in class org.sbml.jsbml.Model
 
hashCode() - Method in class org.sbml.jsbml.QuantityWithUnit
 
hashCode() - Method in class org.sbml.jsbml.Reaction
 
hashCode() - Method in interface org.sbml.jsbml.SBase
 
hashCode() - Method in class org.sbml.jsbml.SBMLDocument
 
hashCode() - Method in class org.sbml.jsbml.SimpleSpeciesReference
 
hashCode() - Method in class org.sbml.jsbml.Species
 
hashCode() - Method in class org.sbml.jsbml.SpeciesReference
 
hashCode() - Method in class org.sbml.jsbml.Symbol
 
hashCode() - Method in class org.sbml.jsbml.Trigger
 
hashCode() - Method in class org.sbml.jsbml.Unit
 
hashCode() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
 
hashCode() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
hashCode() - Method in class org.sbml.jsbml.util.ValuePair
 
hashCode() - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns a hashcode for this XMLAttributes object.
hashCode() - Method in class org.sbml.jsbml.xml.XMLNamespaces
Returns a hashcode for this XMLNamespaces object.
hashCode() - Method in class org.sbml.jsbml.xml.XMLToken
 
hashCode() - Method in class org.sbml.jsbml.xml.XMLTriple
Returns a hashcode for this XMLTriple object.
hasModifier(Species) - Method in class org.sbml.jsbml.Reaction
 
hasNamespaceNS(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether an XML Namespace with the given uri/prefix pair is contained in the XMLNamespaces of this XMLToken.
hasNamespacePrefix(String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether an XML Namespace with the given prefix is contained in the XMLNamespaces of this XMLToken.
hasNamespaceURI(String) - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether an XML Namespace with the given URI is contained in the XMLNamespaces of this XMLToken.
hasNS(String, String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Returns true or false depending on whether an XML Namespace with the given URI and prefix pair is contained in this XMLNamespaces list.
hasOnlySubstanceUnits - Variable in class org.sbml.jsbml.Species
Represents the 'hasOnlySubstanceUnits' attribute of a Species element.
hasOnlySubstanceUnits() - Method in class org.sbml.jsbml.Species
 
hasOnlySubstanceUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
hasPrefix(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Returns true or false depending on whether an XML Namespace with the given prefix is contained in this XMLNamespaces list.
hasProduct(Species) - Method in class org.sbml.jsbml.Reaction
 
hasReactant(Species) - Method in class org.sbml.jsbml.Reaction
 
hasReadCreated - Variable in class org.sbml.jsbml.xml.parsers.DatesParser
Boolean value to know if a 'created' element has been read by this parser.
hasReadEMAIL - Variable in class org.sbml.jsbml.xml.parsers.VCardParser
Boolean value to know if the 'EMAIL' node has been read.
hasReadFamilyName - Variable in class org.sbml.jsbml.xml.parsers.VCardParser
Boolean value to know if the 'Family' node has been read.
hasReadGivenName - Variable in class org.sbml.jsbml.xml.parsers.VCardParser
Boolean value to know if the 'Given' node has been read.
hasReadModified - Variable in class org.sbml.jsbml.xml.parsers.DatesParser
Boolean value to know if a 'modified' element has been read by this parser.
hasReadNNode - Variable in class org.sbml.jsbml.xml.parsers.VCardParser
Boolean value to know if the 'N' node has been read.
hasReadOrgName - Variable in class org.sbml.jsbml.xml.parsers.VCardParser
Boolean value to know if the 'Orgname' node has been read.
hasReadORGNode - Variable in class org.sbml.jsbml.xml.parsers.VCardParser
Boolean value to know if the 'ORG' node has been read.
hasReadW3CDTF - Variable in class org.sbml.jsbml.xml.parsers.DatesParser
Boolean value to know if a 'W3CDTF' element has been read by this parser.
hasRequiredAttributes() - Method in class org.sbml.jsbml.Unit
Predicate returning true or false depending on whether all the required attributes for this Unit object have been set.
hasUnit(String) - Method in class org.sbml.jsbml.Model
Returns true if this model has a reference to the unit with the given identifier.
hasUnits() - Method in class org.sbml.jsbml.ASTNode
Returns true if the current ASTNode or any of his descendant has a unit defined.
hasURI(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Returns true or false depending on whether an XML Namespace with the given URI is contained in this XMLNamespaces list.
hasValidAnnotation() - Method in class org.sbml.jsbml.AbstractSBase
 
hasValidAnnotation() - Method in interface org.sbml.jsbml.SBase
 
hasValidLevelVersionNamespaceCombination() - Method in class org.sbml.jsbml.AbstractSBase
 
hasValidLevelVersionNamespaceCombination() - Method in interface org.sbml.jsbml.SBase
Predicate returning true or false depending on whether this object's level/version and name space values correspond to a valid SBML specification.
heading(String, String, boolean) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Creates head lines.
history - Variable in class org.sbml.jsbml.Annotation
The ModelHistory which represents the history section of a RDF annotation
History - Class in org.sbml.jsbml
Contains all the history information about a Model (or other SBase if level >= 3).
History() - Constructor for class org.sbml.jsbml.History
Creates a History instance.
History(History) - Constructor for class org.sbml.jsbml.History
Creates a History instance from a given History.
history - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
href(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Creates a hyper link to the given target and the text to be visible in the document.
HTMLFormula - Class in org.sbml.jsbml.util.compilers
 
HTMLFormula() - Constructor for class org.sbml.jsbml.util.compilers.HTMLFormula
 
hyperref(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 

I

id - Variable in class org.sbml.jsbml.AbstractNamedSBase
id of the SBML component (can be optional depending on the level and version).
id - Variable in class org.sbml.jsbml.ASTNode
Possible attributes for a MathML element
id - Variable in class org.sbml.jsbml.FunctionDefinition
Represents the "id" attribute of a functionDefinition element.
id - Variable in class org.sbml.jsbml.SBO.Term
The base properties of this SBO.Term.
id - Variable in class org.sbml.jsbml.util.filters.AssignmentVariableFilter
The desired identifier for NamedSBases to be acceptable.
id - Variable in class org.sbml.jsbml.util.filters.NameFilter
The desired identifier for NamedSBases to be acceptable.
id - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
idChar - Static variable in class org.sbml.jsbml.AbstractNamedSBase
 
IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
IdentifierException - Exception in org.sbml.jsbml
This exception is thrown when trying to set or add an identifier to an instance of NamedSBase but if the given identifier is already registered in the containing Model.
IdentifierException(NamedSBase, String) - Constructor for exception org.sbml.jsbml.IdentifierException
 
IdentifierException(SBase, String) - Constructor for exception org.sbml.jsbml.IdentifierException
 
ILLEGAL_ASTNODE_TYPE_MSG - Static variable in class org.sbml.jsbml.FunctionDefinition
Error message to indicate that an incorrect ASTNode.Type has been passed to a method.
ILLEGAL_CONSTANT_VARIABLE_MSG - Static variable in interface org.sbml.jsbml.Assignment
Error message to be displayed in case that a Variable with constant property set to true is to be assigned to this Assignment.
ILLEGAL_STOCHIOMETRY_VALUE - Static variable in class org.sbml.jsbml.SpeciesReference
Message to be displayed in case that an illegal stoichiometric value has been set.
ILLEGAL_UNIT_EXCEPTION_MSG - Static variable in class org.sbml.jsbml.JSBML
Error message for the case that an invalid unit identifier is to be added to this object.
ILLEGAL_UNIT_KIND_EXCEPTION_MSG - Static variable in class org.sbml.jsbml.KineticLaw
Exception to be displayed in case that an illegal variant of unit is to be set for this SBaseWithUnit.
ILLEGAL_VARIABLE_EXCEPTION_MSG - Static variable in interface org.sbml.jsbml.Assignment
Error message to indicate that a SpeciesReference cannot be used as the Variable in this Assignment because the SBML Level < 3.
image - Variable in class org.sbml.jsbml.text.parser.Token
The string image of the token.
inBuf - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
indent - Variable in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
indent - Variable in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
The number of white spaces for the indent if this is to be used.
indent - Variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
The number of white spaces for the indent if this is to be used.
indent - Variable in class org.sbml.jsbml.xml.parsers.XMLNodeWriter
 
indentChar - Variable in class org.sbml.jsbml.xml.stax.SBMLWriter
The symbol for indentation.
indentCount - Variable in class org.sbml.jsbml.xml.stax.SBMLWriter
The number of indentation symbols.
indenting - Variable in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
Decides whether or not the content of the MathML string should be indented.
indenting - Variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
Decides whether or not the content of the MathML string should be indented.
INDEX_EXCEEDS_SIZE - Static variable in class org.sbml.jsbml.JSBML
 
indexOf(TreeNode, TreeNode) - Static method in class org.sbml.jsbml.AbstractTreeNode
Searches the given child in the list of sub-nodes of the parent element.
indexOf(Object) - Method in class org.sbml.jsbml.ListOf
 
info(String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger
 
init() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
Re-initializes the Document object belonging to this class.
init() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
Initializes the Converter
initDefaults() - Method in class org.sbml.jsbml.ASTNode
Initializes the default values/attributes of the node.
initDefaults() - Method in class org.sbml.jsbml.Compartment
Initializes the default values using the current Level/Version configuration.
initDefaults(int, int) - Method in class org.sbml.jsbml.Compartment
Initializes the default values using the current Level/Version configuration.
initDefaults() - Method in class org.sbml.jsbml.Event
Initializes the default values using the current Level/Version configuration.
initDefaults(int, int) - Method in class org.sbml.jsbml.Event
Initializes the default values of this Event.
initDefaults() - Method in class org.sbml.jsbml.ExplicitRule
 
initDefaults() - Method in class org.sbml.jsbml.KineticLaw
 
initDefaults() - Method in class org.sbml.jsbml.Model
Initializes the default values using the current Level/Version configuration.
initDefaults(int, int) - Method in class org.sbml.jsbml.Model
Initializes the default values of the attributes of the Model
initDefaults(int, int) - Method in class org.sbml.jsbml.Parameter
Initializes the default values of this Parameter, i.e., sets it to a constant variable with a NaN value.
initDefaults() - Method in class org.sbml.jsbml.Parameter
Initializes the default values using the current Level/Version configuration.
initDefaults() - Method in class org.sbml.jsbml.Reaction
Initializes the default values using the current Level/Version configuration.
initDefaults(int, int) - Method in class org.sbml.jsbml.Reaction
Initializes the default variables of this Reaction.
initDefaults() - Method in class org.sbml.jsbml.SBMLDocument
 
initDefaults() - Method in class org.sbml.jsbml.Species
Initializes the default values using the current Level/Version configuration.
initDefaults(int, int) - Method in class org.sbml.jsbml.Species
Initializes the default values of this Species.
initDefaults() - Method in class org.sbml.jsbml.SpeciesReference
Initializes the default values using the current Level/Version configuration.
initDefaults(int, int) - Method in class org.sbml.jsbml.SpeciesReference
Initializes the default values of this SpeciesReference.
initDefaults() - Method in class org.sbml.jsbml.Trigger
Sets the properties Trigger.initialValue and Trigger.persistent to null, i.e., undefined.
initDefaults() - Method in class org.sbml.jsbml.Unit
Initializes the default values using the current Level/Version configuration.
initDefaults(int, int) - Method in class org.sbml.jsbml.Unit
Initializes the attributes of this Unit (except for 'kind') to their defaults values.
initialAmount - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
InitialAssignment - Class in org.sbml.jsbml
Represents the initialAssignment XML element of a SBML file.
InitialAssignment() - Constructor for class org.sbml.jsbml.InitialAssignment
Creates an InitialAssignment instance.
InitialAssignment(InitialAssignment) - Constructor for class org.sbml.jsbml.InitialAssignment
Creates an InitialAssignment instance from a given InitialAssignment.
InitialAssignment(int, int) - Constructor for class org.sbml.jsbml.InitialAssignment
Creates an InitialAssignment from level and version.
InitialAssignment(Variable) - Constructor for class org.sbml.jsbml.InitialAssignment
Creates an InitialAssignment instance from a Variable.
InitialAssignment(Variable, ASTNode, int, int) - Constructor for class org.sbml.jsbml.InitialAssignment
Creates an InitialAssignment from a Variable, ASTNode, level and version.
initialise(Token, int[][], String[]) - Static method in exception org.sbml.jsbml.text.parser.ParseException
It uses "currentToken" and "expectedTokenSequences" to generate a parse error message and returns it.
initialisesBiologicalQualifierMap() - Method in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
Initialises the biologicalQualifierMap of this parser.
initialisesModelQualifierMap() - Method in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
Initialises the modelQualifierMap of this parser.
initializeCoreElements() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
initializedParsers - Variable in class org.sbml.jsbml.xml.stax.SBMLReader
Contains all the initialized parsers.
initializePackageParserNamespaces() - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Initializes the packageParser HashMap of this class.
initializePackageParserNamespaces() - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Initializes the packageParser HasMap of this class.
initializePackageParsers() - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Creates the ReadingParser instances and stores them in a HashMap.
initializePackageParsers() - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Creates the ReadingParser instances and stores them in a HashMap.
initialValue - Variable in class org.sbml.jsbml.Trigger
 
initialValue - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
initListOf(SBase, ListOf<T>, ListOf.Type) - Static method in class org.sbml.jsbml.ListOf
Helper method to initialize newly created lists.
input_stream - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
inputStream - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
insertChild(int, ASTNode) - Method in class org.sbml.jsbml.ASTNode
Inserts the given ASTNode at point n in the list of children of this ASTNode.
insertChild(int, XMLNode) - Method in class org.sbml.jsbml.xml.XMLNode
Inserts a node as the nth child of this XMLNode.
insertNoRDFAnnotation(String, int) - Method in class org.sbml.jsbml.Annotation
Inserts 'annotation' to the non RDF annotation StringBuilder at position 'offset'.
instance - Static variable in class org.sbml.jsbml.xml.stax.DateProcessor
 
instance_ - Static variable in class org.sbml.jsbml.util.JAXPFacade
 
instantiatedSBMLParsers - Variable in class org.sbml.jsbml.xml.stax.SBMLWriter
contains the WritingParser instances of this class.
INTEGER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
intToString(int) - Static method in class org.sbml.jsbml.SBO
Returns the integer as a correctly formatted SBO string.
invalid() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
Creates an invalid unit definition encapsulated in an ASTNodeValue.
INVALID_ATTRIBUTE_VALUE - Static variable in class org.sbml.jsbml.JSBML
 
INVALID_LEXICAL_STATE - Static variable in error org.sbml.jsbml.text.parser.TokenMgrError
Tried to change to an invalid lexical state.
INVALID_OBJECT - Static variable in class org.sbml.jsbml.JSBML
 
INVALID_OPERATOR_MSG - Static variable in class org.sbml.jsbml.ASTNode
Message to indicate that an ASTNode.Type type has been chosen which cannot be used as an operator.
INVALID_TYPE_AND_QUALIFIER_COMBINATION_MSG - Static variable in class org.sbml.jsbml.CVTerm
Message to indicate an illegal combination of a CVTerm.Type and a CVTerm.Qualifier attribute.
INVALID_XML_OPERATION - Static variable in class org.sbml.jsbml.JSBML
 
involves(Species) - Method in class org.sbml.jsbml.Reaction
Convenient test if the given species takes part in this reaction as a reactant, product, or modifier.
IOProgressListener - Interface in org.sbml.jsbml.util
 
ioProgressOn(Object) - Method in interface org.sbml.jsbml.util.IOProgressListener
Method to report progress when reading or writing the current object has been finished.
isAlgebraic() - Method in class org.sbml.jsbml.Rule
 
isAmpere() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind ampere.
isAntisenseRNA(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isAssignment() - Method in class org.sbml.jsbml.Rule
 
isAttributesEmpty() - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether the attribute set in this XMLToken set is empty.
isAvogadro() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind avogadro.
isBecquerel() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind becquerel.
isBindingActivator(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isBiologicalQualifier() - Method in class org.sbml.jsbml.CVTerm
Returns true if this qualifier is a biological qualifier.
isBiologicalQualifier() - Method in enum org.sbml.jsbml.CVTerm.Qualifier
Returns true if this qualifier is a biological qualifier.
isBoolean() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node has a boolean type (a logical operator, a relational operator, or the constants true or false).
isBoolean() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
isBoundaryCondition() - Method in class org.sbml.jsbml.Species
 
isBuiltIn(String, int) - Static method in class org.sbml.jsbml.Unit
isBuiltIn(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
isBuiltIn() - Method in class org.sbml.jsbml.UnitDefinition
isCallableSBase() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
isCandela() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind candela
isCatalyst(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isCatalyticActivator(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isCelsius() - Method in class org.sbml.jsbml.Unit
Deprecated.
Unit.Kind.CELSIUS should no longer be used.
isChildOf(int, int) - Static method in class org.sbml.jsbml.SBO
Checks whether the given sboTerm is a member of the SBO subgraph rooted at parent.
isChildOf(SBO.Term, SBO.Term) - Static method in class org.sbml.jsbml.SBO
Traverses the systems biology ontology starting at SBO.Term subject until either the root (SBO:0000000) or the SBO.Term object is reached.
isCompartmentVolume() - Method in class org.sbml.jsbml.AlgebraicRule
 
isCompartmentVolume() - Method in class org.sbml.jsbml.ExplicitRule
 
isCompartmentVolume() - Method in class org.sbml.jsbml.Rule
(SBML Level 1 only) Predicate returning true or false depending on whether this Rule is an CompartmentVolumeRule.
isCompetetiveInhibitor(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isCompleteInhibitor(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isComplex(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isConservationLaw(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the term is-a conservation law, false otherwise
isConstant() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node represents a MathML constant (e.g., true, Pi).
isConstant() - Method in class org.sbml.jsbml.SpeciesReference
 
isConstant() - Method in class org.sbml.jsbml.Symbol
 
isConstant() - Method in interface org.sbml.jsbml.Variable
 
isContinuousFramework(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the term is-a continuous framework, false otherwise
isCoulomb() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind coulomb.
isDebugMode() - Static method in class org.sbml.jsbml.ListOf
If this method returns true, the ListOf.toString() method of this ListOf displays the whole content of the list.
isDefinedIn(int, int) - Method in enum org.sbml.jsbml.ASTNode.Type
Checks whether this type is valid for the given SBML Level/Version combination.
isDefinedIn(int, int) - Method in enum org.sbml.jsbml.Unit.Kind
Tests whether this kind of unit is defined in the given level and version of SBML.
isDifference() - Method in class org.sbml.jsbml.ASTNode
Checks if this ASTNode represents a difference.
isDifference() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
isDimensionless() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the Unit.Kind DIMENSIONLESS.
isDiscreteFramework(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the term is-a discrete framework, false otherwise
isDrug(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isElement() - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether this XMLToken is an XML element.
isEmpty() - Method in class org.sbml.jsbml.Annotation
 
isEmpty() - Method in class org.sbml.jsbml.History
Checks whether at least one attribute has been set for this History.
isEmpty() - Method in class org.sbml.jsbml.ListOf
 
isEmpty() - Method in class org.sbml.jsbml.xml.XMLAttributes
Returns true or false depending on whether this XMLAttributes set is empty.
isEmpty() - Method in class org.sbml.jsbml.xml.XMLNamespaces
Returns true or false depending on whether this XMLNamespaces list is empty.
isEmpty() - Method in class org.sbml.jsbml.xml.XMLTriple
Deprecated.
libSBML internal
isEmptySet(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isEnd() - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether this XMLToken is an XML end element.
isEndElement - Variable in class org.sbml.jsbml.xml.XMLToken
 
isEndFor(XMLToken) - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether this XMLToken is an XML end element for the given start element.
isEntity(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the term is-a Entity, false otherwise
isEnzymaticCatalysis(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isEOF - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
isEOF - Variable in class org.sbml.jsbml.xml.XMLToken
 
isEOF() - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether this XMLToken is an end of file marker.
isError() - Method in exception org.sbml.jsbml.SBMLError
Returns true is the SBMLError severity is of type SBMLError.SEVERITY.ERROR
isError() - Method in exception org.sbml.jsbml.SBMLException
 
isEssentialActivator(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isEvent(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isExplicitlySetConstant - Variable in class org.sbml.jsbml.LocalParameter
This field memorizes whether this LocalParameter has been explicitly set to be constant.
isExplicitlySetConstant() - Method in class org.sbml.jsbml.LocalParameter
In SBML prior to Level 3 it was possible to explicitly state that a local parameter represents a constant Quantity.
isExplicitlySetConstant - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
isFarad() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind farad
isFast() - Method in class org.sbml.jsbml.Reaction
 
isFatal() - Method in exception org.sbml.jsbml.SBMLError
Returns true is the SBMLError severity is of type SBMLError.SEVERITY.FATAL
isFatal() - Method in exception org.sbml.jsbml.SBMLException
 
isFilterForSpecies() - Method in class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
 
isFunction() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node represents a function.
isFunctionalCompartment(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isFunctionalEntity(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isFunctionDefinition - Variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
isGene(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isGeneCodingRegion(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the sboTerm stands for a gene coding region, false otherwise
isGeneOrGeneCodingRegion(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the sboTerm stands for a gene coding region or a gene, false otherwise
isGeneric(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isGram() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind gram
isGray() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind gray
isHasOnlySubstanceUnits() - Method in class org.sbml.jsbml.Species
 
isHenry() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind henry
isHertz() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind hertz
isHillEquation(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isIdMandatory() - Method in class org.sbml.jsbml.CompartmentType
Deprecated.
isIdMandatory() - Method in class org.sbml.jsbml.Event
 
isIdMandatory() - Method in class org.sbml.jsbml.FunctionDefinition
 
isIdMandatory() - Method in class org.sbml.jsbml.Model
 
isIdMandatory() - Method in interface org.sbml.jsbml.NamedSBase
This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.
isIdMandatory() - Method in class org.sbml.jsbml.QuantityWithUnit
 
isIdMandatory() - Method in class org.sbml.jsbml.Reaction
 
isIdMandatory() - Method in class org.sbml.jsbml.SimpleSpeciesReference
 
isIdMandatory() - Method in class org.sbml.jsbml.SpeciesType
Deprecated.
isIdMandatory() - Method in class org.sbml.jsbml.UnitDefinition
 
isInfinity() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node represents the special IEEE 754 value infinity, false otherwise.
isInfo() - Method in exception org.sbml.jsbml.SBMLError
Returns true is the SBMLError severity is of type SBMLError.SEVERITY.INFO
isInfo() - Method in exception org.sbml.jsbml.SBMLException
 
isInhibitor(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isInitialValue() - Method in class org.sbml.jsbml.Trigger
 
isInt(double) - Static method in class org.sbml.jsbml.util.Maths
Checks if the given argument represents an integer number, i.e., if it can be casted to int without loosing information.
isInteger() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node contains an integer value, false otherwise.
isInteraction(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isInternal() - Method in exception org.sbml.jsbml.SBMLError
Returns true is the SBMLError category is of type internal
isInternal() - Method in exception org.sbml.jsbml.SBMLException
 
isInvalid() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind invalid.
isInvalid() - Method in class org.sbml.jsbml.UnitDefinition
This method checks, if this UnitDefinition only contains Invalid as Unit.Kind.
isIon(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isIonChannel(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isItem() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind item
isJoule() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind Joule
isKatal() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind katal
isKelvin() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind kelvin
isKilogram() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind kilogram
isKineticConstant(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isLambda() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node is a MathML <lambda>, false otherwise.
isLeaf() - Method in class org.sbml.jsbml.AbstractTreeNode
 
isLitre() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind litre.
isLog10() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node represents a log10() function, false otherwise.
isLogical() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node is a MathML logical operator (i.e., and, or, not, xor).
isLogicalFramework(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isLumen() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind lumen
isLux() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind lux
isMaterialEntity(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isMathematicalExpression(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isMessengerRNA(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isMetre() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind metre
isMinusOne() - Method in class org.sbml.jsbml.ASTNode
Returns true if this astnode represents the number minus one (either as integer or as real value).
isModellingFramework(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isModelQualifier() - Method in class org.sbml.jsbml.CVTerm
Returns true if this qualifier is a model qualifier.
isModelQualifier() - Method in enum org.sbml.jsbml.CVTerm.Qualifier
Returns true if this qualifier is a model qualifier.
isModifier(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isMole() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind mole.
isName() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node is a user-defined Variable name in SBML L1, L2 (MathML), or the special symbols delay or time.
isNamespacesEmpty() - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether the XMLNamespaces of this XMLToken is empty.
isNaN() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node is a type Real and represents the special IEEE 754 value 'not a number' Double.NaN, false otherwise.
isNegInfinity() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node represents the special IEEE 754 value 'negative infinity' Double.NEGATIVE_INFINITY, false otherwise.
isNewton() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind newton
isNode() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
Checks whether the value encapsulated in this ASTNodeValue is an instance of Node.
isNonCompetetiveInhibitor(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isNonEssentialActivator(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isNumber() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node contains a number, false otherwise.
isNumber() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
ISO_8601_DATE_FORMAT - Static variable in class org.sbml.jsbml.xml.stax.DateProcessor
ISO 8601 [W3CDTF] date format for GMT
isObsolete(int) - Static method in class org.sbml.jsbml.SBO
Function for checking whether the SBO term is obsolete.
isObsolete() - Method in class org.sbml.jsbml.SBO.Term
Checks whether or not this SBO.Term is obsolete.
isOhm() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind ohm
isOne() - Method in class org.sbml.jsbml.ASTNode
Returns true if this ASTNode represents the number one (either as integer or as real value).
isOperator() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node is a mathematical operator, meaning, +, -, *, / or ^ (power).
isOverdetermined() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
Returns a boolean that indicates whether the given model is over determined or not.
isPackageRequired(String, StartElement) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Returns true if there is no 'required' attribute for this namespace URI, false otherwise.
isParameter() - Method in class org.sbml.jsbml.AlgebraicRule
 
isParameter() - Method in class org.sbml.jsbml.ExplicitRule
 
isParameter() - Method in class org.sbml.jsbml.Rule
(SBML Level 1 only) Predicate returning true or false depending on whether this Rule is an ParameterRule.
isPartialInhibitor(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isParticipant(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isParticipantRole(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isPascal() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind pascal
isPersistent() - Method in class org.sbml.jsbml.Trigger
 
isPhenotype(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isPhysicalCompartment(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isPhysicalParticipant(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isPiecewise() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node is the MathML <piecewise> construct, false otherwise.
isPredefined(String, int) - Static method in class org.sbml.jsbml.Unit
Predicate to test whether a given string is the name of a predefined SBML unit.
isPredefined(String, int) - Static method in class org.sbml.jsbml.UnitDefinition
 
isPredefined(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
Test if the given unit is a predefined unit.
isPredefined() - Method in class org.sbml.jsbml.UnitDefinition
This method tests if this unit definition is a predefined unit.
isPredefinedUnitsID(String) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
Checks whether or not a given identifier for a Unit.Kind or UnitDefinition equals a predefined unit identifier for this type.
isPrintNameIfAvailable() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
isProduct(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isProtein(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isQuantitativeParameter(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isRadian() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind radian
isRate() - Method in class org.sbml.jsbml.Rule
 
isRateLaw(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isRational() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node represents a rational number, false otherwise.
isReactant(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isReal() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node can represent a real number, false otherwise.
isReceptor(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isRelational() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node is a MathML relational operator, meaning ==, >=, >, <, and !=.
isReversible() - Method in class org.sbml.jsbml.Reaction
 
isRNA(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isRNAOrMessengerRNA(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isRoot() - Method in class org.sbml.jsbml.AbstractTreeNode
 
isRoot() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
isSBMLNamespaceNeeded(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
isScalar() - Method in class org.sbml.jsbml.AssignmentRule
 
isScalar() - Method in class org.sbml.jsbml.ExplicitRule
Predicate returning true or false depending on whether this Rule is an AssignmentRule (SBML Level 2) or has a 'type' attribute value of 'scalar' (SBML Level 1).
isScalar() - Method in class org.sbml.jsbml.RateRule
 
isScalar() - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
 
isSecond() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind second
isSetAbout() - Method in class org.sbml.jsbml.Annotation
Checks whether the 'about' element has been initialized.
isSetAnnotation() - Method in class org.sbml.jsbml.AbstractSBase
 
isSetAnnotation() - Method in class org.sbml.jsbml.Annotation
Checks if the Annotation is initialised.
isSetAnnotation() - Method in interface org.sbml.jsbml.SBase
Predicate returning true or false depending on whether this object's 'annotation' sub-element exists and has content.
isSetAreaUnits() - Method in class org.sbml.jsbml.Model
Returns true if the area units ID of this Model is not null.
isSetAreaUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns true if the UnitDefinition which has the area units ID of this Model as id is not null.
isSetAttributes() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
isSetBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm
 
