- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
The absolute value represented by the given
ASTNode2
.
- abs(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- abs(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- abs(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- abs(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- ABS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- 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
-
Deprecated.
- abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- AbstractASTNode - Class in org.sbml.jsbml.math
-
A node in the Abstract Syntax Tree (AST) representation
of a mathematical expression.
- AbstractASTNode() - Constructor for class org.sbml.jsbml.math.AbstractASTNode
-
- AbstractASTNode(ASTNode2) - Constructor for class org.sbml.jsbml.math.AbstractASTNode
-
- AbstractASTNode(MathContainer) - Constructor for class org.sbml.jsbml.math.AbstractASTNode
-
- 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
-
- 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
-
Initializes a new object of type
AbstractNamedSBaseWithUnit
whose
identifier and name are set to
null
and whose level and
version are set to -1 each.
- 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
-
- AbstractReaderWriter - Class in org.sbml.jsbml.xml.parsers
-
Contains some code shared by most of the L3 packages parsers.
- AbstractReaderWriter() - Constructor for class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- 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 SBML Level and
Version.
- AbstractSBase(SBase) - Constructor for class org.sbml.jsbml.AbstractSBase
-
- AbstractSBase.NOTES_TYPE - Enum in org.sbml.jsbml
-
- AbstractSBasePlugin - Class in org.sbml.jsbml.ext
-
- AbstractSBasePlugin() - Constructor for class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- AbstractSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- AbstractSBasePlugin(SBasePlugin) - Constructor for class org.sbml.jsbml.ext.AbstractSBasePlugin
-
This method will need to be further tested
- 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.
- accept(SBase) - Method in class org.sbml.jsbml.KineticLaw
-
- accept(SBase) - Method in class org.sbml.jsbml.Model
-
- accept(SBase) - Method in interface org.sbml.jsbml.util.IdManager
-
Returns true if this
IdManager
can register or unregister
the given
SBase
.
- 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.IdenticalUnitDefinitionFilter
-
- 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
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.XMLNodeFilter
-
- 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.math.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.
- 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>, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- addAllChangeListeners(Collection<TreeNodeChangeListener>, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- addAllChangeListeners(Collection<TreeNodeChangeListener>, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- 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(ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
Adds a child to this node.
- addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction
-
Adds a child to this node.
- addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- addChild(XMLNode) - Method in class org.sbml.jsbml.xml.XMLNode
-
- addColor(SBMLRDFAnnotationParser.NODE_COLOR, SBMLRDFAnnotationParser.NODE_COLOR) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Adds the given colors and return the resulting color.
- 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
-
- 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 class org.sbml.jsbml.Annotation
-
Adds an additional namespace 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.math.parser.TokenMgrError
-
Replaces unprintable characters by their escaped (or unicode escaped)
equivalents in the given string
- 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
-
- addExtension(String, SBasePlugin) - Method in class org.sbml.jsbml.AbstractSBase
-
- addExtension(String, SBasePlugin) - Method in interface org.sbml.jsbml.SBase
-
- 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.
- 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, String, String) - Method in class org.sbml.jsbml.SBMLDocument
-
- addNamespace(String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Appends an XML namespace URI 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
.
- addNestedCVTerm(CVTerm) - Method in class org.sbml.jsbml.CVTerm
-
- 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
-
- addPackageDeclaration(String, String, boolean) - Method in class org.sbml.jsbml.SBMLDocument
-
Adds the package namespace declaration in this
SBMLDocument
, adds as well
the required attribute for this package.
- 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.
- addPlugin(String, SBasePlugin) - Method in class org.sbml.jsbml.AbstractSBase
-
- addPlugin(String, SBasePlugin) - Method in interface org.sbml.jsbml.SBase
-
- addPredefinedUnitDefinitions(Model) - Static method in class org.sbml.jsbml.util.SBMLtools
-
- addPredefinedUnits() - Method in class org.sbml.jsbml.Model
-
- addProduct(SpeciesReference) - Method in class org.sbml.jsbml.Reaction
-
- 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
-
- addTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- addTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
- 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.math.parser.SimpleCharStream
-
Method to adjust line and column numbers for the start of a token.
- 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(ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- and(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- AND - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
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.FormulaCompilerLibSBML
-
- 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
-
Deprecated.
- 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(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(XMLNode) - Constructor for class org.sbml.jsbml.Annotation
-
- 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
-
Clone constructor.
- annotationNameSpaces - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- annotationParsers - Variable in class org.sbml.jsbml.xml.stax.SBMLReader
-
- AnnotationReader - Interface in org.sbml.jsbml.xml.parsers
-
The interface to implement for the SBML parsers reading SBML annotations.
- AnnotationWriter - Interface in org.sbml.jsbml.xml.parsers
-
The interface to implement for the SBML parsers writing SBML annotations.
- 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.
- appendAnnotation(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- appendAnnotation(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase
-
- appendAnnotation(String) - Method in interface org.sbml.jsbml.SBase
-
Appends the given annotation to the 'annotation' subelement of this object.
- appendAnnotation(XMLNode) - Method in interface org.sbml.jsbml.SBase
-
Appends the given annotation to the 'annotation' subelement of this object.
- appendNonRDFAnnotation(String) - Method in class org.sbml.jsbml.Annotation
-
Appends some 'annotation' to the non RDF annotation
XMLNode
of this object.
- appendNonRDFAnnotation(XMLNode) - Method in class org.sbml.jsbml.Annotation
-
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arccosh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccoth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccoth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccoth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccoth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccoth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccsc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccsc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccsc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccsc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccsc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccsch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccsch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccsch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccsch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccsch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arcsec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arcsec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arcsec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arcsec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arcsec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arcsech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arcsech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arcsech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arcsech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arcsech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arcsin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arcsin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arcsin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arcsin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arcsin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arcsinh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arcsinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arcsinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arcsinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arcsinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arcsinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arctan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arctan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arctan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arctan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arctan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arctanh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arctanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arctanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arctanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arctanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arctanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.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
-
Deprecated.
- 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.
- areValidModifiedDates(List<XMLNode>) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- arg - Variable in class org.sbml.jsbml.math.parser.FormulaParser.JJCalls
-
- arg - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2.JJCalls
-
- arg - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3.JJCalls
-
- arg - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2.JJCalls
-
- arg - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParser.JJCalls
-
- arg - Variable in class org.sbml.jsbml.text.parser.FormulaParser.JJCalls
-
- arg - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2.JJCalls
-
- arg - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3.JJCalls
-
- arg - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2.JJCalls
-
- arith(char, Object...) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Basic method which links several elements with a mathematical operator.
- arith(Object, Object...) - Static method in class org.sbml.jsbml.math.compiler.HTMLFormula
-
Basic method which links several elements with a mathematical operator.
- 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.
- arithmeticOperation(ASTNode.Type, ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- 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
-
- ASTArithmeticOperatorNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing an arithmetic
operator in a mathematical expression.
- ASTArithmeticOperatorNode() - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- ASTArithmeticOperatorNode(ASTArithmeticOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- ASTArithmeticOperatorNode(MathContainer) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- ASTArithmeticOperatorNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- ASTArithmeticOperatorNode(ASTNode.Type, MathContainer) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- ASTBinaryFunctionNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a function with two
parameters
- ASTBinaryFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- ASTBinaryFunctionNode(ASTBinaryFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- ASTBinaryFunctionNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- ASTBoolean - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a boolean
- ASTBoolean() - Constructor for class org.sbml.jsbml.math.ASTBoolean
-
- ASTBoolean(ASTBoolean) - Constructor for class org.sbml.jsbml.math.ASTBoolean
-
Copy constructor; Creates a deep copy of the given
ASTBoolean
.
- ASTBoolean(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTBoolean
-
- ASTCiFunctionNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML ci element
in a mathematical expression.
- ASTCiFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTCiFunctionNode
-
- ASTCiFunctionNode(ASTCiFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTCiFunctionNode
-
- ASTCiNumberNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML ci element
in a mathematical expression.
- ASTCiNumberNode() - Constructor for class org.sbml.jsbml.math.ASTCiNumberNode
-
- ASTCiNumberNode(ASTCiNumberNode) - Constructor for class org.sbml.jsbml.math.ASTCiNumberNode
-
- ASTCnExponentialNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing an exponent
in a mathematical expression
- ASTCnExponentialNode() - Constructor for class org.sbml.jsbml.math.ASTCnExponentialNode
-
- ASTCnExponentialNode(ASTCnExponentialNode) - Constructor for class org.sbml.jsbml.math.ASTCnExponentialNode
-
- ASTCnIntegerNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing an Integer
in a mathematical expression
- ASTCnIntegerNode() - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode
-
- ASTCnIntegerNode(ASTCnIntegerNode) - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode
-
- ASTCnIntegerNode(int) - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode
-
- ASTCnNumberNode<T> - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML cn element in a
mathematical expression.
- ASTCnNumberNode() - Constructor for class org.sbml.jsbml.math.ASTCnNumberNode
-
- ASTCnNumberNode(ASTCnNumberNode<T>) - Constructor for class org.sbml.jsbml.math.ASTCnNumberNode
-
- ASTCnNumberNode(String) - Constructor for class org.sbml.jsbml.math.ASTCnNumberNode
-
- ASTCnRationalNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a rational number
in a mathematical expression
- ASTCnRationalNode() - Constructor for class org.sbml.jsbml.math.ASTCnRationalNode
-
- ASTCnRationalNode(ASTCnRationalNode) - Constructor for class org.sbml.jsbml.math.ASTCnRationalNode
-
- ASTCnRealNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a real number
in a mathematical expression
- ASTCnRealNode() - Constructor for class org.sbml.jsbml.math.ASTCnRealNode
-
- ASTCnRealNode(ASTCnRealNode) - Constructor for class org.sbml.jsbml.math.ASTCnRealNode
-
Copy constructor; Creates a deep copy of the given
ASTCnRealNode
.
- ASTCnRealNode(double) - Constructor for class org.sbml.jsbml.math.ASTCnRealNode
-
- ASTConstantNumber - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a constant number
in a mathematical expression.
- ASTConstantNumber() - Constructor for class org.sbml.jsbml.math.ASTConstantNumber
-
- ASTConstantNumber(ASTConstantNumber) - Constructor for class org.sbml.jsbml.math.ASTConstantNumber
-
- ASTConstantNumber(double) - Constructor for class org.sbml.jsbml.math.ASTConstantNumber
-
- ASTConstantNumber(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTConstantNumber
-
- ASTCSymbolAvogadroNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing avogadro's number
- ASTCSymbolAvogadroNode() - Constructor for class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- ASTCSymbolAvogadroNode(ASTCSymbolAvogadroNode) - Constructor for class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- ASTCSymbolBaseNode - Interface in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML element
that contains a definitionURL and name attribute.
- ASTCSymbolDelayNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the delay function
- ASTCSymbolDelayNode() - Constructor for class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- ASTCSymbolDelayNode(ASTCSymbolDelayNode) - Constructor for class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- ASTCSymbolNode - Interface in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML csymbol element
in a mathematical expression.
- ASTCSymbolTimeNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the time function
- ASTCSymbolTimeNode() - Constructor for class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- ASTCSymbolTimeNode(ASTCSymbolTimeNode) - Constructor for class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- ASTDivideNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the divide function
- ASTDivideNode() - Constructor for class org.sbml.jsbml.math.ASTDivideNode
-
- ASTDivideNode(ASTDivideNode) - Constructor for class org.sbml.jsbml.math.ASTDivideNode
-
Copy constructor; Creates a deep copy of the given
ASTDivideNode
.
- ASTDivideNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTDivideNode
-
- ASTFactory - Class in org.sbml.jsbml.math
-
A collection of static methods that can be used to create new abstract syntax
trees or alter the topology of existing ones.
- ASTFactory() - Constructor for class org.sbml.jsbml.math.ASTFactory
-
- ASTFunction - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a function
in a mathematical expression.
- ASTFunction() - Constructor for class org.sbml.jsbml.math.ASTFunction
-
- ASTFunction(ASTFunction) - Constructor for class org.sbml.jsbml.math.ASTFunction
-
Copy constructor; Creates a deep copy of the given
ASTFunction
.
- ASTFunction(MathContainer) - Constructor for class org.sbml.jsbml.math.ASTFunction
-
- ASTHyperbolicNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a hyperbolic function
- ASTHyperbolicNode() - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode
-
- ASTHyperbolicNode(ASTHyperbolicNode) - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode
-
- ASTHyperbolicNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode
-
- ASTLambdaFunctionNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a lambda function
in a mathematical expression.
- ASTLambdaFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- ASTLambdaFunctionNode(ASTLambdaFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- ASTLogarithmNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the logarithm function
- ASTLogarithmNode() - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode
-
- ASTLogarithmNode(ASTLogarithmNode) - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode
-
- ASTLogarithmNode(ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode
-
- ASTLogarithmNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode
-
- ASTLogicalOperatorNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a logical operator
in a mathematical expression.
- ASTLogicalOperatorNode() - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- ASTLogicalOperatorNode(ASTLogicalOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- ASTLogicalOperatorNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- ASTMinusNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the minus operator
- ASTMinusNode() - Constructor for class org.sbml.jsbml.math.ASTMinusNode
-
- ASTMinusNode(ASTMinusNode) - Constructor for class org.sbml.jsbml.math.ASTMinusNode
-
Copy constructor; Creates a deep copy of the given
ASTMinusNode
.
- ASTMinusNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTMinusNode
-
- 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(ASTNode2) - 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
-
- ASTNode.Type - Enum in org.sbml.jsbml
-
An enumeration of all possible types that can be represented by an
abstract syntax tree node.
- ASTNode2 - Interface in org.sbml.jsbml.math
-
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
- ASTNode2Compiler - Interface in org.sbml.jsbml.math.compiler
-
A compiler for abstract syntax trees.
- ASTNode2Value<T> - Class in org.sbml.jsbml.math.compiler
-
When interpreting
ASTNode2
s, the
ASTNode2Compiler
takes
elements of this class as arguments and performs its operations on it.
- ASTNode2Value(ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- ASTNode2Value(T, ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- ASTNode2Value(ASTNode.Type, ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- ASTNode2Value(UnitDefinition, ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- ASTNodeCompiler - Interface in org.sbml.jsbml.util.compilers
-
A compiler for abstract syntax trees.
- astNodeParent - Variable in class org.sbml.jsbml.xml.stax.SBMLReader
-
The parent of the mathML we are parsing through the readMathML methods.
- astNodeToTree(ASTNode, String, String) - Static method in class org.sbml.jsbml.ASTNode
-
Returns a simple tree view of the ASTNode internal, including mainly
node type and hierarchy.
- 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
-
- ASTNumber - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a number
in a mathematical expression.
- ASTNumber() - Constructor for class org.sbml.jsbml.math.ASTNumber
-
- ASTNumber(ASTNumber) - Constructor for class org.sbml.jsbml.math.ASTNumber
-
Copy constructor; Creates a deep copy of the given
ASTNumber
.
- ASTPiecewiseFunctionNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML piecewise
element in a mathematical expression.
- ASTPiecewiseFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- ASTPiecewiseFunctionNode(ASTPiecewiseFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- ASTPlusNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the plus operator
- ASTPlusNode() - Constructor for class org.sbml.jsbml.math.ASTPlusNode
-
- ASTPlusNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTPlusNode
-
- ASTPlusNode(ASTPlusNode) - Constructor for class org.sbml.jsbml.math.ASTPlusNode
-
Copy constructor; Creates a deep copy of the given
ASTPlusNode
.
- ASTPowerNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the power function
- ASTPowerNode() - Constructor for class org.sbml.jsbml.math.ASTPowerNode
-
- ASTPowerNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTPowerNode
-
Creates a new
ASTPowerNode
with the specified basis and
exponent.
- ASTPowerNode(ASTPowerNode) - Constructor for class org.sbml.jsbml.math.ASTPowerNode
-
Copy constructor; Creates a deep copy of the given
ASTPowerNode
.
- ASTQualifierNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML qualifier element
in a mathematical expression.
- ASTQualifierNode() - Constructor for class org.sbml.jsbml.math.ASTQualifierNode
-
- ASTQualifierNode(ASTQualifierNode) - Constructor for class org.sbml.jsbml.math.ASTQualifierNode
-
- ASTQualifierNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTQualifierNode
-
- ASTRelationalOperatorNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a relational
operator in a mathematical expression.
- ASTRelationalOperatorNode() - Constructor for class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- ASTRelationalOperatorNode(ASTRelationalOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- ASTRelationalOperatorNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- ASTRootNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a root function
- ASTRootNode() - Constructor for class org.sbml.jsbml.math.ASTRootNode
-
- ASTRootNode(ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTRootNode
-
Creates a new
ASTRootNode
with the specified radicand and
a root exponent of 2.
- ASTRootNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTRootNode
-
Creates a new
ASTRootNode
with the specified radicand and
rootExponent.
- ASTRootNode(ASTRootNode) - Constructor for class org.sbml.jsbml.math.ASTRootNode
-
Copy constructor; Creates a deep copy of the given
ASTRootNode
.
- ASTTimesNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the times operator
- ASTTimesNode() - Constructor for class org.sbml.jsbml.math.ASTTimesNode
-
- ASTTimesNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTTimesNode
-
- ASTTimesNode(ASTTimesNode) - Constructor for class org.sbml.jsbml.math.ASTTimesNode
-
Copy constructor; Creates a deep copy of the given
ASTTimesNode
.
- ASTTrigonometricNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a trigonometric function
- ASTTrigonometricNode() - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode
-
- ASTTrigonometricNode(ASTTrigonometricNode) - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode
-
- ASTTrigonometricNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode
-
- ASTUnaryFunctionNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a function with only one
parameter
- ASTUnaryFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- ASTUnaryFunctionNode(ASTUnaryFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- ASTUnaryFunctionNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- ASTUnknown - Class in org.sbml.jsbml.math
-
An
ASTNode2
with specified neutral behavior.
- ASTUnknown() - Constructor for class org.sbml.jsbml.math.ASTUnknown
-
- 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.math.parser.SimpleCharStream
-
- 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.math.compiler.HTMLFormula
-
Multiplication symbol “⋅”.
- 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
-
- canConvert(Class) - Method in class org.sbml.jsbml.xml.xstream.converter.SBMLErrorConverter
-
- category - Variable in exception org.sbml.jsbml.SBMLError
-
- category - Variable in exception org.sbml.jsbml.SBMLException
-
The category of this exception.
- Category() - Constructor for enum org.sbml.jsbml.SBMLException.Category
-
- category - Variable in class org.sbml.jsbml.util.Detail
-
- ceiling(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- ceiling(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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
-
- CHECK_CATEGORY() - Constructor for enum org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY
-
- checkAbout(SBase) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Checks and Sets about String
, that correspond to the value of the
rdf:about attribute.
- checkAndSetPackageNamespaceAndVersion(SBase) - Method in class org.sbml.jsbml.AbstractSBase
-
Checks whether or not the given
SBase
has the same package
version configuration than this element or the SBMLDocument.
- checkAndSetPackageNamespaceAndVersion(SBasePlugin, SBMLDocument) - Method in class org.sbml.jsbml.AbstractSBase
-
Checks whether or not the given
SBasePlugin
has the same package
configuration than the SBMLDocument.
- 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(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Creates brackets if needed.
- checkBrackets(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Creates brackets if needed.
- 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, Map<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(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Creates brackets if needed.
- checkDenominatorBrackets(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Creates brackets if needed.
- checkForDimensionlessOrInvalidUnits(UnitDefinition) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
Throws an IllegalArgumentException
if the given units do not
represent a dimensionless or invalid unit.
- 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
-
- checkPackages(SBMLDocument) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil
-
Checks the whole
SBMLDocument
, including all siblings, to make sure
that the package version and namespace is set properly.
- checkPackages(SBMLDocument, boolean, boolean) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil
-
Checks the whole
SBMLDocument
, including all siblings, to make sure
that the package version and namespace is set properly.
- checkPackages(SBase, List<String>, boolean, boolean) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil
-
Checks the given
SBase
, including all it's siblings, to make sure
that the package version and namespace is set properly.
