- 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
-
- AbstractNamedSBase(AbstractNamedSBase) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
-
- AbstractNamedSBase(int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
-
- AbstractNamedSBase(String) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- addCreator(Creator) - Method in class org.sbml.jsbml.History
-
- addCVTerm(CVTerm) - Method in class org.sbml.jsbml.AbstractSBase
-
- addCVTerm(CVTerm) - Method in class org.sbml.jsbml.Annotation
-
- 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
-
- 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
-
- 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
-
- 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
-
- addProduct(SpeciesReference) - Method in class org.sbml.jsbml.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
-
- 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
-
- addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- addUnit(String) - Method in class org.sbml.jsbml.UnitDefinition
-
- addUnit(Unit) - Method in class org.sbml.jsbml.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
-
- addWritingParser(List<WritingParser>, WritingParser, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- ASTNode(CallableSBase, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
- 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
-
- ASTNode(double, int) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(double, int, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(double, MathContainer) - Constructor for class org.sbml.jsbml.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
-
- ASTNode(MathContainer) - Constructor for class org.sbml.jsbml.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
-
- 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
ASTNode
s, 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.
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- clone() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
- 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
-
- 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
-
- Constraint(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Constraint
-
- Constraint(Constraint) - Constructor for class org.sbml.jsbml.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
-
- containsUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
ASTNodeValue
s 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
-
- 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
-
- createCompartment(String) - Method in class org.sbml.jsbml.Model
-
- createCompartmentType() - Method in class org.sbml.jsbml.Model
-
- createCompartmentType(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
-
- createFunctionDefinition() - Method in class org.sbml.jsbml.Model
-
- createFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- createKineticLaw() - Method in class org.sbml.jsbml.Model
-
- 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
-
- createKineticParameter(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
-
- createModifier(String) - Method in class org.sbml.jsbml.Model
-
- createModifier() - Method in class org.sbml.jsbml.Reaction
-
- createModifier(Species) - Method in class org.sbml.jsbml.Reaction
-
- createModifier(String) - Method in class org.sbml.jsbml.Reaction
-
- createModifier(String, Species) - Method in class org.sbml.jsbml.Reaction
-
- createModifier(String, String) - Method in class org.sbml.jsbml.Reaction
-
- 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
-
- createParameter(String) - Method in class org.sbml.jsbml.Model
-
- createPriority() - Method in class org.sbml.jsbml.Event
-
- createPriority(ASTNode) - Method in class org.sbml.jsbml.Event
-
- createProduct() - Method in class org.sbml.jsbml.Model
-
- createProduct(String) - Method in class org.sbml.jsbml.Model
-
- createProduct() - Method in class org.sbml.jsbml.Reaction
-
- createProduct(Species) - Method in class org.sbml.jsbml.Reaction
-
- createProduct(String) - Method in class org.sbml.jsbml.Reaction
-
- createProduct(String, Species) - Method in class org.sbml.jsbml.Reaction
-
- createProduct(String, String) - Method in class org.sbml.jsbml.Reaction
-
- createRateRule() - Method in class org.sbml.jsbml.Model
-
- createReactant() - Method in class org.sbml.jsbml.Model
-
- 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
-
- createReactant(Species) - Method in class org.sbml.jsbml.Reaction
-
- createReactant(String) - Method in class org.sbml.jsbml.Reaction
-
- createReactant(String, Species) - Method in class org.sbml.jsbml.Reaction
-
- createReactant(String, String) - Method in class org.sbml.jsbml.Reaction
-
- createReaction() - Method in class org.sbml.jsbml.Model
-
- createReaction(String) - Method in class org.sbml.jsbml.Model
-
- createSpecies() - Method in class org.sbml.jsbml.Model
-
- createSpecies(String) - Method in class org.sbml.jsbml.Model
-
- createSpecies(String, Compartment) - Method in class org.sbml.jsbml.Model
-
- 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
-
- createUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- Creator(Creator) - Constructor for class org.sbml.jsbml.Creator
-
- Creator(String, String, String, String) - Constructor for class org.sbml.jsbml.Creator
-
- 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
-
- CVTerm(CVTerm) - Constructor for class org.sbml.jsbml.CVTerm
-
- CVTerm(CVTerm.Qualifier, String...) - Constructor for class org.sbml.jsbml.CVTerm
-
- CVTerm(CVTerm.Type, CVTerm.Qualifier, String...) - Constructor for class org.sbml.jsbml.CVTerm
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
SBMLError
s 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
-
- 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
-
- getFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- getInitialAssignment(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
-
- 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
SBMLError
s 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
-
- 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
-
- 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
-
- getMessage() - Method in exception org.sbml.jsbml.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
-
- getModelHistory() - Method in class org.sbml.jsbml.Model
-
- 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
-
- getModifier() - Static method in class org.sbml.jsbml.SBO
-
- getModifierForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- 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
-
- 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
-
- getNamespaceURI() - Method in enum org.sbml.jsbml.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
-
- 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
-
- getNumCompartments() - Method in class org.sbml.jsbml.Model
-
- getNumCompartmentTypes() - Method in class org.sbml.jsbml.Model
-
Deprecated.