isSetBoundaryCondition - Variable in class org.sbml.jsbml.Species
 
isSetBoundaryCondition() - Method in class org.sbml.jsbml.Species
 
isSetCharacters() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
isSetCharge - Variable in class org.sbml.jsbml.Species
Boolean value to test if the charge has been set.
isSetCharge() - Method in class org.sbml.jsbml.Species
 
isSetClassName() - Method in class org.sbml.jsbml.ASTNode
 
isSetCompartment() - Method in class org.sbml.jsbml.Reaction
 
isSetCompartment() - Method in class org.sbml.jsbml.Species
 
isSetCompartmentInstance() - Method in class org.sbml.jsbml.Reaction
 
isSetCompartmentInstance() - Method in class org.sbml.jsbml.Species
 
isSetCompartmentType() - Method in class org.sbml.jsbml.Compartment
Returns true if the compartmentID of this compartment is not null.
isSetCompartmentTypeInstance() - Method in class org.sbml.jsbml.Compartment
Deprecated.
isSetConstant - Variable in class org.sbml.jsbml.SpeciesReference
 
isSetConstant() - Method in class org.sbml.jsbml.SpeciesReference
 
isSetConstant - Variable in class org.sbml.jsbml.Symbol
 
isSetConstant() - Method in class org.sbml.jsbml.Symbol
 
isSetConstant() - Method in interface org.sbml.jsbml.Variable
 
isSetConversionFactor() - Method in class org.sbml.jsbml.Model
Returns true if the conversionFactorID of this Model is not null.
isSetConversionFactor() - Method in class org.sbml.jsbml.Species
 
isSetConversionFactorInstance() - Method in class org.sbml.jsbml.Model
Returns true if the Parameter which has the conversionFactorID of this Model as id is not null.
isSetConversionFactorInstance() - Method in class org.sbml.jsbml.Species
 
isSetCreatedDate() - Method in class org.sbml.jsbml.History
Predicate returning true or false depending on whether this History's createdDate has been set.
isSetDefinitionURL() - Method in class org.sbml.jsbml.ASTNode
 
isSetDelay() - Method in class org.sbml.jsbml.Event
 
isSetDenominator - Variable in class org.sbml.jsbml.SpeciesReference
Boolean value to know if the SpeciesReference denominator has been set.
isSetDenominator() - Method in class org.sbml.jsbml.SpeciesReference
 
isSetEmail() - Method in class org.sbml.jsbml.Creator
Returns true or false depending on whether this Creator's email has been set.
isSetEncoding() - Method in class org.sbml.jsbml.ASTNode
 
isSetExponent - Variable in class org.sbml.jsbml.Unit
 
isSetExponent() - Method in class org.sbml.jsbml.Unit
 
isSetExtentUnits() - Method in class org.sbml.jsbml.Model
Returns true if the extentUnitsID of this Model is not null.
isSetExtentUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns true if the UnitDefinition which has the extentUnitsID of this Model as id is not null.
isSetFamilyName() - Method in class org.sbml.jsbml.Creator
Returns true or false depending on whether this Creator's familyName has been set.
isSetFast - Variable in class org.sbml.jsbml.Reaction
Checks whether the Reaction.fast attribute has been set by using a default or by changing its value.
isSetFast() - Method in class org.sbml.jsbml.Reaction
 
isSetGivenName() - Method in class org.sbml.jsbml.Creator
Returns true or false depending on whether this Creator's givenName has been set.
isSetHasOnlySubstanceUnits - Variable in class org.sbml.jsbml.Species
 
isSetHasOnlySubstanceUnits() - Method in class org.sbml.jsbml.Species
 
isSetHistory() - Method in class org.sbml.jsbml.AbstractSBase
 
isSetHistory() - Method in class org.sbml.jsbml.Annotation
Checks if the History is initialised
isSetHistory() - Method in interface org.sbml.jsbml.SBase
 
isSetId() - Method in class org.sbml.jsbml.AbstractNamedSBase
 
isSetId() - Method in class org.sbml.jsbml.ASTNode
 
isSetId() - Method in class org.sbml.jsbml.FunctionDefinition
 
isSetId() - Method in interface org.sbml.jsbml.NamedSBase
 
isSetInitialAmount() - Method in class org.sbml.jsbml.Species
 
isSetInitialConcentration() - Method in class org.sbml.jsbml.Species
 
isSetInitialValue() - Method in class org.sbml.jsbml.Trigger
 
isSetKind() - Method in class org.sbml.jsbml.Unit
Predicate to test whether the 'kind' attribute of this Unit has been set.
isSetKineticLaw() - Method in class org.sbml.jsbml.Reaction
 
isSetL() - Method in class org.sbml.jsbml.util.ValuePair
 
isSetLengthUnits() - Method in class org.sbml.jsbml.Model
Returns true if the lengthUnitsID of this Model is not null.
isSetLengthUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns true if the UnitDefinition which has the lengthUnitsID of this Model as id is not null.
isSetLevel() - Method in class org.sbml.jsbml.AbstractSBase
 
isSetLevel() - Method in interface org.sbml.jsbml.SBase
 
isSetLevelAndVersion() - Method in class org.sbml.jsbml.AbstractSBase
 
isSetLevelAndVersion() - Method in interface org.sbml.jsbml.SBase
Returns true if both, Level and Version are set for this SBase.
isSetListOfCompartments() - Method in class org.sbml.jsbml.Model
Returns true if the listOfCompartments of this Model is not null and not empty.
isSetListOfCompartmentTypes() - Method in class org.sbml.jsbml.Model
Deprecated. 
isSetListOfConstraints() - Method in class org.sbml.jsbml.Model
Returns true if the listOfConstraints of this Model is not null and not empty.
isSetListOfCreators() - Method in class org.sbml.jsbml.History
 
isSetListOfCVTerms() - Method in class org.sbml.jsbml.Annotation
Checks if the list of CVTerm is not empty.
isSetListOfErrors() - Method in class org.sbml.jsbml.SBMLDocument
 
isSetListOfEventAssignments() - Method in class org.sbml.jsbml.Event
 
isSetListOfEvents() - Method in class org.sbml.jsbml.Model
Returns true if the listOfEvents of this Model is not null and not empty.
isSetListOfFunctionDefinitions() - Method in class org.sbml.jsbml.Model
Returns true if the listOfFunctionDefinitions of this Model is not null and not empty.
isSetListOfInitialAssignments() - Method in class org.sbml.jsbml.Model
Returns true if the listOfInitialAssignments of this Model is not null and not empty.
isSetListOfLocalParameters() - Method in class org.sbml.jsbml.KineticLaw
 
isSetListOfModification() - Method in class org.sbml.jsbml.History
 
isSetListOfModifiers() - Method in class org.sbml.jsbml.Reaction
 
isSetListOfParameters() - Method in class org.sbml.jsbml.KineticLaw
isSetListOfParameters() - Method in class org.sbml.jsbml.Model
Returns true if the listOfParameters of this Model is not null and not empty.
isSetListOfProducts() - Method in class org.sbml.jsbml.Reaction
 
isSetListOfReactants() - Method in class org.sbml.jsbml.Reaction
 
isSetListOfReactions() - Method in class org.sbml.jsbml.Model
Returns true if the listOfReactions of this Model is not null and not empty.
isSetListOfRules() - Method in class org.sbml.jsbml.Model
Returns true if the listOfRules of this Model is not null and not empty.
isSetListOfSpecies() - Method in class org.sbml.jsbml.Model
Returns true if the listOfSpecies of this Model is not null and not empty.
isSetListOfSpeciesTypes() - Method in class org.sbml.jsbml.Model
Deprecated. 
isSetListOfUnitDefinitions() - Method in class org.sbml.jsbml.Model
Returns true if the listOfUnitDefinitions of this Model is not null and not empty.
isSetListOfUnits() - Method in class org.sbml.jsbml.UnitDefinition
 
isSetMath() - Method in class org.sbml.jsbml.AbstractMathContainer
 
isSetMath() - Method in interface org.sbml.jsbml.MathContainer
Checks if an ASTNode has been set for this MathContainer.
isSetMessage() - Method in class org.sbml.jsbml.Constraint
Returns true if the message of this Constraint is not null.
isSetMetaId() - Method in class org.sbml.jsbml.AbstractSBase
 
isSetMetaId() - Method in interface org.sbml.jsbml.SBase
Predicate returning true or false depending on whether this object's 'metaid' attribute has been set.
isSetModel() - Method in class org.sbml.jsbml.SBMLDocument
 
isSetModelHistory() - Method in class org.sbml.jsbml.Model
Deprecated.
isSetModelQualifierType() - Method in class org.sbml.jsbml.CVTerm
 
isSetModifiedDate() - Method in class org.sbml.jsbml.History
Predicate returning true or false depending on whether this History's modifiedDate has been set.
isSetMultiplier - Variable in class org.sbml.jsbml.Unit
 
isSetMultiplier() - Method in class org.sbml.jsbml.Unit
 
isSetName() - Method in class org.sbml.jsbml.AbstractNamedSBase
 
isSetName() - Method in class org.sbml.jsbml.ASTNode
 
isSetName() - Method in class org.sbml.jsbml.FunctionDefinition
 
isSetName() - Method in interface org.sbml.jsbml.NamedSBase
 
isSetName() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
isSetNamespace() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
isSetNewValue() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
isSetNonRDFannotation() - Method in class org.sbml.jsbml.Annotation
Checks if the non RDF part of the Annotation is initialised.
isSetNotes() - Method in class org.sbml.jsbml.AbstractSBase
 
isSetNotes() - Method in interface org.sbml.jsbml.SBase
Predicate returning true or false depending on whether this object's 'notes' sub-element exists and has content.
isSetNumberType - Variable in class org.sbml.jsbml.ASTNode
Tells if the type attribute of the cn element was set and we need to write it back or if it is set to the default (REAL).
isSetNumberType() - Method in class org.sbml.jsbml.ASTNode
Returns true if the number type is set.
isSetNumberType - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
isSetOffset - Variable in class org.sbml.jsbml.Unit
 
isSetOffset() - Method in class org.sbml.jsbml.Unit
Deprecated.
the offset attribute should no longer be used.
isSetOldValue() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
isSetOrganisation() - Method in class org.sbml.jsbml.Creator
Returns true or false depending on whether this Creator's organisation has been set.
isSetOrganization() - Method in class org.sbml.jsbml.Creator
Returns true or false depending on whether this Creator's organisation has been set.
isSetOtherAnnotationThanRDF() - Method in class org.sbml.jsbml.Annotation
Deprecated.
isSetOutside() - Method in class org.sbml.jsbml.Compartment
Returns true if the outsideID of this compartment is not null.
isSetOutsideInstance() - Method in class org.sbml.jsbml.Compartment
Returns true if the compartment instance which matches the outsideID of this compartment is not null.
isSetParent() - Method in class org.sbml.jsbml.AbstractTreeNode
 
isSetParent() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
 
isSetParentSBMLObject() - Method in class org.sbml.jsbml.AbstractSBase
 
isSetParentSBMLObject() - Method in class org.sbml.jsbml.ASTNode
Checks if a parent SBML object, i.e., a MathContainer, is set as a parent SBML object for this ASTNode.
isSetParentSBMLObject() - Method in interface org.sbml.jsbml.SBase
Check whether this SBase has been linked to a parent within the hierarchical SBML data structure.
isSetPersistent() - Method in class org.sbml.jsbml.Trigger
 
isSetPrefix() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
isSetPriority() - Method in class org.sbml.jsbml.Event
 
isSetProgramName() - Method in class org.sbml.jsbml.SBMLWriter
Check if a program name has been defined for this SBMLWriter.
isSetProgramVersion() - Method in class org.sbml.jsbml.SBMLWriter
Check if a program version has been defined for this SBMLWriter.
isSetQualifierType() - Method in class org.sbml.jsbml.CVTerm
Checks whether or not the CVTerm.Qualifier has been set for this CVTerm.
isSetRDFannotation() - Method in class org.sbml.jsbml.Annotation
Checks if the RDF part of the Annotation is initialised.
isSetReversible - Variable in class org.sbml.jsbml.Reaction
Checks whether the Reaction.reversible attribute has been set by using a default or by changing its value.
isSetReversible() - Method in class org.sbml.jsbml.Reaction
 
isSetSBOTerm() - Method in class org.sbml.jsbml.AbstractSBase
 
isSetSBOTerm() - Method in interface org.sbml.jsbml.SBase
 
isSetScale - Variable in class org.sbml.jsbml.Unit
 
isSetScale() - Method in class org.sbml.jsbml.Unit
 
isSetSize() - Method in class org.sbml.jsbml.Compartment
Returns true if the size of this compartment has been set by a user.
isSetSource() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
isSetSpatialDimensions - Variable in class org.sbml.jsbml.Compartment
Helper variable to check if spatial dimensions has been set by the user.
isSetSpatialDimensions() - Method in class org.sbml.jsbml.Compartment
Returns true if the spatialDimensions of this compartment has been set by a user.
isSetSpatialSizeUnits() - Method in class org.sbml.jsbml.Species
Deprecated.
Only valid for SBML Level 2 Versions 1 and 2.
isSetSpatialSizeUnitsInstance() - Method in class org.sbml.jsbml.Species
 
isSetSpecies() - Method in class org.sbml.jsbml.SimpleSpeciesReference
 
isSetSpeciesInstance() - Method in class org.sbml.jsbml.SimpleSpeciesReference
 
isSetSpeciesType() - Method in class org.sbml.jsbml.Species
Deprecated.
isSetSpeciesTypeInstance() - Method in class org.sbml.jsbml.Species
Deprecated.
isSetStoichiometry - Variable in class org.sbml.jsbml.SpeciesReference
 
isSetStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference
 
isSetStoichiometryMath() - Method in class org.sbml.jsbml.SpeciesReference
 
isSetStyle() - Method in class org.sbml.jsbml.ASTNode
 
isSetSubstanceUnits() - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
isSetSubstanceUnits() - Method in class org.sbml.jsbml.Model
Returns true if the substanceUnitsID of this Model is not null.
isSetSubstanceUnits() - Method in class org.sbml.jsbml.Species
 
isSetSubstanceUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
Deprecated. 
isSetSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns true if the UnitDefinition which has the substanceUnitsID of this Model as id is not null.
isSetSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Species
 
isSetSymbol() - Method in class org.sbml.jsbml.InitialAssignment
 
isSetTimeUnits() - Method in class org.sbml.jsbml.Event
Deprecated. 
isSetTimeUnits() - Method in class org.sbml.jsbml.KineticLaw
Deprecated. 
isSetTimeUnits() - Method in class org.sbml.jsbml.Model
Returns true if the timeUnitsID of this Model is not null.
isSetTimeUnitsInstance() - Method in class org.sbml.jsbml.Event
Deprecated. 
isSetTimeUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
Deprecated. 
isSetTimeUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns true if the UnitsDefinition which has the timeUnistID of this Model as id is not null.
isSetTrigger() - Method in class org.sbml.jsbml.Event
 
isSetType() - Method in class org.sbml.jsbml.CVTerm
Returns true if the Type of this CVTerm is set.
isSetTypeQualifier() - Method in class org.sbml.jsbml.CVTerm
Returns true if the Qualifier of this CVTerm is set.
isSetUnit() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
Test if this value can be evaluated to a UnitDefinition
isSetUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
isSetUnits() - Method in class org.sbml.jsbml.ASTNode
Returns true if a unit is defined on this node.
isSetUnits() - Method in class org.sbml.jsbml.Event
Deprecated.
isSetUnits() - Method in class org.sbml.jsbml.ExplicitRule
Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
isSetUnits() - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
isSetUnits() - Method in interface org.sbml.jsbml.SBaseWithUnit
 
isSetUnitsInstance() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
isSetUnitsInstance() - Method in class org.sbml.jsbml.Event
Deprecated.
isSetUnitsInstance() - Method in class org.sbml.jsbml.ExplicitRule
Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
isSetUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
isSetUnitsInstance() - Method in interface org.sbml.jsbml.SBaseWithUnit
Checks whether the element referenced by the unitsID attribute of this SBaseWithUnit is either an existing base Unit, i.e., a simple Unit that can directly be addressed via its Unit.Kind element, or the identifier of an existing UnitDefinition in the Model to which this SBaseWithUnit belongs.
isSetUserObject() - Method in class org.sbml.jsbml.ASTNode
 
isSetUserObject() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
 
isSetUseValuesFromTriggerTime - Variable in class org.sbml.jsbml.Event
 
isSetUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event
 
isSetV() - Method in class org.sbml.jsbml.util.ValuePair
 
isSetValue() - Method in interface org.sbml.jsbml.Quantity
Returns true if the value of this Quantity is set.
isSetValue - Variable in class org.sbml.jsbml.QuantityWithUnit
a boolean to help knowing is the value as been set by the user or is the default one.
isSetValue() - Method in class org.sbml.jsbml.QuantityWithUnit
 
isSetValue() - Method in class org.sbml.jsbml.SpeciesReference
 
isSetVariable() - Method in interface org.sbml.jsbml.Assignment
Returns true if the variableID of this Assignment is not null.
isSetVariable() - Method in class org.sbml.jsbml.EventAssignment
 
isSetVariable() - Method in class org.sbml.jsbml.ExplicitRule
 
isSetVariable() - Method in class org.sbml.jsbml.InitialAssignment
 
isSetVariableInstance() - Method in interface org.sbml.jsbml.Assignment
Returns true if the Variable instance which has the variableID of this Assignment as id is not null.
isSetVariableInstance() - Method in class org.sbml.jsbml.EventAssignment
 
isSetVariableInstance() - Method in class org.sbml.jsbml.ExplicitRule
 
isSetVariableInstance() - Method in class org.sbml.jsbml.InitialAssignment
 
isSetVersion() - Method in class org.sbml.jsbml.AbstractSBase
 
isSetVersion() - Method in interface org.sbml.jsbml.SBase
 
isSetVolume() - Method in class org.sbml.jsbml.Compartment
Deprecated.
The volume attribute is only defined in SBML Level 1. Please use Compartment.isSetSize()
isSetVolumeUnits() - Method in class org.sbml.jsbml.Model
Returns true if the volumeUnitsID of this Model is not null.
isSetVolumeUnitsInstance() - Method in class org.sbml.jsbml.Model
Returns true if the UnitDefinition which has the volumeUnitsID of this Model as id is not null.
isSiemens() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind siemens
isSievert() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind sievert
isSimpleMolecule(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isSpeciesConcentration() - Method in class org.sbml.jsbml.AlgebraicRule
 
isSpeciesConcentration() - Method in class org.sbml.jsbml.ExplicitRule
 
isSpeciesConcentration() - Method in class org.sbml.jsbml.Rule
(SBML Level 1 only) Predicate returning true or false depending on whether this Rule is an SpeciesConcentrationRule.
isSpecificActivator(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isSqrt() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node represents a square root function, false otherwise.
isStart() - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether this XMLToken is an XML start element.
isStartElement - Variable in class org.sbml.jsbml.xml.XMLToken
 
isStateTransition(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isSteadyStateExpression(int) - Static method in class org.sbml.jsbml.SBO
Function for checking the SBO term is from correct part of SBO.
isSteradian() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind steradian
isStimulator(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isString() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node is a name or refers to a FunctionDefinition.
isString() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
issuedWarnings - Variable in class org.sbml.jsbml.xml.stax.SBMLWriter
Remember already issued warnings to avoid having multiple lines, saying the same thing (Warning: Skipping detailed parsing of name space 'XYZ'.
isSum() - Method in class org.sbml.jsbml.ASTNode
Checks if this ASTNode represents a sum.
isSum() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
isSystem() - Method in exception org.sbml.jsbml.SBMLError
Returns true is the SBMLError category is of type system
isSystem() - Method in exception org.sbml.jsbml.SBMLException
 
isTesla() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind tesla
isText - Variable in class org.sbml.jsbml.xml.XMLToken
 
isText() - Method in class org.sbml.jsbml.xml.XMLToken
Returns true or false depending on whether this XMLToken is an XML text element.
isTranscription(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTranscriptionalActivation(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTranscriptionalInhibitor(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTransitionOmitted(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTranslation(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTranslationalActivation(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTranslationalInhibitor(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTransport(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTrigger(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTruncated(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isUMinus() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node is a unary minus operator, false otherwise.
isUMinus() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
isUnary() - Method in class org.sbml.jsbml.ASTNode
Checks whether the number of child nodes is exactly one.
isUnary() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
isUnitKind(Unit.Kind, int, int) - Static method in class org.sbml.jsbml.Unit
 
isUnitKind(String, int, int) - Static method in class org.sbml.jsbml.Unit
Predicate to test whether a given string is the name of a valid base unit in SBML (such as 'gram' or 'mole').
isUnitKind() - Method in class org.sbml.jsbml.UnitDefinition
Convenient method to test whether this UnitDefinition contains exactly one Unit that itself represents a Unit.Kind, i.e., multiplier = 1, exponent = 1, scale = 1.
isUnitsDefined - Variable in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
isUnitsDefined() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
isUnknown() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node has an unknown type.
isUnknownMolecule(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isUnknownTransition(int) - Static method in class org.sbml.jsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isUserObjectRecursiveDataType() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
Checks whether or not the user's object has been set (see TreeNodeAdapter.isSetUserObject()) and if so if it belongs to those elements returned by the method TreeNodeAdapter.getChildAt(int).
isUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event
 
isValidId(String, int, int) - Static method in class org.sbml.jsbml.AbstractNamedSBase
Checks whether the given idCandidate is a valid identifier according to the SBML specifications.
isValidLevelAndVersionCombination(int, int) - Static method in class org.sbml.jsbml.AbstractSBase
Returns true is the level and version combination is a valid one, false otherwise.
isValidUnit(Model, String) - Static method in class org.sbml.jsbml.Unit
Returns true if the unit is a valid unit kind name or an identifier of an existing UnitDefinition.
isValidUnitKindString(String, int, int) - Static method in enum org.sbml.jsbml.Unit.Kind
This method is equivalent to converting the String to a Unit.Kind and then calling its Unit.Kind.isDefinedIn(int, int) method.
isVariable() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node represents a Variable.
isVariantOfArea() - Method in class org.sbml.jsbml.Unit
 
isVariantOfArea() - Method in class org.sbml.jsbml.UnitDefinition
 
isVariantOfLength() - Method in class org.sbml.jsbml.Unit
 
isVariantOfLength() - Method in class org.sbml.jsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'length'.
isVariantOfSubstance() - Method in class org.sbml.jsbml.Unit
 
isVariantOfSubstance() - Method in class org.sbml.jsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'substance'.
isVariantOfSubstancePerArea() - Method in class org.sbml.jsbml.UnitDefinition
 
isVariantOfSubstancePerLength() - Method in class org.sbml.jsbml.UnitDefinition
 
isVariantOfSubstancePerTime() - Method in class org.sbml.jsbml.UnitDefinition
 
isVariantOfSubstancePerVolume() - Method in class org.sbml.jsbml.UnitDefinition
 
isVariantOfTime() - Method in class org.sbml.jsbml.Unit
 
isVariantOfTime() - Method in class org.sbml.jsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'time'.
isVariantOfVolume() - Method in class org.sbml.jsbml.Unit
 
isVariantOfVolume() - Method in class org.sbml.jsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'volume'.
isVolt() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind volt
isWarning() - Method in exception org.sbml.jsbml.SBMLError
Returns true is the SBMLError severity is of type SBMLError.SEVERITY.WARNING
isWarning() - Method in exception org.sbml.jsbml.SBMLException
 
isWatt() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind watt
isWeber() - Method in class org.sbml.jsbml.Unit
Predicate for testing whether this Unit is of the kind weber
isXML() - Method in exception org.sbml.jsbml.SBMLError
Returns true is the SBMLError category is of type xml
isXML() - Method in exception org.sbml.jsbml.SBMLException
 
isZero() - Method in class org.sbml.jsbml.ASTNode
Returns true if this node represents the number zero (either as integer or as real value).
iterator() - Method in class org.sbml.jsbml.ListOf
 

J

JAXPFacade - Class in org.sbml.jsbml.util
A convenient Facade to parse and write byte and character streams with XML content using the interfaces and classes defined by the JAXP specification.
JAXPFacade() - Constructor for class org.sbml.jsbml.util.JAXPFacade
 
jj_2_1(int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_2_rtns - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_3_1() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_3R_5() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_add_error_token(int, int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_consume_token(int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_endpos - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_expentries - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_expentry - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_gc - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_gen - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_input_stream - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_kind - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_la - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_la1 - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_la1_0 - Static variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_la1_init_0() - Static method in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_lastpos - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_lasttokens - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_ls - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_nt - Variable in class org.sbml.jsbml.text.parser.FormulaParser
Next token.
jj_ntk - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_ntk() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_rescan - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_rescan_token() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_save(int, int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_scan_token(int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
jj_scanpos - Variable in class org.sbml.jsbml.text.parser.FormulaParser
 
jjAddStates(int, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjCheckNAdd(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjCheckNAddStates(int, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjCheckNAddTwoStates(int, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjFillToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjmatchedKind - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjmatchedPos - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjMoveNfa_0(int, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjMoveStringLiteralDfa0_0() - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjMoveStringLiteralDfa1_0(long) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjMoveStringLiteralDfa2_0(long, long) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjnewStateCnt - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjnextStates - Static variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjround - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjrounds - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjStartNfa_0(int, long) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjStartNfaWithStates_0(int, int, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjstateSet - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjStopAtPos(int, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjStopStringLiteralDfa_0(int, long) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjstrLiteralImages - Static variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
Token literal values.
jjtoSkip - Static variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
jjtoToken - Static variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
JSBML - Class in org.sbml.jsbml
Wrapper class for global methods and constants defined by JSBML.
JSBML() - Constructor for class org.sbml.jsbml.JSBML
 
jsbmlVersion - Static variable in class org.sbml.jsbml.JSBML
The current version number of JSBML.