- checkPackages(SBase, Map<String, PackageInfo>, Map<String, PackageInfo>, boolean, boolean) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil
-
Checks the given
SBase
, including all it's siblings, to make sure
that the package version and namespace is set properly.
- checkRelationalArgumentBrackets(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Creates brackets if needed.
- checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
- checkSize(ArrayList<ASTNode2>, int) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
- checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
- checkSize(ArrayList<ASTNode2>, int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
- checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
- checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
- checkSize(ArrayList<ASTNode2>, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
- checkSize(ArrayList<ASTNode>, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- checkSize(ArrayList<ASTNode2>, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
- 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.
- chemicalFormulaPattern - Static variable in class org.sbml.jsbml.validator.SyntaxChecker
-
- childElements - Variable in class org.sbml.jsbml.xml.XMLNode
-
- childNode - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- children() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- children() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- className - Variable in class org.sbml.jsbml.ASTNode
-
- 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
-
- clearUserObjects() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- clearUserObjects() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- clearUserObjects() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
Removes all of the mappings from the map of user objects (optional
operation).
- 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.ext.AbstractSBasePlugin
-
- clone() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- 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.math.AbstractASTNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTBoolean
-
- clone() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- clone() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTDivideNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTFunction
-
- clone() - Method in class org.sbml.jsbml.math.ASTHyperbolicNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTMinusNode
-
- clone() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Clone ASTNode2
- clone() - Method in class org.sbml.jsbml.math.ASTNumber
-
- clone() - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTPlusNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTQualifierNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTTimesNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTTrigonometricNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- clone() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- clone() - Method in class org.sbml.jsbml.Model
-
- clone() - Method in class org.sbml.jsbml.ModifierSpeciesReference
-
- clone() - Method in class org.sbml.jsbml.ontology.Term
-
- clone() - Method in class org.sbml.jsbml.ontology.Triple
-
- 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 deep copy of this object, i.e., a new
SBase
with the same
properties
like this one.
- 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.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.ListOfWithName
-
- clone() - Method in class org.sbml.jsbml.util.Pair
-
- 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.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- CLOSE_PAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- CobraFormulaParser - Class in org.sbml.jsbml.text.parser
-
Class used to parse infix mathematical formula written by the COBRA toolbox
and returns a representation of it as an Abstract Syntax Tree (AST).
- CobraFormulaParser(InputStream) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Constructor with InputStream.
- CobraFormulaParser(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Constructor with InputStream and supplied encoding
- CobraFormulaParser(Reader) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Constructor.
- CobraFormulaParser(CobraFormulaParserTokenManager) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Constructor with generated Token Manager.
- CobraFormulaParser.JJCalls - Class in org.sbml.jsbml.text.parser
-
- CobraFormulaParser.LookaheadSuccess - Error in org.sbml.jsbml.text.parser
-
- CobraFormulaParserConstants - Interface in org.sbml.jsbml.text.parser
-
Token literal values and constants.
- CobraFormulaParserTokenManager - Class in org.sbml.jsbml.text.parser
-
Token Manager.
- CobraFormulaParserTokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Constructor.
- CobraFormulaParserTokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Constructor.
- CobraUtil - Class in org.sbml.jsbml.util
-
Contains some useful methods to manipulate 'COBRA SBML'
- CobraUtil() - Constructor for class org.sbml.jsbml.util.CobraUtil
-
- code - Variable in exception org.sbml.jsbml.SBMLError
-
- code - Variable in exception org.sbml.jsbml.SBMLException
-
- Code() - Constructor for enum org.sbml.jsbml.SBMLException.Code
-
- 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.math.compiler.LaTeXCompiler
-
- colorbox(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- column - Variable in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- column - Variable in exception org.sbml.jsbml.SBMLError
-
- column - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- column - Variable in class org.sbml.jsbml.xml.XMLToken
-
- command(String, Object) - Static method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- command(String, Object, Object) - Static method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- 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
-
- compareString(String, String) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- compareTo(Term) - Method in class org.sbml.jsbml.ontology.Term
-
- compareTo(Triple) - Method in class org.sbml.jsbml.ontology.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.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- COMPARISON - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
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
-
- CompartmentalizedSBase - Interface in org.sbml.jsbml
-
- 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
-
- 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(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTBoolean
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTDivideNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTFunction
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTHyperbolicNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTMinusNode
-
- compile(ASTNode2Compiler) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Compiles this
ASTNode2
and returns the result.
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTPlusNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTQualifierNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTRootNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTTimesNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTTrigonometricNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- compile(ASTNode2Compiler) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- compile(Compartment) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- compile(double, int, String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Creates an
ASTNode2Value
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.math.compiler.ASTNode2Compiler
-
- compile(int, String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- compile(CallableSBase) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- compile(String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
A compiler will also have to deal with a name.
- compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.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.math.compiler.LaTeXCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- compile(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- compile(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
Compiles this
ASTNode2
and produce an XMLStreamWriter representing this node in mathML.
- compile(boolean) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
Compile boolean values
- compile(Compartment) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(double, int, String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(double, String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(int, String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(CallableSBase) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- compile(String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- compile(double, int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- compile(double, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- compile(int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- compile(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- compile(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- 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(ASTQualifierNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileBvar(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileCi(ASTCSymbolBaseNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileCi(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileConstantElement(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileConstantElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileCSymbol(ASTCSymbolNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileCSymbol(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileElement(ASTFunction) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileElement(String, ASTFunction) - Method in class org.sbml.jsbml.math.compiler.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(ASTConstantNumber) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileExponentiale(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileFunctionElement(ASTFunction) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileFunctionElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileInteger(ASTCnIntegerNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileInteger(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileLambda(ASTLambdaFunctionNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileLambda(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileLog(ASTLogarithmNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileLog(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileLogicalOperator(ASTLogicalOperatorNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileLogicalOperator(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileNegativeInfinity(ASTCnRealNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileNegativeInfinity(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileNotANumber(ASTCnRealNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileNotANumber(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compilePi(ASTConstantNumber) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compilePi(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compilePiecewise(ASTPiecewiseFunctionNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compilePiecewise(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compilePositiveInfinity(ASTCnRealNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compilePositiveInfinity(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compiler - Variable in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- compiler - Variable in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- compileRational(ASTCnRationalNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileRational(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileReal(ASTCnRealNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileReal(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileReal_e(ASTCnExponentialNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileReal_e(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileRelationalOperator(ASTRelationalOperatorNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileRelationalOperator(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileRootElement(ASTRootNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileRootElement(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileUserFunction(ASTCiFunctionNode) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileUserFunction(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- compileVector(ASTFunction) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- compileVector(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
String
s
(obtained by calling Object.toString()
if the current
Object
is not null
) into a new StringBuffer
.
- concatStringBuilder(Object...) - Static method in class org.sbml.jsbml.util.StringTools
-
This method concatenates two or more Object
String
s
(obtained by calling Object.toString()
if the current
Object
is not null
) into a new StringBuilder
.
- 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.math.compiler.LaTeXCompiler
-
- CONSTANT_E - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- CONSTANT_FALSE - Variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- CONSTANT_FALSE - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- CONSTANT_PI - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
The constant pi
- CONSTANT_PI - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
The constant pi
- CONSTANT_TRUE - Variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- 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.math.compiler.FormulaCompiler
-
Tests whether the String representation of the given object contains any
arithmetic symbols and if the given object is already sorrounded by
brackets.
- 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 surrounded 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
.
- containsReaction(String) - Method in class org.sbml.jsbml.Model
-
Returns
true
if this
Model
contains a reference to the
given
Reaction
.
- 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.Compartment
-
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Returns
true
or
false
depending on whether this
ASTCiNumberNode
refers to elements such as parameters or
numbers with undeclared units.
- containsUndeclaredUnits() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
Flag to indicate whether or not units have been fully declared for this
value.
- 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.Species
-
- 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
-
- containsUserObjectKey(Object) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- containsUserObjectKey(Object) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- containsUserObjectKey(Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- 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(T) - Method in interface org.sbml.jsbml.SBMLInputConverter
-
Takes a model in an arbitrary (but type-secure) format and delivers a
corresponding JSBML-compliant model.
- convertSBMLDocument(File) - Method in interface org.sbml.jsbml.SBMLInputConverter
-
- convertSBMLDocument(String) - 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(InputStream, OutputStream) - Method in class org.sbml.jsbml.validator.MultipartPost
-
- cos(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- cos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- cos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- cosh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- cosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.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
-
Deprecated.
- cosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- cot(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- cot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- coth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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.
- countType(ASTNode2, ASTNode.Type) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Counts the number of nodes that have
ASTNode.Type
type
in the tree rooted at node.
- 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
-
Deprecated.
- createApplyNode(Node, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
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
-
Deprecated.
- createApplyNode(String, ASTNodeValue...) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- createApplyNode(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
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
-
Deprecated.
- createCnElement(double, int, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- createCnElement(Number, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- 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
-
Deprecated.
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
-
Deprecated.
- createdDate - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- createDelay() - Method in class org.sbml.jsbml.Event
-
Creates a new
Delay
instance and sets it to this
Event
.
- createDelay(ASTNode) - Method in class org.sbml.jsbml.Event
-
Creates a new
Delay
instance and sets it to this
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.
- 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
-
Creates a new
EventAssignment
element and adds it to the ListOfEventAssignments list.
- createEventAssignment(String, ASTNode) - Method in class org.sbml.jsbml.Event
-
Creates a new
EventAssignment
element and adds it to the ListOfEventAssignments list.
- createEventAssignment(Variable, ASTNode) - Method in class org.sbml.jsbml.Event
-
Creates a new
EventAssignment
element and adds it to the ListOfEventAssignments list.
- 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
-
Creates a new
History
and associates it with the annotation of
this element.
- createHistory() - Method in class org.sbml.jsbml.Annotation
-
- createIndentationString(int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
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
-
- createListOfChild(ListOf<?>, String) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- 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
.
- createMessage(String, String, SBasePlugin) - Static method in exception org.sbml.jsbml.PropertyException
-
- createMessage(String, String, TreeNode) - 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
TreeNode
.
- createModel() - Method in class org.sbml.jsbml.SBMLDocument
-
Creates a new Model inside this
SBMLDocument
, and returns a
pointer to it.
- 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
-
- createModulo(ASTNode, ASTNode) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Returns a piecewise
ASTNode
representing the modulo operation between the left and right child given.
- createModulo(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Returns a piecewise
ASTNode
representing the modulo operation between the left and right child given.
- createModulo(ASTNode, ASTNode) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Returns a piecewise
ASTNode
representing the modulo operation between the left and right child given.
- createModulo(ASTNode, ASTNode) - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
Returns a piecewise
ASTNode
representing the modulo operation between the left and right child given.
- createModulo(ASTNode, ASTNode) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Returns a piecewise
ASTNode
representing the modulo operation between the left and right child given.
- createModulo(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Returns a piecewise
ASTNode
representing the modulo operation between the left and right child given.
- createNestedCVTerm() - Method in class org.sbml.jsbml.CVTerm
-
- createParameter() - Method in class org.sbml.jsbml.Model
-
- createParameter(String) - Method in class org.sbml.jsbml.Model
-
- createPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- createPlugin(String) - Method in interface org.sbml.jsbml.SBase
-
Creates a new
SBasePlugin
for the given package name or URI
and adds it to this
SBase
.
- createPluginFor(SBase) - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
- 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
-
- createSpecies(String, String, Compartment) - Method in class org.sbml.jsbml.Model
-
- createSpeciesType() - Method in class org.sbml.jsbml.Model
-
- createSpeciesType(String) - Method in class org.sbml.jsbml.Model
-
- createStoichiometryMath(ASTNode) - Method in class org.sbml.jsbml.SpeciesReference
-
- 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(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
-
- csc(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- csc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- csch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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.math.parser.FormulaParserASTNode2TokenManager
-
- curChar - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
- curChar - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
- curChar - Variable in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
- curChar - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
- curChar - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
- curChar - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
- curChar - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
- curChar - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
- curLexState - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
- curLexState - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
- curLexState - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
- curLexState - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
- currentToken - Variable in exception org.sbml.jsbml.math.parser.ParseException
-
This is the last token that has been consumed successfully.
- currentToken - Variable in exception org.sbml.jsbml.text.parser.ParseException
-
This is the last token that has been consumed successfully.
- CUSTOM_RDF - Static variable in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
A Constant String
that is used to store any remaining children
or attributes after having removed the standard SBML RDF elements and attributes.
- 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(XMLNode) - Constructor for class org.sbml.jsbml.CVTerm
-
- CVTerm.Qualifier - Enum in org.sbml.jsbml
-
This enum
list all the possible MIRIAM qualifiers.
- CVTerm.Type - Enum in org.sbml.jsbml
-
This enum list all the possible MIRIAM qualifiers 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
-
- factorial(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- factorial(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- factorial(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- factorial(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- factorial(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- factorial(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- FACTORIAL - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- FACTORIAL - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- FACTORIAL - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- FACTORIAL - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- factorial(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML
-
- factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- factorial(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- factorial(int) - Static method in class org.sbml.jsbml.util.Maths
-
This method computes the factorial! function.
- familyName - Variable in class org.sbml.jsbml.Creator
-
Family name of the creator
- familyName - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- fast - Variable in class org.sbml.jsbml.Reaction
-
Represents the 'fast' XML attribute of a reaction element.
- fast - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- fatal(String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger
-
- file - Variable in class org.sbml.jsbml.SBMLErrorLog
-
- fill(int, char, String) - Static method in class org.sbml.jsbml.util.StringTools
-
- fill(int, char) - Static method in class org.sbml.jsbml.util.StringTools
-
- fill(int, char, StringBuilder) - Static method in class org.sbml.jsbml.util.StringTools
-
Ensures a minimum size of length
for the given
stringBuilder
.
- FillBuff() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- FillBuff() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- filter(Filter) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- filter(Filter, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- filter(Filter, boolean, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- filter(Filter) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- filter(Filter, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- filter(Filter, boolean, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- Filter - Interface in org.sbml.jsbml.util.filters
-
A filter is a general interface that allows to check an object for a certain
property.
- filter(Filter) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
Filters this tree data structure recursively and returns a list of all
TreeNode
s that are accepted by the
Filter
.
- filter(Filter, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
Filters this tree data structure recursively and returns a list of all
TreeNode
s that are accepted by the
Filter
.
- filter(Filter, boolean, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
Filters this tree data structure recursively and returns a list of all
TreeNode
s that are accepted by the
Filter
.
- filterCVTerms(CVTerm.Qualifier) - Method in class org.sbml.jsbml.AbstractSBase
-
- filterCVTerms(CVTerm.Qualifier, boolean, String...) - Method in class org.sbml.jsbml.AbstractSBase
-
- filterCVTerms(CVTerm.Qualifier, String) - Method in class org.sbml.jsbml.AbstractSBase
-
- filterCVTerms(CVTerm.Qualifier, String, boolean) - Method in class org.sbml.jsbml.AbstractSBase
-
- filterCVTerms(CVTerm.Qualifier) - Method in class org.sbml.jsbml.Annotation
-
Returns a list of CVTerm having the given qualifier.
- filterCVTerms(CVTerm.Qualifier, String) - Method in class org.sbml.jsbml.Annotation
-
Returns a list of CVTerm having the given qualifier and
where the URI contains the given pattern.
- filterCVTerms(CVTerm.Qualifier) - Method in interface org.sbml.jsbml.SBase
-
- filterCVTerms(CVTerm.Qualifier, String) - Method in interface org.sbml.jsbml.SBase
-
Queries the list of controlled vocabulary terms (
CVTerm
) for those
terms whose
CVTerm.Qualifier
is of the given type and selects only those
resources from
these terms that contain the given pattern.
- filterCVTerms(CVTerm.Qualifier, String, boolean) - Method in interface org.sbml.jsbml.SBase
-
Returns a list of resource URIs for the given
CVTerm.Qualifier
that match
the
given pattern.
- filterCVTerms(CVTerm.Qualifier, boolean, String...) - Method in interface org.sbml.jsbml.SBase
-
Returns a list of resource URIs for the given
CVTerm.Qualifier
that match
the
given patterns.
- filterForSpecies - Variable in class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
-
Decides whether to filter for the identifier of the referenced
Species
or if to use id and name to filter for the instance of
SimpleSpeciesReference
itself.
- filterList(Filter) - Method in class org.sbml.jsbml.ListOf
-
Returns a new List
that contains only those elements that
satisfy a certain filter criterion.
- filterResources(Pattern...) - Method in class org.sbml.jsbml.CVTerm
-
Returns a list of resource URIs that contain the given Pattern
(s).
- filterResources(String...) - Method in class org.sbml.jsbml.CVTerm
-
Returns a list of resource URIs that contain the given pattern(s).
- filters - Variable in class org.sbml.jsbml.util.filters.AndFilter
-
A set of filters whose conditions have to be satisfied to accept an item.
- findCallableSBase(String) - Method in class org.sbml.jsbml.Model
-
Returns a
CallableSBase
element of the
Model
that has the
given 'id' as identifier or
null
if no element is found.
- findFirstNonEmptyTextElementIndex(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Return the first child element of type text that is not empty.
- findIdentical(UnitDefinition) - Method in class org.sbml.jsbml.Model
-
- findLocalParameters(String) - Method in class org.sbml.jsbml.Model
-
- findModifierSpeciesReference(String) - Method in class org.sbml.jsbml.Model
-
- findNamedSBase(String) - Method in class org.sbml.jsbml.Model
-
Returns a
NamedSBase
element of the model that has the given 'id'
as id or
null
if no element is found.
- findNamedSBaseWithDerivedUnit(String) - Method in class org.sbml.jsbml.Model
-
- findQuantity(String) - Method in class org.sbml.jsbml.Model
-
Searches for an instance of
Quantity
within all of this
Model
's components that has the given identifier or name attribute
and returns it.
- findQuantityWithUnit(String) - Method in class org.sbml.jsbml.Model
-
Searches for an instance of
QuantityWithUnit
within all of this
Model
's components that has the given identifier or name attribute
and returns it.
- findReactionsForLocalParameter(String) - Method in class org.sbml.jsbml.Model
-
- findReferencedCallableSBases() - Method in class org.sbml.jsbml.math.ASTFunction
-
Goes through the formula and identifies all global parameters that are
referenced by this rate rule.
- findReferencedGlobalParameters() - Method in class org.sbml.jsbml.ASTNode
-
Goes through the formula and identifies all global parameters that are
referenced by this rate equation.
- findSBase(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- findShortestPath(int, OverdeterminationValidator.Node<SBase>, List<OverdeterminationValidator.Node<SBase>>) - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
-
Finds all paths of the length i whose nodes are part of the matching.
- findSimpleSpeciesReference(String) - Method in class org.sbml.jsbml.Model
-
- findSpeciesReference(String) - Method in class org.sbml.jsbml.Model
-
- findSymbol(String) - Method in class org.sbml.jsbml.Model
-
- findUniqueNamedSBase(String) - Method in class org.sbml.jsbml.Model
-
Returns a
UniqueNamedSBase
element that has the given 'id' within
this
Model
or
null
if no such element can be found.
- findUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
Returns a
UnitDefinition
element that has the given 'id' within
this
Model
or
null
if no such element can be found.
- FindUnitsCompiler - Class in org.sbml.jsbml.math.compiler
-
Finds if an ASTNode is using any units attribute.
- FindUnitsCompiler() - Constructor for class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- findUnitsCompiler - Variable in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- FindUnitsCompiler - Class in org.sbml.jsbml.util.compilers
-
Finds if an ASTNode is using any units attribute.
- FindUnitsCompiler() - Constructor for class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- findUnitsCompiler - Variable in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- findVariable(String) - Method in class org.sbml.jsbml.Model
-
Searches the
Variable
with the given identifier in this model.
- fireNodeAddedEvent() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- fireNodeAddedEvent() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- fireNodeAddedEvent() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- fireNodeAddedEvent() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
All
TreeNodeChangeListener
instances linked to this
TreeNode
are informed about the adding of this
Object
to
an owning parent
Object
.