- getNumConstraints() - Method in class org.sbml.jsbml.Model
-
- getNumCreators() - Method in class org.sbml.jsbml.History
-
- getNumCVTerms() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNumCVTerms() - Method in class org.sbml.jsbml.Annotation
-
- getNumCVTerms() - Method in interface org.sbml.jsbml.SBase
-
- getNumDelays() - Method in class org.sbml.jsbml.Model
-
Returns the number of
Delay
s 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
-
- getNumEvents() - Method in class org.sbml.jsbml.Model
-
Returns the number of
Event
s 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
-
- getNumInitialAssignments() - Method in class org.sbml.jsbml.Model
-
- getNumKineticLaws() - Method in class org.sbml.jsbml.Model
-
- getNumListsOf() - Method in class org.sbml.jsbml.Model
-
Returns the number of
ListOf
s 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
-
- getNumNamedSBases() - Method in class org.sbml.jsbml.Model
-
Returns the number of
NamedSBase
s in the
Model
, so elements
that can have a name.
- getNumNamedSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.Model
-
- getNumParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- getNumParameters() - Method in class org.sbml.jsbml.Model
-
Returns the number of
Parameter
s of this Model.
- getNumProducts() - Method in class org.sbml.jsbml.Reaction
-
- getNumQuantities() - Method in class org.sbml.jsbml.Model
-
Returns the number of
Quantity
s of this Model.
- getNumQuantitiesWithUnit() - Method in class org.sbml.jsbml.Model
-
- getNumReactants() - Method in class org.sbml.jsbml.Reaction
-
- getNumReactions() - Method in class org.sbml.jsbml.Model
-
Returns the number of
Reaction
s 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
Rule
s of this model.
- getNumSBases() - Method in class org.sbml.jsbml.Model
-
Returns the number of
SBase
s of this model.
- getNumSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.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 SpeciesReferences
s 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
-
- 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
-
- getNumUnits() - Method in class org.sbml.jsbml.Model
-
Returns the number of
Unit
s of this Model.
- getNumUnits() - Method in class org.sbml.jsbml.UnitDefinition
-
- getNumVariables() - Method in class org.sbml.jsbml.Model
-
Returns the number of
Variable
s of this Model.
- getObject() - Method in class org.sbml.jsbml.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
-
- 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
-
- 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
-
- 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
-
- getProduct() - Static method in class org.sbml.jsbml.SBO
-
- getProductForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- 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
-
- getReactant() - Static method in class org.sbml.jsbml.SBO
-
- getReactantForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- 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
-
- 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
-
- getSBaseListType() - Method in class org.sbml.jsbml.ListOf
-
- getSBMLDocument() - Method in class org.sbml.jsbml.AbstractSBase
-
- getSBMLDocument() - Method in interface org.sbml.jsbml.SBase
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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 Parameter
s.
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 Parameter
s.
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
-
- 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
-
- getValue() - Method in interface org.sbml.jsbml.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
-
- 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
-
- 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
-
- getVolumeUnits() - Method in class org.sbml.jsbml.Model
-
Returns the volume units ID of this
Model
.
- getVolumeUnitsInstance() - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
n
th 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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 Parameter
s.
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 Parameter
s.
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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
ASTNode
s.
- 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
-
- 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
-
- 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
n
th 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
-
- removeCompartment(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- removeCreator(int) - Method in class org.sbml.jsbml.History
-
If there is no i
th Creator
, it returns null.
- removeEvent(int) - Method in class org.sbml.jsbml.Model
-
- removeEvent(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- removeFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
-
- removeInitialAssignment(int) - Method in class org.sbml.jsbml.Model
-
- removeLocalParameter(int) - Method in class org.sbml.jsbml.KineticLaw
-
- removeLocalParameter(LocalParameter) - Method in class org.sbml.jsbml.KineticLaw
-
- removeLocalParameter(String) - Method in class org.sbml.jsbml.KineticLaw
-
- 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
-
- 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
-
- 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
-
- 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
-
- removeReaction(Reaction) - Method in class org.sbml.jsbml.Model
-
Removes a reaction from the model.