K

kind - Variable in class org.sbml.jsbml.text.parser.Token
An integer that describes the kind of this token.
kind - Variable in class org.sbml.jsbml.Unit
Represents the 'kind' XML attribute of an unit element.
kind - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
KineticLaw - Class in org.sbml.jsbml
Represents the kineticLaw XML element of a SBML file.
KineticLaw() - Constructor for class org.sbml.jsbml.KineticLaw
Creates a KineticLaw instance.
KineticLaw(int, int) - Constructor for class org.sbml.jsbml.KineticLaw
Creates a KineticLaw instance from a level and version.
KineticLaw(KineticLaw) - Constructor for class org.sbml.jsbml.KineticLaw
Creates a KineticLaw instance from a given KineticLaw.
KineticLaw(Reaction) - Constructor for class org.sbml.jsbml.KineticLaw
Creates a KineticLaw instance from a given Reaction.
kineticLaw - Variable in class org.sbml.jsbml.Reaction
Represents the 'kineticLaw' XML subNode of a reaction element.
kineticLaw - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 

L

l - Variable in class org.sbml.jsbml.util.ValuePair
 
label(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
lambda(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
The body of a FunctionDefinition.
lambda(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
lambda(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
lambda(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
lambda(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
lambda(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
lambdaBody(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Creates the body of a lambda function, i.e., the argument list and the actual mathematical operation, all comma separated and surrounded in brackets.
lang - Variable in class org.sbml.jsbml.util.Message
 
lastElementCreated - Variable in class org.sbml.jsbml.util.compilers.MathMLCompiler
The last top Element that has been created in the previous step.
lastElementWasApply - Variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
lastIndexOf(Object) - Method in class org.sbml.jsbml.ListOf
 
LaTeXCompiler - Class in org.sbml.jsbml.util.compilers
Converts ASTNodeValue objects into a LaTeX String to be included into scientific writings or to be displayed in a GUI.
LaTeXCompiler() - Constructor for class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
LaTeXCompiler(boolean) - Constructor for class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
leadingZeros(int, int) - Static method in class org.sbml.jsbml.util.StringTools
This method creates a String representation of the given number and inserts as many zero characters as the prefix of this String as needed to result in a String of the given length.
leftBrace - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Left parenthesis.
leftQuotationMark - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
An opening quotation mark.
LENGTH - Static variable in class org.sbml.jsbml.UnitDefinition
Identifier of the (for SBML Level 2) predefined UnitDefinition length.
length(int, int) - Static method in class org.sbml.jsbml.UnitDefinition
Predefined unit for length.
lengthUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
lengthUnitsID - Variable in class org.sbml.jsbml.Model
Represents the 'lengthUnits' XML attribute of a model element.
leq(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates an ASTNode representing less or equal for the two given left and right child.
leq(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Less equal.
leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
leq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
letter - Static variable in class org.sbml.jsbml.AbstractNamedSBase
 
LETTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
level - Variable in class org.sbml.jsbml.util.compilers.ASTNodeValue
The level of the underlying SBMLDocument.
level - Variable in class org.sbml.jsbml.util.compilers.MathMLCompiler
The SBML level to be used in this class.
level - Variable in class org.sbml.jsbml.util.compilers.UnitsCompiler
SBML level field
level - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
LEVEL_MISMATCH - Static variable in class org.sbml.jsbml.JSBML
 
LEVEL_MISMATCH_MSG - Static variable in exception org.sbml.jsbml.LevelVersionError
Message to display in cases that two objects do not have identical level attributes.
levelMismatchMessage(SBase, SBase) - Static method in exception org.sbml.jsbml.LevelVersionError
Creates an error message if the level fields of both elements are not identical, or an empty String otherwise.
LevelVersionError - Exception in org.sbml.jsbml
An SBMLError that indicates that associated instances of SBase cannot be combined within the same model due to their differently set Level or Version attribute.
LevelVersionError(SBase) - Constructor for exception org.sbml.jsbml.LevelVersionError
 
LevelVersionError(int, int) - Constructor for exception org.sbml.jsbml.LevelVersionError
 
LevelVersionError(String, int, int) - Constructor for exception org.sbml.jsbml.LevelVersionError
 
LevelVersionError(SBase, SBase) - Constructor for exception org.sbml.jsbml.LevelVersionError
 
LEXICAL_ERROR - Static variable in error org.sbml.jsbml.text.parser.TokenMgrError
Lexical error occurred.
LexicalError(boolean, int, int, int, String, char) - Static method in error org.sbml.jsbml.text.parser.TokenMgrError
Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.
lexStateNames - Static variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
Lexer state names.
LibSBMLFormulaCompiler - Class in org.sbml.jsbml.util.compilers
 
LibSBMLFormulaCompiler() - Constructor for class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
line - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
line - Variable in class org.sbml.jsbml.util.Location
 
line - Variable in class org.sbml.jsbml.xml.XMLToken
 
lineBreak - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
This is a LaTeX line break.
listIterator() - Method in class org.sbml.jsbml.ListOf
 
listIterator(int) - Method in class org.sbml.jsbml.ListOf
 
ListOf<T extends SBase> - Class in org.sbml.jsbml
This list implementation is a Java List that extends AbstractSBase.
ListOf() - Constructor for class org.sbml.jsbml.ListOf
Creates a ListOf instance.
ListOf(int, int) - Constructor for class org.sbml.jsbml.ListOf
Creates a ListOf instance from a level and version.
ListOf(ListOf<? extends SBase>) - Constructor for class org.sbml.jsbml.ListOf
creates a ListOf instance from a given ListOf.
listOf - Variable in class org.sbml.jsbml.ListOf
list containing all the SBase elements of this object.
ListOf.Type - Enum in org.sbml.jsbml
This enum lists all the possible names of the listXXX components.
ListOf.Type() - Constructor for enum org.sbml.jsbml.ListOf.Type
 
listOfCompartments - Variable in class org.sbml.jsbml.Model
Represents the listOfCompartments subnode of a model element.
listOfCompartmentTypes - Variable in class org.sbml.jsbml.Model
Deprecated.
only valid in SBML Level 2 for Versions 2 through 4.
listOfConstraints - Variable in class org.sbml.jsbml.Model
Represents the listOfConstraints subnode of a model element.
listOfCreators - Variable in class org.sbml.jsbml.History
Contains all the Creator instances of this History.
listOfCVTerms - Variable in class org.sbml.jsbml.Annotation
contains all the CVTerm of the RDF annotation
listOfErrors - Variable in class org.sbml.jsbml.SBMLDocument
Memorizes all SBMLError when parsing the file containing this document.
listOfEventAssignments - Variable in class org.sbml.jsbml.Event
Represents the listOfEventAssignments sub-element of an event element.
listOfEvents - Variable in class org.sbml.jsbml.Model
Represents the listOfEvents subnode of a model element.
listOfFunctionDefinitions - Variable in class org.sbml.jsbml.Model
Represents the listOfFunctionDefinitions subnode of a model element.
listOfInitialAssignments - Variable in class org.sbml.jsbml.Model
Represents the listOfInitialAssignments subnode of a model element.
listOfListeners - Variable in class org.sbml.jsbml.AbstractTreeNode
List of listeners for this component
listOfLocalParameters - Variable in class org.sbml.jsbml.KineticLaw
Represents the listOfLocalParameters or listOfParameters sub-element of a kineticLaw element.
listOfModification - Variable in class org.sbml.jsbml.History
Contains all the modified date instances of this History.
listOfModifiers - Variable in class org.sbml.jsbml.Reaction
Represents the 'listOfModifiers' XML subNode of a reaction element.
listOfNodes - Variable in class org.sbml.jsbml.ASTNode
Child nodes.
listOfParameters - Variable in class org.sbml.jsbml.Model
Represents the listOfParameters subnode of a model element.
listOfPredefinedUnitDefinitions - Variable in class org.sbml.jsbml.Model
Represents the list of predefined UnitDefinitions for a given SBML level and version.
listOfProducts - Variable in class org.sbml.jsbml.Reaction
Represents the 'listOfProducts' XML subNode of a reaction element.
listOfReactants - Variable in class org.sbml.jsbml.Reaction
Represents the 'listOfReactants' XML subNode of a reaction element.
listOfReactions - Variable in class org.sbml.jsbml.Model
Represents the listOfReactions subnode of a model element.
listOfRules - Variable in class org.sbml.jsbml.Model
Represents the listOfRules subnode of a model element.
listOfSpecies - Variable in class org.sbml.jsbml.Model
Represents the listOfSpecies subnode of a model element.
listOfSpeciesTypes - Variable in class org.sbml.jsbml.Model
Deprecated.
only valid in SBML Level 2 for Versions 2 through 4.
listOfUnitDefinitions - Variable in class org.sbml.jsbml.Model
Represents the listOfUnitDefinitions subnode of a model element.
listOfUnits - Variable in class org.sbml.jsbml.UnitDefinition
Represents the 'listOfUnit' XML sub-element of a UnitDefinition.
listOfUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
listType - Variable in class org.sbml.jsbml.ListOf
name of the list at it appears in the SBMLFile.
ln(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Natural logarithm.
ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
ln(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
ln(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the ln of n
loadClasses(String, Map<String, Class<? extends T>>) - Static method in class org.sbml.jsbml.JSBML
Loads Properties from a configuration file with the given path assuming that all values represent class names.
LocalParameter - Class in org.sbml.jsbml
A local parameter can only be used to specify a constant within a KineticLaw.
LocalParameter() - Constructor for class org.sbml.jsbml.LocalParameter
Creates a new instance of LocalParameter.
LocalParameter(int, int) - Constructor for class org.sbml.jsbml.LocalParameter
 
LocalParameter(LocalParameter) - Constructor for class org.sbml.jsbml.LocalParameter
 
LocalParameter(Parameter) - Constructor for class org.sbml.jsbml.LocalParameter
Creates a new local parameter that will have the same properties than the given global parameter.
LocalParameter(String) - Constructor for class org.sbml.jsbml.LocalParameter
Creates a new instance of LocalParameter with the given identifier.
LocalParameter(String, int, int) - Constructor for class org.sbml.jsbml.LocalParameter
 
LocalParameter(String, String, int, int) - Constructor for class org.sbml.jsbml.LocalParameter
 
location - Variable in exception org.sbml.jsbml.SBMLError
 
Location - Class in org.sbml.jsbml.util
 
Location() - Constructor for class org.sbml.jsbml.util.Location
 
Location(int, int) - Constructor for class org.sbml.jsbml.util.Location
 
log(ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates an ASTNode representing a logarithm to base 10 of the given value.
log(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates an ASTNode that represents the logarithm function with the given base and value.
LOG - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
log(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Logarithm of the given value to base 10.
log(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Logarithm of the given value to the given base.
log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
log(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
log(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
log(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the log of n to the base 10
log(double, double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the logarithm of a number x to a giving base b.
log(Priority, String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger
 
log4jLogger - Variable in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
Log4j logger
logger - Static variable in class org.sbml.jsbml.AbstractMathContainer
A logger for user-messages.
logger - Static variable in class org.sbml.jsbml.AbstractSBase
A logger for this class.
logger - Variable in class org.sbml.jsbml.ASTNode
 
logger - Static variable in exception org.sbml.jsbml.IdentifierException
 
logger - Static variable in class org.sbml.jsbml.KineticLaw
A logger for this class.
logger - Static variable in class org.sbml.jsbml.ListOf
A Logger for this class.
logger - Static variable in class org.sbml.jsbml.Model
 
logger - Variable in class org.sbml.jsbml.SBMLDocument
logger used to print messages
logger - Static variable in class org.sbml.jsbml.Unit
A Logger for this class.
logger - Static variable in class org.sbml.jsbml.UnitDefinition
The logger for this class.
logger - Variable in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
logger - Variable in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
A Logger for this class.
logger - Variable in class org.sbml.jsbml.xml.parsers.AnnotationParser
 
logger - Variable in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
 
logger - Variable in class org.sbml.jsbml.xml.parsers.DatesParser
 
logger - Variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
logger - Variable in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
 
logger - Variable in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
 
logger - Variable in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
The logger of this parser
logger - Variable in class org.sbml.jsbml.xml.parsers.StringParser
 
logger - Variable in class org.sbml.jsbml.xml.parsers.VCardParser
 
logger - Variable in class org.sbml.jsbml.xml.parsers.XMLNodeWriter
 
logger - Variable in class org.sbml.jsbml.xml.stax.SBMLWriter
 
logger - Variable in class org.sbml.jsbml.xml.stax.XMLLogger
logger
logicalOperation(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
logicalOperation(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
longtableHead(String, String, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Creates a head for a longtable in LaTeX.
LOOP_DETECTED - Static variable in error org.sbml.jsbml.text.parser.TokenMgrError
Detected (and bailed out of) an infinite loop in the token manager.
lt(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates an ASTNode that performs a less than comparison between two ASTNodes.
lt(String, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates an ASTNode that performs a less than comparison between a variable and another ASTNode.
lt(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Less than.
lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
lt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
lv - Variable in class org.sbml.jsbml.AbstractSBase
Level and version of the SBML component.

M

main(String[]) - Static method in class org.sbml.jsbml.SBO
Tests method.
main(String[]) - Static method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
main(String[]) - Static method in class org.sbml.jsbml.validator.SBMLValidator
 
main(String[]) - Static method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads the file that is passed as argument and write it to the console, using the method SBMLWriter.write.
main(String[]) - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter
Tests this class
mantissa - Variable in class org.sbml.jsbml.ASTNode
 
mantissa - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
mapOfLocalParameters - Variable in class org.sbml.jsbml.KineticLaw
For internal computation: a mapping between their identifiers and the LocalParameters in KineticLaws themself:
mapOfLocalParameters - Variable in class org.sbml.jsbml.Model
A mapping between the identifiers of LocalParameters and the containing Reaction objects.
mapOfUniqueNamedSBases - Variable in class org.sbml.jsbml.Model
For internal computation: a mapping between their identifiers and the UniqueNamedSBases in Models themself:
mapOfUnitDefinitions - Variable in class org.sbml.jsbml.Model
A mapping between their identifiers and associated UnitDefinition objects.
mappingFromMetaId2SBase - Variable in class org.sbml.jsbml.SBMLDocument
Stores all the meta identifiers within this SBMLDocument to avoid the creation of multiple identical meta identifiers.
marshal(Object, HierarchicalStreamWriter, MarshallingContext) - Method in class org.sbml.jsbml.xml.xstream.converter.MessageConverter
 
maskSpecialChars(String) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Masks all special characters used by LaTeX with a backslash including hyphen symbols.
maskSpecialChars(String, boolean) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
matching - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
HashMap representing the current matching with value of the left node -> value of the right node
math - Variable in class org.sbml.jsbml.AbstractMathContainer
The math formula as an abstract syntax tree.
math(Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Encloses the given formula in dollar symbols (inline math mode).
math - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
MathContainer - Interface in org.sbml.jsbml
Base interface for all the SBML components which contain MathML nodes.
MathMLCompiler - Class in org.sbml.jsbml.util.compilers
With this compiler, an ASTNode can be transformed into a MathML string.
MathMLCompiler() - Constructor for class org.sbml.jsbml.util.compilers.MathMLCompiler
 
MathMLCompiler(ASTNode) - Constructor for class org.sbml.jsbml.util.compilers.MathMLCompiler
 
MathMLParser - Class in org.sbml.jsbml.xml.parsers
Deprecated.
this class should not be used anymore, replaced by MathMLStaxParser. But we keep it in case somebody want to use Document
MathMLParser() - Constructor for class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
MathMLStaxParser - Class in org.sbml.jsbml.xml.parsers
A MathMLStaxParser is used to parse the MathML expressions injected into a SBML file.
MathMLStaxParser() - Constructor for class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
MathMLXMLStreamCompiler - Class in org.sbml.jsbml.util.compilers
Writes an ASTNode the mathML.
MathMLXMLStreamCompiler(XMLStreamWriter, String) - Constructor for class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
Create a new MathMLXMLStreamCompiler.
mathrm(char) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
mathrm(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
Maths - Class in org.sbml.jsbml.util
This class provides several static methods for mathematical operations such as faculty, logarithms and several trigonometric functions, which are not part of standard Java, but necessary to evaluate the content of SBML files.
Maths() - Constructor for class org.sbml.jsbml.util.Maths
Constructor that should not be used; this class provides static methods only.
mathtext(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
mathtt(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Returns the LaTeX code to set the given String in type writer font within a math environment.
maxNextCharInd - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
mbox(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
merge(Unit, Unit) - Static method in class org.sbml.jsbml.Unit
Merges two Unit objects with the same 'kind' attribute value into a single Unit.
message - Variable in class org.sbml.jsbml.Constraint
Represents the subnode message of a constraint element.
message - Variable in exception org.sbml.jsbml.SBMLError
 
Message - Class in org.sbml.jsbml.util
 
Message() - Constructor for class org.sbml.jsbml.util.Message
 
message - Variable in class org.sbml.jsbml.util.Message
 
message - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
messageBuffer - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
MessageConverter - Class in org.sbml.jsbml.xml.xstream.converter
 
MessageConverter(String) - Constructor for class org.sbml.jsbml.xml.xstream.converter.MessageConverter
 
metaId - Variable in class org.sbml.jsbml.AbstractSBase
metaid of the SBML component.
metaId - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
midrule - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Produces a fancy line in tables.
militaryTimezones - Variable in class org.sbml.jsbml.xml.stax.DateProcessor
 
minus(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Subtracts the given ASTNode from this node.
minus(double) - Method in class org.sbml.jsbml.ASTNode
Subtracts the given number from this node.
minus(int) - Method in class org.sbml.jsbml.ASTNode
Subtracts the given integer from this node.
minus(int, String) - Method in class org.sbml.jsbml.ASTNode
 
MINUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
minus(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Subtraction.
minus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
minus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
minus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
minus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
minus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
Model - Class in org.sbml.jsbml
JSBML implementation of SBML's Model construct.
Model() - Constructor for class org.sbml.jsbml.Model
Creates a Model instance.
Model(int, int) - Constructor for class org.sbml.jsbml.Model
Creates a Model instance.
Model(Model) - Constructor for class org.sbml.jsbml.Model
Creates a Model instance from a Model.
Model(String) - Constructor for class org.sbml.jsbml.Model
Creates a Model instance from an id.
Model(String, int, int) - Constructor for class org.sbml.jsbml.Model
Creates a Model instance from an id, level and version.
model - Variable in class org.sbml.jsbml.SBMLDocument
Represents the 'model' XML subnode of a SBML file.
model - Variable in class org.sbml.jsbml.util.compilers.UnitsCompiler
The model associated to this compiler.
model - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
model - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
The given SBML model
ModelOverdeterminedException - Exception in org.sbml.jsbml.validator
This class represents an exception that is thrown when the model to be simulated is overdetermined
ModelOverdeterminedException() - Constructor for exception org.sbml.jsbml.validator.ModelOverdeterminedException
 
ModelOverdeterminedException(String) - Constructor for exception org.sbml.jsbml.validator.ModelOverdeterminedException
 
ModelOverdeterminedException(String, Throwable) - Constructor for exception org.sbml.jsbml.validator.ModelOverdeterminedException
 
ModelOverdeterminedException(Throwable) - Constructor for exception org.sbml.jsbml.validator.ModelOverdeterminedException
 
modelQualifierMap - Variable in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
The map containing all the relationships Miriam qualifier String <=> Miriam qualifier Qualifier.
ModelQualifierParser - Class in org.sbml.jsbml.xml.parsers
A ModelQualifierParser is used to parse the XML elements and attributes which have this namespace URI : http://biomodels.net/model-qualifiers/.
ModelQualifierParser() - Constructor for class org.sbml.jsbml.xml.parsers.ModelQualifierParser
Creates a ModelQualifierParser instance and initialises the modelQualifierMap.
modified - Variable in class org.sbml.jsbml.History
Last date of modification
modified - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
ModifierSpeciesReference - Class in org.sbml.jsbml
Represents the modifierSpeciesReference XML element of a SBML file.
ModifierSpeciesReference() - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
Creates a ModifierSpeciesReference instance.
ModifierSpeciesReference(int, int) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
 
ModifierSpeciesReference(ModifierSpeciesReference) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
Creates a ModifierSpeciesReference instance from a given ModifierSpeciesReference.
ModifierSpeciesReference(Species) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
Creates a ModifierSpeciesReference instance from a given Species.
ModifierSpeciesReference(String) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
 
ModifierSpeciesReference(String, int, int) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
 
MultipartPost - Class in org.sbml.jsbml.validator
Performs a Multipart HTTP post to the given URL.
MultipartPost(String) - Constructor for class org.sbml.jsbml.validator.MultipartPost
 
multiplier - Variable in class org.sbml.jsbml.Unit
Represents the 'multiplier' XML attribute of an unit element.
multiplier - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
multiplyWith(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Multiplies this ASTNode with the given node
multiplyWith(ASTNode...) - Method in class org.sbml.jsbml.ASTNode
Multiplies this ASTNode with the given nodes, i.e., all given nodes will be children of this node, whose type will be set to ASTNode.Type.TIMES.
multiplyWith(CallableSBase) - Method in class org.sbml.jsbml.ASTNode
Multiplies this ASTNode with the given SBML element.
multiplyWith(UnitDefinition) - Method in class org.sbml.jsbml.UnitDefinition
Multiplies this unit with the given unit definition, i.e., adds a clone of each unit object in the list of units of the given definition to the list of this unit.

N

name - Variable in class org.sbml.jsbml.AbstractNamedSBase
name of the SBML component (can be optional depending on the level and version).
name - Variable in class org.sbml.jsbml.ASTNode
If no NamedSBase object exists or can be identified when ASTNode.setName(String) is called, the given name is stored in this field.
name - Variable in class org.sbml.jsbml.FunctionDefinition
Represents the "name" attribute of a functionDefinition element.
name - Variable in class org.sbml.jsbml.SBO.Term
The base properties of this SBO.Term.
name - Variable in class org.sbml.jsbml.util.filters.NameFilter
The desired name for NamedSBases to be acceptable.
name - Variable in class org.sbml.jsbml.util.Option
 
name - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
name - Variable in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
Represents the localName of a SBML component to write.
name - Variable in class org.sbml.jsbml.xml.XMLTriple
 
NamedSBase - Interface in org.sbml.jsbml
Base class for all the SBML components with an id and a name (optional or not).
NamedSBaseWithDerivedUnit - Interface in org.sbml.jsbml
All objects that implement this interface can be referenced in abstract syntax trees as implemented in ASTNode.
NameFilter - Class in org.sbml.jsbml.util.filters
This filter only accepts instances of NamedSBase with the name as given in the constructor of this object.
NameFilter() - Constructor for class org.sbml.jsbml.util.filters.NameFilter
 
NameFilter(String) - Constructor for class org.sbml.jsbml.util.filters.NameFilter
 
NameFilter(String, String) - Constructor for class org.sbml.jsbml.util.filters.NameFilter
 
namespace - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
namespace - Variable in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
Represents the namespace URI of a SBML component to write.
namespaces - Variable in class org.sbml.jsbml.xml.XMLNamespaces
HashMap
namespaces - Variable in class org.sbml.jsbml.xml.XMLToken
 
namespaceURI - Static variable in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
The namespace URI of this ReadingParser.
namespaceURI - Static variable in class org.sbml.jsbml.xml.parsers.CreatorParser
The namespace URI of this ReadingParser.
namespaceURI - Static variable in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
The namespace URI of this ReadingParser.
namespaceURI - Static variable in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
The namespaceURI of this parser.
namespaceURI - Variable in class org.sbml.jsbml.xml.XMLTriple
 
namesToUnits - Variable in class org.sbml.jsbml.util.compilers.UnitsCompiler
Necessary for function definitions to remember the units of the argument list.
NEGATIVE_ININITY - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
neq(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates an ASTNode that performs a not equal comparison between two ASTNodes.
neq(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Not equal.
neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
newInstance(SBase, Class<T>) - Static method in class org.sbml.jsbml.ListOf
Helper method to initialize a new ListOf object for the given parent SBML object and with the given Class as the type of the list.
newLine - Static variable in class org.sbml.jsbml.util.StringTools
New line separator of this operating system
newLine() - Static method in class org.sbml.jsbml.util.StringTools
 
newToken(int, String) - Static method in class org.sbml.jsbml.text.parser.Token
Returns a new Token object, by default.
newToken(int) - Static method in class org.sbml.jsbml.text.parser.Token
 
next - Variable in class org.sbml.jsbml.text.parser.FormulaParser.JJCalls
 
next - Variable in class org.sbml.jsbml.text.parser.Token
A reference to the next regular (non-special) token from the input stream.
nextMetaId() - Method in class org.sbml.jsbml.SBMLDocument
 
NO_SUCH_VARIABLE_EXCEPTION_MSG - Static variable in interface org.sbml.jsbml.Assignment
Message to be displayed if no Variable can be found in the associated Model that would have the desired identifier.
nodeAdded(TreeNode) - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
 
nodeAdded(TreeNode) - Method in interface org.sbml.jsbml.util.TreeNodeChangeListener
The TreeNode passed to this method has just been added to the a containing element.
nodeRemoved(TreeNodeRemovedEvent) - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
 
nodeRemoved(TreeNodeRemovedEvent) - Method in interface org.sbml.jsbml.util.TreeNodeChangeListener
The TreeNodeRemovedEvent passed to this method provides information about the node that has been removed from a containing parent and does hence no longer belong to the SBMLDocument anymore.
nodes - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
Adjacent nodes
nodes - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
 
NodeWriter - Interface in org.sbml.jsbml.util
A writer for XML DOM nodes.
nonRDFannotation - Variable in class org.sbml.jsbml.Annotation
contains all the annotation information which are not RDF.
nonRDFAnnotation - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
NOT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
not(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
not(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
not(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
not(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
not(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
not(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
notes - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
notesBuffer - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
notesReader - Static variable in class org.sbml.jsbml.xml.XMLNode
This reader is used to parse all notes-Strings.
notesXMLNode - Variable in class org.sbml.jsbml.AbstractSBase
notes of the SBML component.
notifyChildChange(TreeNode, TreeNode) - Method in class org.sbml.jsbml.AbstractSBase
 
notifyChildChange(TreeNode, TreeNode) - Method in class org.sbml.jsbml.AbstractTreeNode
This method is called when one child has been swapped with another one and can be used to check certain properties of the resulting changed tree.
NotImplementedException - Error in org.sbml.jsbml.util
This kind of Exception indicates currently missing functionality in JSBML.
NotImplementedException() - Constructor for error org.sbml.jsbml.util.NotImplementedException
 
NotImplementedException(String) - Constructor for error org.sbml.jsbml.util.NotImplementedException
 
NotImplementedException(Throwable) - Constructor for error org.sbml.jsbml.util.NotImplementedException
 
NotImplementedException(String, Throwable) - Constructor for error org.sbml.jsbml.util.NotImplementedException
 
NUMBER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
numerator - Variable in class org.sbml.jsbml.ASTNode
This value stores the numerator if this.isRational() is true, or the value of an integer if this.isInteger() is true.
numerator - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 

O

offset - Variable in class org.sbml.jsbml.Unit
Deprecated.
the offset attribute should no longer be used.
offset - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
omitXMLDeclaration - Variable in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
If true no XML declaration will be written into the MathML output, otherwise the XML version will appear at the beginning of the output.
omitXMLDeclaration - Variable in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
If true no XML declaration will be written into the MathML output, otherwise the XML version will appear at the beginning of the output.
OPEN_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
OPERATION_FAILED - Static variable in class org.sbml.jsbml.JSBML
 
OPERATION_SUCCESS - Static variable in class org.sbml.jsbml.JSBML
 
Option - Class in org.sbml.jsbml.util
Stores the options sent by the SBML online validator.
Option() - Constructor for class org.sbml.jsbml.util.Option
 
Option(String, String) - Constructor for class org.sbml.jsbml.util.Option
 
options - Variable in class org.sbml.jsbml.SBMLErrorLog
 
OR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
or(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
or - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
OrFilter - Class in org.sbml.jsbml.util.filters
This filter accepts an item if at least one of its filters accepts the given item.
OrFilter() - Constructor for class org.sbml.jsbml.util.filters.OrFilter
 
OrFilter(Filter...) - Constructor for class org.sbml.jsbml.util.filters.OrFilter
 
org.sbml.jsbml - package org.sbml.jsbml
Pure Java implementation of the data structures to represent all SBML constructs.
org.sbml.jsbml.resources - package org.sbml.jsbml.resources
Contains classes to deal with and to manage non-Java resources, such as configuration files.
org.sbml.jsbml.text.parser - package org.sbml.jsbml.text.parser
Provides classes to parse formula Strings and to convert these into abstract syntax tree data structures.
org.sbml.jsbml.util - package org.sbml.jsbml.util
A collection of handy utilities when working with JSBML classes, such as classes for String manipulation or mathematical operations.
org.sbml.jsbml.util.compilers - package org.sbml.jsbml.util.compilers
The classes in this package can be used to evaluate the information represented by abstract syntax trees (ASTNode objects).
org.sbml.jsbml.util.filters - package org.sbml.jsbml.util.filters
Filter are useful to decide whether or not to accept a certain item.
org.sbml.jsbml.validator - package org.sbml.jsbml.validator
This package provides methods to validate the content of SBML models, whether given in a file or as a data structure.
org.sbml.jsbml.xml - package org.sbml.jsbml.xml
This package provides classes and methods to deal with SBML in form of XML elements, i.e., here you can find parsers and writers for SBML and also elements to define XML nodes to be used for notes or annotations.
org.sbml.jsbml.xml.parsers - package org.sbml.jsbml.xml.parsers
Contains classes that implement ReaderParser and/or WritingParser to read or write some specific parts of an SBML file.
org.sbml.jsbml.xml.stax - package org.sbml.jsbml.xml.stax
Contains classes that use the Streaming API for XML (StAX) to read or write an SBML file.
org.sbml.jsbml.xml.xstream.converter - package org.sbml.jsbml.xml.xstream.converter
Contains classes that uses the XStream to read or write XML.
organisation - Variable in class org.sbml.jsbml.Creator
Organisation name of the creator.
organisation - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
orReplacement - Variable in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
 
outside - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
outsideID - Variable in class org.sbml.jsbml.Compartment
Deprecated.
OverdeterminationValidator - Class in org.sbml.jsbml.validator
This class creates a bipartite graph and a matching for the given model using the algorithm by Hopcroft and Karp (1973).
OverdeterminationValidator(Model) - Constructor for class org.sbml.jsbml.validator.OverdeterminationValidator
Creates a new OverdeterminationValidator for the given model
OverdeterminationValidator.InnerNode<T extends SBase> - Class in org.sbml.jsbml.validator
This class represents an inner node in the bipartite graph, e.g., a varibale or an reaction
OverdeterminationValidator.InnerNode(T) - Constructor for class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
Creates a new inner node
OverdeterminationValidator.Node<S> - Interface in org.sbml.jsbml.validator
This Interface represents a node in the bipartite graph
OverdeterminationValidator.StartNode<T extends SBase> - Class in org.sbml.jsbml.validator
This class represents the start node in the bipartite graph
OverdeterminationValidator.StartNode() - Constructor for class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
Creates a new start node
OverdeterminationValidator.TerminalNode<T extends SBase> - Class in org.sbml.jsbml.validator
This class represents the end node in the bipartite graph
OverdeterminationValidator.TerminalNode() - Constructor for class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
Creates a new terminal node