- fireNodeRemovedEvent() - Method in class org.sbml.jsbml.AbstractSBase
-
- fireNodeRemovedEvent() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- fireNodeRemovedEvent() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- fireNodeRemovedEvent() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- fireNodeRemovedEvent() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
All
TreeNodeChangeListener
instances linked to this
TreeNode
are informed about the deletion of this
TreeNode
from a parent
Object
.
- firePropertyChange(String, Object, Object) - Method in class org.sbml.jsbml.AbstractSBase
-
- firePropertyChange(String, Object, Object) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- firePropertyChange(String, Object, Object) - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- firePropertyChange(String, Object, Object) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- firePropertyChange(String, Object, Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- first - Variable in class org.sbml.jsbml.math.parser.FormulaParser.JJCalls
-
- first - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2.JJCalls
-
- first - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3.JJCalls
-
- first - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2.JJCalls
-
- first - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParser.JJCalls
-
- first - Variable in class org.sbml.jsbml.text.parser.FormulaParser.JJCalls
-
- first - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2.JJCalls
-
- first - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3.JJCalls
-
- first - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2.JJCalls
-
- firstHit(Filter) - Method in class org.sbml.jsbml.ListOf
-
Returns the first element in this list that satisfies a certain filter
criterion.
- firstLetterLowerCase(String) - Static method in class org.sbml.jsbml.util.StringTools
-
Returns a String whose first letter is now in lower case.
- firstLetterUpperCase(String) - Static method in class org.sbml.jsbml.util.StringTools
-
Returns a String who's first letter is now in upper case.
- floor(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- floor(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- floor(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- floor(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- floor(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- floor(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- floor(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- format(double) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
This method returns a StringBuffer
representing a properly
LaTeX formatted number.
- format(double) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
This method returns a StringBuffer
representing a properly
LaTeX formatted number.
- formatToW3CDTF(Date) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
-
- formatToW3CDTF(String) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
-
Format datetime string to
W3CDTF.
- formatToW3CDTF(Timestamp) - Method in class org.sbml.jsbml.xml.stax.DateProcessor
-
- formula - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- FORMULA_ARGUMENT_SEPARATOR - Static variable in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- FormulaCompiler - Class in org.sbml.jsbml.math.compiler
-
This class creates C-like infix formula
String
s that represent the
content of
ASTNode2
s.
- FormulaCompiler() - Constructor for class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- FormulaCompiler - Class in org.sbml.jsbml.util.compilers
-
This class creates C-like infix formula
String
s that represent the
content of
ASTNode
s.
- FormulaCompiler() - Constructor for class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- FormulaCompilerLibSBML - Class in org.sbml.jsbml.util.compilers
-
This class creates C-like infix formula
String
s that represent the
content of
ASTNode
s and try to reproduce the output generated by the LibSBML L3 parser.
- FormulaCompilerLibSBML() - Constructor for class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML
-
- FormulaCompilerNoPiecewise - Class in org.sbml.jsbml.util.compilers
-
Produces an infix formula like
FormulaCompiler
but removes all the
piecewise functions.
- FormulaCompilerNoPiecewise() - Constructor for class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
-
- FormulaParser - Class in org.sbml.jsbml.math.parser
-
Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
- FormulaParser(InputStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParser
-
Constructor with InputStream.
- FormulaParser(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.FormulaParser
-
Constructor with InputStream and supplied encoding
- FormulaParser(Reader) - Constructor for class org.sbml.jsbml.math.parser.FormulaParser
-
Constructor.
- FormulaParser(FormulaParserTokenManager) - Constructor for class org.sbml.jsbml.math.parser.FormulaParser
-
Constructor with generated Token Manager.
- FormulaParser - Class in org.sbml.jsbml.text.parser
-
Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
- FormulaParser(InputStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser
-
Constructor with InputStream.
- FormulaParser(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser
-
Constructor with InputStream and supplied encoding
- FormulaParser(Reader) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser
-
Constructor.
- FormulaParser(FormulaParserTokenManager) - Constructor for class org.sbml.jsbml.text.parser.FormulaParser
-
Constructor with generated Token Manager.
- FormulaParser.JJCalls - Class in org.sbml.jsbml.math.parser
-
- FormulaParser.JJCalls - Class in org.sbml.jsbml.text.parser
-
- FormulaParser.LookaheadSuccess - Error in org.sbml.jsbml.math.parser
-
- FormulaParser.LookaheadSuccess - Error in org.sbml.jsbml.text.parser
-
- FormulaParserASTNode2 - Class in org.sbml.jsbml.math.parser
-
Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
- FormulaParserASTNode2(InputStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Constructor with InputStream.
- FormulaParserASTNode2(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Constructor with InputStream and supplied encoding
- FormulaParserASTNode2(Reader) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Constructor.
- FormulaParserASTNode2(FormulaParserASTNode2TokenManager) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Constructor with generated Token Manager.
- FormulaParserASTNode2 - Class in org.sbml.jsbml.text.parser
-
Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
- FormulaParserASTNode2(InputStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Constructor with InputStream.
- FormulaParserASTNode2(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Constructor with InputStream and supplied encoding
- FormulaParserASTNode2(Reader) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Constructor.
- FormulaParserASTNode2(FormulaParserASTNode2TokenManager) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Constructor with generated Token Manager.
- FormulaParserASTNode2.JJCalls - Class in org.sbml.jsbml.math.parser
-
- FormulaParserASTNode2.JJCalls - Class in org.sbml.jsbml.text.parser
-
- FormulaParserASTNode2.LookaheadSuccess - Error in org.sbml.jsbml.math.parser
-
- FormulaParserASTNode2.LookaheadSuccess - Error in org.sbml.jsbml.text.parser
-
- FormulaParserASTNode2Constants - Interface in org.sbml.jsbml.math.parser
-
Token literal values and constants.
- FormulaParserASTNode2Constants - Interface in org.sbml.jsbml.text.parser
-
Token literal values and constants.
- FormulaParserASTNode2TokenManager - Class in org.sbml.jsbml.math.parser
-
Token Manager.
- FormulaParserASTNode2TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
Constructor.
- FormulaParserASTNode2TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
Constructor.
- FormulaParserASTNode2TokenManager - Class in org.sbml.jsbml.text.parser
-
Token Manager.
- FormulaParserASTNode2TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
Constructor.
- FormulaParserASTNode2TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
Constructor.
- FormulaParserConstants - Interface in org.sbml.jsbml.math.parser
-
Token literal values and constants.
- FormulaParserConstants - Interface in org.sbml.jsbml.text.parser
-
Token literal values and constants.
- FormulaParserLL3 - Class in org.sbml.jsbml.math.parser
-
Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
- FormulaParserLL3(InputStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Constructor with InputStream.
- FormulaParserLL3(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Constructor with InputStream and supplied encoding
- FormulaParserLL3(Reader) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Constructor.
- FormulaParserLL3(FormulaParserLL3TokenManager) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Constructor with generated Token Manager.
- FormulaParserLL3 - Class in org.sbml.jsbml.text.parser
-
Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
- FormulaParserLL3(InputStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Constructor with InputStream.
- FormulaParserLL3(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Constructor with InputStream and supplied encoding
- FormulaParserLL3(Reader) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Constructor.
- FormulaParserLL3(FormulaParserLL3TokenManager) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Constructor with generated Token Manager.
- FormulaParserLL3.JJCalls - Class in org.sbml.jsbml.math.parser
-
- FormulaParserLL3.JJCalls - Class in org.sbml.jsbml.text.parser
-
- FormulaParserLL3.LookaheadSuccess - Error in org.sbml.jsbml.math.parser
-
- FormulaParserLL3.LookaheadSuccess - Error in org.sbml.jsbml.text.parser
-
- FormulaParserLL3ASTNode2 - Class in org.sbml.jsbml.math.parser
-
Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
- FormulaParserLL3ASTNode2(InputStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Constructor with InputStream.
- FormulaParserLL3ASTNode2(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Constructor with InputStream and supplied encoding
- FormulaParserLL3ASTNode2(Reader) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Constructor.
- FormulaParserLL3ASTNode2(FormulaParserLL3ASTNode2TokenManager) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Constructor with generated Token Manager.
- FormulaParserLL3ASTNode2 - Class in org.sbml.jsbml.text.parser
-
Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
- FormulaParserLL3ASTNode2(InputStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Constructor with InputStream.
- FormulaParserLL3ASTNode2(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Constructor with InputStream and supplied encoding
- FormulaParserLL3ASTNode2(Reader) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Constructor.
- FormulaParserLL3ASTNode2(FormulaParserLL3ASTNode2TokenManager) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Constructor with generated Token Manager.
- FormulaParserLL3ASTNode2.JJCalls - Class in org.sbml.jsbml.math.parser
-
- FormulaParserLL3ASTNode2.JJCalls - Class in org.sbml.jsbml.text.parser
-
- FormulaParserLL3ASTNode2.LookaheadSuccess - Error in org.sbml.jsbml.math.parser
-
- FormulaParserLL3ASTNode2.LookaheadSuccess - Error in org.sbml.jsbml.text.parser
-
- FormulaParserLL3ASTNode2Constants - Interface in org.sbml.jsbml.math.parser
-
Token literal values and constants.
- FormulaParserLL3ASTNode2Constants - Interface in org.sbml.jsbml.text.parser
-
Token literal values and constants.
- FormulaParserLL3ASTNode2TokenManager - Class in org.sbml.jsbml.math.parser
-
Token Manager.
- FormulaParserLL3ASTNode2TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
Constructor.
- FormulaParserLL3ASTNode2TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
Constructor.
- FormulaParserLL3ASTNode2TokenManager - Class in org.sbml.jsbml.text.parser
-
Token Manager.
- FormulaParserLL3ASTNode2TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
Constructor.
- FormulaParserLL3ASTNode2TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
Constructor.
- FormulaParserLL3Constants - Interface in org.sbml.jsbml.math.parser
-
Token literal values and constants.
- FormulaParserLL3Constants - Interface in org.sbml.jsbml.text.parser
-
Token literal values and constants.
- FormulaParserLL3TokenManager - Class in org.sbml.jsbml.math.parser
-
Token Manager.
- FormulaParserLL3TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
Constructor.
- FormulaParserLL3TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
Constructor.
- FormulaParserLL3TokenManager - Class in org.sbml.jsbml.text.parser
-
Token Manager.
- FormulaParserLL3TokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
Constructor.
- FormulaParserLL3TokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
Constructor.
- FormulaParserTokenManager - Class in org.sbml.jsbml.math.parser
-
Token Manager.
- FormulaParserTokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
Constructor.
- FormulaParserTokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
Constructor.
- FormulaParserTokenManager - Class in org.sbml.jsbml.text.parser
-
Token Manager.
- FormulaParserTokenManager(SimpleCharStream) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
Constructor.
- FormulaParserTokenManager(SimpleCharStream, int) - Constructor for class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
Constructor.
- formulaToString(ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
Returns the formula from the given ASTNode as an SBML Level 1 text-string
mathematical formula.
- formulaToString(ASTNode, FormulaCompiler) - Static method in class org.sbml.jsbml.ASTNode
-
Returns the formula from the given
ASTNode
as an
infix mathematical formula produce by the given
FormulaCompiler
.
- formulaToString(ASTNode) - Static method in class org.sbml.jsbml.JSBML
-
Converts an
ASTNode
formula to a text string using a specific
syntax for mathematical formulas.
- formulaToString(ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Returns the formula from the given ASTNode2 as an SBML Level 1 text-string
mathematical formula.
- frac(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
Creates a new
ASTNode
of type DIVIDE with the given nodes as children.
- frac(int, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
Creates a new
ASTNode
that of type DIVIDE with the given numerator and
denominator.
- frac(MathContainer, CallableSBase, CallableSBase) - Static method in class org.sbml.jsbml.ASTNode
-
- frac(MathContainer, String, String) - Static method in class org.sbml.jsbml.ASTNode
-
Returns a new
ASTNode
that of type DIVIDE with the two entities as numerator and denominator.
- frac(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- frac(int, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Creates a new
ASTDivideNode
with the given numerator
and denominator.
- frac(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- frac(int, int) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
A fraction of two int values.
- frac(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- frac(int, int) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- frac(Object, Object) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Returns a fraction with the given elements as numerator and denominator.
- frac(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- frac(int, int) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- frac(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- frac(int, int) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- frac(Object, Object) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- frac(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- frac(int, int) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- frac(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- frac(int, int) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
A fraction of two int values.
- frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- frac(int, int) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- frac(Object, Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Returns a fraction with the given elements as numerator and denominator.
- frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- frac(int, int) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- frac(int, int) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- frac(Object, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- frac(int, int) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- frac(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- frac(int, int) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- function(FunctionDefinition, List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- function(T, List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- function(String, List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- function(FunctionDefinition, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- function(String, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- function(T, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- function(FunctionDefinition, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- function(String, ASTNode2...) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- function(String, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- function(T, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- function(FunctionDefinition, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- function(String, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Decides whether to produce brackets.
- function(String, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- function(String, Object) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Without brackets.
- function(T, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- function(String, ASTNode2...) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- function(String, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- function(FunctionDefinition, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- function(String, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- function(T, List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- function(FunctionDefinition, List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- function(String, List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- function(FunctionDefinition, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- function(FunctionDefinition, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- function(String, ASTNode...) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- function(FunctionDefinition, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- function(String, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Decides whether to produce brackets.
- function(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Without brackets.
- function(FunctionDefinition, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- function(String, ASTNode...) - Method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- function(FunctionDefinition, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- function(String, List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- FunctionDefinition - Class in org.sbml.jsbml
-
Represents the functionDefinition XML element of a SBML file.
- FunctionDefinition() - Constructor for class org.sbml.jsbml.FunctionDefinition
-
Creates a FunctionDefinition instance.
- FunctionDefinition(FunctionDefinition) - Constructor for class org.sbml.jsbml.FunctionDefinition
-
Creates a FunctionDefinition instance from a given FunctionDefinition.
- FunctionDefinition(int, int) - Constructor for class org.sbml.jsbml.FunctionDefinition
-
Creates a FunctionDefinition instance from a level and version.
- FunctionDefinition(String, ASTNode, int, int) - Constructor for class org.sbml.jsbml.FunctionDefinition
-
Creates a FunctionDefinition instance from an id, ASTNode, level and
version.
- FunctionDefinition(String, int, int) - Constructor for class org.sbml.jsbml.FunctionDefinition
-
Creates a FunctionDefinition instance from an id, level and version.
- gen - Variable in class org.sbml.jsbml.math.parser.FormulaParser.JJCalls
-
- gen - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2.JJCalls
-
- gen - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3.JJCalls
-
- gen - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2.JJCalls
-
- gen - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParser.JJCalls
-
- gen - Variable in class org.sbml.jsbml.text.parser.FormulaParser.JJCalls
-
- gen - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2.JJCalls
-
- gen - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3.JJCalls
-
- gen - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2.JJCalls
-
- generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Generate ParseException.
- generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
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(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- geq(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Greater equal.
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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.FormulaCompilerLibSBML
-
- 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
-
Deprecated.
- 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.
- getActivator() - Static method in class org.sbml.jsbml.SBO
-
- 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.math.ASTBoolean
-
- getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTFunction
-
- getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTNumber
-
- getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
Deprecated.
- 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
-
- 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
-
- getArgumentCount() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getAssociation() - Static method in class org.sbml.jsbml.SBO
-
Interaction between several biochemical entities that results in the
formation of a non-covalent complex
- 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
.
- getBase() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- getBasis() - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- getBeginColumn() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get token beginning column number.
- getBeginColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Get token beginning column number.
- getBeginLine() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get token beginning line 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
-
An essential activator that affects the apparent value of the Michaelis
constant(s).
- getBiologicalQualifierFor(String) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier
-
- getBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- getBody() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getBoundaryCondition() - Method in class org.sbml.jsbml.Species
-
- getBundle(String) - Static method in class org.sbml.jsbml.util.ResourceManager
-
Loads the ResourceBundle
with the given name for the default
Locale
.
- getBundle(String, Locale) - Static method in class org.sbml.jsbml.util.ResourceManager
-
Loads the ResourceBundle
with the given name for the given
Locale
.
- getBvarCount() - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- 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
-
Modification of the velocity of a reaction by lowering the energy of the
transition state.
- getCatalyst() - Static method in class org.sbml.jsbml.SBO
-
Substance that accelerates the velocity of a chemical reaction without
itself being consumed or transformed.
- 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() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
Get the child of this node
- getChild(int) - Method in class org.sbml.jsbml.xml.XMLNode
-
Returns the child
XMLNode
at index childIndex.
- 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.math.AbstractASTNode
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTBoolean
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTFunction
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTNumber
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- getChildAt(int) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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.math.ASTBoolean
-
- getChildCount() - Method in class org.sbml.jsbml.math.ASTFunction
-
- getChildCount() - Method in class org.sbml.jsbml.math.ASTNumber
-
- getChildCount() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
- getChildElement(String, String) - Method in class org.sbml.jsbml.xml.XMLNode
-
Gets the first direct child element of this
XMLNode
with the given local name and namespace.
- getChildElements(String, String) - Method in class org.sbml.jsbml.xml.XMLNode
-
Gets all the direct children of this
XMLNode
with the given local
name and namespace.
- getChildren() - Method in class org.sbml.jsbml.ASTNode
-
Returns the list of children of the current ASTNode.
- getChildren() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the list of children of the current ASTFunction.
- getChildren() - Method in class org.sbml.jsbml.ontology.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 class org.sbml.jsbml.math.parser.SimpleCharStream
-
Deprecated.
- 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.xml.XMLToken
-
Returns the column at which this
XMLToken
occurred in the input
document or data stream.
- getCompartment() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
Returns the value of the referenced compartment.
- getCompartment(int) - Method in class org.sbml.jsbml.Model
-
Gets the n
th 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() - Static method in class org.sbml.jsbml.SBO
-
Physical compartment.
- getCompartment() - Method in class org.sbml.jsbml.Species
-
- getCompartmentCount() - Method in class org.sbml.jsbml.Model
-
- getCompartmentInstance() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
- getCompartmentInstance() - Method in class org.sbml.jsbml.Reaction
-
- getCompartmentInstance() - Method in class org.sbml.jsbml.Species
-
- getCompartmentType() - Method in class org.sbml.jsbml.Compartment
-
- getCompartmentType(int) - Method in class org.sbml.jsbml.Model
-
- getCompartmentType(String) - Method in class org.sbml.jsbml.Model
-
- getCompartmentTypeCount() - Method in class org.sbml.jsbml.Model
-
- 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.math.compiler.ASTNode2Compiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getConstantE() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getConstantE() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- getConstantE() - Method in class org.sbml.jsbml.math.compiler.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
-
Deprecated.
- getConstantE() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getConstantFalse() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.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
-
Deprecated.
- getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getConstantPi() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getConstantPi() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantPi() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantPi() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantPi() - Method in class org.sbml.jsbml.math.compiler.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
-
Deprecated.
- getConstantPi() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getConstantTrue() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.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
-
Deprecated.
- 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.
- getConstraintCount() - Method in class org.sbml.jsbml.Model
-
- getConsumption() - Static method in class org.sbml.jsbml.SBO
-
Decrease in amount of a material or conceptual entity.
- 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
-
- getCreatorCount() - 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
-
Returns the
CVTerm
instance at the position 'index' in the list of
CVTerm
s of this object.
- getCVTermCount() - Method in class org.sbml.jsbml.AbstractSBase
-
- getCVTermCount() - Method in class org.sbml.jsbml.Annotation
-
- getCVTermCount() - Method in interface org.sbml.jsbml.SBase
-
- getCVTerms() - Method in class org.sbml.jsbml.AbstractSBase
-
- getCVTerms() - Method in interface org.sbml.jsbml.SBase
-
Returns the list of
CVTerm
s of this object.
- getDeclaredNamespaces() - Method in class org.sbml.jsbml.AbstractSBase
-
- getDeclaredNamespaces() - Method in class org.sbml.jsbml.Annotation
-
- 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
-
Returns the default symbol to be used to indent new elements in the XML
representation of SBML data structures.
- getDefaultIndentCount() - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Returns the default number of indent symbols to be concatenated at the
beginning of a new block in an XML representation of SBML data
structures.