- removeReaction(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
-
- removeSpecies(Species) - Method in class org.sbml.jsbml.Model
-
Removes a species from the model.
- removeSpecies(String) - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
-
- removeUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
- removeUnitDefinition(UnitDefinition) - Method in class org.sbml.jsbml.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
-
- 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
-
- 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
.
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- setAssignmentRuleVariable(AssignmentRule, Model) - Method in class org.sbml.jsbml.xml.parsers.SBMLLevel1Version1Parser
-
- setAttributes(XMLAttributes) - Method in class org.sbml.jsbml.xml.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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- setExplicitlyConstant(boolean) - Method in class org.sbml.jsbml.LocalParameter
-
- setExponent(double) - Method in class org.sbml.jsbml.Unit
-
Sets the exponent of this
Unit
- setExponent(int) - Method in class org.sbml.jsbml.Unit
-
- 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
-
- setFamilyName(String) - Method in class org.sbml.jsbml.Creator
-
Sets the family name
- setFast(boolean) - Method in class org.sbml.jsbml.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
-
- setKineticLaw(KineticLaw) - Method in class org.sbml.jsbml.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
-
- 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
-
- 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
-
- 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
-
- setListOfRules(ListOf<Rule>) - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
-
- setMessage(String) - Method in class org.sbml.jsbml.Constraint
-
- setMessage(XMLNode) - Method in class org.sbml.jsbml.Constraint
-
- setMessage(Message) - Method in exception org.sbml.jsbml.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
-
- 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
-
- 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
-
- setSBaseListType(ListOf.Type) - Method in class org.sbml.jsbml.ListOf
-
- 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
-
- 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
-
- 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
-
- 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
-
- setUnits(Unit) - Method in class org.sbml.jsbml.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 Parameter
s.
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 Parameter
s.
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
-
- setUnits(Unit) - Method in interface org.sbml.jsbml.SBaseWithUnit
-
- setUnits(Unit.Kind) - Method in interface org.sbml.jsbml.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
-
- 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
-
- 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
-
- 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
-
- simplify(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
-
- simplify() - Method in class org.sbml.jsbml.UnitDefinition
-
- 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
-
- SpeciesReferenceFilter() - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
-
- SpeciesReferenceFilter(Species) - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
-
- 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
-
- 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
-
- 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
-
- SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
Switch to specified lex state.
- Symbol - Class in org.sbml.jsbml
-
- 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
-
- 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 Parameter
s.
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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- unsetLengthUnits() - Method in class org.sbml.jsbml.Model
-
Sets the lengthUnitsID of this
Model
to null.
- unsetListOfCompartments() - Method in class org.sbml.jsbml.Model
-
- unsetListOfCompartmentTypes() - Method in class org.sbml.jsbml.Model
-
Deprecated.
- unsetListOfConstraints() - Method in class org.sbml.jsbml.Model
-
- unsetListOfEventAssignments() - Method in class org.sbml.jsbml.Event
-
- unsetListOfEvents() - Method in class org.sbml.jsbml.Model
-
- unsetListOfFunctionDefinitions() - Method in class org.sbml.jsbml.Model
-
- unsetListOfInitialAssignments() - Method in class org.sbml.jsbml.Model
-
- unsetListOfLocalParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- unsetListOfModifiedDates() - Method in class org.sbml.jsbml.History
-
Sets the created of this
History
to null.
- unsetListOfModifiers() - Method in class org.sbml.jsbml.Reaction
-
- unsetListOfParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- unsetListOfParameters() - Method in class org.sbml.jsbml.Model
-
- unsetListOfProducts() - Method in class org.sbml.jsbml.Reaction
-
- unsetListOfReactants() - Method in class org.sbml.jsbml.Reaction
-
- unsetListOfReactions() - Method in class org.sbml.jsbml.Model
-
- unsetListOfRules() - Method in class org.sbml.jsbml.Model
-
- unsetListOfSpecies() - Method in class org.sbml.jsbml.Model
-
- unsetListOfSpeciesTypes() - Method in class org.sbml.jsbml.Model
-
Deprecated.
- unsetListOfUnitDefinitions() - Method in class org.sbml.jsbml.Model
-
- unsetListOfUnits() - Method in class org.sbml.jsbml.UnitDefinition
-
- unsetMath() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- unsetMath() - Method in interface org.sbml.jsbml.MathContainer
-
- unsetMessage() - Method in class org.sbml.jsbml.Constraint
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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 Parameter
s.
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
-
- 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
-
- 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
-
- 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
-