P

packageParsers - Variable in class org.sbml.jsbml.xml.stax.SBMLReader
Contains all the relationships namespace URI <=> ReadingParser implementation classes.
packageParsers - Variable in class org.sbml.jsbml.xml.stax.SBMLWriter
contains all the relationships name space URI <=> WritingParser class.
Parameter - Class in org.sbml.jsbml
Represents a globally valid parameter in the model, i.e., a variable that may change during a simulation or that provides a constant value.
Parameter() - Constructor for class org.sbml.jsbml.Parameter
Creates a Parameter instance.
Parameter(int, int) - Constructor for class org.sbml.jsbml.Parameter
Creates a Parameter instance from an id, level and version.
Parameter(LocalParameter) - Constructor for class org.sbml.jsbml.Parameter
This constructor allows the creation of a global Parameter based on a LocalParameter.
Parameter(Parameter) - Constructor for class org.sbml.jsbml.Parameter
Creates a Parameter instance from a given Parameter.
Parameter(String) - Constructor for class org.sbml.jsbml.Parameter
 
Parameter(String, int, int) - Constructor for class org.sbml.jsbml.Parameter
 
parent - Variable in class org.sbml.jsbml.AbstractTreeNode
The parent element of this Annotation.
parentSBMLObject - Variable in class org.sbml.jsbml.ASTNode
The container that holds this ASTNode.
parentSBMLObject - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
parse() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
parse(InputStream, DefaultHandler, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
Parses the content of a byte stream as XML, using a nonvalidating parser and the specified SAX2 default event handler.
parse(InputStream, DefaultHandler, Object[]) - Method in class org.sbml.jsbml.util.JAXPFacade
Parses the content of a byte stream as XML, using a validating parser and the specified SAX2 default event handler.
parse(Reader, DefaultHandler, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
Parses the content of a character stream as XML, using a nonvalidating parser and the specified SAX2 default event handler.
parse(Reader, DefaultHandler, Object[]) - Method in class org.sbml.jsbml.util.JAXPFacade
Parses the content of a character stream as XML, using a validating parser and the specified SAX2 default event handler.
parse(InputStream, DefaultHandler, boolean) - Method in interface org.sbml.jsbml.util.SAX2Parser
Parses the content of a byte stream as XML, using a nonvalidating parser and the specified SAX2 default event handler.
parse(InputStream, DefaultHandler, Object[]) - Method in interface org.sbml.jsbml.util.SAX2Parser
Parses the content of a byte stream as XML, using a validating parser and the specified SAX2 default event handler.
parse(Reader, DefaultHandler, boolean) - Method in interface org.sbml.jsbml.util.SAX2Parser
Parses the content of a character stream as XML, using a nonvalidating parser and the specified SAX2 default event handler.
parse(Reader, DefaultHandler, Object[]) - Method in interface org.sbml.jsbml.util.SAX2Parser
Parses the content of a character stream as XML, using a validating parser and the specified SAX2 default event handler.
ParseException - Exception in org.sbml.jsbml.text.parser
This exception is thrown when parse errors are encountered.
ParseException(Token, int[][], String[]) - Constructor for exception org.sbml.jsbml.text.parser.ParseException
This constructor is used by the method "generateParseException" in the generated parser.
ParseException() - Constructor for exception org.sbml.jsbml.text.parser.ParseException
The following constructors are for use by you for whatever purpose you can think of.
ParseException(String) - Constructor for exception org.sbml.jsbml.text.parser.ParseException
Constructor with message.
parseFormula(String) - Static method in class org.sbml.jsbml.ASTNode
Parses a text-string mathematical formula and returns a representation as an Abstract Syntax Tree.
parseFormula(String) - Static method in class org.sbml.jsbml.JSBML
Parses a text-string mathematical formula and returns a representation as an Abstract Syntax Tree.
parseSBMLBoolean(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into a boolean following the rules of the SBML specifications, section 3.1.2.
parseSBMLDouble(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into a double number following the rules of the SBML specifications, section 3.1.5.
parseSBMLInt(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into an int number following the rules of the SBML specifications, section 3.1.3.
parseSBMLShort(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into an short number following the rules of the SBML specifications, section 3.1.3.
paths - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
A list of all paths of a certain length in the graph
pattern - Variable in class org.sbml.jsbml.util.filters.CVTermFilter
 
persistent - Variable in class org.sbml.jsbml.Trigger
 
persistent - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
piecewise(ASTNode, ASTNode...) - Static method in class org.sbml.jsbml.ASTNode
Creates a piecewise ASTNode.
piecewise(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
piecewiseMap - Variable in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
 
plus(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Adds a given node to this node.
plus(CallableSBase) - Method in class org.sbml.jsbml.ASTNode
Adds an SBML element to this node.
plus(double) - Method in class org.sbml.jsbml.ASTNode
Adds a number to this node.
plus(int) - Method in class org.sbml.jsbml.ASTNode
Adds an integer number to this node.
PLUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
plus(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
POSITIVE_INFINITY - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
pow(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates a power ASTNode.
pow(ASTNode, double) - Static method in class org.sbml.jsbml.ASTNode
Creates a power ASTNode.
pow(ASTNode, int) - Static method in class org.sbml.jsbml.ASTNode
Creates a power ASTNode.
pow(MathContainer, CallableSBase, CallableSBase) - Static method in class org.sbml.jsbml.ASTNode
Raises the given basis by the power of the given exponent.
pow(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
pow(Object, Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Returns the basis to the power of the exponent as StringBuffer.
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
pow(Object, Object) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula
Returns the basis to the power of the exponent as StringBuffer.
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
pow(ASTNodeValue, ASTNodeValue) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
POWER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
prefix - Static variable in class org.sbml.jsbml.SBO
the prefix of all SBO ids.
prefix - Variable in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
Represents the prefix of a SBML component to write.
prefix - Variable in class org.sbml.jsbml.xml.XMLTriple
 
prependChild(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Adds the given node as a child of this ASTNode.
prevCharIsCR - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
prevCharIsLF - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
previosParent - Variable in class org.sbml.jsbml.util.TreeNodeRemovedEvent
The previous parent node in the tree, i.e., the node that was the parent of the deleted node (see TreeNodeRemovedEvent.getSource()) before the deletion.
previousElement - Variable in class org.sbml.jsbml.xml.parsers.DatesParser
Stores the localName of the last element read by this parser.
previousElements - Variable in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
A map containing the history of the previous element within a RDF node this parser has been read.
Primary() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
print(InputStream, OutputStream) - Static method in class org.sbml.jsbml.validator.SBMLValidator
 
print(Reader, Writer) - Static method in class org.sbml.jsbml.validator.SBMLValidator
 
printChildren(SBO.Term, String) - Static method in class org.sbml.jsbml.SBO
Prints to the console all the sub-tree of terms, starting from the children of the given parent term.
printErrors() - Method in class org.sbml.jsbml.SBMLDocument
 
printErrors(PrintStream) - Method in class org.sbml.jsbml.SBMLDocument
 
printNameIfAvailable - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Important for LaTeX export to decide whether the name or the id of a NamedSBase should be printed.
printTerm(SBO.Term) - Static method in class org.sbml.jsbml.SBO.Term
Returns a String representing a term the same way as in the OBO file.
printUnits(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
Returns a string that expresses the unit definition represented by this UnitDefinition object.
printUnits(UnitDefinition, boolean) - Static method in class org.sbml.jsbml.UnitDefinition
Returns a string that expresses the unit definition represented by this UnitDefinition object.
printValueAndUnit() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
priority - Variable in class org.sbml.jsbml.Event
Represents the priority sub-element of an event.
Priority - Class in org.sbml.jsbml
This class represents the priority element in SBML.
Priority() - Constructor for class org.sbml.jsbml.Priority
 
Priority(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Priority
 
Priority(int, int) - Constructor for class org.sbml.jsbml.Priority
 
Priority(Priority) - Constructor for class org.sbml.jsbml.Priority
 
priority - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AnnotationParser
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.CreatorParser
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.DatesParser
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
 
processAttribute(String, String, String, String, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the XML attribute and modify 'contextObject' in consequence.
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.StringParser
 
processAttribute(String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.VCardParser
 
processAttributes(Iterator<Attribute>, QName, Stack<Object>, ReadingParser, boolean, boolean, int, boolean) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Process Attributes of the current element on the stack.
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.AnnotationParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.CreatorParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.DatesParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
 
processCharactersOf(String, String, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the text of a XML element and modify 'contextObject' in consequence.
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.StringParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.VCardParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.AnnotationParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.CreatorParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.DatesParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
Checks if the sbmlDocument and all the SBML components have a valid rdf:about value.
processEndDocument(SBMLDocument) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the end of the document.
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.StringParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.VCardParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AnnotationParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.CreatorParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.DatesParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
 
processEndElement(String, String, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the end of the element 'elementName'.
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.StringParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.VCardParser
 
processEndElement(QName, Boolean, Boolean, Boolean, int, int, ReadingParser, Stack<Object>, boolean, int, boolean) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Process the end of an element.
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AnnotationParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.CreatorParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.DatesParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the namespace and modify the contextObject in consequence.
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.StringParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.VCardParser
 
processNamespaces(Iterator<Namespace>, QName, Stack<Object>, ReadingParser, boolean) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Process Namespaces of the current element on the stack.
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AnnotationParser
 
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.BiologicalQualifierParser
 
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.CreatorParser
 
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.DatesParser
 
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.ModelQualifierParser
 
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
 
processStartElement(String, String, boolean, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the XML element and modify 'contextObject' in consequence.
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.StringParser
 
processStartElement(String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.VCardParser
 
processStartElement(StartElement, QName, Boolean, Stack<Object>, boolean, int, boolean) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Process a StartElement event.
processUnitsMap(Map<String, UnitDefinition>, Model, String) - Static method in class org.sbml.jsbml.util.SubModel
 
processUnitsMap(Map<String, UnitDefinition>, Model, KineticLaw) - Static method in class org.sbml.jsbml.util.SubModel
 
programName - Variable in class org.sbml.jsbml.SBMLWriter
The name of the program that has been used to create an SBML String representation (possibly in a File) with the help of JSBML.
programVersion - Variable in class org.sbml.jsbml.SBMLWriter
The version of the program using JSBML to serialize a model in an SBML String or File.
PROPERTY_UNDEFINED_EXCEPTION_MSG - Static variable in exception org.sbml.jsbml.PropertyNotAvailableException
Message to indicate that a certain property cannot be set for the current level/version combination.
PROPERTY_UNDEFINED_EXCEPTION_MSG - Static variable in exception org.sbml.jsbml.PropertyUndefinedError
Message to indicate that a certain property has not been set for the current SBase in its level/version combination.
propertyChange(PropertyChangeEvent) - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
 
PropertyException - Exception in org.sbml.jsbml
This is an error of an undefined property or value for a propterty in some instance of SBase.
PropertyException() - Constructor for exception org.sbml.jsbml.PropertyException
 
PropertyException(String) - Constructor for exception org.sbml.jsbml.PropertyException
 
PropertyNotAvailableException - Exception in org.sbml.jsbml
An error that indicates that a property of an SBase is not available for the current SBML Level/Version combination.
PropertyNotAvailableException(String, SBase) - Constructor for exception org.sbml.jsbml.PropertyNotAvailableException
 
PropertyUndefinedError - Exception in org.sbml.jsbml
This PropertyException indicates that the value belonging to a mandatory property, for which there is no default value, has not been declared by the user.
PropertyUndefinedError(String, SBase) - Constructor for exception org.sbml.jsbml.PropertyUndefinedError
 

Q

qualifier - Variable in class org.sbml.jsbml.CVTerm
Represents the MIRIAM qualifier node in the annotation node of a SBML component.
qualifier - Variable in class org.sbml.jsbml.util.filters.CVTermFilter
 
qualifier - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
Quantity - Interface in org.sbml.jsbml
A quantity is an element that represents a value with an associated unit that can be addressed through the identifier or name attribute of this element.
QuantityWithUnit - Class in org.sbml.jsbml
This object represents an element with identifier and name, a value, and a defined unit.
QuantityWithUnit() - Constructor for class org.sbml.jsbml.QuantityWithUnit
 
QuantityWithUnit(int, int) - Constructor for class org.sbml.jsbml.QuantityWithUnit
 
QuantityWithUnit(QuantityWithUnit) - Constructor for class org.sbml.jsbml.QuantityWithUnit
 
QuantityWithUnit(String) - Constructor for class org.sbml.jsbml.QuantityWithUnit
 
QuantityWithUnit(String, int, int) - Constructor for class org.sbml.jsbml.QuantityWithUnit
 
QuantityWithUnit(String, String, int, int) - Constructor for class org.sbml.jsbml.QuantityWithUnit
 

R

R - Static variable in class org.sbml.jsbml.util.Maths
Universal gas constant of 8.314472 J ⋅ mol-1 ⋅ K-1 according to D.
raiseByThePowerOf(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Raises this ASTNode by the power of the value of the given node.
raiseByThePowerOf(CallableSBase) - Method in class org.sbml.jsbml.ASTNode
Raises this ASTNode by the power of the value of this named SBase object.
raiseByThePowerOf(double) - Method in class org.sbml.jsbml.ASTNode
Raises this ASTNode by the power of the given number.
raiseByThePowerOf(double) - Method in class org.sbml.jsbml.UnitDefinition
Raises this unit definition by the power of the given exponent, i.e., the exponents of every unit contained by this unit definition are multiplied with the given exponent.
RateRule - Class in org.sbml.jsbml
Represents the rateRule XML element of a SBML file.
RateRule() - Constructor for class org.sbml.jsbml.RateRule
Creates a RateRule instance.
RateRule(ASTNode, int, int) - Constructor for class org.sbml.jsbml.RateRule
 
RateRule(ASTNode, Parameter) - Constructor for class org.sbml.jsbml.RateRule
 
RateRule(ASTNode, Variable) - Constructor for class org.sbml.jsbml.RateRule
 
RateRule(int, int) - Constructor for class org.sbml.jsbml.RateRule
Creates a RateRule instance from a given RateRule.
RateRule(Parameter) - Constructor for class org.sbml.jsbml.RateRule
 
RateRule(Parameter, ASTNode) - Constructor for class org.sbml.jsbml.RateRule
 
RateRule(RateRule) - Constructor for class org.sbml.jsbml.RateRule
 
RateRule(Variable) - Constructor for class org.sbml.jsbml.RateRule
Creates a RateRule instance from a given Symbol.
RateRule(ExplicitRule) - Constructor for class org.sbml.jsbml.RateRule
Creates a RateRule instance cloned from the given ExplicitRule
RateRule(Variable, ASTNode) - Constructor for class org.sbml.jsbml.RateRule
Creates a RateRule instance from a given Symbol and ASTNode.
rdfAnnotationNamespaces - Variable in class org.sbml.jsbml.Annotation
contains all the name spaces of the matching XML RDF annotation node
rdfAnnotationNamespaces - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
RDFAnnotationParser - Class in org.sbml.jsbml.xml.parsers
A RDFAnnotationParser is used to parser the subNodes of an annotation which have the namespace URI : "http://www.w3.org/1999/02/22-rdf-syntax-ns#".
RDFAnnotationParser() - Constructor for class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
 
reactants - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
A set with the ids of all reactants in the model
Reaction - Class in org.sbml.jsbml
Represents the reaction XML element of a SBML file.
Reaction() - Constructor for class org.sbml.jsbml.Reaction
Creates a Reaction instance.
Reaction(int, int) - Constructor for class org.sbml.jsbml.Reaction
 
Reaction(Reaction) - Constructor for class org.sbml.jsbml.Reaction
Creates a Reaction instance from a given reaction.
Reaction(String) - Constructor for class org.sbml.jsbml.Reaction
 
Reaction(String, int, int) - Constructor for class org.sbml.jsbml.Reaction
Creates a Reaction instance from an id, level and version.
reactionEquation(Reaction) - Method in class org.sbml.jsbml.util.compilers.HTMLFormula
 
read(File) - Static method in class org.sbml.jsbml.SBMLReader
Factory method for reading SBML from a given File.
read(File, TreeNodeChangeListener) - Static method in class org.sbml.jsbml.SBMLReader
Factory method for reading SBML from a given File.
read(InputStream) - Static method in class org.sbml.jsbml.SBMLReader
Factory method for reading SBML from a given InputStream.
read(String) - Static method in class org.sbml.jsbml.SBMLReader
Factory method for reading SBML from given XML code in its String representation.
readAttribute(String, String, String) - Method in class org.sbml.jsbml.AbstractMathContainer
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.AbstractNamedSBase
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.AbstractSBase
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.Annotation
Sets the about instance of this object if the attributeName is equal to 'about'.
readAttribute(String, String, String) - Method in class org.sbml.jsbml.Compartment
 
readAttribute(String, String, String, String) - Method in class org.sbml.jsbml.Creator
Returns true if the XML attribute is known by this Creator.
readAttribute(String, String, String, String) - Method in class org.sbml.jsbml.CVTerm
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.Event
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.EventAssignment
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ExplicitRule
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.FunctionDefinition
 
readAttribute(String, String, String, String) - Method in class org.sbml.jsbml.History
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.InitialAssignment
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.KineticLaw
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ListOf
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.LocalParameter
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.Model
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.Parameter
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.Reaction
 
readAttribute(String, String, String) - Method in interface org.sbml.jsbml.SBase
If the attribute is an id or name attribute, it will set the id or name of this object with the value of the XML attribute ('value').
readAttribute(String, String, String) - Method in class org.sbml.jsbml.SBMLDocument
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.SimpleSpeciesReference
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.Species
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.SpeciesReference
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.Trigger
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.Unit
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
 
readChar() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Read a character.
ReadingParser - Interface in org.sbml.jsbml.xml.parsers
The interface to implement for the SBML parsers reading SBML files.
readMathML(String, TreeNodeChangeListener) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads a mathML String into an ASTNode.
readMathML(String) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
 
readMathMLFromString(String) - Static method in class org.sbml.jsbml.ASTNode
Reads the MathML from the given XML string.
readMathMLFromString(String) - Static method in class org.sbml.jsbml.JSBML
Reads the MathML from the given XML string, constructs a corresponding abstract syntax tree, and returns a pointer to the root of the tree.
readNotes(String, TreeNodeChangeListener) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads a notes XML String into an XMLNode.
readNotes(String) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
 
readProperties(String) - Static method in class org.sbml.jsbml.resources.Resource
 
readSBML(String) - Static method in class org.sbml.jsbml.JSBML
Reads an SBML document from the given file.
readSBML(File, TreeNodeChangeListener) - Method in class org.sbml.jsbml.SBMLReader
 
readSBML(File) - Method in class org.sbml.jsbml.SBMLReader
Reads an SBML document from a File.
readSBML(String) - Method in class org.sbml.jsbml.SBMLReader
Reads an SBML document from a file.
readSBML(File) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
 
readSBML(File, TreeNodeChangeListener) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads a SBML String from the given file.
readSBML(String) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads SBML from a given file.
readSBML(XMLEventReader, TreeNodeChangeListener) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads an SBMLDocument from the given XMLEventReader
readSBML(XMLEventReader) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
 
readSBMLFile(String) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads the SBML file 'fileName' and creates/initialises a SBMLDocument instance.
readSBMLFromFile(String) - Static method in class org.sbml.jsbml.JSBML
Reads an SBML document from the given file.
readSBMLFromFile(String) - Method in class org.sbml.jsbml.SBMLReader
Reads an SBML document from a file.
readSBMLFromStream(InputStream) - Method in class org.sbml.jsbml.SBMLReader
Reads an SBML document from a data stream.
readSBMLFromStream(InputStream, TreeNodeChangeListener) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads a SBML document from the given stream.
readSBMLFromStream(InputStream) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
 
readSBMLFromString(String) - Static method in class org.sbml.jsbml.JSBML
Reads an SBML document from a string assumed to be in XML format.
readSBMLFromString(String) - Method in class org.sbml.jsbml.SBMLReader
Reads an SBML document from the given XML string.
readSBMLFromString(String, TreeNodeChangeListener) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads a SBML model from the given XML String.
readSBMLFromString(String) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
 
readXMLFromStream(InputStream, TreeNodeChangeListener) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads a XML document from the given stream.
readXMLFromString(String, TreeNodeChangeListener) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads an XML String that should the part of a SBML model.
readXMLFromXMLEventReader(XMLEventReader, TreeNodeChangeListener) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
Reads an XML document from the given XMLEventReader.
REAL_FORMAT - Static variable in class org.sbml.jsbml.util.StringTools
 
realFormat - Variable in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
Formats the real number in a valid way for mathML.
reduceToBinary() - Method in class org.sbml.jsbml.ASTNode
Reduces this ASTNode to a binary tree, e.g., if the formula in this ASTNode is and(x, y, z) then the formula of the reduced node would be and(and(x, y), z).
references(ListOf<? extends SimpleSpeciesReference>, Species) - Method in class org.sbml.jsbml.Reaction
Checks whether the given list references the given species.
refersTo(String) - Method in class org.sbml.jsbml.ASTNode
Returns true if this node or one of its descendants contains some identifier with the given id.
registerChild(SBase) - Method in class org.sbml.jsbml.AbstractSBase
 
registerChild(SBase) - Method in interface org.sbml.jsbml.SBase
Sets this object as SBML parent of 'sbase'.
registerId(KineticLaw, LocalParameter, boolean, boolean) - Method in class org.sbml.jsbml.Model
Registration of LocalParameter instances in the Model.
registerId(NamedSBase, boolean) - Method in class org.sbml.jsbml.Model
Registers the identifier of a NamedSBase and its associated object in this Model.
registerId(UniqueNamedSBase, boolean) - Method in class org.sbml.jsbml.Model
 
registerId(UnitDefinition, boolean) - Method in class org.sbml.jsbml.Model
Registers the identifier and the corresponding UnitDefinition itself in this Model.
registerIds(SBase, SBase, boolean, boolean) - Method in class org.sbml.jsbml.Model
Registers the given element in this Model.
registerLocalParameter(LocalParameter, boolean) - Method in class org.sbml.jsbml.KineticLaw
 
registerMetaId(SBase, boolean) - Method in class org.sbml.jsbml.SBMLDocument
Saves or removes the given meta identifier in this SBMLDocument's SBMLDocument.mappingFromMetaId2SBase.
registerMetaIds(SBase, boolean, boolean) - Method in class org.sbml.jsbml.SBMLDocument
Collects all meta identifiers of this AbstractSBase and all of its sub-elements if recursively is true.
ReInit(InputStream) - Method in class org.sbml.jsbml.text.parser.FormulaParser
Reinitialise.
ReInit(InputStream, String) - Method in class org.sbml.jsbml.text.parser.FormulaParser
Reinitialise.
ReInit(Reader) - Method in class org.sbml.jsbml.text.parser.FormulaParser
Reinitialise.
ReInit(FormulaParserTokenManager) - Method in class org.sbml.jsbml.text.parser.FormulaParser
Reinitialise.
ReInit(SimpleCharStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
Reinitialise parser.
ReInit(SimpleCharStream, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
Reinitialise parser.
ReInit(Reader, int, int, int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Reinitialise.
ReInit(Reader, int, int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Reinitialise.
ReInit(Reader) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream, String, int, int, int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream, int, int, int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream, String) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream, String, int, int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Reinitialise.
ReInit(InputStream, int, int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
Reinitialise.
ReInitRounds() - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
 
relation(ASTNode, String, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
relation(ASTNode, String, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Creates a relation between two ASTNodes.
relational(ASTNode.Type, ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates a relational ASTNode of the given type with the two given children left and right.
remove(int) - Method in class org.sbml.jsbml.ListOf
 
remove(NamedSBase) - Method in class org.sbml.jsbml.ListOf
Removes a NamedSBase according to its unique id.
remove(Object) - Method in class org.sbml.jsbml.ListOf
 
remove(String) - Method in class org.sbml.jsbml.ListOf
Specialized method to remove a named SBase according to its unique id.
remove(ListOf<? extends SimpleSpeciesReference>, String) - Method in class org.sbml.jsbml.Reaction
 
remove(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
Removes an attribute with the given index from this XMLAttributes set.
remove(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Removes an attribute with the given local name and namespace URI from this XMLAttributes set.
remove(String) - Method in class org.sbml.jsbml.xml.XMLAttributes
Removes an attribute with the given local name from this XMLAttributes set.
remove(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLAttributes
Removes an attribute with the given XMLTriple from this XMLAttributes set.
remove(int) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Removes an XML Namespace stored in the given position of this list.
remove(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
Removes an XML Namespace with the given prefix.
removeAll(Collection<?>) - Method in class org.sbml.jsbml.ListOf
 
removeAll(Filter) - Method in class org.sbml.jsbml.ListOf
Removes all elements from this list that fulfill the filter property of the given filter.
removeAllTreeNodeChangeListeners() - Method in class org.sbml.jsbml.AbstractTreeNode
 
removeAllTreeNodeChangeListeners() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
Removes all SBase change listeners from this element.
removeAttr(int) - Method in class org.sbml.jsbml.xml.XMLToken
Removes an attribute with the given index from the attribute set in this XMLToken.
removeAttr(String) - Method in class org.sbml.jsbml.xml.XMLToken
Removes an attribute with the given local name from the attribute set in this XMLToken.
removeAttr(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
Removes an attribute with the given local name and namespace URI from the attribute set in this XMLToken.
removeAttr(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLToken
Removes an attribute with the given XMLTriple from the attribute set in this XMLToken.
removeChild(int) - Method in class org.sbml.jsbml.ASTNode
Removes child n of this ASTNode.
removeChild(long) - Method in class org.sbml.jsbml.xml.XMLNode
Removes the nth child of this XMLNode and returns the removed node.
removeChildren() - Method in class org.sbml.jsbml.xml.XMLNode
Removes all children from this node.
removeCompartment(int) - Method in class org.sbml.jsbml.Model
Removes the i-th Compartment of the Model.
removeCompartment(String) - Method in class org.sbml.jsbml.Model
Removes the Compartment of the Model with 'id' as id.
removeCompartmentType(int) - Method in class org.sbml.jsbml.Model
Deprecated.
removeCompartmentType(String) - Method in class org.sbml.jsbml.Model
Deprecated.
removeConstraint(int) - Method in class org.sbml.jsbml.Model
Removes the n-th Constraint of the Model.
removeCreator(int) - Method in class org.sbml.jsbml.History
If there is no ith Creator, it returns null.
removeEvent(int) - Method in class org.sbml.jsbml.Model
Removes the n-th Event of the Model.
removeEvent(String) - Method in class org.sbml.jsbml.Model
Removes the Event of the Model with 'id' as id.
removeEventAssignment(int) - Method in class org.sbml.jsbml.Event
 
removeEventAssignment(String) - Method in class org.sbml.jsbml.Event
 
removeFilter(Filter) - Method in class org.sbml.jsbml.util.filters.AndFilter
 
removeFirst(Filter) - Method in class org.sbml.jsbml.ListOf
Removes the first element from this list that fulfills the filter property of the given filter.
removeFunctionDefinition(int) - Method in class org.sbml.jsbml.Model
Removes the n-th FunctionDefinition of the Model.
removeFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
Removes the FunctionDefinition of the Model with 'id' as id.
removeInitialAssignment(int) - Method in class org.sbml.jsbml.Model
Removes the n-th InitialAssignment of the Model.
removeLocalParameter(int) - Method in class org.sbml.jsbml.KineticLaw
Removes the ith LocalParameter from this object.
removeLocalParameter(LocalParameter) - Method in class org.sbml.jsbml.KineticLaw
Removes the LocalParameter 'p' from the KineticLaw.listOfLocalParameters of this KineticLaw according to its 'id'.
removeLocalParameter(String) - Method in class org.sbml.jsbml.KineticLaw
Removes a LocalParameter from this object based on its 'id'.
removeModifiedDate(int) - Method in class org.sbml.jsbml.History
If there is no ith modified Date, it returns null.
removeModifier(int) - Method in class org.sbml.jsbml.Reaction
Removes the nth modifier species (ModifierSpeciesReference object) in the list of modifiers in this Reaction and returns it.
removeModifier(ModifierSpeciesReference) - Method in class org.sbml.jsbml.Reaction
Removes the ModifierSpeciesReference 'modspecref' from this Reaction.
removeModifier(String) - Method in class org.sbml.jsbml.Reaction
Removes the modifier species (ModifierSpeciesReference object) having the given 'species' attribute in the list of modifiers in this Reaction and returns it.
removeNamespace(String) - Method in class org.sbml.jsbml.AbstractSBase
 