- getDefaultLevel() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns 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
-
Returns the default Version of new SBMLDocument objects.
- getDefinition() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the definition of this
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
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
Returns the definitionURL of the MathML element represented by this ASTCiFunctionNode
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getDefinitionURL() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- getDelay() - Method in class org.sbml.jsbml.Event
-
- getDelayCount() - Method in class org.sbml.jsbml.Model
-
- getDenominator() - Method in class org.sbml.jsbml.ASTNode
-
Gets the value of the denominator of this node.
- getDenominator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
Get the denominator value of this node.
- getDenominator() - Method in class org.sbml.jsbml.SpeciesReference
-
- 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
-
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
-
Derives the unit of this quantity.
- getDerivedUnits() - Method in class org.sbml.jsbml.Species
-
- 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
-
- getDissociation() - Static method in class org.sbml.jsbml.SBO
-
Transformation of a non-covalent complex that results in the formation of
several independent biochemical entities.
- getDocument() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getDrug() - Static method in class org.sbml.jsbml.SBO
-
- getElementByMetaId(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- 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
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.jsbml.SBMLDocument
-
- getElementName() - Method in class org.sbml.jsbml.Species
-
- getElementName() - Method in class org.sbml.jsbml.SpeciesReference
-
- getElementName() - Method in class org.sbml.jsbml.util.ListOfWithName
-
- 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
-
- getElementNamespace() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getElementNamespace() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the XML namespace (URI) of the package extension of this plugin object.
- getEmail() - Method in class org.sbml.jsbml.Creator
-
Returns the email from the
Creator
.
- getEmptySet() - Static method in class org.sbml.jsbml.SBO
-
Empty set is used to represent the source of a creation process or the
result of a degradation process.
- getEnabledPackageNamespace(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Return the package namespace enabled on this SBMLDocument or null if the package
is not enabled.
- getEncoding() - Method in class org.sbml.jsbml.ASTNode
-
Returns the encoding of the mathML element represented by this ASTNode.
- getEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- getEncoding() - Method in interface org.sbml.jsbml.math.ASTCSymbolNode
-
Returns the encoding of the MathML element represented by
this
ASTCSymbolNode
- getEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- getEndColumn() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get token end column number.
- getEndColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Get token end column number.
- getEndLine() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get token end line 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
-
Returns the ith error or warning encountered during consistency checking.
- getError(long) - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the
nth
SBMLError
object in this log.
- getErrorCount() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the number of errors or warnings encountered during consistency checking.
- getErrorCount() - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the number of errors that have been logged.
- getErrorId() - Method in exception org.sbml.jsbml.xml.XMLException
-
- getErrorLog() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns a collection of all
SBMLError
s reflecting
problems in the overall data structure of this
SBMLDocument
.
- getErrorsBySeverity(SBMLError.SEVERITY) - Method in class org.sbml.jsbml.SBMLErrorLog
-
- 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
-
Gets an element from the listOfEventAssignments at the given index.
- getEventAssignment(String) - Method in class org.sbml.jsbml.Event
-
Gets an element from the listOfEventAssignments, with the given id.
- getEventAssignmentCount() - Method in class org.sbml.jsbml.Event
-
- getEventAssignmentCount() - Method in class org.sbml.jsbml.Model
-
- getEventCount() - Method in class org.sbml.jsbml.Model
-
- 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.math.ASTCnExponentialNode
-
Get the exponent value of this node.
- getExponent() - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- getExponent() - Method in class org.sbml.jsbml.Unit
-
- getExponentAsDouble() - Method in class org.sbml.jsbml.Unit
-
- getExtendedSBase() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getExtendedSBase() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the SBase object that is extended by this plug-in.
- getExtension(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- getExtension(String) - Method in interface org.sbml.jsbml.SBase
-
Returns the
SBasePlugin
extension object which matches this package
name or URI.
- getExtensionCount() - Method in class org.sbml.jsbml.AbstractSBase
-
- getExtensionCount() - Method in interface org.sbml.jsbml.SBase
-
- getExtensionPackages() - Method in class org.sbml.jsbml.AbstractSBase
-
- getExtensionPackages() - Method in interface org.sbml.jsbml.SBase
-
- 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.
- getFirstElementIndex(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase
-
Return the index of the first child of type 'Element' for the given
XMLNode
.
- getFormats(String) - Method in class org.sbml.jsbml.util.XMLResourceBundleControl
-
- getFormula() - Method in class org.sbml.jsbml.AbstractMathContainer
-
Deprecated.
- getFormula() - Method in interface org.sbml.jsbml.MathContainer
-
- getFullAnnotation() - Method in class org.sbml.jsbml.Annotation
-
- getFullAnnotationString() - Method in class org.sbml.jsbml.Annotation
-
- 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
-
- getFunctionDefinitionCount() - Method in class org.sbml.jsbml.Model
-
- getGene() - Static method in class org.sbml.jsbml.SBO
-
A gene is an informational molecule segment.
- 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
-
Returns the
History
instance of this object.
- 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 class org.sbml.jsbml.math.AbstractASTNode
-
- getId() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Get the id of this node
- getId() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getId() - Method in interface org.sbml.jsbml.NamedSBase
-
- getId() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the SBO identifier of this
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
-
- getIdManager(SBase) - Method in class org.sbml.jsbml.AbstractSBase
-
- getIdOrName(NamedSBase) - Static method in class org.sbml.jsbml.util.SBMLtools
-
- GetImage() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get token literal value.
- 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(TreeNode) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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.
- getInhibition() - Static method in class org.sbml.jsbml.SBO
-
Negative modulation of the execution of a process.
- getInhibitor() - Static method in class org.sbml.jsbml.SBO
-
Substance that decreases the probability of a chemical reaction without
itself being consumed or transformed by the reaction.
- 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
-
- getInitialAssignmentCount() - 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.math.ASTUnknown
-
- 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() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
Get the integer value of this node.
- getInteger(ASTNode) - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
- getInteger(ASTNode2) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
- getInteger(ASTNode) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
- getInteger(ASTNode2) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
- getInteger(ASTNode) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
- getInteger(ASTNode) - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
- getInteger(ASTNode2) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
- getInteger(ASTNode) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- getInteger(ASTNode2) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
- 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'.
- getKey() - Method in class org.sbml.jsbml.util.Pair
-
- getKeys() - Method in class org.sbml.jsbml.util.XMLResourceBundleControl.XMLResourceBundle
-
- 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
-
- getKineticLawCount() - Method in class org.sbml.jsbml.Model
-
- 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.
- getLastIndexOf(XMLNode, String, String) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getLeftChild() - Method in class org.sbml.jsbml.ASTNode
-
Gets the left child of this node.
- getLeftChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- 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 class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getLevel() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- getLevel() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
Returns the level of the SBML document that was the basis to create this
ASTNode2Value
.
- 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
-
Deprecated.
- 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 class org.sbml.jsbml.math.parser.SimpleCharStream
-
Deprecated.
- 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.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
-
- getListOfConstraints() - Method in class org.sbml.jsbml.Model
-
Returns the listOfConstraints of this
Model
.
- getListOfCount() - Method in class org.sbml.jsbml.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
-
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
-
Returns the listOfEventAssignments.
- 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
-
- getListOfNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm
-
- 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.
- getListOfNodes() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the list of children of the current ASTFunction.
- getListOfNodes(Filter) - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the list of children of the current ASTFunction that satisfy the
given filter.
- getListOfParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- getListOfParameters() - Method in class org.sbml.jsbml.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.AbstractReaderWriter
-
- 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 interface org.sbml.jsbml.xml.parsers.WritingParser
-
Returns the list of children of the objectToWrite
.
- getListOfSpecies() - Method in class org.sbml.jsbml.Model
-
- getListOfSpeciesTypes() - Method in class org.sbml.jsbml.Model
-
- getListOfTreeNodeChangeListeners() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getListOfTreeNodeChangeListeners() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
- getLocalParameterCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of parameters that are contained within kineticLaws in
the reactions of this model.
- 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
-
- getMacromolecule() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO term id for macromolecule.
- getManager() - Static method in class org.sbml.jsbml.xml.parsers.ParserManager
-
- getMantissa() - Method in class org.sbml.jsbml.ASTNode
-
Gets the mantissa value of this node.
- getMantissa() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
Get 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
-
- getMathContainerCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of elements that can contain math in the
Model
.
- getMathematicalExpression() - Static method in class org.sbml.jsbml.SBO
-
- getMathMLClass() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- getMathMLClass() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns the class of the MathML element represented by
this
ASTNode2
- getMathMLClass() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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 error org.sbml.jsbml.math.parser.TokenMgrError
-
You can also modify the body of this method to customize your error messages.
- 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
-
Returns the metaid of this element.
- 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
-
- getModel() - Method in class org.sbml.jsbml.util.ModelBuilder
-
- getModelHistory() - Method in class org.sbml.jsbml.Model
-
- getModellingFramework() - Static method in class org.sbml.jsbml.SBO
-
- getModelQualifierFor(String) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier
-
- getModelQualifierType() - Method in class org.sbml.jsbml.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
.
- getModifiedDateCount() - Method in class org.sbml.jsbml.History
-
Get the number of ModifiedDate objects 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
-
Substance that changes the velocity of a process without itself being
consumed or transformed by the reaction.
- getModifierCount() - Method in class org.sbml.jsbml.Reaction
-
- getModifierForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- getModifierSpeciesReferenceCount() - Method in class org.sbml.jsbml.Model
-
- getModifierSpeciesReferences() - Method in class org.sbml.jsbml.Model
-
- getModulation() - Static method in class org.sbml.jsbml.SBO
-
Modification of the execution of an event or a process.
- 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 class org.sbml.jsbml.math.ASTCiNumberNode
-
Deprecated.
- getName() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getName() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
- getName() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- getName() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the name of the MathML element represented by
this
ASTFunction
- getName() - Method in interface org.sbml.jsbml.NamedSBase
-
- getName() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the name of this
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
-
- getNamedSBaseCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of
NamedSBase
s in the
Model
, so elements
that can have a name.
- getNamedSBaseWithDerivedUnitCount() - Method in class org.sbml.jsbml.Model
-
- getNameOrID(NamedSBase) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
If the field printNameIfAvailable is false this method returns a the id
of the given SBase.
- 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.
- getNameOrId(NamedSBase) - Static method in class org.sbml.jsbml.util.SBMLtools
-
- getNamespace() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNamespace() - Method in interface org.sbml.jsbml.SBase
-
Returns the namespace to which this
SBase
belong to.
- getNamespace() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- getNamespaceFor(int, int, int) - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
Gets the namespace for this package that correspond to the given SBML level, version
and the package version.
- getNamespaceFor(int, int, int, String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
Gets the namespace for the given package name that correspond to the SBML level, version
and package version.
- 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.xml.parsers.MathMLParser
-
Deprecated.
- getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- getNamespaces() - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
-
Returns a List
of all the namespaces that this parser is handling.
- getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- getNamespaces() - Method in interface org.sbml.jsbml.xml.parsers.WritingParser
-
Returns a List
of all the namespaces that this parser is handling
- getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- getNamespaces() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
- 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() - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
Return the namespace URI of the namespace parsed by this class.
- getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- 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.
- getNecessaryStimulation() - Static method in class org.sbml.jsbml.SBO
-
Control that is necessary to the execution of a process.
- getNegativeInfinity() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getNestedCVTerm(int) - Method in class org.sbml.jsbml.CVTerm
-
- getNestedCVTermCount() - Method in class org.sbml.jsbml.CVTerm
-
- 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.math.parser.FormulaParser
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
Get the next Token.
- getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
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
-
- getNonCovalentComplex() - 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
XMLNode
containing annotations other than
the official RDF annotation, as defined in the SBML specifications.
- getNonRDFannotationAsString() - 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
-
Returns the notes sub-element of this object as a String
.
- getNumArguments() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getNumber() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Get the numerical base of MathML element.
- getNumbering(long) - Static method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getNumbering(long) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getNumChildren() - Method in class org.sbml.jsbml.AbstractTreeNode
-
Returns the number of child elements of this TreeNode
.
- 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
-
- getNumerator() - Method in class org.sbml.jsbml.ASTNode
-
Gets the value of the numerator of this node.
- getNumerator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
Get the numerator value of this node.
- getNumErrors() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the number of errors or warnings encountered during consistency checking.
- getNumErrors() - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the number of errors that have been logged.
- getNumEventAssignments() - Method in class org.sbml.jsbml.Event
-
- getNumEventAssignments() - Method in class org.sbml.jsbml.Model
-
- getNumEvents() - Method in class org.sbml.jsbml.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
-
- 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
-
- getNumNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm
-
- getNumParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- getNumParameters() - Method in class org.sbml.jsbml.Model
-
- getNumPlugins() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNumPlugins() - Method in interface org.sbml.jsbml.SBase
-
- getNumProducts() - Method in class org.sbml.jsbml.Reaction
-
- getNumQuantities() - Method in class org.sbml.jsbml.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
-
- getNumResources() - Method in class org.sbml.jsbml.CVTerm
-
Returns the number of resources for this
CVTerm
.
- getNumRules() - Method in class org.sbml.jsbml.Model
-
- getNumSBases() - Method in class org.sbml.jsbml.Model
-
- getNumSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.Model
-
- getNumSpecies() - Method in class org.sbml.jsbml.Model
-
- getNumSpeciesReferences() - Method in class org.sbml.jsbml.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
-
- getNumUnitDefinitions() - Method in class org.sbml.jsbml.Model
-
- getNumUnits() - Method in class org.sbml.jsbml.Model
-
- getNumUnits() - Method in class org.sbml.jsbml.UnitDefinition
-
- getNumVariables() - Method in class org.sbml.jsbml.Model
-
- getObject() - Method in class org.sbml.jsbml.ontology.Triple
-
Returns the object of this
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.
- getOrCreate(XMLNode, String, String, String) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getOrCreate(XMLNode, int, String, String, String) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getOrCreateAfter(XMLNode, String, String, String, String, String) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getOrCreateCVTerm(XMLNode, int, String, String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- getOrCreateDescription(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- 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.
- getOtherAttribute(String) - Method in class org.sbml.jsbml.Creator
-
- getOtherAttributes() - Method in class org.sbml.jsbml.Creator
-
- 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.
- getPackage() - Method in exception org.sbml.jsbml.SBMLError
-
- getPackageInfo(SBase, String, int, String, Map<String, PackageInfo>, Map<String, PackageInfo>, boolean, boolean) - Static method in class org.sbml.jsbml.xml.parsers.PackageUtil
-
- getPackageName() - Method in class org.sbml.jsbml.AbstractSBase
-
- getPackageName() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the package name of this plugin object.
- getPackageName() - Method in interface org.sbml.jsbml.SBase
-
- getPackageName() - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
Returns the short name of this package.
- getPackageName(String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
Returns the name of the SBML package corresponding to the given namespace URI.
- getPackageNamespaces() - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
Returns a List
of all the valid namespaces for the package.
- getPackageParser(String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
Returns the
PackageParser
corresponding to the given name or namespace.
- getPackageRequired(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the required attribute of the given package extension.
- getPackageRequired(String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
Returns the required attribute corresponding to the given name or namespace.
- getPackageVersion() - Method in class org.sbml.jsbml.AbstractSBase
-
- getPackageVersion() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getPackageVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the package version of the package extension of this plugin object.
- getPackageVersion() - Method in interface org.sbml.jsbml.SBase
-
Returns the version of the SBML Level 3 package to which this element belongs.
- 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
-
- getParameterCount() - Method in class org.sbml.jsbml.Model
-
- 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.math.ASTUnknown
-
- 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.ext.AbstractSBasePlugin
-
- getParentSBMLObject() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the parent
SBase
object to which this plugin object connected.
- 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 class org.sbml.jsbml.math.AbstractASTNode
-
- getParentSBMLObject() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Return the parentSBMLObject of this
ASTNode2
- getParentSBMLObject() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getParentSBMLObject() - Method in interface org.sbml.jsbml.SBase
-
Returns the parent of this
SBase
.
- getParentTerms() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the parent Terms.
- 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
-
The function of a physical or conceptual entity, that is its role, in the
execution of an event or process.
- getPattern() - Method in class org.sbml.jsbml.util.filters.CVTermFilter
-
- getPersistent() - Method in class org.sbml.jsbml.Trigger
-
- getPertubingAgent() - Static method in class org.sbml.jsbml.SBO
-
Perturbing agent.
- 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
-
- getPieceCount() - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- getPiecewiseMap() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
-
Gets a Map
of the piecewise expressions that have been
transformed.
- getPkgRequired(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- getPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- getPlugin(String) - Method in interface org.sbml.jsbml.SBase
-
Returns an
SBasePlugin
for an SBML Level 3 package extension
with the given package name or URI.
- getPositiveInfinity() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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.ontology.Triple
-
Returns the predicate of this
Triple
.
- getPrefix() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the prefix of the package extension of this plugin object.
- 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
-
- getProcess() - Static method in class org.sbml.jsbml.SBO
-
- 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
-
Substance that is produced in a reaction.
- getProductCount() - Method in class org.sbml.jsbml.Reaction
-
- getProductForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- getProduction() - Static method in class org.sbml.jsbml.SBO
-
Generation of a material or conceptual entity.
- 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.CVTerm
-
- getQualifier() - Method in class org.sbml.jsbml.util.filters.CVTermFilter
-
- getQualifierFor(String, String, CVTerm.Qualifier) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier
-
- getQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- getQuantitativeParameter() - Static method in class org.sbml.jsbml.SBO
-
- getQuantityCount() - Method in class org.sbml.jsbml.Model
-
- getQuantityWithUnitCount() - Method in class org.sbml.jsbml.Model
-
- getRadicand() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- getRateLaw() - Static method in class org.sbml.jsbml.SBO
-
- 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
-
Substance consumed by a chemical reaction.
- getReactantCount() - Method in class org.sbml.jsbml.Reaction
-
- 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
-
- getReactionCount() - Method in class org.sbml.jsbml.Model
-
- getReadingParsers() - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
- getReal() - Method in class org.sbml.jsbml.ASTNode
-
Gets the real-numbered value of this node.
- getReal() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
Get the real 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.
- getReferenceInstance() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- getReferenceInstance() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- getRefId() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
Get refId attribute
- getRefId() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Get refId attribute
- 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
-
- getReservedNamesL1V1() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
- getResourceCount() - Method in class org.sbml.jsbml.CVTerm
-
Returns the number of resources for this
CVTerm
.
- 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.
- getRightChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- getRNA() - Static method in class org.sbml.jsbml.SBO
-
- getRoot() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getRoot() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getRoot() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- getRootExponent() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- getRule(int) - Method in class org.sbml.jsbml.Model
-
Gets the n
th Rule
of the listOfRules.
- getRule(String) - Method in class org.sbml.jsbml.Model
-
- getRuleCount() - Method in class org.sbml.jsbml.Model
-
- getSBaseCount() - Method in class org.sbml.jsbml.Model
-
- getSBaseListType() - Method in class org.sbml.jsbml.ListOf
-
- getSBaseWithDerivedUnitCount() - Method in class org.sbml.jsbml.Model
-
- getSBMLDocument() - Method in class org.sbml.jsbml.AbstractSBase
-
- getSBMLDocument() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getSBMLDocument() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- getSBMLDocument() - Method in interface org.sbml.jsbml.SBase
-
- getSBMLDocument() - Method in class org.sbml.jsbml.util.ModelBuilder
-
- getSBMLDocumentAttributes() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the map of attribute names and values of this 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
-
- getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
Returns the shortLabel of the namespace parsed by this class.
- getShortMessage() - Method in exception org.sbml.jsbml.SBMLError
-
- getShortMessage() - Method in exception org.sbml.jsbml.SBMLException
-
- getSideProduct() - Static method in class org.sbml.jsbml.SBO
-
Returns the side product SBO term
- getSideSubstrate() - Static method in class org.sbml.jsbml.SBO
-
Returns the side substrate SBO term
- 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
-
- getSpatialSizeUnitsInstance() - Method in class org.sbml.jsbml.Species
-
- getSpecies(SpeciesReference) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Returns the id of a PluginSpeciesReference object's belonging species as
an object of type StringBuffer.
- 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
-
- 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.