removeNamespace - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
removeNamespace(int) - Method in class org.sbml.jsbml.xml.XMLToken
Removes an XML Namespace stored in the given position of the XMLNamespaces of this XMLToken.
removeNamespace(String) - Method in class org.sbml.jsbml.xml.XMLToken
Removes an XML Namespace with the given prefix.
removeParameter(int) - Method in class org.sbml.jsbml.KineticLaw
removeParameter(Parameter) - Method in class org.sbml.jsbml.KineticLaw
removeParameter(String) - Method in class org.sbml.jsbml.KineticLaw
removeParameter(int) - Method in class org.sbml.jsbml.Model
Removes the n-th Parameter of the Model.
removeParameter(Parameter) - Method in class org.sbml.jsbml.Model
Removes the Parameter 'parameter' from this Model.
removeParameter(String) - Method in class org.sbml.jsbml.Model
Removes the Parameter of the Model with 'id' as id.
removeProduct(int) - Method in class org.sbml.jsbml.Reaction
Removes the nth product species (SpeciesReference object) in the list of products in this Reaction and returns it.
removeProduct(SpeciesReference) - Method in class org.sbml.jsbml.Reaction
Removes the SpeciesReference 'modspecref' from the listOfProducts of this Reaction.
removeProduct(String) - Method in class org.sbml.jsbml.Reaction
Removes the product species (SpeciesReference object) having the given 'species' attribute in the list of products in this Reaction and returns it.
removeReactant(int) - Method in class org.sbml.jsbml.Reaction
Removes the nth reactant species (SpeciesReference object) in the list of reactants in this Reaction and returns it.
removeReactant(SpeciesReference) - Method in class org.sbml.jsbml.Reaction
Removes the SpeciesReference 'modspecref' from the listOfReactants of this Reaction.
removeReactant(String) - Method in class org.sbml.jsbml.Reaction
Removes the reactant species (SpeciesReference object) having the given 'species' attribute in the list of reactants in this Reaction and returns it.
removeReaction(int) - Method in class org.sbml.jsbml.Model
Removes the n-th Reaction of the Model.
removeReaction(Reaction) - Method in class org.sbml.jsbml.Model
Removes a reaction from the model.
removeReaction(String) - Method in class org.sbml.jsbml.Model
Removes the Reaction of the Model with 'id' as id.
removeResource(String) - Method in class org.sbml.jsbml.CVTerm
Removes a resource from the CVTerm.
removeResource(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
Removes an attribute with the given index from this XMLAttributes set.
removeRule(int) - Method in class org.sbml.jsbml.Model
Removes the i-th Rule of the Model.
removeRule(String) - Method in class org.sbml.jsbml.Model
Removes the Rule of the Model with 'variableId' as variable.
removeScale(Unit) - Static method in class org.sbml.jsbml.Unit
Manipulates the attributes of the Unit to express the unit with the value of the scale attribute reduced to zero.
removeScale() - Method in class org.sbml.jsbml.Unit
Manipulates the attributes of the Unit to express the unit with the value of the scale attribute reduced to zero.
removeSpecies(int) - Method in class org.sbml.jsbml.Model
Removes the i-th Species of the Model.
removeSpecies(Species) - Method in class org.sbml.jsbml.Model
Removes a species from the model.
removeSpecies(String) - Method in class org.sbml.jsbml.Model
Removes the Species of the Model with 'id' as id.
removeSpeciesType(int) - Method in class org.sbml.jsbml.Model
Deprecated.
removeSpeciesType(String) - Method in class org.sbml.jsbml.Model
Deprecated.
removeTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.AbstractTreeNode
 
removeTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
 
removeTreeNodeChangeListener(TreeNodeChangeListener) - Method in interface org.sbml.jsbml.SBase
Removes the given TreeNodeChangeListener from this element.
removeTreeNodeChangeListener(TreeNodeChangeListener) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
Removes recursively the given change listener from this element.
removeTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
Removes the given change listener from this element.
removeUnit(int) - Method in class org.sbml.jsbml.UnitDefinition
Removes the nth Unit object from this UnitDefinition object and returns a pointer to it.
removeUnitDefinition(int) - Method in class org.sbml.jsbml.Model
Removes the n-th UnitDefinition of the Model.
removeUnitDefinition(String) - Method in class org.sbml.jsbml.Model
Removes the UnitDefinition of the Model with 'id' as id.
removeUnitDefinition(UnitDefinition) - Method in class org.sbml.jsbml.Model
Removes a UnitDefinition of the Model.
removeUnneccessaryElements(Model, Object) - Method in interface org.sbml.jsbml.SBMLOutputConverter
Deletes those elements that are not referenced or not needed within the model.
reorder(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
Orders alphabetically the Unit objects within the ListOfUnits of a UnitDefinition.
replaceArgument(String, ASTNode) - Method in class org.sbml.jsbml.ASTNode
Replaces occurrences of a name within this ASTNode with the name/value/formula represented by the second argument ASTNode, e.g., if the formula in this ASTNode is x + y; bvar is x and arg is an ASTNode representing the real value 3 ReplaceArgument substitutes 3 for x within this ASTNode.
replaceChild(int, ASTNode) - Method in class org.sbml.jsbml.ASTNode
Replaces the nth child of this ASTNode with the given ASTNode.
reset() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
reset() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
Allows to re-use this object to compile another ASTNode.
resetParentSBMLObject(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Resets the parentSBMLObject to null recursively.
Resource - Class in org.sbml.jsbml.resources
Dummy class that just loads resource files if required.
Resource() - Constructor for class org.sbml.jsbml.resources.Resource
 
resource - Static variable in class org.sbml.jsbml.resources.Resource
 
resource - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
resourceURIs - Variable in class org.sbml.jsbml.CVTerm
Contains all the MIRIAM URI associated with the qualifier of this CVTerm instance.
retainAll(Collection<?>) - Method in class org.sbml.jsbml.ListOf
 
reversible - Variable in class org.sbml.jsbml.Reaction
Represents the 'reversible' XML attribute of a reaction element.
reversible - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
REVERSIBLE_REACTION_ARROW - Static variable in class org.sbml.jsbml.util.compilers.HTMLFormula
HTML code for the reversible reaction arrow whose upper side is directed to the right “⇌”.
RIGHT_ARROW - Static variable in class org.sbml.jsbml.util.compilers.HTMLFormula
HTML code for the right arrow “→”.
rightBrace - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
rightQuotationMark - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
An closing quotation mark.
root(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates a root ASTNode.
root(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
root(double, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
root(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
root(double, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
root(Object, Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Returns the exponent-th root of the basis as StringBuffer.
root(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
root(double, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
root(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
root(double, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
root(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
root(double, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
root(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
root(ASTNodeValue, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
root(double, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
root(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
root(double, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
root(double, ASTNodeValue) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
root(double, double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the rootExponent-th root of the radiant
Rule - Class in org.sbml.jsbml
The base class for the AlgebraicRule, RateRule, AssignmentRule.
Rule() - Constructor for class org.sbml.jsbml.Rule
Creates a Rule instance.
Rule(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Rule
Creates a Rule instance from an id, level and version.
Rule(int, int) - Constructor for class org.sbml.jsbml.Rule
Creates a Rule instance from a level and version.
Rule(Rule) - Constructor for class org.sbml.jsbml.Rule
Creates a new Rule instance from a given Rule.

S

saveChanges(Model, Object) - Method in interface org.sbml.jsbml.SBMLOutputConverter
Save the changes in the model.
saveChanges(Reaction, Object) - Method in interface org.sbml.jsbml.SBMLOutputConverter
 
saveToString(Object) - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
Tries to call the Object.toString() method on the given object.
SAX2Parser - Interface in org.sbml.jsbml.util
An interface for XML SAX2 parsers.
SBase - Interface in org.sbml.jsbml
The interface to implement for each SBML component.
SBaseWithDerivedUnit - Interface in org.sbml.jsbml
This type represents an SBase object that is associated to a unit.
SBaseWithUnit - Interface in org.sbml.jsbml
Defines a kind of SBase that is equipped with a defined unit.
sbmlCoreElements - Variable in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
This map contains all the relationships XML element name <=> matching java class.
SBMLCoreElements - Variable in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
SBMLCoreParser - Class in org.sbml.jsbml.xml.parsers
Parses the SBML core elements of an SBML file.
SBMLCoreParser() - Constructor for class org.sbml.jsbml.xml.parsers.SBMLCoreParser
Creates a SBMLCoreParser instance.
sbmlCoreParser - Static variable in class org.sbml.jsbml.xml.stax.SBMLReader
Initialize a static instance of the core parser.
SBMLDocument - Class in org.sbml.jsbml
Represents the 'sbml' root node of a SBML file.
SBMLDocument() - Constructor for class org.sbml.jsbml.SBMLDocument
Creates a SBMLDocument instance.
SBMLDocument(int, int) - Constructor for class org.sbml.jsbml.SBMLDocument
Creates a SBMLDocument instance from a level and version.
SBMLDocument(SBMLDocument) - Constructor for class org.sbml.jsbml.SBMLDocument
Creates a new SBMLDocument instance from a given SBMLDocument.
SBMLDocumentAttributes - Variable in class org.sbml.jsbml.SBMLDocument
Contains all the XML attributes of the sbml XML node.
SBMLDocumentAttributes - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
SBMLDocumentNamespaces - Variable in class org.sbml.jsbml.SBMLDocument
Contains all the namespaces of the sbml XML node and their prefixes.
SBMLError - Exception in org.sbml.jsbml
Representation of errors, warnings and other diagnostics.
SBMLError() - Constructor for exception org.sbml.jsbml.SBMLError
Constructs a new SBMLError.
SBMLError(String) - Constructor for exception org.sbml.jsbml.SBMLError
Constructs a new SBMLError with the given message.
SBMLError.SEVERITY - Enum in org.sbml.jsbml
 
SBMLError.SEVERITY() - Constructor for enum org.sbml.jsbml.SBMLError.SEVERITY
 
SBMLErrorLog - Class in org.sbml.jsbml
Log of errors and other events encountered during SBML processing.
SBMLErrorLog() - Constructor for class org.sbml.jsbml.SBMLErrorLog
 
SBMLException - Exception in org.sbml.jsbml
This class roughly corresponds to libSBML's SBMLError class.
SBMLException() - Constructor for exception org.sbml.jsbml.SBMLException
 
SBMLException(String) - Constructor for exception org.sbml.jsbml.SBMLException
 
SBMLException(String, Throwable) - Constructor for exception org.sbml.jsbml.SBMLException
 
SBMLException(Throwable) - Constructor for exception org.sbml.jsbml.SBMLException
 
SBMLException.Category - Enum in org.sbml.jsbml
Category of this exception.
SBMLException.Category() - Constructor for enum org.sbml.jsbml.SBMLException.Category
 
SBMLException.Code - Enum in org.sbml.jsbml
Error codes.
SBMLException.Code() - Constructor for enum org.sbml.jsbml.SBMLException.Code
 
SBMLException.Type - Enum in org.sbml.jsbml
 
SBMLException.Type() - Constructor for enum org.sbml.jsbml.SBMLException.Type
 
SBMLInputConverter - Interface in org.sbml.jsbml
This interface allows the implementing class to create a JSBML model based on some other data structure.
SBMLLevel1Rule - Class in org.sbml.jsbml.xml.parsers
Represent a level 1 rule.
SBMLLevel1Rule() - Constructor for class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
 
SBMLLevel1Rule(SBMLLevel1Rule) - Constructor for class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
Creates a new ExplicitRule
SBMLLevel1Version1Parser - Class in org.sbml.jsbml.xml.parsers
 
SBMLLevel1Version1Parser() - Constructor for class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
sbmlNS - Static variable in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
The SBML attribute for the additional namespace.
SBMLObjectForXML - Class in org.sbml.jsbml.xml.stax
An SBMLObjectForXML is an object to store the localName, prefix, namespace URI, attributes and text of a SBML component we want to write.
SBMLObjectForXML() - Constructor for class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
SBMLOutputConverter - Interface in org.sbml.jsbml
This interface allows the implementing class to convert a JSBML model into another data structure.
SBMLReader - Class in org.sbml.jsbml
Provides methods for reading SBML from files, text strings or streams.
SBMLReader() - Constructor for class org.sbml.jsbml.SBMLReader
Creates a new SBMLReader.
SBMLReader(SBMLReader) - Constructor for class org.sbml.jsbml.SBMLReader
Clone constructor.
SBMLReader - Class in org.sbml.jsbml.xml.stax
Provides all the methods to read a SBML file.
SBMLReader() - Constructor for class org.sbml.jsbml.xml.stax.SBMLReader
 
sbmlUnits - Static variable in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
The attribute for SBML units.
SBMLValidator - Class in org.sbml.jsbml.validator
Validates the SBML document given by filename.xml or located at the http:// URL.
SBMLValidator() - Constructor for class org.sbml.jsbml.validator.SBMLValidator
 
SBMLValidator.CHECK_CATEGORY - Enum in org.sbml.jsbml.validator
Enumerates the different possible check categories when performing the validation of an SBML document.
SBMLValidator.CHECK_CATEGORY() - Constructor for enum org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY
 
SBMLWriter - Class in org.sbml.jsbml
Provides methods for writing SBML to files, text strings or streams.
SBMLWriter() - Constructor for class org.sbml.jsbml.SBMLWriter
Creates a new SBMLwriter.
SBMLWriter(char, short) - Constructor for class org.sbml.jsbml.SBMLWriter
Creates a new SBMLwriter that uses the given character for indentation of the XML representation of SBML data structures (with the given number of such symbols).
SBMLWriter(SBMLWriter) - Constructor for class org.sbml.jsbml.SBMLWriter
Clone constructor.
SBMLWriter(String, String) - Constructor for class org.sbml.jsbml.SBMLWriter
Creates a new SBMLwriter for the program with the given name and version.
SBMLWriter(String, String, char, short) - Constructor for class org.sbml.jsbml.SBMLWriter
Creates a new SBMLwriter for the program with the given name and version that uses the given character for indentation of the XML representation of SBML data structures (with the given number of such symbols).
sbmlWriter - Variable in class org.sbml.jsbml.SBMLWriter
The actual writer.
SBMLWriter - Class in org.sbml.jsbml.xml.stax
A SBMLWriter provides the methods to write a SBML file.
SBMLWriter() - Constructor for class org.sbml.jsbml.xml.stax.SBMLWriter
Creates a new SBMLWriter with default configuration for SBMLWriter.indentChar and SBMLWriter.indentCount.
SBMLWriter(char, short) - Constructor for class org.sbml.jsbml.xml.stax.SBMLWriter
Creates a new SBMLWriter with the given configuration for the SBMLWriter.indentChar and SBMLWriter.indentCount, i.e., the symbol to be used to indent elements in the XML representation of SBML data objects and the number of these symbols to be concatenated at the beginning of each new line for a new element.
SBO - Class in org.sbml.jsbml
Methods for interacting with Systems Biology Ontology (SBO) terms.
SBO() - Constructor for class org.sbml.jsbml.SBO
 
sbo - Static variable in class org.sbml.jsbml.SBO
 
SBO.Term - Class in org.sbml.jsbml
This is a convenient wrapper class for the corresponding implementation of org.biojava.ontology.Term in BioJava as it provides specialized methods to obtain the information from the SBO OBO file directly and under the same name as the keys are given in that file.
SBO.Term(org.biojava.ontology.Term) - Constructor for class org.sbml.jsbml.SBO.Term
Creates a new Term instance.
SBO.Triple - Class in org.sbml.jsbml
This is a wrapper class for the corresponding BioJava class org.biojava.ontology.Triple, to allow for simplified access to the properties of a subject-predicate-object triple in this ontology.
SBO.Triple(org.biojava.ontology.Triple) - Constructor for class org.sbml.jsbml.SBO.Triple
Creates a new SBO.Triple from a given corresponding object from BioJava.
sbo2alias - Static variable in class org.sbml.jsbml.SBO
 
SBOFilter - Class in org.sbml.jsbml.util.filters
A Filter that accepts only instances of SBase whose SBO term field is set to a certain value of interest.
SBOFilter() - Constructor for class org.sbml.jsbml.util.filters.SBOFilter
Generates a new Filter for SBO terms but with an invalid SBO term as filter criterion.
SBOFilter(int) - Constructor for class org.sbml.jsbml.util.filters.SBOFilter
Creates an SBO term filter with the given term as filter criterion.
sboNumberString(int) - Static method in class org.sbml.jsbml.SBO
Creates and returns a 7 digit SBO number for the given SBO.Term identifier (if this is a valid identifier).
sboTerm - Variable in class org.sbml.jsbml.AbstractSBase
sbo term of the SBML component.
sboTerm - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
scale - Variable in class org.sbml.jsbml.Unit
Represents the 'scale' XML attribute of an unit element.
scale - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
SCIENTIFIC_FORMAT - Static variable in class org.sbml.jsbml.util.StringTools
 
sec(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
sec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
sec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
sec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
sec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
sec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
sec(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the secant of a double value.
sech(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
sech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
sech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
sech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
sech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
sech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
sech(double) - Static method in class org.sbml.jsbml.util.Maths
This method computes the sech of n
section(String, boolean) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
serialVersionUID - Static variable in class org.sbml.jsbml.AbstractMathContainer
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.AbstractNamedSBase
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
serialVersionUID - Static variable in class org.sbml.jsbml.AbstractSBase
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.AbstractTreeNode
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.AlgebraicRule
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Annotation
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.AnnotationElement
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.AssignmentRule
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.ASTNode
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Compartment
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.CompartmentType
Deprecated.
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Constraint
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Creator
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.CVTerm
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Delay
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Event
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.EventAssignment
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.ExplicitRule
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.FunctionDefinition
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.History
Generated serial version identifier.
serialVersionUID - Static variable in exception org.sbml.jsbml.IdentifierException
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.InitialAssignment
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.KineticLaw
Generated serial version identifier.
serialVersionUID - Static variable in exception org.sbml.jsbml.LevelVersionError
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.ListOf
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.LocalParameter
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Model
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.ModifierSpeciesReference
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Parameter
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Priority
Generated serial version identifier.
serialVersionUID - Static variable in exception org.sbml.jsbml.PropertyException
Generated serial version identifier
serialVersionUID - Static variable in exception org.sbml.jsbml.PropertyNotAvailableException
Generated serial version identifier.
serialVersionUID - Static variable in exception org.sbml.jsbml.PropertyUndefinedError
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.QuantityWithUnit
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.RateRule
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Reaction
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Rule
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.SBMLDocument
Generated serial version identifier.
serialVersionUID - Static variable in exception org.sbml.jsbml.SBMLError
Generated serial version identifier.
serialVersionUID - Static variable in exception org.sbml.jsbml.SBMLException
Generated serial version id.
serialVersionUID - Static variable in class org.sbml.jsbml.SBMLReader
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.SBMLWriter
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.SBO.Term
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.SBO.Triple
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.SimpleSpeciesReference
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Species
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.SpeciesReference
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.SpeciesType
Deprecated.
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.StoichiometryMath
Deprecated.
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Symbol
Generated serial version identifier.
serialVersionUID - Static variable in error org.sbml.jsbml.text.parser.FormulaParser.LookaheadSuccess
 
serialVersionUID - Static variable in exception org.sbml.jsbml.text.parser.ParseException
The version identifier for this Serializable class.
serialVersionUID - Static variable in class org.sbml.jsbml.text.parser.Token
The version identifier for this Serializable class.
serialVersionUID - Static variable in error org.sbml.jsbml.text.parser.TokenMgrError
The version identifier for this Serializable class.
serialVersionUID - Static variable in class org.sbml.jsbml.Trigger
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.Unit
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.UnitDefinition
Generated serial version identifier.
serialVersionUID - Static variable in exception org.sbml.jsbml.util.compilers.UnitException
Generated serial version identifier.
serialVersionUID - Static variable in error org.sbml.jsbml.util.NotImplementedException
Generated serial version identifier
serialVersionUID - Static variable in class org.sbml.jsbml.util.TreeNodeAdapter
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
Generated serial version identifier
serialVersionUID - Static variable in class org.sbml.jsbml.util.TreeNodeRemovedEvent
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.util.ValuePair
Generated serial version identifier.
serialVersionUID - Static variable in exception org.sbml.jsbml.validator.ModelOverdeterminedException
 
serialVersionUID - Static variable in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
Generated serial version identifier.
serialVersionUID - Static variable in exception org.sbml.jsbml.xml.XMLException
Generated serial version identifier.
serialVersionUID - Static variable in class org.sbml.jsbml.xml.XMLNode
Generated serial version identifier
serialVersionUID - Static variable in class org.sbml.jsbml.xml.XMLToken
Generated serial version identifier
set(int, T) - Method in class org.sbml.jsbml.ListOf
 
setAbout(String) - Method in class org.sbml.jsbml.Annotation
Sets the value of the about String of this object.
setAndReplacement(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
Sets the String that will be used to replace ' and ' (the mathML <and> element) in the boolean expressions.
setAnnotation(Annotation) - Method in class org.sbml.jsbml.AbstractSBase
 
setAnnotation(Annotation) - Method in interface org.sbml.jsbml.SBase
Sets the value of the 'annotation' sub-element of this SBML object to a copy of annotation given as an Annotation instance.
setAnnotation - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
setAnnotationAttributes(NamedNodeMap) - Method in class org.sbml.jsbml.Annotation
Sets the annotationNamespaces.
setAnnotationNamespaces(Map<String, String>) - Method in class org.sbml.jsbml.Annotation
Sets the annotationNamespaces.
setAreaUnits(String) - Method in class org.sbml.jsbml.Model
Sets the areaUnitsID of this Model to 'areaUnitsID'
setAreaUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model
Sets the areaUnitsID of this Model to the id of the UnitDefinition 'areaUnits'.
setAssignmentRuleVariable(AssignmentRule, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setAttributes(XMLAttributes) - Method in class org.sbml.jsbml.xml.XMLToken
Sets an XMLAttributes to this XMLToken.
setBiologicalQualifierType(int) - Method in class org.sbml.jsbml.CVTerm
Sets the biological qualifier type.
setBiologicalQualifierType(CVTerm.Qualifier) - Method in class org.sbml.jsbml.CVTerm
Sets the biological qualifier type of this CVTerm.
setBoundaryCondition(boolean) - Method in class org.sbml.jsbml.Species
Sets the boundaryCondition Boolean.
setCategory(String) - Method in exception org.sbml.jsbml.SBMLError
Sets the category of this SBMLError.
setCategory(SBMLException.Category) - Method in exception org.sbml.jsbml.SBMLException
 
setCategory(int) - Method in class org.sbml.jsbml.util.Detail
 
setCharacter(char) - Method in class org.sbml.jsbml.ASTNode
Sets the value of this ASTNode to the given character.
setCharacters(String) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
setCharacters(String) - Method in class org.sbml.jsbml.xml.XMLToken
 
setCharge(int) - Method in class org.sbml.jsbml.Species
Deprecated.
Only defined in SBML Level 1, Version 1 and 2, and Level 2 Version 1. Since Level 2 Version 2 it has been marked as a deprecated property, but has been completely removed in SBML Level 3.
setClassName(String) - Method in class org.sbml.jsbml.ASTNode
Sets the class name of the mathML element represented by this ASTNode.
setCode(int) - Method in exception org.sbml.jsbml.SBMLError
Sets the error code of this SBMLError.
setCode(SBMLException.Code) - Method in exception org.sbml.jsbml.SBMLException
 
setColumn(int) - Method in class org.sbml.jsbml.util.Location
 
setCompartment(Compartment) - Method in class org.sbml.jsbml.Reaction
Sets the compartmentID of this Reaction to the id of the Compartment 'compartment'.
setCompartment(String) - Method in class org.sbml.jsbml.Reaction
Sets the compartmentID of this Reaction to 'compartmentID'.
setCompartment(Compartment) - Method in class org.sbml.jsbml.Species
Sets the compartmentID of this Species to the id of 'compartment'.
setCompartment(String) - Method in class org.sbml.jsbml.Species
Sets the compartmentID of this Species to 'compartment'.
setCompartmentCompartmentType(Compartment, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setCompartmentOutside(Compartment, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setCompartmentType(CompartmentType) - Method in class org.sbml.jsbml.Compartment
Deprecated.
setCompartmentType(String) - Method in class org.sbml.jsbml.Compartment
Deprecated.
Only valid in Level 2.
setCompartmentUnits(Compartment, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setConsistencyChecks(SBMLValidator.CHECK_CATEGORY, boolean) - Method in class org.sbml.jsbml.SBMLDocument
Controls the consistency checks that are performed when SBMLDocument.checkConsistency() is called.
setConstant(boolean) - Method in class org.sbml.jsbml.SpeciesReference
 
setConstant(boolean) - Method in class org.sbml.jsbml.Symbol
 
setConstant(boolean) - Method in interface org.sbml.jsbml.Variable
Sets the constant boolean of this Variable.
setConversionFactor(Parameter) - Method in class org.sbml.jsbml.Model
Sets the conversionFactorID of this Model to the id of the Parameter 'conversionFactor'.
setConversionFactor(String) - Method in class org.sbml.jsbml.Model
Sets the conversionFactorID of this Model to 'conversionFactorID'.
setConversionFactor(Parameter) - Method in class org.sbml.jsbml.Species
Sets the conversionFactorID of this Species to the id of 'conversionFactor'.
setConversionFactor(String) - Method in class org.sbml.jsbml.Species
Sets the conversionFactorID of this Species to 'conversionFactorID'.
setCreatedDate(Date) - Method in class org.sbml.jsbml.History
Sets the createdDate.
setDebugMode(boolean) - Static method in class org.sbml.jsbml.ListOf
Allows you to influence the behavior of the ListOf.toString() method.
setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
Set debug output.
setDefinitionURL(String) - Method in class org.sbml.jsbml.ASTNode
 
setDelay(Delay) - Method in class org.sbml.jsbml.Event
Sets the delay of this Event to 'delay'.
setDenominator(int) - Method in class org.sbml.jsbml.SpeciesReference
Deprecated. 
setDetail(Detail) - Method in exception org.sbml.jsbml.SBMLError
 
setEmail(String) - Method in class org.sbml.jsbml.Creator
Sets the email
setEncoding(String) - Method in class org.sbml.jsbml.ASTNode
Sets the encoding of the mathML element represented by this ASTNode.
setEnd() - Method in class org.sbml.jsbml.xml.XMLToken
Declares this XML start element is also an end element.
setEOF() - Method in class org.sbml.jsbml.xml.XMLToken
Declares this XMLToken is an end-of-file (input) marker.
setError(boolean) - Method in exception org.sbml.jsbml.SBMLException
 
setEventAssignmentVariable(EventAssignment, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setEventTimeUnits(Event, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setExcerpt(String) - Method in exception org.sbml.jsbml.SBMLError
Sets the excerpt of this SBMLError.
setExplicitlyConstant(boolean) - Method in class org.sbml.jsbml.LocalParameter
Deprecated.
Since SBML Level 3 it is no longer possible to explicitly set a LocalParameter to constant = true because LocalParameter instances always represent constant a Quantity.
setExponent(double) - Method in class org.sbml.jsbml.Unit
Sets the exponent of this Unit
setExponent(int) - Method in class org.sbml.jsbml.Unit
Deprecated.
setExtentUnits(String) - Method in class org.sbml.jsbml.Model
Sets the extendUnitsID of this Model to 'extentUnitsID'.
setExtentUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model
Sets the extentUnitsID of this Model to the id of the UnitDefinition 'extentUnits'.
setFamilyName(String) - Method in class org.sbml.jsbml.Creator
Sets the family name
setFast(boolean) - Method in class org.sbml.jsbml.Reaction
Sets the fast Boolean of this Reaction.
setFatal(boolean) - Method in exception org.sbml.jsbml.SBMLException
 
setFile(File) - Method in class org.sbml.jsbml.SBMLErrorLog
Sets the file.
setFilterForSpecies(boolean) - Method in class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
 
setFilters(Set<Filter>) - Method in class org.sbml.jsbml.util.filters.AndFilter
 
setFormula(String) - Method in class org.sbml.jsbml.AbstractMathContainer
Deprecated.
setFormula(String) - Method in class org.sbml.jsbml.FunctionDefinition
 
setFormula(String) - Method in interface org.sbml.jsbml.MathContainer
Deprecated.
As this is part of SBML Level 1, it is strongly recommended not to work with the String representation of a formula, but to deal with a more flexible ASTNode. Please use ASTNode.parseFormula(String) to create an ASTNode object from your formula String.
setGivenName(String) - Method in class org.sbml.jsbml.Creator
Sets the given name
setHasOnlySubstanceUnits(boolean) - Method in class org.sbml.jsbml.Species
Sets hasOnlySubstanceUnits Boolean
setHistory(History) - Method in class org.sbml.jsbml.AbstractSBase
 
setHistory(History) - Method in class org.sbml.jsbml.Annotation
Changes the History instance to 'history'
setHistory(History) - Method in interface org.sbml.jsbml.SBase
 
setId(String) - Method in class org.sbml.jsbml.AbstractNamedSBase
 
setId(String) - Method in class org.sbml.jsbml.ASTNode
Sets the id of the mathML element represented by this ASTNode.
setId(String) - Method in class org.sbml.jsbml.FunctionDefinition
 
setId(String) - Method in class org.sbml.jsbml.LocalParameter
 
setId(String) - Method in interface org.sbml.jsbml.NamedSBase
sets the id value with 'id'
setId(String) - Method in class org.sbml.jsbml.UnitDefinition
 
setId(String) - Method in class org.sbml.jsbml.util.filters.AssignmentVariableFilter
 
setId(String) - Method in class org.sbml.jsbml.util.filters.NameFilter
 
setIndent(int) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
setIndent(int) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
setIndentationChar(char) - Method in class org.sbml.jsbml.SBMLWriter
Influences the way how SBML data structures are represented in XML.
setIndentationChar(char) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Allows you to set another blank character for indentation.
setIndentationCount(short) - Method in class org.sbml.jsbml.SBMLWriter
Influences the way how SBML data structures are represented in XML.
setIndentationCount(int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
setIndentationCount(short) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
setIndenting(boolean) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
setIndenting(boolean) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
setInfo(boolean) - Method in exception org.sbml.jsbml.SBMLException
 
setInitialAmount(double) - Method in class org.sbml.jsbml.Species
Sets the initialAmount of this Species.
setInitialAssignmentSymbol(InitialAssignment, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setInitialConcentration(double) - Method in class org.sbml.jsbml.Species
Sets the initialConcentration of this Species.
setInitialValue(boolean) - Method in class org.sbml.jsbml.Trigger
Can only be set if Level >= 3.
setInternal(boolean) - Method in exception org.sbml.jsbml.SBMLException
 
setIsSetNumberType(boolean) - Method in class org.sbml.jsbml.ASTNode
 
setKind(Unit.Kind) - Method in class org.sbml.jsbml.Unit
Sets the Unit.Kind of this Unit
setKineticLaw(KineticLaw) - Method in class org.sbml.jsbml.Reaction
Sets the kineticLaw of this Reaction.
setL(L) - Method in class org.sbml.jsbml.util.ValuePair
 
setLang(String) - Method in class org.sbml.jsbml.util.Message
 
setLengthUnits(String) - Method in class org.sbml.jsbml.Model
Sets the lengthUnitsID of this Model to 'lengthUnitsID'.
setLengthUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model
Sets the lengthUnitsID of this Model to the id of the UnitDefinition 'lengthUnits'.
setLevel(int) - Method in class org.sbml.jsbml.AbstractSBase
 
setLevel(int) - Method in interface org.sbml.jsbml.SBase
Sets the level of this object with 'level'.
setLevel(int) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setLevel(int) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
setLevelAndVersion(int, int, boolean) - Method in class org.sbml.jsbml.AbstractSBase
Sets recursively the level and version attribute for this element and all sub-elements.
setLevelAndVersion(int, int) - Method in class org.sbml.jsbml.SBMLDocument
Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.
setLevelAndVersion(int, int, boolean) - Method in class org.sbml.jsbml.SBMLDocument
Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.
setLevelAndVersion(UnitDefinition) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
Ensures that level and version combination of a unit are the same then these that are defined here.
setLevelAndVersionFor(Object, SBase) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
Sets level and version properties of the new object according to the value in the model.
setLine(int) - Method in class org.sbml.jsbml.util.Location
 
setListOf(List<T>) - Method in class org.sbml.jsbml.ListOf
Clears this ListOf if not empty and then adds all elements in the given List to this ListOf.
setListOfCompartments(ListOf<Compartment>) - Method in class org.sbml.jsbml.Model
Sets the listOfCompartments of this Model to 'listOfCompartments'.
setListOfCompartmentTypes(ListOf<CompartmentType>) - Method in class org.sbml.jsbml.Model
Deprecated. 
setListOfConstraints(ListOf<Constraint>) - Method in class org.sbml.jsbml.Model
Sets the listOfConstraints of this Model to 'listOfConstraints'.
setListOfEventAssignments(ListOf<EventAssignment>) - Method in class org.sbml.jsbml.Event
Sets the Event.listOfEventAssignments of this Event to 'listOfEventAssignments'.
setListOfEvents(ListOf<Event>) - Method in class org.sbml.jsbml.Model
Sets the listOfEvents of this Model to 'listOfEvents'.
setListOfFunctionDefinitions(ListOf<FunctionDefinition>) - Method in class org.sbml.jsbml.Model
Sets the listOfFunctionDefinitions of this Model to 'listOfFunctionDefinitions'.
setListOfInitialAssignments(ListOf<InitialAssignment>) - Method in class org.sbml.jsbml.Model
Sets the Model.listOfInitialAssignments of this Model to 'listOfInitialAssignments'.
setListOfLocalParameters(ListOf<LocalParameter>) - Method in class org.sbml.jsbml.KineticLaw
Sets the listOfParameters of this KineticLaw to 'list'.
setListOfModifiers(ListOf<ModifierSpeciesReference>) - Method in class org.sbml.jsbml.Reaction
Sets the listOfModifiers of this Reaction.
setListOfParameters(ListOf<Parameter>) - Method in class org.sbml.jsbml.Model
Sets the Model.listOfParameters of this Model to 'listOfParameters'.
setListOfProducts(ListOf<SpeciesReference>) - Method in class org.sbml.jsbml.Reaction
setListOfReactants(ListOf<SpeciesReference>) - Method in class org.sbml.jsbml.Reaction
Sets the listOfReactants of this Reaction.
setListOfReactions(ListOf<Reaction>) - Method in class org.sbml.jsbml.Model
Sets the Model.listOfReactions of this Model to 'listOfReactions'.
setListOfRules(ListOf<Rule>) - Method in class org.sbml.jsbml.Model
Sets the Model.listOfRules of this Model to 'listOfRules'.
setListOfSpecies(ListOf<Species>) - Method in class org.sbml.jsbml.Model
Sets the listOfSpecies of this Model to 'listOfSpecies'.
setListOfSpeciesTypes(ListOf<SpeciesType>) - Method in class org.sbml.jsbml.Model
Deprecated. 
setListOfUnitDefinitions(ListOf<UnitDefinition>) - Method in class org.sbml.jsbml.Model
Sets the listOfUnitDefinitions of this Model to 'listOfUnitDefinitions'.
setListOfUnits(ListOf<Unit>) - Method in class org.sbml.jsbml.UnitDefinition
setLocation(Location) - Method in exception org.sbml.jsbml.SBMLError
Sets the location of this SBMLError.
setLogger(XMLLogger) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
setMath(ASTNode) - Method in class org.sbml.jsbml.AbstractMathContainer
 
setMath(ASTNode) - Method in class org.sbml.jsbml.FunctionDefinition
 
setMath(ASTNode) - Method in interface org.sbml.jsbml.MathContainer
Sets the math ASTNode of this MathContainer to the given value.
setMessage(String) - Method in class org.sbml.jsbml.Constraint
Sets the message of this Constraint to 'message'.
setMessage(XMLNode) - Method in class org.sbml.jsbml.Constraint
Sets the message of this Constraint to 'message'.
setMessage(Message) - Method in exception org.sbml.jsbml.SBMLError
Sets the message of this SBMLError.
setMessage(String) - Method in class org.sbml.jsbml.util.Message
 
setMetaId(String) - Method in class org.sbml.jsbml.AbstractSBase
 
setMetaId(String) - Method in interface org.sbml.jsbml.SBase
Sets the metaid value with 'metaid'.
setModel(Model) - Method in class org.sbml.jsbml.SBMLDocument
Sets the Model for this SBMLDocument to the given Model.
setModelHistory(History) - Method in class org.sbml.jsbml.Model
setModelQualifierType(int) - Method in class org.sbml.jsbml.CVTerm
Sets the model qualifier type of this CVTerm.
setModelQualifierType(CVTerm.Qualifier) - Method in class org.sbml.jsbml.CVTerm
Sets the model qualifier type of this CVTerm.
setModifiedDate(Date) - Method in class org.sbml.jsbml.History
Sets the modifiedDate.
setMultiplier(double) - Method in class org.sbml.jsbml.Unit
Sets the multiplier of this Unit
setName(String) - Method in class org.sbml.jsbml.AbstractNamedSBase
 
setName(String) - Method in class org.sbml.jsbml.ASTNode
Sets the value of this ASTNode to the given name.
setName(String) - Method in class org.sbml.jsbml.FunctionDefinition
 
setName(String) - Method in interface org.sbml.jsbml.NamedSBase
sets the name value with 'name'.
setName(String) - Method in class org.sbml.jsbml.util.filters.NameFilter
 
setName(String) - Method in class org.sbml.jsbml.util.Option
 
setName(String) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
setNamespace(String) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
setNamespaces(XMLNamespaces) - Method in class org.sbml.jsbml.xml.XMLToken
Sets an XMLnamespaces to this XML element.
setNonRDFAnnotation(String) - Method in class org.sbml.jsbml.Annotation
Sets the value of the non RDF annotations
setNotes(String) - Method in class org.sbml.jsbml.AbstractSBase
 
setNotes(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase
 
setNotes(String) - Method in interface org.sbml.jsbml.SBase
Sets the notes with 'notes'.
setNotes(XMLNode) - Method in interface org.sbml.jsbml.SBase
Sets the XMLNode containing the notes sub-element of this object.
setOffset(double) - Method in class org.sbml.jsbml.Unit
Deprecated.
Only defined for SBML Level 2 Version 1.
setOmitXMLDeclaration(boolean) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
setOmitXMLDeclaration(boolean) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
setOptions(List<Option>) - Method in class org.sbml.jsbml.SBMLErrorLog
Sets the list of options.
setOrganisation(String) - Method in class org.sbml.jsbml.Creator
Sets the organisation
setOrganization(String) - Method in class org.sbml.jsbml.Creator
Sets the organisation
setOrReplacement(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
Sets the String that will be used to replace ' or ' (the mathML <or> element) in the boolean expressions.
setOutside(Compartment) - Method in class org.sbml.jsbml.Compartment
Deprecated.
setOutside(String) - Method in class org.sbml.jsbml.Compartment
Deprecated.
since Level 3 Version 1
setParameterUnits(QuantityWithUnit, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setParent(TreeNode) - Method in class org.sbml.jsbml.AbstractTreeNode
 
setParentSBML(SBase) - Method in class org.sbml.jsbml.AbstractSBase
 
setParentSBMLObject(SBase) - Method in class org.sbml.jsbml.AbstractSBase
Checks the Level/Version configuration of the new parent (if it is compliant to the one of this SBase), adds all changeListeners from the parent to this SBase, fires a TreeNodeChangeListener.nodeAdded(TreeNode) event, and and finally, it will forward the new parent to AbstractSBase.setParentSBML(SBase).
setParentSBMLObject(ASTNode, MathContainer) - Static method in class org.sbml.jsbml.ASTNode
Sets the Parent of the node and its children to the given value
setParentSBMLObject(ASTNode, MathContainer, int) - Static method in class org.sbml.jsbml.ASTNode
Sets the Parent of the node and its children to the given value
setPattern(String) - Method in class org.sbml.jsbml.util.filters.CVTermFilter
 
setPersistent(boolean) - Method in class org.sbml.jsbml.Trigger
Can only be set if Level >= 3.
setPrefix(String) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
setPrintNameIfAvailable(boolean) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
setPriority(Priority) - Method in class org.sbml.jsbml.Event
 
setProgramName(String) - Method in class org.sbml.jsbml.SBMLWriter
Sets the name of this program, i.e., the program that is about to write out the SBMLDocument.
setProgramVersion(String) - Method in class org.sbml.jsbml.SBMLWriter
Sets the version of this program, i.e., the program that is about to write out the SBMLDocument.
setQualifier(CVTerm.Qualifier) - Method in class org.sbml.jsbml.util.filters.CVTermFilter
 
setQualifierType(int) - Method in class org.sbml.jsbml.CVTerm
Sets the type of this CVTerm to the Type represented by 'qualifierType'.
setQualifierType(CVTerm.Type) - Method in class org.sbml.jsbml.CVTerm
Sets the type of this CVTerm to 'type'
setRateRuleVariable(RateRule, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setRDFAbout(SBase) - Method in class org.sbml.jsbml.xml.parsers.RDFAnnotationParser
 
setRdfAnnotationNamespaces(Map<String, String>) - Method in class org.sbml.jsbml.Annotation
Sets the rdfAnnotationNamespace map to 'rdfAnnotationNamespaces'.
setReactionCompartment(Reaction, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setReversible(boolean) - Method in class org.sbml.jsbml.Reaction
Sets the reversible Boolean of this Reaction.
setSBaseListType(Class<T>) - Method in class org.sbml.jsbml.ListOf
Sets the ListOf.Type of this ListOf instance to the ListOf.Type defined by the given Class.
setSBaseListType(ListOf.Type) - Method in class org.sbml.jsbml.ListOf
Sets the ListOf.Type of this ListOf instance to 'listType'.
setSBMLDocumentAttributes(Map<String, String>) - Method in class org.sbml.jsbml.SBMLDocument
Sets the SBMLDocumentAttributes.
setSBOTerm(int) - Method in class org.sbml.jsbml.AbstractSBase
 
setSBOTerm(String) - Method in class org.sbml.jsbml.AbstractSBase
 
setSBOTerm(int) - Method in interface org.sbml.jsbml.SBase
Sets the value of the 'sboTerm' attribute.
setSBOTerm(String) - Method in interface org.sbml.jsbml.SBase
Sets the value of the 'sboTerm' attribute.
setScale(int) - Method in class org.sbml.jsbml.Unit
Sets the scale of this Unit
setSeverity(String) - Method in exception org.sbml.jsbml.SBMLError
Sets the severity of this SBMLError.
setSeverity(int) - Method in class org.sbml.jsbml.util.Detail
 
setShortMessage(Message) - Method in exception org.sbml.jsbml.SBMLError
 
setShortMessage(String) - Method in exception org.sbml.jsbml.SBMLException
 
setSize(double) - Method in class org.sbml.jsbml.Compartment
Sets the size of this compartment to 'size'.
setSpatialDimensions(double) - Method in class org.sbml.jsbml.Compartment
Sets the spatialDimensions of this compartment to 'i'.
setSpatialDimensions(int) - Method in class org.sbml.jsbml.Compartment
 
setSpatialDimensions(short) - Method in class org.sbml.jsbml.Compartment
Sets the spatialDimensions of this compartment to 'spatialDimensiosn'.
setSpatialSizeUnits(String) - Method in class org.sbml.jsbml.Species
Deprecated.
This property is only valid for SBML Level 2 Versions 1 and 2.
setSpatialSizeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Species
Deprecated. 
setSpecies(Species) - Method in class org.sbml.jsbml.SimpleSpeciesReference
Sets the speciesID to the id of the Species 'species'.
setSpecies(String) - Method in class org.sbml.jsbml.SimpleSpeciesReference
Sets the speciesID to 'spec'.
setSpeciesCompartment(Species, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setSpeciesConversionFactor(Species, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setSpeciesReferenceSpecies(SimpleSpeciesReference, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setSpeciesSpeciesType(Species, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setSpeciesSubstanceUnits(Species, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
setSpeciesType(SpeciesType) - Method in class org.sbml.jsbml.Species
Deprecated. 
setSpeciesType(String) - Method in class org.sbml.jsbml.Species
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
setStatus(String) - Method in class org.sbml.jsbml.SBMLErrorLog
Sets the status.
setStatus(String) - Method in class org.sbml.jsbml.util.Option
 
setStoichiometry(double) - Method in class org.sbml.jsbml.SpeciesReference
Sets the stoichiometry of this SpeciesReference.
setStoichiometryMath(StoichiometryMath) - Method in class org.sbml.jsbml.SpeciesReference
Deprecated. 
setStyle(String) - Method in class org.sbml.jsbml.ASTNode
Sets the style of the mathML element represented by this ASTNode.
setSubstanceUnits(String) - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
Only defined for SBML Level 1 and Level 2 Version 1 and 2.
setSubstanceUnits(Unit) - Method in class org.sbml.jsbml.KineticLaw
Deprecated. 
setSubstanceUnits(String) - Method in class org.sbml.jsbml.Model
Sets the substanceUnitsID of this Model to 'substanceUnitsID'
setSubstanceUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model
Sets the substanceUnitsID of this Model to the id of 'substanceUnits'.
setSubstanceUnits(String) - Method in class org.sbml.jsbml.Species
Sets the substanceUnitsID to 'unit'.
setSubstanceUnits(Unit) - Method in class org.sbml.jsbml.Species
Sets the substanceUnits.
setSubstanceUnits(Unit.Kind) - Method in class org.sbml.jsbml.Species
Sets the substanceUnits.
setSubstanceUnits(UnitDefinition) - Method in class org.sbml.jsbml.Species
Sets the substanceUnitsID to the id of 'units'.
setSymbol(String) - Method in class org.sbml.jsbml.InitialAssignment
setSystem(boolean) - Method in exception org.sbml.jsbml.SBMLException
 
setTabSize(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
 
setTerm(int) - Method in class org.sbml.jsbml.util.filters.SBOFilter
 
setThisAsParentSBMLObject(SBase) - Method in class org.sbml.jsbml.AbstractSBase
 
setThisAsParentSBMLObject(SBase) - Method in interface org.sbml.jsbml.SBase
Sets this object as SBML parent of 'sbase'.
setTimeUnits(String) - Method in class org.sbml.jsbml.Event
Deprecated.
This is only applicable for SBML Level 2, Versions 1 and 2.
setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Event
Deprecated.
setTimeUnits(String) - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
Only defined for Level 1 and Level 2 Version 1.
setTimeUnits(Unit) - Method in class org.sbml.jsbml.KineticLaw
Deprecated. 
setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
Only defined for Level 1 and Level 2 Version 1.
setTimeUnits(String) - Method in class org.sbml.jsbml.Model
Sets the timeUnits of this Model to 'timeUnistID'
setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model
Sets the timeUnitsID of this Model to the id of the UnitDefinition 'timeUnits'.
setTimeUnitsID(String) - Method in class org.sbml.jsbml.Event
Deprecated. 
setTrigger(Trigger) - Method in class org.sbml.jsbml.Event
Sets the trigger of this Event to 'trigger'.
setTriple(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLToken
Sets the XMLTripe (name, uri and prefix) of this XML element.
setType(String) - Method in class org.sbml.jsbml.ASTNode
Sets the type from a String.
setType(ASTNode.Type) - Method in class org.sbml.jsbml.ASTNode
Sets the type of this ASTNode to the given Type.
setType(ASTNode.Type) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setType(String) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
 
setTypeOfNotes(String) - Method in class org.sbml.jsbml.xml.parsers.StringParser
Sets the typeOfNote of this parser.
setUIFlag(boolean) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
setUnits(String) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
setUnits(Unit) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
setUnits(String) - Method in class org.sbml.jsbml.ASTNode
Sets the units attribute.
setUnits(String) - Method in class org.sbml.jsbml.Compartment
Sets the unitsID of this QuantityWithUnit.
setUnits(Unit) - Method in class org.sbml.jsbml.Compartment
Sets the Unit of this Compartment.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.Compartment
Sets the unit of this Compartment.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.Compartment
Set the unit attribute of this Compartment to the given unit definition.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.Event
Deprecated.
setUnits(String) - Method in class org.sbml.jsbml.Event
Deprecated.
setUnits(Unit) - Method in class org.sbml.jsbml.Event
Deprecated.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.Event
Deprecated.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.ExplicitRule
Deprecated.
setUnits(String) - Method in class org.sbml.jsbml.ExplicitRule
Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
setUnits(Unit) - Method in class org.sbml.jsbml.ExplicitRule
Deprecated.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.ExplicitRule
Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
setUnits(String) - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
setUnits(Unit) - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
setUnits(String) - Method in interface org.sbml.jsbml.SBaseWithUnit
Sets the unitsID of this SBaseWithUnit.
setUnits(Unit) - Method in interface org.sbml.jsbml.SBaseWithUnit
Sets the Unit of this SBaseWithUnit.
setUnits(Unit.Kind) - Method in interface org.sbml.jsbml.SBaseWithUnit
Sets the unit of this SBaseWithUnit.
setUnits(UnitDefinition) - Method in interface org.sbml.jsbml.SBaseWithUnit
Set the unit attribute of this SBaseWithUnit to the given unit definition.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setUserObject(Object) - Method in class org.sbml.jsbml.ASTNode
 
setUserObject(Object) - Method in class org.sbml.jsbml.util.TreeNodeAdapter
 
setUseValuesFromTriggerTime(boolean) - Method in class org.sbml.jsbml.Event
Sets the useValuesFromTriggerTime of this Event to 'useValuesFromTriggerTime'.
setV(V) - Method in class org.sbml.jsbml.util.ValuePair
 
setValidationErrors(List<SBMLError>) - Method in class org.sbml.jsbml.SBMLErrorLog
Sets the list of errors.
setValue(double) - Method in class org.sbml.jsbml.ASTNode
Sets the value of this ASTNode to the given double number and sets the node type to REAL.
setValue(double, int) - Method in class org.sbml.jsbml.ASTNode
Sets the value of this ASTNode to the given real (double) in two parts: the mantissa and the exponent.
setValue(int) - Method in class org.sbml.jsbml.ASTNode
Sets the value of this ASTNode to the given (long) integer and sets the node type to INTEGER.
setValue(int, int) - Method in class org.sbml.jsbml.ASTNode
Sets the value of this ASTNode to the given rational in two parts: the numerator and denominator.
setValue(double) - Method in class org.sbml.jsbml.Compartment
 
setValue(double) - Method in interface org.sbml.jsbml.Quantity
Sets the value of this Quantity.
setValue(double) - Method in class org.sbml.jsbml.QuantityWithUnit
 
setValue(double) - Method in class org.sbml.jsbml.SpeciesReference
 
setValue(boolean) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setValue(Boolean) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setValue(double) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setValue(int) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setValue(long) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setValue(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setValue(Node) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setValue(Number) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setValue(short) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setValue(String) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setVariable(String) - Method in interface org.sbml.jsbml.Assignment
Sets the variableID of this Assignment to the given value.
setVariable(Variable) - Method in interface org.sbml.jsbml.Assignment
Sets the variableID of this Assignment to the id of the Variable 'variable'.Listeners are notified about this change.
setVariable(CallableSBase) - Method in class org.sbml.jsbml.ASTNode
 
setVariable(String) - Method in class org.sbml.jsbml.EventAssignment
 
setVariable(Variable) - Method in class org.sbml.jsbml.EventAssignment
 
setVariable(String) - Method in class org.sbml.jsbml.ExplicitRule
 
setVariable(Variable) - Method in class org.sbml.jsbml.ExplicitRule
 
setVariable(String) - Method in class org.sbml.jsbml.InitialAssignment
 
setVariable(Variable) - Method in class org.sbml.jsbml.InitialAssignment
 
setVersion(int) - Method in class org.sbml.jsbml.AbstractSBase
 
setVersion(int) - Method in interface org.sbml.jsbml.SBase
Sets the version of this object with 'version'.
setVersion(int) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
setVolume(double) - Method in class org.sbml.jsbml.Compartment
Deprecated.
This method is only available for SBML Level 1. You should either use Compartment.setSize(double) or Compartment.setValue(double).
setVolumeUnits(String) - Method in class org.sbml.jsbml.Model
Sets the volumeUnitsID of this Model to 'volumeUnitsID'
setVolumeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model
Sets the volumeUnitsID of this Model to the id of the UnitDefinition 'volumeUnits'.
setWarning(boolean) - Method in exception org.sbml.jsbml.SBMLException
 
setXML(boolean) - Method in exception org.sbml.jsbml.SBMLException
 
severity - Variable in exception org.sbml.jsbml.SBMLError
 
severity - Variable in class org.sbml.jsbml.util.Detail
 
shortmessage - Variable in exception org.sbml.jsbml.SBMLError
 
shortMessage - Variable in exception org.sbml.jsbml.SBMLException
 
SIdL2 - Static variable in class org.sbml.jsbml.AbstractNamedSBase
 
SIdL2Pattern - Static variable in class org.sbml.jsbml.AbstractNamedSBase
 
SimpleCharStream - Class in org.sbml.jsbml.text.parser
An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
SimpleCharStream(Reader, int, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream
Constructor.
SimpleCharStream(Reader, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream
Constructor.
SimpleCharStream(Reader) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, int, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream
Constructor.
SimpleCharStream(InputStream) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream
Constructor.
SimpleSpeciesReference - Class in org.sbml.jsbml
SimpleSpeciesReference() - Constructor for class org.sbml.jsbml.SimpleSpeciesReference
Creates a SimpleSpeciesReference instance.
SimpleSpeciesReference(int, int) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference
 
SimpleSpeciesReference(SimpleSpeciesReference) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference
Creates a SimpleSpeciesReference instance from a given SimpleSpeciesReference.
SimpleSpeciesReference(Species) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference
Creates a SimpleSpeciesReference instance from a given Species.
SimpleSpeciesReference(String) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference
 
SimpleSpeciesReference(String, int, int) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference
 
SimpleSpeciesReference(String, String, int, int) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference
 
SimpleTreeNodeChangeListener - Class in org.sbml.jsbml.util
This very simple implementation of an TreeNodeChangeListener writes all the events to the standard out stream.
SimpleTreeNodeChangeListener() - Constructor for class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
Creates an TreeNodeChangeListener that writes all events to the standard output.
simplify(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
 
simplify() - Method in class org.sbml.jsbml.UnitDefinition
Simplifies the UnitDefinition so that any Unit objects occurring within the UnitDefinition.listOfUnits occurs only once.
sin(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
sinh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
sinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
sinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
sinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
sinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
sinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
size() - Method in class org.sbml.jsbml.ListOf
 
size - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
SLPITTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
spatialDimensions - Variable in class org.sbml.jsbml.Compartment
Represents the spatialDimensions XML attribute of a compartment element.
spatialDimensions - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
spatialSizeUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
spatialSizeUnitsID - Variable in class org.sbml.jsbml.Species
Deprecated.
specialToken - Variable in class org.sbml.jsbml.text.parser.Token
This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
Species - Class in org.sbml.jsbml
Represents the species XML element of a SBML file.
Species() - Constructor for class org.sbml.jsbml.Species
Creates a Species instance.
Species(int, int) - Constructor for class org.sbml.jsbml.Species
Creates a Species instance from a level and version.
Species(Species) - Constructor for class org.sbml.jsbml.Species
Creates a Species instance from a Species.
Species(String) - Constructor for class org.sbml.jsbml.Species
 
Species(String, int, int) - Constructor for class org.sbml.jsbml.Species
Creates a Species instance from a level and verison.
Species(String, String, int, int) - Constructor for class org.sbml.jsbml.Species
 
species - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
speciesID - Variable in class org.sbml.jsbml.SimpleSpeciesReference
Represents the 'species' XML attribute.
SpeciesReference - Class in org.sbml.jsbml
Represents the speciesReference XML element of a SBML file.
SpeciesReference() - Constructor for class org.sbml.jsbml.SpeciesReference
Creates a SpeciesReference instance.
SpeciesReference(int, int) - Constructor for class org.sbml.jsbml.SpeciesReference
 
SpeciesReference(Species) - Constructor for class org.sbml.jsbml.SpeciesReference
Creates a SpeciesReference instance from a Species.
SpeciesReference(SpeciesReference) - Constructor for class org.sbml.jsbml.SpeciesReference
Creates a SpeciesReference instance from a given SpeciesReference.
SpeciesReference(String) - Constructor for class org.sbml.jsbml.SpeciesReference
 
SpeciesReference(String, int, int) - Constructor for class org.sbml.jsbml.SpeciesReference
 
SpeciesReference(String, String, int, int) - Constructor for class org.sbml.jsbml.SpeciesReference
 
SpeciesReferenceFilter - Class in org.sbml.jsbml.util.filters
This is a special NameFilter that allows users to search for a SimpleSpeciesReference that refers to a Species with the given identifier attribute.
SpeciesReferenceFilter() - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
Creates a new SpeciesReferenceFilter with undefined properties.
SpeciesReferenceFilter(Species) - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
Creates a new SpeciesReferenceFilter that only accepts instances of SpeciesReference pointing to the id of the given Species.
SpeciesReferenceFilter(String) - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
 
SpeciesReferenceFilter(String, String) - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
 