- getSpeciesCount() - Method in class org.sbml.jsbml.Model
-
- getSpeciesInstance() - Method in class org.sbml.jsbml.SimpleSpeciesReference
-
- getSpeciesReferenceCount() - Method in class org.sbml.jsbml.Model
-
- getSpeciesType(int) - Method in class org.sbml.jsbml.Model
-
- getSpeciesType(String) - Method in class org.sbml.jsbml.Model
-
- getSpeciesType() - Method in class org.sbml.jsbml.Species
-
- getSpeciesTypeCount() - Method in class org.sbml.jsbml.Model
-
- getSpeciesTypeInstance() - Method in class org.sbml.jsbml.Species
-
- getSpeciesWithBoundaryConditionCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of
Species
whose boundary condition is set to
true
.
- 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
-
- getStimulation() - Static method in class org.sbml.jsbml.SBO
-
Positive modulation of the execution of a process.
- 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
-
- getStoichiometryMathCount() - Method in class org.sbml.jsbml.Model
-
- 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.
- getStyle() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- getStyle() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Return the style of this node
- getStyle() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getSubject() - Method in class org.sbml.jsbml.ontology.Triple
-
Returns the subject of this
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
-
- getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Species
-
- GetSuffix(int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get the suffix.
- 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
-
- getSymbolCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of all instances of
Symbol
referenced within the
model.
- getSynonyms() - Method in class org.sbml.jsbml.ontology.Term
-
Returns all
Synonym
s of this
Term
.
- getTabSize(int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- getTabSize(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- getTerm() - Method in class org.sbml.jsbml.ontology.Term
-
Grants access to the underlying BioJava
org.biojava3.ontology.Term
.
- 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'.
- getTerms() - Static method in class org.sbml.jsbml.SBO
-
Return the set of terms of the SBO Ontology.
- getTerms() - Method in class org.sbml.jsbml.util.filters.SBOFilter
-
- 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.math.parser.FormulaParser
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Get the specific Token.
- getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
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 class org.sbml.jsbml.math.ASTUnknown
-
- 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'
- getTriggerCount() - Method in class org.sbml.jsbml.Model
-
- getTriple() - Method in class org.sbml.jsbml.ontology.Triple
-
Grants access to the original BioJava
org.biojava3.ontology.Triple
.
- getTriples(Term, Term, Term) - Static method in class org.sbml.jsbml.SBO
-
Returns a set of Triple which match the supplied subject, predicate and object.
- getTrueIndexOf(XMLNode, String, String, int) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- 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 class org.sbml.jsbml.math.AbstractASTNode
-
- getType() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns the type of this ASTNode2.
- getType() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getType() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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.XMLNodeReader
-
- getUnit(int) - Method in class org.sbml.jsbml.UnitDefinition
-
Returns a specific Unit instance belonging to this UnitDefinition.
- getUnitCount() - Method in class org.sbml.jsbml.Model
-
- getUnitCount() - Method in class org.sbml.jsbml.UnitDefinition
-
- getUnitDefinition(int) - Method in class org.sbml.jsbml.Model
-
- getUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
- getUnitDefinitionCount() - Method in class org.sbml.jsbml.Model
-
- 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.Compartment
-
- getUnits() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- getUnits() - Method in class org.sbml.jsbml.ExplicitRule
-
- getUnits() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- getUnits() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Returns the units of the MathML element represented by this ASTCnNumberNode
- getUnits() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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.Compartment
-
- getUnitsInstance() - Method in class org.sbml.jsbml.Event
-
Deprecated.
- getUnitsInstance() - Method in class org.sbml.jsbml.ExplicitRule
-
- getUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- getUnitsInstance() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- 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() - Method in class org.sbml.jsbml.AbstractSBase
-
- getURI() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Gets the URI to which this element belongs to.
- getURI() - Method in interface org.sbml.jsbml.SBase
-
Returns the namespace to which this
SBase
belong to.
- 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(Object) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getUserObject(Object) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getUserObject() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- getUserObject(Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- 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 class org.sbml.jsbml.math.ASTBoolean
-
- getValue() - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- getValue() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getValue() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- getValue() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- getValue() - Method in class org.sbml.jsbml.math.parser.Token
-
An optional attribute value of the Token.
- 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.util.Pair
-
- 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
-
- getVariable() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- getVariableCount() - Method in class org.sbml.jsbml.Model
-
- 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 class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- getVersion() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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
-
Creates an SBML error report and returns the list of errors.
- getWordForNumber(long) - Static method in class org.sbml.jsbml.util.StringTools
-
Returns the number as an English word.
- getWriteWarnings(T) - Method in interface org.sbml.jsbml.SBMLOutputConverter
-
- getWritingParsers() - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
- getWritingParsers(Object, String) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Gets all the writing parsers necessary to write the given object.
- getXMLnamespaceSBML() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
The additional MathML name space for units to numbers.
- getXMLNode() - Method in class org.sbml.jsbml.Annotation
-
- 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(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- gt(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Greater than.
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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.FormulaCompilerLibSBML
-
- 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
-
Deprecated.
- 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.math.AbstractASTNode
-
The style of this MathML element
- id - Variable in class org.sbml.jsbml.ontology.Term
-
The base properties of this
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 interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- IDCHAR - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- IdenticalUnitDefinitionFilter - Class in org.sbml.jsbml.util.filters
-
- IdenticalUnitDefinitionFilter(UnitDefinition) - Constructor for class org.sbml.jsbml.util.filters.IdenticalUnitDefinitionFilter
-
- 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
-
- IdManager - Interface in org.sbml.jsbml.util
-
Manages an id namespace.
- IFormulaParser - Interface in org.sbml.jsbml.math.parser
-
An interface for the FormulaParser generated by JavaCC to parse infix math formula.
- IFormulaParser - Interface in org.sbml.jsbml.text.parser
-
An interface for the FormulaParser generated by JavaCC to parse infix math formula.
- ignoreCase - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
- ignoreCase - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
- ignoreCase - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
- ignoreCase - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- ignoreCase - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
- ignoredExtensions - Variable in class org.sbml.jsbml.AbstractSBase
-
Map
containing the ignored package objects.
- ignoredXMLElements - Variable in class org.sbml.jsbml.AbstractSBase
-
Contains the unknown XML attributes or elements.
- 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_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
.
- image - Variable in class org.sbml.jsbml.math.parser.Token
-
The string image of the token.
- image - Variable in class org.sbml.jsbml.text.parser.Token
-
The string image of the token.
- IMPLEMENTATION_ASTNODE2 - Static variable in class org.sbml.jsbml.ASTNode
-
The String representing the facade implementation for the new
ASTNode2
implementation.
- IMPLEMENTATION_HISTORIC - Static variable in class org.sbml.jsbml.ASTNode
-
The String representing the first implementation of the ASTNode, since 0.8.
- IMPLEMENTATION_VERSION - Static variable in class org.sbml.jsbml.ASTNode
-
- inBuf - Variable in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- inBuf - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- indent - Variable in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- 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.
- indentChar - 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.parsers.XMLNodeWriter
-
- 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
-
Deprecated.
Re-initializes the Document
object belonging to this class.
- init() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator
-
Initializes the Converter
- init() - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
- initChemicalFormulaPattern() - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
- 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.CompartmentType
-
Deprecated.
Initializes the default settings of this class.
- 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.math.ASTFunction
-
Initializes the default values/attributes of the node.
- 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
Double.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.SpeciesType
-
Deprecated.
Initializes the default settings of this class.
- 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.
- initDefaults(int, int, boolean) - Method in class org.sbml.jsbml.Unit
-
- 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.math.parser.ParseException
-
It uses "currentToken" and "expectedTokenSequences" to generate a parse
error message and returns it.
- 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.
- initializeAnnotationParsers() - Method in class org.sbml.jsbml.xml.stax.SBMLReader
-
Initializes the packageParser HashMap
of this class.
- initializedParsers - Variable in class org.sbml.jsbml.xml.stax.SBMLReader
-
Contains all the initialized parsers.
- 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
-
- initL1V1SNamePattern() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
Initializes the pattern for the type SName (described in SBML L1V1
specification, p.
- initL1V2SNamePattern() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
Creates the pattern for SName as defined in SBML specification for L1V2
page 7.
- initListOf(SBase, ListOf<T>, ListOf.Type) - Static method in class org.sbml.jsbml.ListOf
-
Helper method to initialize newly created lists.
- initMetaIdPatterns() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
Build the pattern for metaIds according to the definition in SBML
L2V2R1 p.
- initReservedNamesL1V1() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
These reserved words can occur in case of
UnitDefinition
s:
"substance"
,
"time"
,
"volume"
.
- initReservedNamesL1V2() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
- initSIdL2Pattern() - Method in class org.sbml.jsbml.validator.SyntaxChecker
-
- InnerNode(T) - Constructor for class org.sbml.jsbml.validator.OverdeterminationValidator.InnerNode
-
Creates a new inner node
- input_stream - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
- input_stream - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
- input_stream - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
- input_stream - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
- inputStream - Variable in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- 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, ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction
-
- insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- insertChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- insertChild(int, XMLNode) - Method in class org.sbml.jsbml.xml.XMLNode
-
Inserts a node as the
n
th child of this
XMLNode
.
- instance - Static variable in class org.sbml.jsbml.math.ASTUnknown
-
- 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.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- INTEGER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
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.math.compiler.UnitsCompiler
-
Creates an invalid unit definition encapsulated in an ASTNode2Value.
- 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.math.parser.TokenMgrError
-
Tried to change to an invalid lexical state.
- 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_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.
- isAlgebraic() - Method in class org.sbml.jsbml.Rule
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTBoolean
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTDivideNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTFunction
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTHyperbolicNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTMinusNode
-
- isAllowableType(ASTNode.Type) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns
true
iff type is allowed in this
ASTNode2
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTPlusNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTQualifierNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTRootNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTTimesNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTTrigonometricNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- isAllowableType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
- isAssociation(int) - Static method in class org.sbml.jsbml.SBO
-
- 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.math.compiler.ASTNode2Value
-
- 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.math.compiler.ASTNode2Value
-
- 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(Term, Term) - Static method in class org.sbml.jsbml.SBO
-
Traverses the systems biology ontology starting at
Term
subject until
either the root (SBO:0000000) or the
Term
object is reached.
- isCompartmentMandatory() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
- isCompartmentMandatory() - Method in class org.sbml.jsbml.Reaction
-
- isCompartmentMandatory() - Method in class org.sbml.jsbml.Species
-
- 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.math.compiler.ASTNode2Value
-
- isDifference() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- isDimensionless() - Method in class org.sbml.jsbml.Unit
-
- isDiscreteFramework(int) - Static method in class org.sbml.jsbml.SBO
-
Returns true
if the term is-a discrete framework, false
otherwise
- isDissociation(int) - Static method in class org.sbml.jsbml.SBO
-
- 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
-
- isEmptyListOf(Object) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Returns
true
if the given
Object
is an empty
ListOf
,
false
otherwise.
- 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
-
- isExtendedByOtherPackages() - Method in class org.sbml.jsbml.AbstractSBase
-
- isExtendedByOtherPackages() - Method in interface org.sbml.jsbml.SBase
-
Returns true
if this object is extended by other packages.
- 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
-
- isIgnoredPackage(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns true
if the given package extension is one of an ignored
packages, otherwise returns false
.
- isIgnoredPkg(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- isInfinity() - Method in class org.sbml.jsbml.ASTNode
-
Returns true
if this node represents the special IEEE 754 value infinity,
false
otherwise.
- isInfinity() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
Returns
true
if this
ASTCnRealNode
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
-
- isLeaf() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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.
- isNegInfinity() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
Returns
true
if this
ASTCnRealNode
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.math.compiler.ASTNode2Value
-
Checks whether the value encapsulated in this
ASTNodeValue
is an
instance of
Node
.
- 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.math.compiler.ASTNode2Value
-
- 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() - Method in class org.sbml.jsbml.ontology.Term
-
Checks whether or not this
Term
is obsolete.
- isObsolete(int) - Static method in class org.sbml.jsbml.SBO
-
Function for checking whether the 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.
- isPackageEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- isPackageEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
Returns
true
if the given SBML Level 3 package is enabled within
the containing
SBMLDocument
.
- isPackageEnabled(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns
true
if the given SBML Level 3 package is enabled within
the
SBMLDocument
.
- isPackageEnabledOrDisabled(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- isPackageURIEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- isPackageURIEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
Returns
true
if the given SBML Level 3 package is enabled within
the containing
SBMLDocument
.
- 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.
- isPkgEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
Deprecated.
- isPkgEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
- isPkgURIEnabled(String) - Method in class org.sbml.jsbml.AbstractSBase
-
Deprecated.
- isPkgURIEnabled(String) - Method in interface org.sbml.jsbml.SBase
-
- 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(UnitDefinition) - Static method in class org.sbml.jsbml.Unit
-
Tests whether the given
UnitDefinition
belongs to the predefined
SBML units.
- 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.
- isPrefixNotationInLogicalOperations() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- isPrintNameIfAvailable() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- isPrintNameIfAvailable() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- isProcess(int) - Static method in class org.sbml.jsbml.SBO
-
- 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 !=.
- isRequired() - Method in interface org.sbml.jsbml.xml.parsers.PackageParser
-
Returns the value of the required
attribute for this package.
- 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 class org.sbml.jsbml.math.ASTUnknown
-
- isRoot() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- isSBMLNamespaceNeeded(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- 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
-
- isSetAnnotation() - Method in interface org.sbml.jsbml.SBase
-
Returns true
or false
depending on whether this object's
'annotation' sub-elements exists and have some 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
-
- isSetChild() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
Returns true iff the child of this node has been set
- isSetClassName() - Method in class org.sbml.jsbml.ASTNode
-
- isSetCompartment() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
- isSetCompartment() - Method in class org.sbml.jsbml.Reaction
-
- isSetCompartment() - Method in class org.sbml.jsbml.Species
-
- isSetCompartmentInstance() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
- 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
-
- 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
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isSetDefinitionURL() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
Returns True iff definitionURL has been set
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- isSetDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- isSetDelay() - Method in class org.sbml.jsbml.Event
-
- isSetDenominator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
Returns true
iff denominator has been set
- 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
-
- isSetEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isSetEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- isSetEncoding() - Method in interface org.sbml.jsbml.math.ASTCSymbolNode
-
Returns true iff encoding has been set
- isSetEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- isSetExponent() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
Returns True iff exponent has been set
- isSetExponent - Variable in class org.sbml.jsbml.Unit
-
- isSetExponent() - Method in class org.sbml.jsbml.Unit
-
- isSetExtendedSBase() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- isSetExtendedSBase() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Check whether an extended SBase has been set.
- 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 initialized
- isSetHistory() - Method in interface org.sbml.jsbml.SBase
-
Returns
true
if the
History
instance of this object is set.
- 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 class org.sbml.jsbml.math.AbstractASTNode
-
- isSetId() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns true iff id has been set
- isSetId() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
- isSetInteger() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
Returns True iff value has been set
- isSetKey() - Method in class org.sbml.jsbml.util.Pair
-
- 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
-
- isSetLeftChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
Return true iff left child has been set
- isSetLeftChild() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- isSetLeftChild() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- 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
-
Returns true
if the level is set.
- 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
.
- isSetList() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns true
iff listOfNodes has been set
- 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
-
- 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
-
Returns true
if the list of errors is defined and contain at least one error.
- isSetListOfEventAssignments() - Method in class org.sbml.jsbml.Event
-
Returns true
, if listOfEventAssignments contains at least one element.
- 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
-
- isSetListOfNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm
-
- 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
-
- 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
-
- isSetMantissa() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
Returns true
iff mantissa has been set
- isSetMath() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- isSetMath() - Method in interface org.sbml.jsbml.MathContainer
-
- isSetMathMLClass() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isSetMathMLClass() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns true iff mathMLClass has been set
- isSetMathMLClass() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
Returns 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 class org.sbml.jsbml.math.ASTCiNumberNode
-
Deprecated.
- isSetName() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isSetName() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
Returns True iff name has been set
- isSetName() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- isSetName() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns True iff name has been set
- 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 initialized.
- isSetNotes() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetNotes() - Method in interface org.sbml.jsbml.SBase
-
Returns true
or false
depending on whether this object's
'notes' sub-element exists and has content.
- isSetNumber() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Returns True iff base has been set
- 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
-
- isSetNumerator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
Returns true
iff numerator has been set
- isSetOffset - Variable in class org.sbml.jsbml.Unit
-
- isSetOffset() - Method in class org.sbml.jsbml.Unit
-
- 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
-
- isSetOtherAttributes() - Method in class org.sbml.jsbml.Creator
-
- 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
.
- isSetPackageRequired(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns true
.
- isSetPackageVErsion() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetPackageVersion() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- isSetPackageVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- isSetPackageVErsion() - Method in interface org.sbml.jsbml.SBase
-
Returns true
if the package version is not equals to '-1'.
- isSetParent() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- isSetParent() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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 class org.sbml.jsbml.math.AbstractASTNode
-
- isSetParentSBMLObject() - Method in interface org.sbml.jsbml.math.ASTNode2
-
- isSetParentSBMLObject() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
- isSetPkgRequired(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- isSetPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetPlugin(String) - Method in interface org.sbml.jsbml.SBase
-
Returns
true
if an
SBasePlugin
is defined
for the given package.
- 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
.
- isSetQualifier() - Method in class org.sbml.jsbml.CVTerm
-
- 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 initialized.
- isSetReal() - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
Returns true
iff a value has been set
- isSetRefId() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
Return true iff refId is set
- isSetRefId() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Return true iff refId is set
- 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
-
- isSetRightChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
Return true iff right child has been set
- isSetRightChild() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- isSetRightChild() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- isSetSBOTerm() - Method in class org.sbml.jsbml.AbstractSBase
-
- isSetSBOTerm() - Method in interface org.sbml.jsbml.SBase
-
Returns true
if the SBOTerm is set.
- 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
-
- 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
-
- isSetStyle() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isSetStyle() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns true iff style has been set
- isSetStyle() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
- isSetType() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isSetType() - Method in class org.sbml.jsbml.math.ASTBoolean
-
- isSetType() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- isSetType() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- isSetType() - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- isSetType() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- isSetType() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns true iff type has been set
- isSetType() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isSetTypeQualifier() - Method in class org.sbml.jsbml.CVTerm
-
- isSetUnit() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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
-
- isSetUnits() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- isSetUnits() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Returns True iff units has been set
- 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
-
- isSetUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- isSetUnitsInstance() - Method in interface org.sbml.jsbml.SBaseWithUnit
-
- isSetUserObject() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- isSetUserObjects() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- isSetUserObjects() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isSetUserObjects() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
Checks whether any user-defined key-value pairs have been attached
to this object.
- 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 class org.sbml.jsbml.math.ASTConstantNumber
-
Returns true iff value has been set
- 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
-
- isSetValue() - Method in class org.sbml.jsbml.util.Pair
-
- 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
-
- isSetVariable() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Returns true iff this
ASTNumber
node
represents a variable.
- 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
-
Returns true
if the version is not null
.
- 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.
- isStrict() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- isStrict() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Specifies strictness.
- isStrict() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- isString() - Method in class org.sbml.jsbml.ASTNode
-
- isString() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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.math.compiler.ASTNode2Value
-
- 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.math.compiler.ASTNode2Value
-
- 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.math.compiler.ASTNode2Value
-
- 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.math.compiler.FindUnitsCompiler
-
- isUnitsDefined() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- 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
-
- 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
-
- isValidChemicalFormula(String) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
- isValidCreatedDate(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidCreator(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidEmailAddress(String) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
Definition of valid e-mail address String
s.
- isValidId(String, int, int) - Static method in class org.sbml.jsbml.AbstractNamedSBase
-
- isValidId(String, int, int) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
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
if the level and version combination is a valid one, false
otherwise.
- isValidMetaId(String) - Static method in class org.sbml.jsbml.AbstractSBase
-
- isValidMetaId(String) - Static method in class org.sbml.jsbml.validator.SyntaxChecker
-
Checks if the given identifier candidate satisfies the requirements for a
valid meta identifier (see SBML L2V4 p.