SpeciesType - Class in org.sbml.jsbml
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
SpeciesType() - Constructor for class org.sbml.jsbml.SpeciesType
Deprecated.
SpeciesType(int, int) - Constructor for class org.sbml.jsbml.SpeciesType
Deprecated.
SpeciesType(SpeciesType) - Constructor for class org.sbml.jsbml.SpeciesType
Deprecated.
SpeciesType(String) - Constructor for class org.sbml.jsbml.SpeciesType
Deprecated. 
SpeciesType(String, int, int) - Constructor for class org.sbml.jsbml.SpeciesType
Deprecated.
SpeciesType(String, String, int, int) - Constructor for class org.sbml.jsbml.SpeciesType
Deprecated.
speciesType - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
speciesTypeID - Variable in class org.sbml.jsbml.Species
Deprecated.
sqrt(ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates a root ASTNode.
sqrt() - Method in class org.sbml.jsbml.ASTNode
Applies the square root function on this syntax tree and returns the resulting tree.
sqrt(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Square root.
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
sqrt(Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
STATIC_LEXER_ERROR - Static variable in error org.sbml.jsbml.text.parser.TokenMgrError
An attempt was made to create a second instance of a static token manager.
staticFlag - Static variable in class org.sbml.jsbml.text.parser.SimpleCharStream
Whether parser is static.
status - Variable in class org.sbml.jsbml.SBMLErrorLog
 
status - Variable in class org.sbml.jsbml.util.Option
 
stoichiometry - Variable in class org.sbml.jsbml.SpeciesReference
Represents the 'stoichiometry' XML attribute of this SpeciesReference.
stoichiometry - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
stoichiometryMath - Variable in class org.sbml.jsbml.SpeciesReference
Deprecated. 
StoichiometryMath - Class in org.sbml.jsbml
Deprecated.
Use AssignmentRule with instances of SpeciesReference as Variable instead.
StoichiometryMath() - Constructor for class org.sbml.jsbml.StoichiometryMath
Deprecated.
StoichiometryMath(int, int) - Constructor for class org.sbml.jsbml.StoichiometryMath
Deprecated.
StoichiometryMath(StoichiometryMath) - Constructor for class org.sbml.jsbml.StoichiometryMath
Deprecated.
stream - Variable in class org.sbml.jsbml.validator.MultipartPost
 
string() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
STRING - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
StringParser - Class in org.sbml.jsbml.xml.parsers
A StringParser can be used to store the HTML expressions into an XMLNode in the SBML component.
StringParser() - Constructor for class org.sbml.jsbml.xml.parsers.StringParser
 
stringToInt(String) - Static method in class org.sbml.jsbml.SBO
Returns the string as a correctly formatted SBO integer portion.
StringTools - Class in org.sbml.jsbml.util
This class provides a collection of convenient methods for manipulating Strings.
StringTools() - Constructor for class org.sbml.jsbml.util.StringTools
 
stringToTimestamp(String) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
Convert timezone of datetime string to GMT.
style - Variable in class org.sbml.jsbml.ASTNode
Possible attributes for a MathML element
style - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
subList(int, int) - Method in class org.sbml.jsbml.ListOf
 
SubModel - Class in org.sbml.jsbml.util
Generates a sub-Model containing the elements passed as argument and all the necessary dependencies.
SubModel() - Constructor for class org.sbml.jsbml.util.SubModel
 
subsection(String, boolean) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
SUBSTANCE - Static variable in class org.sbml.jsbml.UnitDefinition
Identifier of the (for the SBML Levels 1 and 2) predefined UnitDefinition substance.
substance(int, int) - Static method in class org.sbml.jsbml.UnitDefinition
Predefined unit for substance.
substanceUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
substanceUnitsID - Variable in class org.sbml.jsbml.KineticLaw
Deprecated. 
substanceUnitsID - Variable in class org.sbml.jsbml.Model
Represents the 'substanceUnits' XML attribute of a model element.
subsubsection(String, boolean) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
sum(ASTNode...) - Static method in class org.sbml.jsbml.ASTNode
Creates a new ASTNode of type Plus with the given nodes as children.
sum(MathContainer, CallableSBase...) - Static method in class org.sbml.jsbml.ASTNode
Sum of several NamedSBase objects.
sum(Object...) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Returns the sum of the given elements as StringBuffer.
sum(Object...) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula
Returns the sum of the given elements as StringBuffer.
svariables - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
A list where the ids of all global species in an MathML expression are saved temporarily
swapChildren(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Swaps the children of this ASTNode with the children of that ASTNode.
SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
Switch to specified lex state.
Symbol - Class in org.sbml.jsbml
The base class for Compartment, Species, Parameter.
Symbol() - Constructor for class org.sbml.jsbml.Symbol
Creates a Symbol instance.
Symbol(int, int) - Constructor for class org.sbml.jsbml.Symbol
Creates a Symbol instance from a level and version.
Symbol(QuantityWithUnit) - Constructor for class org.sbml.jsbml.Symbol
 
Symbol(String) - Constructor for class org.sbml.jsbml.Symbol
 
Symbol(String, int, int) - Constructor for class org.sbml.jsbml.Symbol
Creates a Symbol instance from an id, level and version.
Symbol(String, String, int, int) - Constructor for class org.sbml.jsbml.Symbol
Creates a Symbol instance from an id, name, level and version.
Symbol(Symbol) - Constructor for class org.sbml.jsbml.Symbol
Creates a Symbol instance from a given Symbol.
symbol - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
symbolTime(String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
The simulation time.
symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 

T

tabSize - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
tan(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
tan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
tan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
tan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
tan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
tan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
tanh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
tanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
tanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
tanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
tanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
tanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
term - Variable in class org.sbml.jsbml.SBO.Term
The underlying BioJava org.biojava.ontology.Term.
term - Variable in class org.sbml.jsbml.util.filters.SBOFilter
The SBO term of interest.
TermLvl1() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
TermLvl2() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
TermLvl3() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
terms - Static variable in class org.sbml.jsbml.SBO
 
text - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
textcolor(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
texttt(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Returns the LaTeX code to set the given String in type writer font.
TIME - Static variable in class org.sbml.jsbml.UnitDefinition
Identifier of the (for the SBML Levels 1 and 2) predefined UnitDefinition time.
time(int, int) - Static method in class org.sbml.jsbml.UnitDefinition
Predefined unit for time.
timeDerivative(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
times(ASTNode...) - Static method in class org.sbml.jsbml.ASTNode
Creates an ASTNode of type times and adds the given nodes as children.
times(MathContainer, CallableSBase...) - Static method in class org.sbml.jsbml.ASTNode
Multiplies several NamedSBase objects.
TIMES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
times(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Product of all given ASTNodes.
times(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
times(Object...) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Returns the product of the given elements as StringBuffer.
times(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
times(Object...) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula
Returns the product of the given elements as StringBuffer.
times(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
times(ASTNodeValue...) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
Convenient method to perform internal changes.
times(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
times(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
timeUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
timeUnitsID - Variable in class org.sbml.jsbml.KineticLaw
Deprecated. 
timeUnitsID - Variable in class org.sbml.jsbml.Model
Represents the 'timeUnits' XML attribute of a model element.
toArray() - Method in class org.sbml.jsbml.ListOf
 
toArray(T[]) - Method in class org.sbml.jsbml.ListOf
 
toBoolean() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
Analog to the toDouble() method but this method tries to evaluate the value contained in this object to a boolean value.
toCallableSBase() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
toClass() - Method in enum org.sbml.jsbml.ListOf.Type
Gives the corresponding Class object for this ListOf.Type.
toDouble() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
toFloat() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
toFormula() - Method in class org.sbml.jsbml.ASTNode
Converts this ASTNode to a text string using a specific syntax for mathematical formulas.
toHTML(Unit) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula
 
toHTML(UnitDefinition) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula
Creates an HTML string representation of this UnitDefinition.
toHTML(String) - Static method in class org.sbml.jsbml.util.StringTools
Returns a HTML formated String, in which each line is at most lineBreak symbols long.
toHTML(String, int) - Static method in class org.sbml.jsbml.util.StringTools
Returns a HTML formated String, in which each line is at most lineBreak symbols long.
toInteger() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
This method is analog to the toDouble method but tries to convert this value into an integer.
token - Variable in class org.sbml.jsbml.text.parser.FormulaParser
Current token.
Token - Class in org.sbml.jsbml.text.parser
Describes the input token stream.
Token() - Constructor for class org.sbml.jsbml.text.parser.Token
No-argument constructor
Token(int) - Constructor for class org.sbml.jsbml.text.parser.Token
Constructs a new token for the specified Image.
Token(int, String) - Constructor for class org.sbml.jsbml.text.parser.Token
Constructs a new token for the specified Image and Kind.
token_source - Variable in class org.sbml.jsbml.text.parser.FormulaParser
Generated Token Manager.
tokenBegin - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
 
tokenImage - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
Literal token values.
tokenImage - Variable in exception org.sbml.jsbml.text.parser.ParseException
This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
TokenMgrError - Error in org.sbml.jsbml.text.parser
Token Manager Error.
TokenMgrError() - Constructor for error org.sbml.jsbml.text.parser.TokenMgrError
No arg constructor.
TokenMgrError(String, int) - Constructor for error org.sbml.jsbml.text.parser.TokenMgrError
Constructor with message and reason.
TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.sbml.jsbml.text.parser.TokenMgrError
Full Constructor.
toLaTeX() - Method in class org.sbml.jsbml.ASTNode
Converts this node recursively into a LaTeX formatted String.
toLong() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
toMathML() - Method in class org.sbml.jsbml.ASTNode
Converts this node recursively into a MathML string that corresponds to the subset of MathML defined in the SBML specification.
toMathML(boolean, boolean, int) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
toMathML(ASTNode) - Static method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
Writes an ASTNode the mathML.
toMathML(Document, boolean, boolean, int) - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
Write output as String.
toMathML(Writer, Document, boolean, boolean, int) - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
toNode() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
toNumber() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
Tries to convert the value contained in this object into a double number.
toprule - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Needed for the beginning of a table.
toString() - Method in class org.sbml.jsbml.AbstractMathContainer
 
toString() - Method in class org.sbml.jsbml.AbstractNamedSBase
Returns the name of the component, if it is available.
toString() - Method in class org.sbml.jsbml.AbstractSBase
 
toString() - Method in class org.sbml.jsbml.AbstractTreeNode
 
toString() - Method in class org.sbml.jsbml.ASTNode
 
toString() - Method in class org.sbml.jsbml.Creator
Returns the information about the creator as a String.
toString() - Method in class org.sbml.jsbml.CVTerm
Returns a String containing the qualifier and all the resource URIs of this CVTerm.
toString() - Method in class org.sbml.jsbml.EventAssignment
 
toString() - Method in class org.sbml.jsbml.FunctionDefinition
 
toString() - Method in class org.sbml.jsbml.KineticLaw
 
toString() - Method in exception org.sbml.jsbml.LevelVersionError
 
toString() - Method in class org.sbml.jsbml.ListOf
 
toString() - Method in exception org.sbml.jsbml.PropertyException
 
toString() - Method in class org.sbml.jsbml.SBMLDocument
 
toString() - Method in exception org.sbml.jsbml.SBMLError
 
toString() - Method in class org.sbml.jsbml.SBMLReader
 
toString() - Method in class org.sbml.jsbml.SBMLWriter
 
toString() - Method in class org.sbml.jsbml.SBO.Term
 
toString() - Method in class org.sbml.jsbml.SBO.Triple
 
toString() - Method in class org.sbml.jsbml.SimpleSpeciesReference
 
toString() - Method in class org.sbml.jsbml.text.parser.Token
Returns the image.
toString() - Method in class org.sbml.jsbml.Unit
Produces a text formula representation of this unit.
toString() - Method in class org.sbml.jsbml.UnitDefinition
 
toString() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
toString() - Method in class org.sbml.jsbml.util.Location
 
toString() - Method in class org.sbml.jsbml.util.Message
 
toString() - Method in class org.sbml.jsbml.util.Option
 
toString(double) - Static method in class org.sbml.jsbml.util.StringTools
Returns a String from the given value that does not contain a point zero at the end if the given value represents an integer number.
toString(Locale, double) - Static method in class org.sbml.jsbml.util.StringTools
Allows for Locale-dependent number formatting.
toString() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
 
toString() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent
 
toString() - Method in class org.sbml.jsbml.util.ValuePair
 
toString() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
 
toString() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
 
toString() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator.TerminalNode
 
toString() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
 
toString() - Method in class org.sbml.jsbml.xml.XMLToken
 
toXML(String, StringBuffer) - Method in class org.sbml.jsbml.Creator
Converts the Creator into XML
toXML(String, StringBuffer) - Method in class org.sbml.jsbml.CVTerm
Writes all the MIRIAM annotations of the CVTerm in 'buffer'
toXML(XMLNode) - Static method in class org.sbml.jsbml.xml.parsers.XMLNodeWriter
 
toXMLMessageString(String) - Static method in class org.sbml.jsbml.util.StringTools
Checks whether a given String fits into the definition of the XML message String in SBML.
toXMLNotesString(String) - Static method in class org.sbml.jsbml.util.StringTools
Checks whether a given String fits into the definition of the XML notes String in SBML.
toXMLString(String, String) - Static method in class org.sbml.jsbml.util.StringTools
Checks whether a given String contain the given surrounding tag.
toXMLString() - Method in class org.sbml.jsbml.xml.XMLNode
Returns a string representation of this XMLNode.
transformer_factory - Static variable in class org.sbml.jsbml.util.JAXPFacade
 
TreeNodeAdapter - Class in org.sbml.jsbml.util
This class is a wrapper element for any Object that should be linked into a tree data structure as represented by AbstractTreeNode, but that might by itself not be an instance of TreeNode, i.e., not compatible with the remaining tree data structure.
TreeNodeAdapter(Object, TreeNode) - Constructor for class org.sbml.jsbml.util.TreeNodeAdapter
Creates a new TreeNode wrapper for the given TreeNodeAdapter.userObject that will be linked to the given AbstractTreeNode.parent within an exisiting tree.
TreeNodeAdapter(TreeNodeAdapter) - Constructor for class org.sbml.jsbml.util.TreeNodeAdapter
Copy constructor for the given node.
TreeNodeChangeEvent - Class in org.sbml.jsbml.util
This event tells an TreeNodeChangeListener which values have been changed in an SBase and also provides the old and the new value.
TreeNodeChangeEvent(TreeNode, String, Object, Object) - Constructor for class org.sbml.jsbml.util.TreeNodeChangeEvent
 
TreeNodeChangeEvent(TreeNodeChangeEvent) - Constructor for class org.sbml.jsbml.util.TreeNodeChangeEvent
 
TreeNodeChangeListener - Interface in org.sbml.jsbml.util
A listener interface that allows applications to get notified if the state of any TreeNode object changes.
TreeNodeRemovedEvent - Class in org.sbml.jsbml.util
A special EventObject to notify a TreeNodeChangeListener about a removed node and its previous position within the tree.
TreeNodeRemovedEvent(TreeNode, TreeNode) - Constructor for class org.sbml.jsbml.util.TreeNodeRemovedEvent
Creates a new TreeNodeRemovedEvent that contains information about an element that has just been removed from a tree together with its previous parent node.
TreeNodeRemovedEvent(TreeNodeRemovedEvent) - Constructor for class org.sbml.jsbml.util.TreeNodeRemovedEvent
Clone constructor.
TreeNodeWithChangeSupport - Interface in org.sbml.jsbml.util
This interface extends the regular recursively defined TreeNode by adding methods to keep track of changes within the tree, such as adding/removing, or exchanging of child nodes or the change of any other attributes.
trigger - Variable in class org.sbml.jsbml.Event
Represents the trigger sub-element of an event element.
Trigger - Class in org.sbml.jsbml
Represents the trigger XML element of a SBML file.
Trigger() - Constructor for class org.sbml.jsbml.Trigger
Creates a Trigger instance.
Trigger(int, int) - Constructor for class org.sbml.jsbml.Trigger
Creates a Trigger instance from a level and version.
Trigger(Trigger) - Constructor for class org.sbml.jsbml.Trigger
Creates a Trigger instance from a given Trigger.
triple - Variable in class org.sbml.jsbml.SBO.Triple
The BioJava org.biojava.ontology.Triple.
triple - Variable in class org.sbml.jsbml.xml.XMLToken
the XMLTripe (name, uri and prefix) of this XML element.
type - Variable in class org.sbml.jsbml.ASTNode
The type of this ASTNode.
type - Variable in class org.sbml.jsbml.CVTerm
Represents the type of MIRIAM qualifier for this CVTerm.
type - Variable in exception org.sbml.jsbml.SBMLException
 
type - Variable in class org.sbml.jsbml.util.compilers.ASTNodeValue
The type of the underlying ASTNode.
type - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
type - Variable in class org.sbml.jsbml.xml.parsers.SBMLLevel1Rule
 
typeOfNotes - Variable in class org.sbml.jsbml.xml.parsers.StringParser
String to be able to detect what type of String this parser is parsing.

U

uFlag - Variable in class org.sbml.jsbml.util.compilers.ASTNodeValue
Flag to indicate whether the underlying ASTNode was an unary node.
uMinus(ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates a new ASTNode that has exactly one child and which is of type minus, i.e., this negates what is encoded in ast.
uMinus(MathContainer, CallableSBase) - Static method in class org.sbml.jsbml.ASTNode
Creates a new ASTNode that has exactly one child and which is of type minus, i.e., this negates what is encoded in ast.
uMinus(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Unary minus, i.e., negation of the given ASTNode.
uMinus(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
uMinus(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
uMinus(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
uMinus(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
uMinus(ASTNodeValue) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
uMinus(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
UNDEFINED_LEVEL_VERSION_COMBINATION_MSG - Static variable in exception org.sbml.jsbml.LevelVersionError
Message to indicate that an invalid combination of the level and version attribute has been set.
UNDEFINED_MODEL_MSG - Static variable in class org.sbml.jsbml.JSBML
This indicates that the Model has not been set properly or that an element tries to access its containing model but this is not possible.
UNDEFINED_PARSE_ERROR_MSG - Static variable in class org.sbml.jsbml.JSBML
This message indicates that a problem occurred but the current class cannot give any more precise information about the reasons.
UNDEFINED_PARSING_ERROR_MSG - Static variable in class org.sbml.jsbml.JSBML
This message indicates that a problem occurred but the current class cannot give any more precise information about the reasons.
underscore - Static variable in class org.sbml.jsbml.AbstractNamedSBase
 
underscore - Static variable in class org.sbml.jsbml.util.StringTools
The Character '_' as a String.
UNEXPECTED_ATTRIBUTE - Static variable in class org.sbml.jsbml.JSBML
 
unifyUnits(ASTNodeValue, ASTNodeValue) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
This method tries to unify the units of two ASTNodeValues so that they have the same units and their value thus is also adjusted.
UniqueNamedSBase - Interface in org.sbml.jsbml
This interface is used to tag all those elements whose identifier must be unique within an SBML Model.
Unit - Class in org.sbml.jsbml
Represents the unit XML element of a SBML file.
Unit() - Constructor for class org.sbml.jsbml.Unit
Creates a Unit instance.
Unit(double, int, Unit.Kind, double, int, int) - Constructor for class org.sbml.jsbml.Unit
Creates a Unit instance from a multiplier, scale, kind and exponent.
Unit(int, int) - Constructor for class org.sbml.jsbml.Unit
Creates a Unit instance from a level and version.
Unit(int, Unit.Kind, double, int, int) - Constructor for class org.sbml.jsbml.Unit
Creates a Unit instance from a scale, kind, exponent, level and version.
Unit(int, Unit.Kind, int, int) - Constructor for class org.sbml.jsbml.Unit
Creates a Unit instance from a scale, kind, level and version.
Unit(Unit.Kind, double, int, int) - Constructor for class org.sbml.jsbml.Unit
Creates a Unit instance from a kind, exponent, level and version.
Unit(Unit.Kind, int, int) - Constructor for class org.sbml.jsbml.Unit
Creates a Unit instance from a kind, level and version.
Unit(String, int, int) - Constructor for class org.sbml.jsbml.Unit
 
Unit(Unit) - Constructor for class org.sbml.jsbml.Unit
Creates a Unit instance from a given Unit.
Unit.Kind - Enum in org.sbml.jsbml
This enumeration contains an exhaustive list of all available unit kinds within all Levels and Versions of SBML.
Unit.Kind() - Constructor for enum org.sbml.jsbml.Unit.Kind
 
unitDef - Variable in class org.sbml.jsbml.util.compilers.ASTNodeValue
The unit associated to the value of this object.
UnitDefinition - Class in org.sbml.jsbml
Represents the unitDefinition XML element of a SBML file.
UnitDefinition() - Constructor for class org.sbml.jsbml.UnitDefinition
Creates an UnitDefinition instance.
UnitDefinition(int, int) - Constructor for class org.sbml.jsbml.UnitDefinition
 
UnitDefinition(String) - Constructor for class org.sbml.jsbml.UnitDefinition
 
UnitDefinition(String, int, int) - Constructor for class org.sbml.jsbml.UnitDefinition
Creates an UnitDefinition instance from an id, level and version.
UnitDefinition(String, String, int, int) - Constructor for class org.sbml.jsbml.UnitDefinition
Creates an UnitDefinition instance from an id, level and version.
UnitDefinition(UnitDefinition) - Constructor for class org.sbml.jsbml.UnitDefinition
Creates an UnitDefinition instance from a given UnitDefinition.
UnitException - Exception in org.sbml.jsbml.util.compilers
Exception to be thrown if inconsistent units are used in mathematical expressions, i.e., instances of ASTNode.
UnitException() - Constructor for exception org.sbml.jsbml.util.compilers.UnitException
 
UnitException(String) - Constructor for exception org.sbml.jsbml.util.compilers.UnitException
 
UnitException(Throwable) - Constructor for exception org.sbml.jsbml.util.compilers.UnitException
 
UnitException(String, Throwable) - Constructor for exception org.sbml.jsbml.util.compilers.UnitException
 
unitId - Variable in class org.sbml.jsbml.ASTNode
Since Level 3 SBML allows to equip numbers with unit identifiers.
units - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
UnitsCompiler - Class in org.sbml.jsbml.util.compilers
Derives the units from mathematical operations.
UnitsCompiler() - Constructor for class org.sbml.jsbml.util.compilers.UnitsCompiler
 
UnitsCompiler(int, int) - Constructor for class org.sbml.jsbml.util.compilers.UnitsCompiler
 
UnitsCompiler(Model) - Constructor for class org.sbml.jsbml.util.compilers.UnitsCompiler
 
unitsID - Variable in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
The unit attribute of this variable.
unitsID - Variable in class org.sbml.jsbml.ExplicitRule
Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
unitsID - Variable in class org.sbml.jsbml.KineticLaw
Deprecated. 
unknownValue() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Dealing with a malformed ASTNode.
unknownValue() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
unknownValue() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
unknownValue() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
unknownValue() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
unknownValue() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
unmarshal(HierarchicalStreamReader, UnmarshallingContext) - Method in class org.sbml.jsbml.xml.xstream.converter.MessageConverter
 
unregister(SBase) - Method in class org.sbml.jsbml.AbstractSBase
 
unregister(SBase) - Method in interface org.sbml.jsbml.SBase
Unregisters recursively the given SBase from the Model and SBMLDocument.
unsetAnnotation() - Method in class org.sbml.jsbml.AbstractSBase
 
unsetAnnotation() - Method in interface org.sbml.jsbml.SBase
Unsets the value of the 'annotation' sub-element of this SBML object.
unsetAreaUnits() - Method in class org.sbml.jsbml.Model
Sets the areaUnitsID of this Model to null.
unsetBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm
Unsets the biological qualifier if it is set.
unsetCharge() - Method in class org.sbml.jsbml.Species
Deprecated. 
unsetCompartment() - Method in class org.sbml.jsbml.Species
Remove the reference to a comparmtent.
unsetCompartmentType() - Method in class org.sbml.jsbml.Compartment
Sets the compartmentTypeID of this Compartment to null.
unsetConstant() - Method in class org.sbml.jsbml.SpeciesReference
 
unsetConstant() - Method in class org.sbml.jsbml.Symbol
 
unsetConstant() - Method in interface org.sbml.jsbml.Variable
With this method the constant property of this variable will be set to an undefined state.
unsetConversionFactor() - Method in class org.sbml.jsbml.Model
Sets the conversionFactorID of this Model to null.
unsetConversionFactor() - Method in class org.sbml.jsbml.Species
Unsets the conversionFactorID of this Species.
unsetCreatedDate() - Method in class org.sbml.jsbml.History
Sets the created of this History to null.
unsetCVTerms() - Method in class org.sbml.jsbml.AbstractSBase
 
unsetCVTerms() - Method in class org.sbml.jsbml.Annotation
Clears the List of CVTerms and removes unnecessary entries from the Annotation.rdfAnnotationNamespaces.
unsetCVTerms() - Method in interface org.sbml.jsbml.SBase
Unsets the list of CVTerm of this object.
unsetCVTerms - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
unsetDelay() - Method in class org.sbml.jsbml.Event
Sets the delay of this Event to null.
unsetEmail() - Method in class org.sbml.jsbml.Creator
Unsets the email of this Creator.
unsetEnd() - Method in class org.sbml.jsbml.xml.XMLToken
Declares this XML start/end element is no longer an end element.
unsetExponent() - Method in class org.sbml.jsbml.Unit
 
unsetExtentUnits() - Method in class org.sbml.jsbml.Model
Sets the extentUnitsID of this Model to null.
unsetFamilyName() - Method in class org.sbml.jsbml.Creator
Unsets the familyName of this Creator.
unsetFast() - Method in class org.sbml.jsbml.Reaction
Sets the fast Boolean of this Reaction to null.
unsetFormula() - Method in class org.sbml.jsbml.AbstractMathContainer
Deprecated.
unsetFormula() - Method in interface org.sbml.jsbml.MathContainer
Deprecated.
unsetGivenName() - Method in class org.sbml.jsbml.Creator
Unsets the givenName of this Creator.
unsetHistory() - Method in class org.sbml.jsbml.AbstractSBase
 
unsetHistory() - Method in class org.sbml.jsbml.Annotation
Sets the History instance of this object to null.
unsetHistory() - Method in interface org.sbml.jsbml.SBase
Unsets the History of this object.
unsetId() - Method in class org.sbml.jsbml.AbstractNamedSBase
 
unsetId() - Method in class org.sbml.jsbml.FunctionDefinition
 
unsetId() - Method in interface org.sbml.jsbml.NamedSBase
sets the id value to null.
unsetInitialAmount() - Method in class org.sbml.jsbml.Species
Unsets the initialAmount of this Species.
unsetInitialConcentration() - Method in class org.sbml.jsbml.Species
Unsets the initialConcentration of this Species.
unsetKind() - Method in class org.sbml.jsbml.Unit
 
unsetKineticLaw() - Method in class org.sbml.jsbml.Reaction
Sets the KineticLaw of this Reaction to null and notifies all TreeNodeChangeListener about changes.
unsetLengthUnits() - Method in class org.sbml.jsbml.Model
Sets the lengthUnitsID of this Model to null.
unsetListOfCompartments() - Method in class org.sbml.jsbml.Model
Removes the Model.listOfCompartments from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfCompartmentTypes() - Method in class org.sbml.jsbml.Model
Deprecated. 
unsetListOfConstraints() - Method in class org.sbml.jsbml.Model
Removes the Model.listOfConstraints from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfEventAssignments() - Method in class org.sbml.jsbml.Event
Removes the Event.listOfEventAssignments from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfEvents() - Method in class org.sbml.jsbml.Model
Removes the Model.listOfEvents from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfFunctionDefinitions() - Method in class org.sbml.jsbml.Model
Removes the Model.listOfFunctionDefinitions from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfInitialAssignments() - Method in class org.sbml.jsbml.Model
Removes the Model.listOfInitialAssignments from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfLocalParameters() - Method in class org.sbml.jsbml.KineticLaw
Removes the KineticLaw.listOfLocalParameters from this KineticLaw and notifies all registered instances of TreeNodeChangeListener.
unsetListOfModifiedDates() - Method in class org.sbml.jsbml.History
Sets the created of this History to null.
unsetListOfModifiers() - Method in class org.sbml.jsbml.Reaction
Removes the Reaction.listOfModifiers from this Reaction and notifies all registered instances of TreeNodeChangeListener.
unsetListOfParameters() - Method in class org.sbml.jsbml.KineticLaw
unsetListOfParameters() - Method in class org.sbml.jsbml.Model
Removes the Model.listOfParameters from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfProducts() - Method in class org.sbml.jsbml.Reaction
Removes the Reaction.listOfProducts from this Reaction and notifies all registered instances of TreeNodeChangeListener.
unsetListOfReactants() - Method in class org.sbml.jsbml.Reaction
Removes the Reaction.listOfReactants from this Reaction and notifies all registered instances of TreeNodeChangeListener.
unsetListOfReactions() - Method in class org.sbml.jsbml.Model
Removes the Model.listOfReactions from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfRules() - Method in class org.sbml.jsbml.Model
Removes the Model.listOfRules from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfSpecies() - Method in class org.sbml.jsbml.Model
Removes the Model.listOfSpecies from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfSpeciesTypes() - Method in class org.sbml.jsbml.Model
Deprecated. 
unsetListOfUnitDefinitions() - Method in class org.sbml.jsbml.Model
Removes the Model.listOfUnitDefinitions from this Model and notifies all registered instances of TreeNodeChangeListener.
unsetListOfUnits() - Method in class org.sbml.jsbml.UnitDefinition
Removes the UnitDefinition.listOfUnits from this UnitDefinition and notifies all registered instances of TreeNodeChangeListener.
unsetMath() - Method in class org.sbml.jsbml.AbstractMathContainer
 
unsetMath() - Method in interface org.sbml.jsbml.MathContainer
 
unsetMessage() - Method in class org.sbml.jsbml.Constraint
Sets the message of this Constraint to null.
unsetMetaId() - Method in class org.sbml.jsbml.AbstractSBase
 
unsetMetaId() - Method in interface org.sbml.jsbml.SBase
Unsets the value of the 'metaid' attribute of this SBML object.
unsetModel() - Method in class org.sbml.jsbml.SBMLDocument
Sets the Model of this SBMLDocument to null and notifies all TreeNodeChangeListener about changes.
unsetModelHistory() - Method in class org.sbml.jsbml.Model
unsetModelQualifierType() - Method in class org.sbml.jsbml.CVTerm
Unsets the model qualifier if it is set.
unsetMultiplier() - Method in class org.sbml.jsbml.Unit
 
unsetName() - Method in class org.sbml.jsbml.AbstractNamedSBase
 
unsetName() - Method in class org.sbml.jsbml.FunctionDefinition
 
unsetName() - Method in interface org.sbml.jsbml.NamedSBase
sets the name value to null.
unsetNonRDFannotation() - Method in class org.sbml.jsbml.Annotation
Sets the non RDF annotation String to null.
unsetNotes() - Method in class org.sbml.jsbml.AbstractSBase
 
unsetNotes() - Method in interface org.sbml.jsbml.SBase
Unsets the value of the 'notes' sub-element of this SBML object.
unsetOffset() - Method in class org.sbml.jsbml.Unit
Deprecated.
the offset attribute should no longer be used.
unsetOrganization() - Method in class org.sbml.jsbml.Creator
Unsets the organisation of this Creator.
unsetOutside() - Method in class org.sbml.jsbml.Compartment
Deprecated.
since Level 3 Version 1
unsetPriority() - Method in class org.sbml.jsbml.Event
Sets the Priority of this Event to null and notifies TreeNodeChangeListeners.
unsetProgramName() - Method in class org.sbml.jsbml.SBMLWriter
 
unsetProgramVersion() - Method in class org.sbml.jsbml.SBMLWriter
 
unsetQualifierType() - Method in class org.sbml.jsbml.CVTerm
Unsets the qualifier type if it is set.
unsetReversible() - Method in class org.sbml.jsbml.Reaction
Sets the reversible Boolean of this Reaction to null.
unsetSBaseListType() - Method in class org.sbml.jsbml.ListOf
Sets the SBaseListType of this ListOf to SBaseListType.none.
unsetSBOTerm() - Method in class org.sbml.jsbml.AbstractSBase
 
unsetSBOTerm() - Method in interface org.sbml.jsbml.SBase
Unsets the value of the 'sboTerm' attribute of this SBML object.
unsetScale() - Method in class org.sbml.jsbml.Unit
 
unsetSize() - Method in class org.sbml.jsbml.Compartment
Unsets the value of the 'size' attribute of this Compartment.
unsetSpatialDimensions() - Method in class org.sbml.jsbml.Compartment
Sets the spatialDimensions of this compartment to null.
unsetSpatialSizeUnits() - Method in class org.sbml.jsbml.Species
Deprecated. 
unsetStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference
Unsets the stoichiometry property of this element.
unsetStoichiometryMath() - Method in class org.sbml.jsbml.SpeciesReference
Deprecated. 
unsetSubstanceUnits() - Method in class org.sbml.jsbml.KineticLaw
Deprecated. 
unsetSubstanceUnits() - Method in class org.sbml.jsbml.Model
Sets the Model.substanceUnitsID of this Model to null.
unsetSubstanceUnits() - Method in class org.sbml.jsbml.Species
Unsets the substanceUnits of this Species.
unsetTimeUnits() - Method in class org.sbml.jsbml.Event
Sets the timeUnitsID of this Event to null.
unsetTimeUnits() - Method in class org.sbml.jsbml.KineticLaw
Deprecated. 
unsetTimeUnits() - Method in class org.sbml.jsbml.Model
Sets the timeUnitsID of this Model to null.
unsetTrigger() - Method in class org.sbml.jsbml.Event
Sets the trigger of this Event to null and notifies TreeNodeChangeListeners.
unsetUnit() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
Removes the unit of this element, i.e., the unit will become invalid.
unsetUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
 
unsetUnits() - Method in class org.sbml.jsbml.ASTNode
Unset the units attribute.
unsetUnits() - Method in class org.sbml.jsbml.ExplicitRule
Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this ExplicitRule represents the SBML element ParameterRule.
unsetUnits() - Method in class org.sbml.jsbml.KineticLaw
Deprecated.
unsetUnits() - Method in interface org.sbml.jsbml.SBaseWithUnit
Sets the unitsID of this SBaseWithUnit to null.
unsetUserObject() - Method in class org.sbml.jsbml.ASTNode
 
unsetUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event
Sets the useValuesFromTriggerTime of this Event to null.
unsetValue() - Method in interface org.sbml.jsbml.Quantity
Unsets the value of this Quantity.
unsetValue() - Method in class org.sbml.jsbml.QuantityWithUnit
 
unsetValue() - Method in class org.sbml.jsbml.SpeciesReference
 
unsetVariable() - Method in interface org.sbml.jsbml.Assignment
Removes the reference from this InitialAssignment to its Variable if there was any, i.e., the Variable is set to null.
unsetVariable() - Method in class org.sbml.jsbml.EventAssignment
 
unsetVariable() - Method in class org.sbml.jsbml.ExplicitRule
 
unsetVariable() - Method in class org.sbml.jsbml.InitialAssignment
 
unsetVolume() - Method in class org.sbml.jsbml.Compartment
Deprecated.
The volume attribute is only defined in SBML Level 1. Please use Compartment.unsetSize()
unsetVolumeUnits() - Method in class org.sbml.jsbml.Model
Sets the volumeUnitsID of this Model to null.
UpdateLineColumn(char) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
 
updateMatching(List<OverdeterminationValidator.Node<SBase>>) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
Updates the matching of the model on the basis of the found augmented path.
updateVariables() - Method in class org.sbml.jsbml.ASTNode
For a better performance ASTNodes can store a direct pointer to a variable element.
URI_AVOGADRO_DEFINITION - Static variable in class org.sbml.jsbml.ASTNode
The URI for the definition of the csymbol for avogadro.
URI_BIOMODELS_NET_BIOLOGY_QUALIFIERS - Static variable in class org.sbml.jsbml.CVTerm
 
URI_BIOMODELS_NET_MODEL_QUALIFIERS - Static variable in class org.sbml.jsbml.CVTerm
 
URI_DELAY_DEFINITION - Static variable in class org.sbml.jsbml.ASTNode
The URI for the definition of the csymbol for delay.
URI_MATHML_DEFINITION - Static variable in class org.sbml.jsbml.ASTNode
URI for the definition of MathML.
URI_MATHML_PREFIX - Static variable in class org.sbml.jsbml.ASTNode
URI prefix for the definition of MathML, it will be used to write the sbml file
URI_NAMESPACE_L1 - Static variable in class org.sbml.jsbml.SBMLDocument
The namespace URI of SBML Level 1 Version 1 and 2.
URI_NAMESPACE_L2V1 - Static variable in class org.sbml.jsbml.SBMLDocument
The namespace URI of SBML Level 2 Version 1.
URI_NAMESPACE_L2V2 - Static variable in class org.sbml.jsbml.SBMLDocument
The namespace URI of SBML Level 2 Version 2.
URI_NAMESPACE_L2V3 - Static variable in class org.sbml.jsbml.SBMLDocument
The namespace URI of SBML Level 2 Version 3.
URI_NAMESPACE_L2V4 - Static variable in class org.sbml.jsbml.SBMLDocument
The namespace URI of SBML Level 2 Version 4.
URI_NAMESPACE_L3V1Core - Static variable in class org.sbml.jsbml.SBMLDocument
The namespace URI of SBML Level 3 Version 1.
URI_PURL_ELEMENTS - Static variable in class org.sbml.jsbml.JSBML
URI for the definition of purl elements
URI_PURL_TERMS - Static variable in class org.sbml.jsbml.JSBML
URI for purl terms.
URI_RDF_SYNTAX_NS - Static variable in class org.sbml.jsbml.Annotation
The RDF syntax name space definition URI.
URI_RDF_VCARD_NS - Static variable in class org.sbml.jsbml.Creator
URI for the RDF syntax name space definition for VCards.
URI_TIME_DEFINITION - Static variable in class org.sbml.jsbml.ASTNode
The URI for the definition of the csymbol for time.
URI_XHTML_DEFINITION - Static variable in class org.sbml.jsbml.JSBML
URI for the definition of XHTML.
usage() - Static method in class org.sbml.jsbml.validator.SBMLValidator
 
usedNamespaces - Variable in class org.sbml.jsbml.AbstractSBase
Contains all the namespaces used by this SBase element.
usepackage(String, String...) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
Creates a usepackage command for the given package with the optional options.
userObject - Variable in class org.sbml.jsbml.ASTNode
Any kind of Object that can be stored in addition to all other features of this ASTNode.
userObject - Variable in class org.sbml.jsbml.util.TreeNodeAdapter
The object to be wrapped.
userObject - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
useValuesFromTriggerTime - Variable in class org.sbml.jsbml.Event
Represents the 'useValuesFromTriggerTime' XML attribute of an event element.
useValuesFromTriggerTime - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 

V

v - Variable in class org.sbml.jsbml.util.ValuePair
 
validateSBML(String, Map<String, String>) - Static method in class org.sbml.jsbml.validator.Validator
Validates the given SBML filename (or http:// URL) by calling the SBML.org online validator.
validationErrors - Variable in class org.sbml.jsbml.SBMLErrorLog
 
Validator - Class in org.sbml.jsbml.validator
Validator is simply a container for the static method validateSBML(filename, parameters).
Validator() - Constructor for class org.sbml.jsbml.validator.Validator
 
validatorURL - Static variable in class org.sbml.jsbml.validator.Validator
 
value - Variable in class org.sbml.jsbml.QuantityWithUnit
The size, initial amount or concentration, or the actual value of this variable.
value - Variable in class org.sbml.jsbml.util.compilers.ASTNodeValue
The actual value of this element.
value - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
value - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
Value of this Node
valueOf(String) - Static method in enum org.sbml.jsbml.AbstractSBase.NOTES_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.ASTNode.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.CVTerm.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.ListOf.Type
Returns the enum constant of this type with the specified name.
valueOf(Class<? extends SBase>) - Static method in enum org.sbml.jsbml.ListOf.Type
Gives the corresponding ListOf.Type for the given Class object.
valueOf(String) - Static method in enum org.sbml.jsbml.SBMLError.SEVERITY
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.SBMLException.Category
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.SBMLException.Code
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.SBMLException.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.Unit.Kind
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY
Returns the enum constant of this type with the specified name.
ValuePair<L extends java.lang.Comparable<? super L>,V extends java.lang.Comparable<? super V>> - Class in org.sbml.jsbml.util
A pair of two values with type parameters.
ValuePair() - Constructor for class org.sbml.jsbml.util.ValuePair
Creates a new ValuePair with both attributes set to null.
ValuePair(L, V) - Constructor for class org.sbml.jsbml.util.ValuePair
 
ValuePair(ValuePair<L, V>) - Constructor for class org.sbml.jsbml.util.ValuePair
 
values() - Static method in enum org.sbml.jsbml.AbstractSBase.NOTES_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.ASTNode.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.CVTerm.Qualifier
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.CVTerm.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.ListOf.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.SBMLError.SEVERITY
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.SBMLException.Category
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.SBMLException.Code
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.SBMLException.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.Unit.Kind
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY
Returns an array containing the constants of this enum type, in the order they are declared.
variable - Variable in class org.sbml.jsbml.ASTNode
A direct pointer to a referenced variable.
variable - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
Variable - Interface in org.sbml.jsbml
A variable of the system is a Quantity whose value may change during a simulation.
variableHash - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
HashMap with id -> node for variables
variableID - Variable in class org.sbml.jsbml.EventAssignment
Represents the 'variable' XML attribute of an eventAssignment element.
variableID - Variable in class org.sbml.jsbml.ExplicitRule
Represents the id of a Variable.
variableID - Variable in class org.sbml.jsbml.InitialAssignment
Represents the 'symbol' XML attribute of an initialAssignmnent element.
variables - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
List with nodes representing an variable in the model
VCardParser - Class in org.sbml.jsbml.xml.parsers
A VCardParser is used to parser the subNodes of an annotation which have this namespace URI : "http://www.w3.org/2001/vcard-rdf/3.0#".
VCardParser() - Constructor for class org.sbml.jsbml.xml.parsers.VCardParser
 
version - Variable in class org.sbml.jsbml.util.compilers.ASTNodeValue
The version of the underlying SBMLDocument.
version - Variable in class org.sbml.jsbml.util.compilers.UnitsCompiler
SBML version field
version - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
VERSION_MISMATCH - Static variable in class org.sbml.jsbml.JSBML
 
VERSION_MISMATCH_MSG - Static variable in exception org.sbml.jsbml.LevelVersionError
Message to display in cases that two objects do not have identical version attributes.
versionMismatchMessage(SBase, SBase) - Static method in exception org.sbml.jsbml.LevelVersionError
Creates an error message if the version fields of both elements are not identical, or an empty String otherwise.
VOLUME - Static variable in class org.sbml.jsbml.UnitDefinition
Identifier of the (for some SBML Levels 1 and 2) predefined UnitDefinition volume.
volume(int, int) - Static method in class org.sbml.jsbml.UnitDefinition
Predefined unit for volume.
volume - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
volumeUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
volumeUnitsID - Variable in class org.sbml.jsbml.Model
Represents the 'volumeUnits' XML attribute of a model element.

W

wedge - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
write(SBMLDocument, File, char, short) - Static method in class org.sbml.jsbml.SBMLWriter
Writes the given SBML document to a File.
write(SBMLDocument, File, String, String) - Static method in class org.sbml.jsbml.SBMLWriter
Writes the given SBML document to a File.
write(SBMLDocument, File, String, String, char, short) - Static method in class org.sbml.jsbml.SBMLWriter
Writes the given SBML document to a File.
write(SBMLDocument, OutputStream, char, short) - Static method in class org.sbml.jsbml.SBMLWriter
Writes the given SBMLDocument to the OutputStream.
write(SBMLDocument, OutputStream, String, String) - Static method in class org.sbml.jsbml.SBMLWriter
Writes the given SBMLDocument to the OutputStream.
write(SBMLDocument, OutputStream, String, String, char, short) - Static method in class org.sbml.jsbml.SBMLWriter
Writes the given SBMLDocument to the OutputStream.
write(SBMLDocument, String, char, short) - Static method in class org.sbml.jsbml.SBMLWriter
Writes the given SBMLDocument to file name.
write(SBMLDocument, String, String, String) - Static method in class org.sbml.jsbml.SBMLWriter
Writes the given SBMLDocument to file name.
write(SBMLDocument, String, String, String, char, short) - Static method in class org.sbml.jsbml.SBMLWriter
Writes the given SBMLDocument to file name.
write(SBMLDocument, File) - Method in class org.sbml.jsbml.SBMLWriter
Writes the given SBML document to a File.
write(SBMLDocument, OutputStream) - Method in class org.sbml.jsbml.SBMLWriter
Writes the given SBML document to the OutputStream.
write(SBMLDocument, String) - Method in class org.sbml.jsbml.SBMLWriter
Writes the given SBMLDocument to file name.
write(Node, Writer, StreamSource, boolean) - Static method in class org.sbml.jsbml.util.JAXPFacade
Writes an XML DOM node to the specified character stream, using a javax.xml.transform.Transformer instance created from streamSource.
write(Node, OutputStream, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
Writes an XML DOM node to the specified byte stream.
write(Node, OutputStream, StreamSource, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
Writes an XML DOM node to the specified byte stream, using a javax.xml.transform.Transformer instance created from streamSource.
write(Node, Writer, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
Writes an XML DOM node to the specified character stream.
write(Node, OutputStream, boolean) - Method in interface org.sbml.jsbml.util.NodeWriter
Writes an XML DOM node to a byte stream.
write(Node, Writer, boolean) - Method in interface org.sbml.jsbml.util.NodeWriter
Writes an XML DOM node to a character stream.
write(char) - Method in class org.sbml.jsbml.validator.MultipartPost
 
write(String) - Method in class org.sbml.jsbml.validator.MultipartPost
 
write(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeWriter
 
write(SBMLDocument, File) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
write(SBMLDocument, File, String, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
write(SBMLDocument, OutputStream) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the SBMLDocument in a SBML file.
write(SBMLDocument, OutputStream, String, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
write(SBMLDocument, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the XML representation of an SBMLDocument in a SBML file.
write(SBMLDocument, String, String, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
writeAnnotation(SBase) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
writeAnnotation(SBase, SMOutputContainer, XMLStreamWriter, int, boolean) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the annotation of this sbase component.
writeAttributes(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
writeAttributes(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
writeAttributes(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
writeAttributes(SBMLObjectForXML, Object) - Method in interface org.sbml.jsbml.xml.parsers.WritingParser
Adds the XML attributes of the sbmlElementToWrite to the attributes HashMap of the xmlObject.
writeCharacters(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
writeCharacters(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
writeCharacters(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
writeCharacters(SBMLObjectForXML, Object) - Method in interface org.sbml.jsbml.xml.parsers.WritingParser
Sets the characters of xmlObject depending on the sbml element to write.
writeCVTerms(List<CVTerm>, Map<String, String>, XMLStreamWriter, int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the listOfCVTerms.
writeElement(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
writeElement(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
writeElement(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
writeElement(SBMLObjectForXML, Object) - Method in interface org.sbml.jsbml.xml.parsers.WritingParser
Sets the name of xmlObject (if it is not set) to the element name of sbmlElementToWrite.
writeEndElement() - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
writeHistory(History, Map<String, String>, XMLStreamWriter, int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the history represented by this History instance.
writeln(String) - Method in class org.sbml.jsbml.validator.MultipartPost
 
writeln() - Method in class org.sbml.jsbml.validator.MultipartPost
 
writeMathML(MathContainer, SMOutputElement, XMLStreamWriter, int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the MathML expression for the math element of this sbase component.
writeMathMLToString(ASTNode) - Static method in class org.sbml.jsbml.JSBML
Writes the given ASTNode (and its children) to a string as MathML, and returns the string.
writeMessage(Constraint, SMOutputElement, XMLStreamWriter, String, int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the message of this Constraint.
writeModel(Model) - Method in interface org.sbml.jsbml.SBMLOutputConverter
 
writeName(Object) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
Converts the given Object into a String.
writeNamespaces(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
writeNamespaces(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
writeNamespaces(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
 
writeNamespaces(SBMLObjectForXML, Object) - Method in interface org.sbml.jsbml.xml.parsers.WritingParser
Sets the namespace of xmlObject (if it is not set) to the namespace of sbmlElementToWrite.
writeNotes(SBase, SMOutputElement, XMLStreamWriter, String, int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the notes of this sbase component.
writeParameter(String, String) - Method in class org.sbml.jsbml.validator.MultipartPost
 
writeParameter(String, File) - Method in class org.sbml.jsbml.validator.MultipartPost
 
writer - Variable in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
 
writer - Variable in class org.sbml.jsbml.xml.parsers.XMLNodeWriter
 
writeRDFAnnotation(Annotation, SMOutputElement, XMLStreamWriter, int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the RDF annotation contained in 'annotation'.
writeSBML(SBMLDocument, String) - Static method in class org.sbml.jsbml.JSBML
Writes the XML representation of an SBML document to a file.
writeSBML(Object, String) - Method in interface org.sbml.jsbml.SBMLOutputConverter
 
writeSBML(Object, String, String, String) - Method in interface org.sbml.jsbml.SBMLOutputConverter
 
writeSBML(SBMLDocument, File) - Method in class org.sbml.jsbml.SBMLWriter
Writes the given SBML document to a File.
writeSBMLElements(SBMLObjectForXML, SMOutputElement, XMLStreamWriter, Object, int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the SBML elements.
writeSBMLToFile(SBMLDocument, String) - Method in class org.sbml.jsbml.SBMLWriter
Writes the given SBML document to file name.
writeSBMLToString(SBMLDocument) - Static method in class org.sbml.jsbml.JSBML
Writes the given SBML document to an in-memory string.
writeSBMLToString(SBMLDocument) - Method in class org.sbml.jsbml.SBMLWriter
Writes the given SBML document to an in-memory String and returns it.
writeSBMLToString(SBMLDocument) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
Writes the given SBML document to an in-memory string.
writeSBMLToString(SBMLDocument, String, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
writeW3CDate(XMLStreamWriter, int, String, String, String, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
 
writeXMLAttributes() - Method in class org.sbml.jsbml.AbstractMathContainer
 
writeXMLAttributes() - Method in class org.sbml.jsbml.AbstractNamedSBase
 
writeXMLAttributes() - Method in class org.sbml.jsbml.AbstractSBase
 
writeXMLAttributes() - Method in class org.sbml.jsbml.Compartment
 
writeXMLAttributes() - Method in class org.sbml.jsbml.Event
 
writeXMLAttributes() - Method in class org.sbml.jsbml.EventAssignment
 
writeXMLAttributes() - Method in class org.sbml.jsbml.ExplicitRule
 
writeXMLAttributes() - Method in class org.sbml.jsbml.FunctionDefinition
 
writeXMLAttributes() - Method in class org.sbml.jsbml.InitialAssignment
 
writeXMLAttributes() - Method in class org.sbml.jsbml.KineticLaw
 
writeXMLAttributes() - Method in class org.sbml.jsbml.LocalParameter
 
writeXMLAttributes() - Method in class org.sbml.jsbml.Model
 
writeXMLAttributes() - Method in class org.sbml.jsbml.Parameter
 
writeXMLAttributes() - Method in class org.sbml.jsbml.Reaction
 
writeXMLAttributes() - Method in interface org.sbml.jsbml.SBase
 
writeXMLAttributes() - Method in class org.sbml.jsbml.SBMLDocument
 
writeXMLAttributes() - Method in class org.sbml.jsbml.SimpleSpeciesReference
 
writeXMLAttributes() - Method in class org.sbml.jsbml.Species
 
writeXMLAttributes() - Method in class org.sbml.jsbml.SpeciesReference
 
writeXMLAttributes() - Method in class org.sbml.jsbml.Trigger
 
writeXMLAttributes() - Method in class org.sbml.jsbml.Unit
 
WritingParser - Interface in org.sbml.jsbml.xml.parsers
The interface to implement for a parser which writes a SBML file.

X

XMLAttributes - Class in org.sbml.jsbml.xml
Representation of the attributes on an XML node.
XMLAttributes() - Constructor for class org.sbml.jsbml.xml.XMLAttributes
Creates a new empty XMLAttributes set.
XMLAttributes(XMLAttributes) - Constructor for class org.sbml.jsbml.xml.XMLAttributes
Copy constructor; creates a copy of this XMLAttributes set.
XMLException - Exception in org.sbml.jsbml.xml
This kind of Error indicates that an XML file could not be parsed correctly.
XMLException() - Constructor for exception org.sbml.jsbml.xml.XMLException
 
XMLException(String) - Constructor for exception org.sbml.jsbml.xml.XMLException
 
XMLException(String, Throwable) - Constructor for exception org.sbml.jsbml.xml.XMLException
 
XMLException(Throwable) - Constructor for exception org.sbml.jsbml.xml.XMLException
 
XMLLogger - Class in org.sbml.jsbml.xml.stax
TODO: Comment missing
XMLLogger() - Constructor for class org.sbml.jsbml.xml.stax.XMLLogger
 
XMLNamespaces - Class in org.sbml.jsbml.xml
Representation of XML Namespaces.
XMLNamespaces() - Constructor for class org.sbml.jsbml.xml.XMLNamespaces
Creates a new empty list of XML namespace declarations.
XMLNamespaces(XMLNamespaces) - Constructor for class org.sbml.jsbml.xml.XMLNamespaces
Copy constructor; creates a copy of this XMLNamespaces list.
XMLNode - Class in org.sbml.jsbml.xml
Representation of a node in an XML document tree.
XMLNode() - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a new empty XMLNode with no children.
XMLNode(String) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a text XMLNode.
XMLNode(String, long) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a text XMLNode.
XMLNode(String, long, long) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a text XMLNode.
XMLNode(XMLNode) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a copy of this XMLNode.
XMLNode(XMLToken) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a new XMLNode by copying token.
XMLNode(XMLTriple) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates an end element XMLNode.
XMLNode(XMLTriple, long) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates an end element XMLNode.
XMLNode(XMLTriple, long, long) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates an end element XMLNode.
XMLNode(XMLTriple, XMLAttributes) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a start element XMLNode with the given set of attributes.
XMLNode(XMLTriple, XMLAttributes, long) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a start element XMLNode with the given set of attributes.
XMLNode(XMLTriple, XMLAttributes, long, long) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a start element XMLNode with the given set of attributes.
XMLNode(XMLTriple, XMLAttributes, XMLNamespaces) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a new start element XMLNode with the given set of attributes and namespace declarations.
XMLNode(XMLTriple, XMLAttributes, XMLNamespaces, long) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a new start element XMLNode with the given set of attributes and namespace declarations.
XMLNode(XMLTriple, XMLAttributes, XMLNamespaces, long, long) - Constructor for class org.sbml.jsbml.xml.XMLNode
Creates a new start element XMLNode with the given set of attributes and namespace declarations.
XMLNodeWriter - Class in org.sbml.jsbml.xml.parsers
 
XMLNodeWriter(XMLStreamWriter, String) - Constructor for class org.sbml.jsbml.xml.parsers.XMLNodeWriter
 
XMLToken - Class in org.sbml.jsbml.xml
Representation of a token in an XML stream.
XMLToken() - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates a new empty XMLToken.
XMLToken(String) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates a text XMLToken.
XMLToken(String, long) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates a text XMLToken.
XMLToken(String, long, long) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates a text XMLToken.
XMLToken(XMLToken) - Constructor for class org.sbml.jsbml.xml.XMLToken
Copy constructor; creates a copy of this XMLToken.
XMLToken(XMLTriple) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates an end element XMLToken.
XMLToken(XMLTriple, long) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates an end element XMLToken.
XMLToken(XMLTriple, long, long) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates an end element XMLToken.
XMLToken(XMLTriple, XMLAttributes) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates a start element XMLToken with the given set of attributes.
XMLToken(XMLTriple, XMLAttributes, long) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates a start element XMLToken with the given set of attributes.
XMLToken(XMLTriple, XMLAttributes, long, long) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates a start element XMLToken with the given set of attributes.
XMLToken(XMLTriple, XMLAttributes, XMLNamespaces) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates a start element XMLToken with the given set of attributes and namespace declarations.
XMLToken(XMLTriple, XMLAttributes, XMLNamespaces, long) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates a start element XMLToken with the given set of attributes and namespace declarations.
XMLToken(XMLTriple, XMLAttributes, XMLNamespaces, long, long) - Constructor for class org.sbml.jsbml.xml.XMLToken
Creates a start element XMLToken with the given set of attributes and namespace declarations.
xmlTriple - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
XMLTriple - Class in org.sbml.jsbml.xml
Representation of a qualified XML name.
XMLTriple() - Constructor for class org.sbml.jsbml.xml.XMLTriple
Creates a new, empty XMLTriple.
XMLTriple(String, String, String) - Constructor for class org.sbml.jsbml.xml.XMLTriple
Creates a new XMLTriple with the given name, uri and and prefix.
XMLTriple(String, char) - Constructor for class org.sbml.jsbml.xml.XMLTriple
Creates a new XMLTriple by splitting the given triplet on the separator character sepchar.
XMLTriple(String) - Constructor for class org.sbml.jsbml.xml.XMLTriple
Creates a new XMLTriple by splitting the given triplet separated by space.
XMLTriple(XMLTriple) - Constructor for class org.sbml.jsbml.xml.XMLTriple
Creates a copy of this XMLTriple set.
XOR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
xor(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
Exclusive or.
xor(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
xor(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
xor - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
xor(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
xor(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
xor(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
 
xor(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
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