- isValidRDF(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidRDFDescription(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidRDFHistory(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidRDFURIs(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- isValidSBMLRDF(SBase) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Returns true if the SBML RDF block is recognized as valid or partially valid.
- 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
-
- isValidVCard(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Returns
SBMLRDFAnnotationParser.NODE_COLOR.GREEN
if at least one of these three nodes is present: vCard:N, vCard:EMAIL or vCard:ORG,
meaning that we consider that the VCard is at least partially defined.
- 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'.
- isVector() - Method in class org.sbml.jsbml.ASTNode
-
Checks if this
ASTNode
represents a vector.
- 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
-
- PACKAGE_VERSION_MISMATCH_MSG - Static variable in exception org.sbml.jsbml.LevelVersionError
-
Message to display in cases that two objects do not have identical
package version attributes.
- PackageInfo - Class in org.sbml.jsbml.xml.parsers
-
- PackageInfo() - Constructor for class org.sbml.jsbml.xml.parsers.PackageInfo
-
- packageName - Variable in class org.sbml.jsbml.AbstractSBase
-
the name of the package which this SBase element belong to, 'core' by default.
- packageName - Variable in exception org.sbml.jsbml.SBMLError
-
- packageName - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- PackageParser - Interface in org.sbml.jsbml.xml.parsers
-
Interface that define some common methods that the parsers for SBML packages need
to implement in order to provide some basic information about them.
- packageParsers - Variable in class org.sbml.jsbml.xml.parsers.ParserManager
-
- PackageUtil - Class in org.sbml.jsbml.xml.parsers
-
- PackageUtil() - Constructor for class org.sbml.jsbml.xml.parsers.PackageUtil
-
- packageVersion - Variable in class org.sbml.jsbml.AbstractSBase
-
the version of the package which this SBase element belong to, '0' by default for core.
- packageVersion - Variable in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- packageVersion - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- packageVersionMismatchMessage(SBase, SBase) - Static method in exception org.sbml.jsbml.LevelVersionError
-
Creates an error message showing the different package versions of the given SBase elements.
- packageVersionMismatchMessage(SBasePlugin, SBase) - Static method in exception org.sbml.jsbml.LevelVersionError
-
Creates an error message showing the different package versions of the given SBase elements.
- Pair<L,V> - Class in org.sbml.jsbml.util
-
A general implementation of a 2-tuple, i.e., two arbitrary objects.
- Pair() - Constructor for class org.sbml.jsbml.util.Pair
-
- Pair(L, V) - Constructor for class org.sbml.jsbml.util.Pair
-
- Pair(Pair<L, V>) - Constructor for class org.sbml.jsbml.util.Pair
-
- pairOf(L, V) - Static method in class org.sbml.jsbml.util.Pair
-
Can be used for static import in your class to easily create
Pair
s
of arbitrary data types with a simple method call, e.g.,
pairOf(1, 2)
.
- Parameter - Class in org.sbml.jsbml
-
Represents a globally valid parameter in the model, i.e., a variable that
may change during a simulation or that provides a constant value.
- Parameter() - Constructor for class org.sbml.jsbml.Parameter
-
- Parameter(int, int) - Constructor for class org.sbml.jsbml.Parameter
-
Creates a
Parameter
instance from a level and version.
- Parameter(LocalParameter) - Constructor for class org.sbml.jsbml.Parameter
-
- Parameter(Parameter) - Constructor for class org.sbml.jsbml.Parameter
-
- Parameter(String) - Constructor for class org.sbml.jsbml.Parameter
-
- Parameter(String, int, int) - Constructor for class org.sbml.jsbml.Parameter
-
Creates a
Parameter
instance from an id, level and version.
- parent - Variable in class org.sbml.jsbml.AbstractTreeNode
-
- parentSBMLObject - Variable in class org.sbml.jsbml.ASTNode
-
The container that holds this ASTNode.
- parentSBMLObject - Variable in class org.sbml.jsbml.math.AbstractASTNode
-
- parentSBMLObject - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- parse() - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
- parse() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
- parse() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
- parse() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
- parse() - Method in interface org.sbml.jsbml.math.parser.IFormulaParser
-
- parse() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
- parse() - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
- parse() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
- parse() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- parse() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
- parse() - Method in interface org.sbml.jsbml.text.parser.IFormulaParser
-
- parse(InputStream, DefaultHandler, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
-
Parses the content of a byte stream as XML, using a nonvalidating
parser and the specified SAX2 default event handler.
- parse(InputStream, DefaultHandler, Object[]) - Method in class org.sbml.jsbml.util.JAXPFacade
-
Parses the content of a byte stream as XML, using a validating
parser and the specified SAX2 default event handler.
- parse(Reader, DefaultHandler, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
-
Parses the content of a character stream as XML, using a
nonvalidating parser and the specified SAX2 default event handler.
- parse(Reader, DefaultHandler, Object[]) - Method in class org.sbml.jsbml.util.JAXPFacade
-
Parses the content of a character stream as XML, using a
validating parser and the specified SAX2 default event handler.
- parse(InputStream, DefaultHandler, boolean) - Method in interface org.sbml.jsbml.util.SAX2Parser
-
Parses the content of a byte stream as XML, using a nonvalidating
parser and the specified SAX2 default event handler.
- parse(InputStream, DefaultHandler, Object[]) - Method in interface org.sbml.jsbml.util.SAX2Parser
-
Parses the content of a byte stream as XML, using a validating
parser and the specified SAX2 default event handler.
- parse(Reader, DefaultHandler, boolean) - Method in interface org.sbml.jsbml.util.SAX2Parser
-
Parses the content of a character stream as XML, using a
nonvalidating parser and the specified SAX2 default event handler.
- parse(Reader, DefaultHandler, Object[]) - Method in interface org.sbml.jsbml.util.SAX2Parser
-
Parses the content of a character stream as XML, using a
validating parser and the specified SAX2 default event handler.
- parseCobraNotes(SBase) - Static method in class org.sbml.jsbml.util.CobraUtil
-
Parses the notes of the given
SBase
element.
- ParseException - Exception in org.sbml.jsbml.math.parser
-
This exception is thrown when parse errors are encountered.
- ParseException(Token, int[][], String[]) - Constructor for exception org.sbml.jsbml.math.parser.ParseException
-
Creates a new
ParseException
instance with the fields "currentToken",
"expectedTokenSequences", and "tokenImage" set.
- ParseException() - Constructor for exception org.sbml.jsbml.math.parser.ParseException
-
- ParseException(String) - Constructor for exception org.sbml.jsbml.math.parser.ParseException
-
- ParseException(Throwable) - Constructor for exception org.sbml.jsbml.math.parser.ParseException
-
Creates a new
ParseException
instance that will warp the given
Throwable
.
- ParseException - Exception in org.sbml.jsbml.text.parser
-
This exception is thrown when parse errors are encountered.
- ParseException(Token, int[][], String[]) - Constructor for exception org.sbml.jsbml.text.parser.ParseException
-
Creates a new
ParseException
instance with the fields "currentToken",
"expectedTokenSequences", and "tokenImage" set.
- ParseException() - Constructor for exception org.sbml.jsbml.text.parser.ParseException
-
- ParseException(String) - Constructor for exception org.sbml.jsbml.text.parser.ParseException
-
- ParseException(Throwable) - Constructor for exception org.sbml.jsbml.text.parser.ParseException
-
Creates a new
ParseException
instance that will warp the given
Throwable
.
- parseFormula(String) - Static method in class org.sbml.jsbml.ASTNode
-
Parses a text-string mathematical formula and returns a representation as
an Abstract Syntax Tree.
- parseFormula(String, IFormulaParser) - Static method in class org.sbml.jsbml.ASTNode
-
Parses a text-string mathematical formula, using the given
IFormulaParser
and returns a representation as
an Abstract Syntax Tree.
- parseFormula(String) - Static method in class org.sbml.jsbml.JSBML
-
Parses a text-string mathematical formula and returns a representation as
an Abstract Syntax Tree.
- parseFormula(String) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Parses a text-string mathematical formula and an Abstract Syntax Tree
representation.
- parseMathML(String) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Return String representation of specified MathML file
- parserDefaults - Variable in class org.sbml.jsbml.xml.parsers.ParserManager
-
- ParserManager - Class in org.sbml.jsbml.xml.parsers
-
- ParserManager() - Constructor for class org.sbml.jsbml.xml.parsers.ParserManager
-
Private constructor to make sure that we have only one
ParserManager
per JVM.
- parseSBMLBoolean(String) - Static method in class org.sbml.jsbml.util.StringTools
-
Parses a String into a boolean following the rules of the SBML
specifications, section 3.1.2.
- parseSBMLDouble(String) - Static method in class org.sbml.jsbml.util.StringTools
-
Parses a String into a double number following the rules of the SBML
specifications, section 3.1.5.
- parseSBMLInt(String) - Static method in class org.sbml.jsbml.util.StringTools
-
Parses a String
into an int number following the rules of the SBML
specifications, section 3.1.3.
- parseSBMLShort(String) - Static method in class org.sbml.jsbml.util.StringTools
-
Parses a String
into an short number following the rules of the
SBML specifications, section 3.1.3.
- paths - Variable in class org.sbml.jsbml.validator.OverdeterminationValidator
-
A list of all paths of a certain length in the graph
- pattern - Variable in class org.sbml.jsbml.util.filters.CVTermFilter
-
- persistent - Variable in class org.sbml.jsbml.Trigger
-
- persistent - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- piecewise(ASTNode, ASTNode...) - Static method in class org.sbml.jsbml.ASTNode
-
- piecewise(MathContainer, ASTNode[]) - Static method in class org.sbml.jsbml.ASTNode
-
- piecewise(ASTQualifierNode, ASTQualifierNode...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- piecewise(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- piecewise(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- piecewise(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- piecewise(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- piecewise(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- piecewise(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
-
- piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- piecewiseMap - Variable in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
-
- plus(ASTNode) - Method in class org.sbml.jsbml.ASTNode
-
Adds a given node to this node.
- plus(CallableSBase) - Method in class org.sbml.jsbml.ASTNode
-
Adds an SBML element to this node.
- plus(double) - Method in class org.sbml.jsbml.ASTNode
-
Adds a number to this node.
- plus(int) - Method in class org.sbml.jsbml.ASTNode
-
Adds an integer number to this node.
- plus(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- plus(ASTNode2, double) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- plus(ASTNode2, int) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- plus(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- plus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- plus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- plus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- plus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- PLUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- PLUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- PLUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- PLUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- PLUS - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- PLUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- PLUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- PLUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- PLUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- plus(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- POSITIVE_INFINITY - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- POSITIVE_INFINITY - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- pow(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
- pow(ASTNode, double) - Static method in class org.sbml.jsbml.ASTNode
-
- pow(ASTNode, int) - Static method in class org.sbml.jsbml.ASTNode
-
- pow(MathContainer, CallableSBase, CallableSBase) - Static method in class org.sbml.jsbml.ASTNode
-
Raises the given basis by the power of the given exponent.
- pow(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- pow(ASTNode2, double) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- pow(ASTNode2, int) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- pow(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- pow(Object, Object) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Returns the basis to the power of the exponent as StringBuffer.
- pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- pow(Object, Object) - Static method in class org.sbml.jsbml.math.compiler.HTMLFormula
-
Returns the basis to the power of the exponent as StringBuffer.
- pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- pow(ASTNode2Value, ASTNode2Value) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- pow(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- pow(Object, Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Returns the basis to the power of the exponent as StringBuffer.
- pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- pow(Object, Object) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula
-
Returns the basis to the power of the exponent as StringBuffer.
- pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- pow(ASTNodeValue, ASTNodeValue) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- POWER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- POWER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- POWER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- POWER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- POWER - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- POWER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- POWER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- POWER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- POWER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- prefix - Static variable in class org.sbml.jsbml.SBO
-
the prefix of all SBO ids.
- prefix - Variable in class org.sbml.jsbml.xml.parsers.PackageInfo
-
- prefix - Variable in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
Represents the prefix of a SBML component to write.
- prefix - Variable in class org.sbml.jsbml.xml.XMLTriple
-
- prefixNotationInLogicalOperations - Variable in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Decides whether prefix or infix notation should be used for the logical
operations "and", "or", and "xor".
- prependChild(ASTNode) - Method in class org.sbml.jsbml.ASTNode
-
Adds the given node as a child of this ASTNode.
- prependChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- prependChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction
-
- prependChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- prevCharIsCR - Variable in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- prevCharIsCR - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- prevCharIsLF - Variable in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- prevCharIsLF - Variable in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- previousParent - Variable in class org.sbml.jsbml.util.TreeNodeRemovedEvent
-
- Primary() - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
- Primary() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
- Primary() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
- Primary() - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
- Primary() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
- Primary() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
- print(InputStream, OutputStream) - Static method in class org.sbml.jsbml.validator.SBMLValidator
-
- print(Reader, Writer) - Static method in class org.sbml.jsbml.validator.SBMLValidator
-
- printErrors(PrintStream) - Method in class org.sbml.jsbml.SBMLDocument
-
Prints all the errors or warnings encountered trying to check this SBML document.
- printNameIfAvailable - Variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Important for LaTeX export to decide whether the name or the id of a
NamedSBase should be printed.
- printNameIfAvailable - Variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Important for LaTeX export to decide whether the name or the id of a
NamedSBase should be printed.
- printTerm(Term) - Static method in class org.sbml.jsbml.ontology.Term
-
Returns a String representing a term the same way as in the OBO file.
- printUnits(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
-
Returns a string that expresses the unit definition represented by this
UnitDefinition object.
- printUnits(UnitDefinition, boolean) - Static method in class org.sbml.jsbml.UnitDefinition
-
Returns a string that expresses the unit definition represented by this
UnitDefinition object.
- printValueAndUnit() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- printValueAndUnit() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- priority - Variable in class org.sbml.jsbml.Event
-
Represents the priority sub-element of an event.
- Priority - Class in org.sbml.jsbml
-
This class represents the priority element in SBML.
- Priority() - Constructor for class org.sbml.jsbml.Priority
-
- Priority(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Priority
-
- Priority(int, int) - Constructor for class org.sbml.jsbml.Priority
-
- Priority(Priority) - Constructor for class org.sbml.jsbml.Priority
-
- priority - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- processAnnotation(SBase) - Method in interface org.sbml.jsbml.xml.parsers.AnnotationReader
-
Process the annotation of the given
SBase
object.
- processAnnotation(SBase) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- processAttribute(String, String, String, String, String, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
-
Process the XML attribute and modify 'contextObject' in consequence.
- processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- processAttributes(Iterator<Attribute>, QName, Stack<Object>, ReadingParser, boolean, boolean) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
-
Process Attributes of the current element on the stack.
- processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- processCharactersOf(String, String, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
-
Process the text of a XML element and modify 'contextObject' in
consequence.
- processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- processEndDocument(SBMLDocument) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
-
Process the end of the document.
- processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- processEndElement(String, String, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
-
Process the end of the element 'elementName'.
- processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- processEndElement(QName, Boolean, Boolean, Boolean, int, int, ReadingParser, Stack<Object>, boolean) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
-
Process the end of an element.
- processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- processNamespace(String, String, String, String, boolean, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
-
Process the namespace and modify the contextObject in consequence.
- processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- processNamespaces(Iterator<Namespace>, QName, Stack<Object>, ReadingParser, boolean) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
-
Process Namespaces of the current element on the stack.
- processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- processStartElement(String, String, String, boolean, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
-
Process the XML element and modify 'contextObject' in consequence.
- processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- processStartElement(StartElement, QName, Boolean, Stack<Object>, boolean) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
-
Process a StartElement
event.
- processUnitsMap(Map<String, UnitDefinition>, Model, String) - Static method in class org.sbml.jsbml.util.SubModel
-
- processUnitsMap(Map<String, UnitDefinition>, Model, KineticLaw) - Static method in class org.sbml.jsbml.util.SubModel
-
- processUnknownAttribute(String, String, String, Object) - Static method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- processValue(ASTNode2Value<?>) - Method in class org.sbml.jsbml.math.AbstractASTNode
-
Set the type, level and version of the specified
ASTNode2Value
value.
- product(ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- programName - Variable in class org.sbml.jsbml.SBMLWriter
-
The name of the program that has been used to create an SBML
String
representation (possibly in a File
) with the help
of JSBML.
- programVersion - Variable in class org.sbml.jsbml.SBMLWriter
-
The version of the program using JSBML to serialize a model in an SBML
String
or File
.
- progressFinish() - Method in interface org.sbml.jsbml.util.ProgressListener
-
This method is called when the process is finished, irrespective of the
progress/total ratio.
- ProgressListener - Interface in org.sbml.jsbml.util
-
The listener interface for receiving progress events.
- progressStart(int) - Method in interface org.sbml.jsbml.util.ProgressListener
-
Reports the total number of expected steps.
- progressUpdate(int, String) - Method in interface org.sbml.jsbml.util.ProgressListener
-
Reports the current progress to this listener, i.e., progress < total.
- properties - Variable in class org.sbml.jsbml.util.XMLResourceBundleControl.XMLResourceBundle
-
The wrapped element.
- PROPERTY_UNDEFINED_EXCEPTION_MSG - Static variable in exception org.sbml.jsbml.PropertyNotAvailableException
-
Message to indicate that a certain property cannot be set for the current
level/version combination.
- PROPERTY_UNDEFINED_EXCEPTION_MSG_SBASE - Static variable in exception org.sbml.jsbml.PropertyUndefinedError
-
Message to indicate that a certain property has not been set for the
current
SBase
in its level/version combination.
- PROPERTY_UNDEFINED_EXCEPTION_MSG_TREE_NODE - Static variable in exception org.sbml.jsbml.PropertyUndefinedError
-
Message to indicate that a certain property has not been set for the
current TreeNode
in its level/version combination.
- propertyChange(PropertyChangeEvent) - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
-
- PropertyException - Exception in org.sbml.jsbml
-
This is an error of an undefined property or value for a property in some
instance of
SBase
.
- PropertyException() - Constructor for exception org.sbml.jsbml.PropertyException
-
- PropertyException(String) - Constructor for exception org.sbml.jsbml.PropertyException
-
- PropertyNotAvailableException - Exception in org.sbml.jsbml
-
An error that indicates that a property of an
SBase
is
not available for the current SBML Level/Version combination.
- PropertyNotAvailableException(String, SBase) - Constructor for exception org.sbml.jsbml.PropertyNotAvailableException
-
- PropertyUndefinedError - Exception in org.sbml.jsbml
-
This
PropertyException
indicates that the value belonging to a
mandatory property, for which there is no default value, has not been
declared by the user.
- PropertyUndefinedError(String, SBase) - Constructor for exception org.sbml.jsbml.PropertyUndefinedError
-
- PropertyUndefinedError(String, SBasePlugin) - Constructor for exception org.sbml.jsbml.PropertyUndefinedError
-
- PropertyUndefinedError(String, TreeNode) - Constructor for exception org.sbml.jsbml.PropertyUndefinedError
-
- putUserObject(Object, Object) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- putUserObject(Object, Object) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- putUserObject(Object, Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- 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
-
- 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
-
- RateRule(Variable, ASTNode) - Constructor for class org.sbml.jsbml.RateRule
-
Creates a
RateRule
instance from a given Symbol and ASTNode.
- RDF_NODE_COLOR - Static variable in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
A Constant
String
that is used to store a
XMLNode
color in the user objects map.
- 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
-
Creates a new Reaction instance from a given SBML level and version.
- 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.math.compiler.HTMLFormula
-
- 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 interface org.sbml.jsbml.ext.SBasePlugin
-
Reads and sets the attribute if it is know from this
SBasePlugin
.
- 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
-
Sets the given attribute in this
SBase
.
- 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.math.parser.SimpleCharStream
-
Read a character.
- readChar() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Read a character.
- readCreatedDate(SBase, XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Reads the 'dcterms:created' part of the SBML RDF annotation into a java Date
.
- readCreator(SBase, XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Reads the 'dc:creator' part of the SBML RDF annotation into
Creator
s.
- reader - Static variable in class org.sbml.jsbml.SBMLReader
-
The singleton actual reader.
- ReadingParser - Interface in org.sbml.jsbml.xml.parsers
-
The interface to implement for the SBML parsers reading SBML files.
- readingParsers - Variable in class org.sbml.jsbml.xml.parsers.ParserManager
-
- readMathML(String, TreeNodeChangeListener) - Method in class org.sbml.jsbml.xml.stax.SBMLReader
-
Reads a mathML String into an
ASTNode
.
- readMathML(String, TreeNodeChangeListener, MathContainer) - 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.
- readModifiedDate(SBase, XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Reads the 'dcterms:modified' part of the SBML RDF annotation into java Date
(s).
- 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
-
- readRDFHistory(SBase, XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Reads the 'rdf:Description' to extract the
History
part of the SBML RDF annotation.
- readRDFURIs(Object, XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Reads the relation elements part of the SBML RDF annotation into
CVTerm
s.
- 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
-
- readSBMLRDF(SBase) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Reads the 'rdf:RDF' block, if present in the
Annotation
, to extract the
History
and the
CVTerm
(s) as defined in the SBML specifications, section 6: 'A standard format for the annotation element'.
- 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.math.compiler.MathMLXMLStreamCompiler
-
Formats the real number in a valid way for mathML.
- 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).
- reduceToBinary(ASTFunction) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Reduces an
ASTFunction
to a binary tree, e.g., if the formula in the
ASTFunction
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.
- refersTo(String) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- refersTo(String) - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- refersTo(String) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- refersTo(String) - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
Returns true
if this node or one of its descendants contains some
identifier with the given id.
- refersTo(String) - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- refersTo(String) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- refId - Variable in class org.sbml.jsbml.math.ASTCiFunctionNode
-
refId attribute for MathML element
- refId - Variable in class org.sbml.jsbml.math.ASTCiNumberNode
-
- refId - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- register(SBase) - Method in class org.sbml.jsbml.KineticLaw
-
- register(SBase, boolean) - Method in class org.sbml.jsbml.KineticLaw
-
- register(SBase) - Method in class org.sbml.jsbml.Model
-
- register(SBase) - Method in interface org.sbml.jsbml.util.IdManager
-
Registers the given
SBase
element and all of it's children in this
IdManager
.
- registerChild(SBase) - Method in class org.sbml.jsbml.AbstractSBase
-
- registerChild(SBasePlugin) - 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(UniqueNamedSBase, boolean) - Method in class org.sbml.jsbml.Model
-
- registerId(UnitDefinition, boolean) - Method in class org.sbml.jsbml.Model
-
- registerIds(SBase, SBase, boolean, boolean, List<IdManager>) - 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.math.parser.FormulaParser
-
Reinitialise.
- ReInit(InputStream, String) - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
Reinitialise.
- ReInit(Reader) - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
Reinitialise.
- ReInit(FormulaParserTokenManager) - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
Reinitialise.
- ReInit(InputStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Reinitialise.
- ReInit(InputStream, String) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Reinitialise.
- ReInit(Reader) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Reinitialise.
- ReInit(FormulaParserASTNode2TokenManager) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Reinitialise.
- ReInit(SimpleCharStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream, int) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
Reinitialise parser.
- ReInit(InputStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Reinitialise.
- ReInit(InputStream, String) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Reinitialise.
- ReInit(Reader) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Reinitialise.
- ReInit(FormulaParserLL3TokenManager) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Reinitialise.
- ReInit(InputStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Reinitialise.
- ReInit(InputStream, String) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Reinitialise.
- ReInit(Reader) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Reinitialise.
- ReInit(FormulaParserLL3ASTNode2TokenManager) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Reinitialise.
- ReInit(SimpleCharStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream, int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream, int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream, int) - Method in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
Reinitialise parser.
- ReInit(Reader) - Method in interface org.sbml.jsbml.math.parser.IFormulaParser
-
- ReInit(InputStream, String) - Method in interface org.sbml.jsbml.math.parser.IFormulaParser
-
- ReInit(InputStream) - Method in interface org.sbml.jsbml.math.parser.IFormulaParser
-
- ReInit(Reader, int, int, int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Reinitialise.
- ReInit(Reader, int, int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Reinitialise.
- ReInit(Reader) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Reinitialise.
- ReInit(InputStream, String, int, int, int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Reinitialise.
- ReInit(InputStream, int, int, int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Reinitialise.
- ReInit(InputStream, String) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Reinitialise.
- ReInit(InputStream) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Reinitialise.
- ReInit(InputStream, String, int, int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Reinitialise.
- ReInit(InputStream, int, int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Reinitialise.
- ReInit(InputStream) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Reinitialise.
- ReInit(InputStream, String) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Reinitialise.
- ReInit(Reader) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Reinitialise.
- ReInit(CobraFormulaParserTokenManager) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Reinitialise.
- ReInit(SimpleCharStream) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream, int) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Reinitialise parser.
- 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(InputStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Reinitialise.
- ReInit(InputStream, String) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Reinitialise.
- ReInit(Reader) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Reinitialise.
- ReInit(FormulaParserASTNode2TokenManager) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Reinitialise.
- ReInit(SimpleCharStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
Reinitialise parser.
- ReInit(InputStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Reinitialise.
- ReInit(InputStream, String) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Reinitialise.
- ReInit(Reader) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Reinitialise.
- ReInit(FormulaParserLL3TokenManager) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Reinitialise.
- ReInit(InputStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Reinitialise.
- ReInit(InputStream, String) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Reinitialise.
- ReInit(Reader) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Reinitialise.
- ReInit(FormulaParserLL3ASTNode2TokenManager) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Reinitialise.
- ReInit(SimpleCharStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
Reinitialise parser.
- ReInit(SimpleCharStream, int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
Reinitialise parser.
- 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) - Method in interface org.sbml.jsbml.text.parser.IFormulaParser
-
- ReInit(InputStream, String) - Method in interface org.sbml.jsbml.text.parser.IFormulaParser
-
- ReInit(InputStream) - Method in interface org.sbml.jsbml.text.parser.IFormulaParser
-
- 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.math.parser.FormulaParserASTNode2TokenManager
-
- ReInitRounds() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
- ReInitRounds() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
- ReInitRounds() - Method in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
- ReInitRounds() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
- ReInitRounds() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
- ReInitRounds() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
- ReInitRounds() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
- ReInitRounds() - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
- relation(ASTNode2, String, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- relation(ASTNode2, String, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Creates a relation between two
ASTNode2
s.
- 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.
- relational(ASTNode.Type, ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- 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(Class<T>, String) - Method in class org.sbml.jsbml.Model
-
Removes the element with the given id from this model if such an element
can be found.
- remove(String) - Method in class org.sbml.jsbml.Model
-
Removes any
UniqueNamedSBase
with the given identifier from this
Model
and returns the removed element if the operation was
successfull.
- remove(ListOf<T>, 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(boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- removeAllTreeNodeChangeListeners() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- removeAllTreeNodeChangeListeners(boolean) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- removeAllTreeNodeChangeListeners() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
Removes all tree node change listeners from this element.
- removeAllTreeNodeChangeListeners(boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
Removes all tree node change listeners recursively 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(int) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- removeChild(int) - Method in class org.sbml.jsbml.math.ASTFunction
-
- removeChild(int) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- removeChild(int) - Method in class org.sbml.jsbml.xml.XMLNode
-
Removes the
n
th child of this
XMLNode
and returns the
removed node.
- removeChild(XMLNode) - Method in class org.sbml.jsbml.xml.XMLNode
-
Removes the first occurrence of the specified element from this list.
- 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
-
- removeCompartmentType(String) - Method in class org.sbml.jsbml.Model
-
- 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
.
- removeCVTerm(CVTerm) - Method in class org.sbml.jsbml.AbstractSBase
-
- removeCVTerm(int) - Method in class org.sbml.jsbml.AbstractSBase
-
Removes the
CVTerm
at the given index.
- removeCVTerm(CVTerm) - Method in class org.sbml.jsbml.Annotation
-
- removeCVTerm(int) - Method in class org.sbml.jsbml.Annotation
-
Removes the
CVTerm
at the given index.
- removeCVTerm(CVTerm) - Method in interface org.sbml.jsbml.SBase
-
- removeCVTerm(int) - Method in interface org.sbml.jsbml.SBase
-
Removes the
CVTerm
at the given index.
- removeCVTerm - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- 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
-
Removes an element from the listOfEventAssignments at the given index.
- removeEventAssignment(String) - Method in class org.sbml.jsbml.Event
-
Removes an element from the listOfEventAssignments.
- removeEventAssignment(EventAssignment) - Method in class org.sbml.jsbml.Event
-
Removes an element from the listOfEventAssignments.
- 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.
- removeFromParent() - Method in class org.sbml.jsbml.AbstractTreeNode
-
This method is designed to be overridden for non-independent child nodes
- removeFromParent() - Method in class org.sbml.jsbml.CVTerm
-
- removeFromParent() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- removeFromParent() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- removeFromParent() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
Removes itself from its parent.
- 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.
- removeMultiplier() - Method in class org.sbml.jsbml.Unit
-
- 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.
- removeNestedCVTerm(CVTerm) - Method in class org.sbml.jsbml.CVTerm
-
- removeNestedCVTerm(int) - Method in class org.sbml.jsbml.CVTerm
-
- removeOffset() - Method in class org.sbml.jsbml.Unit
-
- removePackageDeclaration(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Removes the package namespace declaration in this
SBMLDocument
, removes as well
the required attribute for this package.
- 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(int) - Method in class org.sbml.jsbml.CVTerm
-
Removes the ith resource URI from the
CVTerm
.
- removeResource(String) - Method in class org.sbml.jsbml.CVTerm
-
Removes the first occurrence of the given resource URI 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.
- removeRule(Rule) - Method in class org.sbml.jsbml.Model
-
- 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
-
- removeSpeciesType(String) - Method in class org.sbml.jsbml.Model
-
- removeTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- removeTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- removeTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- removeTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
- 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
-
- removeUserObject(Object) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- removeUserObject(Object) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- removeUserObject(Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- removeXmlNodeIfEmpty(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
Removes an
XMLNode
from its parent if it has no child elements, no attributes
and no namespaces declared any more.
- reorder(UnitDefinition) - Static method in class org.sbml.jsbml.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.
- replaceArgument(String, ASTNode2) - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- replaceChild(int, ASTNode) - Method in class org.sbml.jsbml.ASTNode
-
Replaces the nth child of this ASTNode with the given ASTNode.
- replaceChild(int, ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction
-
Replaces the nth child of this ASTNode2 with the given ASTNode2.
- reservedNamesL1V1 - Variable in class org.sbml.jsbml.validator.SyntaxChecker
-
Collection of reserved names that must not be used as identifiers (names)
in SBML documents in SBML Level 1 Version 1.
- reservedNamesL1V2 - Variable in class org.sbml.jsbml.validator.SyntaxChecker
-
Collection of reserved names that must not be used as identifiers (names)
in SBML documents in SBML Level 1 Version 2.
- reset() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- reset() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- reset() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
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
-
Since this is a singleton class, nobody should be able to instanciate it.
- resource - Static variable in class org.sbml.jsbml.resources.Resource
-
The singleton element.
- resourceBundle - Static variable in class org.sbml.jsbml.AbstractTreeNode
-
Localization support.
- ResourceManager - Class in org.sbml.jsbml.util
-
A
ResourceManager
avoids loading instances of
ResourceBundle
multiple times by keeping these in a
Map
data structure.
- ResourceManager() - Constructor for class org.sbml.jsbml.util.ResourceManager
-
- 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.math.compiler.HTMLFormula
-
HTML code for the reversible reaction arrow whose upper side is directed
to the right “⇌”.
- 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.math.compiler.HTMLFormula
-
HTML code for the right arrow “→”.
- RIGHT_ARROW - Static variable in class org.sbml.jsbml.util.compilers.HTMLFormula
-
HTML code for the right arrow “→”.
- RIGHT_BRACES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- RIGHT_BRACES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- RIGHT_BRACES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- RIGHT_BRACES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- RIGHT_BRACES - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- RIGHT_BRACES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- RIGHT_BRACES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- RIGHT_BRACES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- RIGHT_BRACES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- RIGHT_BRACKET - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- RIGHT_BRACKET - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- RIGHT_BRACKET - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- RIGHT_BRACKET - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- RIGHT_BRACKET - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- RIGHT_BRACKET - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- RIGHT_BRACKET - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- RIGHT_BRACKET - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- RIGHT_BRACKET - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- rightBrace - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- rightBrace - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- rightQuotationMark - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
An closing quotation mark.
- 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(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- root(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- root(double, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- root(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- root(double, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- root(Object, Object) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Returns the exponent-th root of the basis as StringBuffer.
- root(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- root(double, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- root(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- root(double, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- root(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- root(double, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- root(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- root(double, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- root(double, ASTNode2Value) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- root(ASTNodeValue, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- root(double, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- 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
.
- 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 element.
- SBasePlugin - Interface in org.sbml.jsbml.ext
-
Defines the methods necessary for an SBase Plugin.
- 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.
- 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
-
- 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
-
- SBMLErrorConverter - Class in org.sbml.jsbml.xml.xstream.converter
-
- SBMLErrorConverter() - Constructor for class org.sbml.jsbml.xml.xstream.converter.SBMLErrorConverter
-
- 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.Code - Enum in org.sbml.jsbml
-
Error codes.
- SBMLException.Type - Enum in org.sbml.jsbml
-
- SBMLInputConverter<T> - 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
-
- 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<T> - Interface in org.sbml.jsbml
-
This interface allows the implementing class to convert a JSBML model into
another data structure.
- SBMLRDFAnnotationParser - Class in org.sbml.jsbml.xml.parsers
-
Parses the RDF annotations as defined in the SBML specifications and put them into objects.
- SBMLRDFAnnotationParser() - Constructor for class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
-
- SBMLRDFAnnotationParser.NODE_COLOR - Enum in org.sbml.jsbml.xml.parsers
-
- 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
-
- SBMLtools - Class in org.sbml.jsbml.util
-
- SBMLtools() - Constructor for class org.sbml.jsbml.util.SBMLtools
-
- SBMLTypeUndefinedException - Exception in org.sbml.jsbml
-
This error can be thrown whenever a data type is being initialized that is
undefined for a certain SBML Level/Version combination.
- SBMLTypeUndefinedException(Class<?>, int, int) - Constructor for exception org.sbml.jsbml.SBMLTypeUndefinedException
-
- 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.
- 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
-
- 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
-
- 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
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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- sec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- sec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- sec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- sec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- sech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- sech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- sech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- sech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- 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.math.compiler.LaTeXCompiler
-
- section(String, boolean) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- selector(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- selector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- selector(Object...) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Returns the given selector as StringBuffer.
- selector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- selector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- selector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- selector(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- selector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- selector(Object...) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Returns the given selector as StringBuffer
.
- selector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- selector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- selector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- selector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- 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.ext.AbstractSBasePlugin
-
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.math.AbstractASTNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTBoolean
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTCiNumberNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTCnExponentialNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTCnIntegerNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTCnNumberNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTCnRationalNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTCnRealNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTConstantNumber
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTDivideNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTFunction
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTHyperbolicNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTLogarithmNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTMinusNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTNumber
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTPlusNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTPowerNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTQualifierNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTRootNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTTimesNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTTrigonometricNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- serialVersionUID - Static variable in class org.sbml.jsbml.math.ASTUnknown
-
- serialVersionUID - Static variable in exception org.sbml.jsbml.math.compiler.UnitException
-
Generated serial version identifier.
- serialVersionUID - Static variable in exception org.sbml.jsbml.math.parser.ParseException
-
The version identifier for this Serializable class.
- serialVersionUID - Static variable in class org.sbml.jsbml.math.parser.Token
-
The version identifier for this Serializable class.
- serialVersionUID - Static variable in error org.sbml.jsbml.math.parser.TokenMgrError
-
The version identifier for this Serializable class.
- 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.ontology.Term
-
Generated serial version identifier.
- serialVersionUID - Static variable in class org.sbml.jsbml.ontology.Triple
-
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 exception org.sbml.jsbml.SBMLTypeUndefinedException
-
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.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 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 class org.sbml.jsbml.util.ListOfWithName
-
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.Pair
-
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(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- setAnnotation(XMLNode) - 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(XMLNode) - Method in interface org.sbml.jsbml.SBase
-
- setAnnotation(String) - Method in interface org.sbml.jsbml.SBase
-
- setAnnotation - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- setAreaUnits(String) - Method in class org.sbml.jsbml.Model
-
Sets the areaUnitsID of this
Model
to 'areaUnitsID'
- setAreaUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model
-
- setAreaUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model
-
- setAttributes(XMLAttributes) - Method in class org.sbml.jsbml.xml.XMLToken
-
- setBiologicalQualifierType(int) - Method in class org.sbml.jsbml.CVTerm
-
- 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.
- setCaseSensitive(boolean) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Sets the case sensitivity of the parser, for the mathml elements.
- setCaseSensitive(boolean) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Sets the case sensitivity of the parser, for the mathml elements.
- setCaseSensitive(boolean) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Sets the case sensitivity of the parser, for the mathml elements.
- setCaseSensitive(boolean) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Sets the case sensitivity of the parser, for the mathml elements.
- setCaseSensitive(boolean) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Sets the case sensitivity of the parser, for the mathml elements.
- 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.
- setCharacter(char) - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- 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
-
- setChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
Set the child of this node
- 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 exception org.sbml.jsbml.SBMLError
-
- setCompartment(Compartment) - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
- setCompartment(String) - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
Sets the compartment attribute.
- 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
-
- setCompartment(String) - Method in class org.sbml.jsbml.Species
-
- setCompartmentType(CompartmentType) - Method in class org.sbml.jsbml.Compartment
-
Deprecated.
- setCompartmentType(String) - Method in class org.sbml.jsbml.Compartment
-
- 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.math.parser.FormulaParserASTNode2TokenManager
-
Set debug output.
- setDebugStream(PrintStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
Set debug output.
- setDebugStream(PrintStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
Set debug output.
- setDebugStream(PrintStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
Set debug output.
- setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Set debug output.
- setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
Set debug output.
- setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
Set debug output.
- setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
Set debug output.
- setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
Set debug output.
- setDefinitionURL(String) - Method in class org.sbml.jsbml.ASTNode
-
- setDefinitionURL(String) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- setDefinitionURL(String) - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Set the definitionURL of the MathML element represented by
this
ASTCiNumberNode
- setDefinitionURL(String) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- setDefinitionURL(String) - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- setDefinitionURL(String) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- 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.math.ASTCnRationalNode
-
Set the value of the denominator
- 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
-
- setEncoding(String) - Method in class org.sbml.jsbml.ASTNode
-
Sets the encoding of the mathML element represented by this ASTNode.
- setEncoding(String) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- setEncoding(String) - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- setEncoding(String) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- 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
-
- setExcerpt(String) - Method in exception org.sbml.jsbml.SBMLError
-
- setExplicitlyConstant(boolean) - Method in class org.sbml.jsbml.LocalParameter
-
- setExponent(int) - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
Set the exponent value of this node
- setExponent(double) - Method in class org.sbml.jsbml.Unit
-
Sets the exponent of this
Unit
- setExponent(int) - Method in class org.sbml.jsbml.Unit
-
- setExtendedSBase(SBase) - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- setExtentUnits(String) - Method in class org.sbml.jsbml.Model
-
Sets the extendUnitsID of this
Model
to 'extentUnitsID'.
- setExtentUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model
-
- 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 interface org.sbml.jsbml.MathContainer
-
- 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
-
Sets the history.
- 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.math.AbstractASTNode
-
- setId(String) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Set the id of this node
- setId(String) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
Sets other blank character(s) 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
.
- 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.
- setInteger(int) - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
Set the value of this node
- setInternal(boolean) - Method in exception org.sbml.jsbml.SBMLException
-
- setIsSetNumberType(boolean) - Method in class org.sbml.jsbml.ASTNode
-
- setKey(L) - Method in class org.sbml.jsbml.util.Pair
-
- 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
-
- setLeftChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- setLeftChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- setLengthUnits(String) - Method in class org.sbml.jsbml.Model
-
Sets the lengthUnitsID of this
Model
to 'lengthUnitsID'.
- setLengthUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model
-
- 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 class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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
-
Deprecated.
- 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(UnitDefinition) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
Ensures that level and version combination of a unit are the same then
these that are defined here.
- setLevelAndVersion(int, int) - Method in class org.sbml.jsbml.SBMLDocument
-
Sets the SBML Level and Version of this
SBMLDocument
instance,
without attempting to convert the model.
- 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.
- setLevelAndVersion(T, int, int) - Static method in class org.sbml.jsbml.util.SBMLtools
-
- 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 exception org.sbml.jsbml.SBMLError
-
- setListener(ProgressListener) - Method in interface org.sbml.jsbml.SBMLInputConverter
-
- 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
-
- setListOfConstraints(ListOf<Constraint>) - Method in class org.sbml.jsbml.Model
-
Sets the listOfConstraints of this
Model
to 'listOfConstraints'.
- setListOfEventAssignments(ListOf<EventAssignment>) - Method in class org.sbml.jsbml.Event
-
Sets the given ListOf<EventAssignment>
.
- 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
.
- setListOfNestedCVTerms(List<CVTerm>) - Method in class org.sbml.jsbml.CVTerm
-
Sets the given ListOf<CVTerm>
.
- 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
-
- 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
-
- setLogger(XMLLogger) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- setMantissa(double) - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
Get the mantissa value of this node
- 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
-
- setMathMLClass(String) - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- setMathMLClass(String) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Set the class of the MathML element represented by
this
ASTNode2
- setMathMLClass(String) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
-
- 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 class org.sbml.jsbml.math.ASTCiNumberNode
-
Deprecated.
- setName(String) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- setName(String) - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
- setName(String) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- setName(String) - Method in class org.sbml.jsbml.math.ASTFunction
-
Set the name of the MathML element represented by
this
ASTFunction
- 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.AbstractSBase
-
Sets the XML namespace to which this
SBase
belong.
- setNamespace(String) - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
Sets the XML namespace to which this
SBasePlugin
belong.
- 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
- setNonRDFAnnotation(XMLNode) - 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.
- setNumber(T) - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Set the numerical base of MathML element.
- setNumerator(int) - Method in class org.sbml.jsbml.math.ASTCnRationalNode
-
Set the value of the numerator
- setOffset(double) - Method in class org.sbml.jsbml.Unit
-
- 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.
- setOtherAttribute(String, String) - Method in class org.sbml.jsbml.Creator
-
- setOutside(Compartment) - Method in class org.sbml.jsbml.Compartment
-
Deprecated.
- setOutside(String) - Method in class org.sbml.jsbml.Compartment
-
- setPackage(String) - Method in exception org.sbml.jsbml.SBMLError
-
- setPackageName(String) - Method in class org.sbml.jsbml.ListOf
-
Sets the name of the package to which this
SBase
belong.
- setPackageNamespaceAndVersion(String, String, int) - Method in class org.sbml.jsbml.AbstractSBase
-
Sets recursively the package namespace and version.
- setPackageRequired(String, boolean) - Method in class org.sbml.jsbml.SBMLDocument
-
Sets the required attribute value of the given package extension (does nothing in fact!).
- setPackageVersion(int) - Method in class org.sbml.jsbml.AbstractSBase
-
- setPackageVersion(int) - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- setPackageVersion(int) - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- setPackageVersion(int) - Method in interface org.sbml.jsbml.SBase
-
Sets the version of the SBML Level 3 package to which this element belongs.
- setParent(TreeNode) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- setParent(TreeNode) - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- setParent(TreeNode) - Method in interface org.sbml.jsbml.math.ASTNode2
-
- setParent(TreeNode) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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
- setParentSBMLObject(MathContainer) - Method in class org.sbml.jsbml.ASTNode
-
Sets the Parent of the node to the given value
- setParentSBMLObject(MathContainer) - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- setParentSBMLObject(ASTNode2, MathContainer) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Sets the Parent of the node and its children to the given value
- setParentSBMLObject(MathContainer) - Method in class org.sbml.jsbml.math.ASTFunction
-
- setParentSBMLObject(MathContainer) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Sets the parentSBMLObject to container recursively
- setParentSBMLObject(MathContainer) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- 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.
- setPkgRequired(String, boolean) - Method in class org.sbml.jsbml.SBMLDocument
-
- setPrefix(String) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- setPrefixNotationInLogicalOperations(boolean) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- setPrintNameIfAvailable(boolean) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- 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.CVTerm
-
- setQualifier(CVTerm.Qualifier) - Method in class org.sbml.jsbml.util.filters.CVTermFilter
-
- setQualifierType(int) - Method in class org.sbml.jsbml.CVTerm
-
- setQualifierType(CVTerm.Type) - Method in class org.sbml.jsbml.CVTerm
-
- setRadicand(ASTNode2) - Method in class org.sbml.jsbml.math.ASTRootNode
-
- setReal(double) - Method in class org.sbml.jsbml.math.ASTCnRealNode
-
Set the value of this node
- setReference(FunctionDefinition) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- setReference(CallableSBase) - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- setRefId(String) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
Set refId attribute
- setRefId(String) - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Set refId attribute
- setReversible(boolean) - Method in class org.sbml.jsbml.Reaction
-
Sets the reversible Boolean of this
Reaction
.
- setRightChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- setRootExponent(ASTNode2) - Method in class org.sbml.jsbml.math.ASTRootNode
-
- 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
-
- 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
-
- setSpatialSizeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Species
-
- 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'.
- setSpeciesType(SpeciesType) - Method in class org.sbml.jsbml.Species
-
Deprecated.
- setSpeciesType(String) - Method in class org.sbml.jsbml.Species
-
- 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.
- setStrictness(boolean) - Method in class org.sbml.jsbml.math.AbstractASTNode
-
Set the strictness of this node
- setStrictness(boolean) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Set the strictness of this node
- setStrictness(boolean) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- setStyle(String) - Method in class org.sbml.jsbml.ASTNode
-
Sets the style of the mathML element represented by this
ASTNode
.
- setStyle(String) - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- setStyle(String) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Set the style of this node
- setStyle(String) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- setSubstanceUnits(String) - Method in class org.sbml.jsbml.KineticLaw
-
- setSubstanceUnits(Unit) - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- setSubstanceUnits(String) - Method in class org.sbml.jsbml.Model
-
- setSubstanceUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model
-
Sets the substanceUnitsID of this
Model
to the id of
'substanceUnits'.
- setSubstanceUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model
-
- 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.math.parser.SimpleCharStream
-
- setTabSize(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
- setTerms(int...) - Method in class org.sbml.jsbml.util.filters.SBOFilter
-
- setThisAsParentSBMLObject(SBase) - Method in class org.sbml.jsbml.AbstractSBase
-
Deprecated.
- setThisAsParentSBMLObject(SBase) - Method in interface org.sbml.jsbml.SBase
-
- setTimeUnits(String) - Method in class org.sbml.jsbml.Event
-
- setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Event
-
Deprecated.
- setTimeUnits(String) - Method in class org.sbml.jsbml.KineticLaw
-
- setTimeUnits(Unit) - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.KineticLaw
-
- 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
-
- setTimeUnits(Unit.Kind) - 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(String) - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- setType(ASTNode.Type) - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- setType(String) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Sets the type from a String.
- setType(ASTNode.Type) - Method in interface org.sbml.jsbml.math.ASTNode2
-
Set the type of the MathML element represented by this
ASTNode2
- setType(String) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- setType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- setType(ASTNode.Type) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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.XMLNodeReader
-
Sets the typeOfNote of this parser.
- setUIFlag(boolean) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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(Unit.Kind) - Method in class org.sbml.jsbml.ASTNode
-
- setUnits(UnitDefinition) - Method in class org.sbml.jsbml.ASTNode
-
- 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
-
- setUnits(Unit) - Method in class org.sbml.jsbml.ExplicitRule
-
Deprecated.
- setUnits(UnitDefinition) - Method in class org.sbml.jsbml.ExplicitRule
-
- 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 class org.sbml.jsbml.math.ASTCnNumberNode
-
Set the units of the MathML element represented by this ASTCnNumberNode
- setUnits(UnitDefinition) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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.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(boolean) - Method in class org.sbml.jsbml.math.ASTBoolean
-
- setValue(double) - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- setValue(boolean) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- setValue(T) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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
-
- setValue(V) - Method in class org.sbml.jsbml.util.Pair
-
- 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
-
- setVariable(String) - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- setVersion(int) - Method in class org.sbml.jsbml.AbstractSBase
-
- setVersion(int) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- 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(Unit.Kind) - Method in class org.sbml.jsbml.Model
-
- 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
-
- setXMLNode(XMLNode) - Method in class org.sbml.jsbml.Annotation
-
- severity - Variable in exception org.sbml.jsbml.SBMLError
-
- SEVERITY() - Constructor for enum org.sbml.jsbml.SBMLError.SEVERITY
-
- 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
-
- SIdL2Pattern - Variable in class org.sbml.jsbml.validator.SyntaxChecker
-
Pattern to recognize valid SIds, i.e., identifier strings for SBML elements.
- SimpleCharStream - Class in org.sbml.jsbml.math.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.math.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(Reader, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(Reader) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, int, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream
-
Constructor.
- 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.
- simpleMetaIdPattern - Variable in class org.sbml.jsbml.validator.SyntaxChecker
-
Simplified Pattern
to recognize valid meta-identifier strings for
SBML elements.
- 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
-
Creates a SimpleSpeciesReference instance.
- 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
-
Creates a SimpleSpeciesReference instance.
- SimpleSpeciesReference(String, int, int) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference
-
Creates a SimpleSpeciesReference instance.
- SimpleSpeciesReference(String, String, int, int) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference
-
Creates a SimpleSpeciesReference instance.
- 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(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- sin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- sin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- sin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- sin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- sinh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- sinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- sinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- sinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- sinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.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
-
Deprecated.
- 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
-
- size() - Method in class org.sbml.jsbml.xml.XMLAttributes
-
- SLPITTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- SLPITTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- SLPITTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- SLPITTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- SLPITTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- SLPITTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- SNameL1V1 - Variable in class org.sbml.jsbml.validator.SyntaxChecker
-
Name Pattern
for SBML Level 1 version 1.
- SNameL1V2 - Variable in class org.sbml.jsbml.validator.SyntaxChecker
-
Name Pattern
for SBML Level 1 version 2.
- 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
-
- specialToken - Variable in class org.sbml.jsbml.math.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.
- 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
-
Creates a SpeciesReference instance.
- 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
-
Creates a SpeciesReference instance.
- SpeciesReference(String, int, int) - Constructor for class org.sbml.jsbml.SpeciesReference
-
Creates a SpeciesReference instance.
- SpeciesReference(String, String, int, int) - Constructor for class org.sbml.jsbml.SpeciesReference
-
Creates a SpeciesReference instance.
- 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
-
- 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.
- SPLITTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- SPLITTER - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- SPLITTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- 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(ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- sqrt(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Square root.
- sqrt(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- sqrt(Object) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- sqrt(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- sqrt(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- sqrt(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- sqrt(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- StartNode() - Constructor for class org.sbml.jsbml.validator.OverdeterminationValidator.StartNode
-
Creates a new start node
- STATIC_LEXER_ERROR - Static variable in error org.sbml.jsbml.math.parser.TokenMgrError
-
An attempt was made to create a second instance of a static token manager.
- 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.math.parser.SimpleCharStream
-
Whether parser is static.
- 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
-
- strict - Variable in class org.sbml.jsbml.math.AbstractASTNode
-
Specifies strictness.
- string() - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
- string() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
- STRING - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- STRING - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- string() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
- string() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
- STRING - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- STRING - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- string() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
- STRING - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- string() - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
- string() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
- STRING - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- STRING - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- string() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- string() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
- STRING - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- STRING - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- 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.
- stringToType - Static variable in class org.sbml.jsbml.math.parser.FormulaParser
-
- stringToType - Static variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
- stringToType - Static variable in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
- stringToType - Static variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
- stringToType - Static variable in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
- stringToType - Static variable in class org.sbml.jsbml.text.parser.FormulaParser
-
- stringToType - Static variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
- stringToType - Static variable in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
- stringToType - Static variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
- style - Variable in class org.sbml.jsbml.ASTNode
-
- style - Variable in class org.sbml.jsbml.math.AbstractASTNode
-
The style of this 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.math.compiler.LaTeXCompiler
-
- 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.math.compiler.LaTeXCompiler
-
- 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(ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- sum(Object...) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Returns the sum of the given elements as StringBuffer.
- sum(Object...) - Static method in class org.sbml.jsbml.math.compiler.HTMLFormula
-
Returns the sum of the given elements as StringBuffer.
- 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
-
- swapChildren(ASTFunction) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- swapChildren(ASTFunction) - Method in class org.sbml.jsbml.math.ASTFunction
-
- swapChildren(ASTFunction) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- SwitchTo(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
Switch to specified lex state.
- SwitchTo(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
Switch to specified lex state.
- SwitchTo(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
Switch to specified lex state.
- SwitchTo(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
Switch to specified lex state.
- SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Switch to specified lex state.
- SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
Switch to specified lex state.
- SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
Switch to specified lex state.
- SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
Switch to specified lex state.
- 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
-
Creates a Symbol instance.
- Symbol(String) - Constructor for class org.sbml.jsbml.Symbol
-
Creates a Symbol instance.
- 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.math.compiler.ASTNode2Compiler
-
The simulation time.
- symbolTime(String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- symbolTime(String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- symbolTime(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- symbolTime(String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- SyntaxChecker - Class in org.sbml.jsbml.validator
-
A collection of methods for checking the validity of SBML identifiers.
- SyntaxChecker() - Constructor for class org.sbml.jsbml.validator.SyntaxChecker
-
This is a singleton class and should only be used through static methods.
- syntaxChecker - Static variable in class org.sbml.jsbml.validator.SyntaxChecker
-
The only instance of this class.
- ud - Variable in class org.sbml.jsbml.util.filters.IdenticalUnitDefinitionFilter
-
- uFlag - Variable in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
Flag to indicate whether the underlying
ASTNode2
was an unary
node.
- 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(ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- uMinus(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Unary minus, i.e., negation of the given
ASTNode2
.
- uMinus(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- uMinus(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- uMinus(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- uMinus(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- uMinus(ASTNodeValue) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- 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.util.StringTools
-
The Character
'_'
as a String
.
- UNEXPECTED_ATTRIBUTE - Static variable in class org.sbml.jsbml.JSBML
-
- unifyUnits(ASTNode2Value, ASTNode2Value) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
This method tries to unify the units of two ASTNode2Values so that they
have the same units and their value thus is also adjusted.
- 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.
- unitDef - Variable in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
The unit associated to the value of this object.
- 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.math.compiler
-
Exception to be thrown if inconsistent units are used in mathematical
expressions, i.e., instances of
ASTNode2
.
- UnitException() - Constructor for exception org.sbml.jsbml.math.compiler.UnitException
-
- UnitException(String) - Constructor for exception org.sbml.jsbml.math.compiler.UnitException
-
- UnitException(Throwable) - Constructor for exception org.sbml.jsbml.math.compiler.UnitException
-
- UnitException(String, Throwable) - Constructor for exception org.sbml.jsbml.math.compiler.UnitException
-
- 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 - Variable in class org.sbml.jsbml.math.ASTCnNumberNode
-
units attribute for MathML element
- units - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- UnitsCompiler - Class in org.sbml.jsbml.math.compiler
-
Derives the units from mathematical operations.
- UnitsCompiler() - Constructor for class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- UnitsCompiler(int, int) - Constructor for class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- UnitsCompiler(Model) - Constructor for class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
- unitsID - Variable in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- UNKNOWN_ATTRIBUTES - Static variable in class org.sbml.jsbml.AbstractTreeNode
-
- UNKNOWN_ELEMENTS - Static variable in class org.sbml.jsbml.AbstractTreeNode
-
- UNKNOWN_XML_NODE - Static variable in class org.sbml.jsbml.SBMLReader
-
String used when reading an SBML file, to store XMLNode as user object
when the XMLNode does not represents something known from the 'core'.
- unknownValue() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- unknownValue() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- unknownValue() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- unknownValue() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- unknownValue() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
Deprecated.
- unknownValue() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- unmarshal(HierarchicalStreamReader, UnmarshallingContext) - Method in class org.sbml.jsbml.xml.xstream.converter.MessageConverter
-
- unmarshal(HierarchicalStreamReader, UnmarshallingContext) - Method in class org.sbml.jsbml.xml.xstream.converter.SBMLErrorConverter
-
- unregister(SBase) - Method in class org.sbml.jsbml.KineticLaw
-
- unregister(SBase) - Method in class org.sbml.jsbml.Model
-
- unregister(SBase) - Method in interface org.sbml.jsbml.util.IdManager
-
Unregisters the given
SBase
element and all of it's children in this
IdManager
.
- unregisterChild(SBase) - Method in class org.sbml.jsbml.AbstractSBase
-
- unregisterChild(SBasePlugin) - Method in class org.sbml.jsbml.AbstractSBase
-
- unregisterChild(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
-
- unsetBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- unsetCharge() - Method in class org.sbml.jsbml.Species
-
Deprecated.
- unsetCompartment() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
Remove the reference to a compartment, i.e., unset the value of the
variable 'compartment'.
- unsetCompartment() - Method in class org.sbml.jsbml.Reaction
-
- unsetCompartment() - Method in class org.sbml.jsbml.Species
-
- 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
-
- 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
-
- unsetExtension(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- unsetExtension(String) - Method in interface org.sbml.jsbml.SBase
-
Unsets the
SBasePlugin
extension object which matches this package
name or URI.
- unsetExtentUnits() - Method in class org.sbml.jsbml.Model
-
- 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
-
- unsetListOfCompartments() - Method in class org.sbml.jsbml.Model
-
- unsetListOfCompartmentTypes() - Method in class org.sbml.jsbml.Model
-
- 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
-
- unsetListOfNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm
-
- 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
-
- 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
-
- 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
.
- unsetNamespace() - Method in class org.sbml.jsbml.AbstractSBase
-
Unsets the namespace that is associated to this
SBase
.
- 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
-
- unsetOrganization() - Method in class org.sbml.jsbml.Creator
-
Unsets the organisation of this
Creator
.
- unsetOutside() - Method in class org.sbml.jsbml.Compartment
-
- unsetParentSBMLObject() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- unsetParentSBMLObject() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Unsets the parentSBMLObject to null
recursively.
- unsetParentSBMLObject() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- unsetPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- unsetPlugin(String) - Method in interface org.sbml.jsbml.SBase
-
Unsets the
SBasePlugin
extension object which matches this package
name or URI.
- unsetPriority() - Method in class org.sbml.jsbml.Event
-
- unsetProgramName() - Method in class org.sbml.jsbml.SBMLWriter
-
- unsetProgramVersion() - Method in class org.sbml.jsbml.SBMLWriter
-
- unsetQualifier() - Method in class org.sbml.jsbml.CVTerm
-
Unsets the qualifier if it is set.
- 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
-
- 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.math.compiler.ASTNode2Value
-
Removes the unit of this element, i.e., the unit will become invalid.
- 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
-
- unsetUnits() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- unsetUnits() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Unset the units attribute.
- unsetUnits() - Method in interface org.sbml.jsbml.SBaseWithUnit
-
- 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
-
- UpdateLineColumn(char) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
- 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
ASTNode
s 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_L2V5 - Static variable in class org.sbml.jsbml.SBMLDocument
-
The namespace URI of SBML Level 2 Version 5.
- URI_NAMESPACE_L3V1Core - Static variable in class org.sbml.jsbml.SBMLDocument
-
The namespace URI of SBML Level 3 Version 1.
- URI_NAMESPACE_L3V2Core - Static variable in class org.sbml.jsbml.SBMLDocument
-
The namespace URI of SBML Level 3 Version 2.
- 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
-
- usepackage(String, String...) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Creates a usepackage command for the given package with the optional
options.
- 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.util.TreeNodeAdapter
-
The object to be wrapped.
- userObject - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- userObjectKeySet() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- userObjectKeySet() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- userObjectKeySet() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- userObjects - Variable in class org.sbml.jsbml.AbstractTreeNode
-
Any kind of
Object
that can be stored in addition to all other
features of this
AbstractTreeNode
in form of key-value pairs.
- 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
-