libSBML
5.8.0
A B C D E F G H I K L M N O P R S T U V W X Y Z 

A

acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.CompModelPlugin
 
acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.CompSBasePlugin
 
acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.Deletion
 
acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.ExternalModelDefinition
 
acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
 
acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.ModelDefinition
 
acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.Port
 
acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.ReplacedBy
 
acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.ReplacedElement
 
acceptComp(SWIGTYPE_p_CompVisitor) - Method in class org.sbml.libsbml.Submodel
 
acceptFbc(SWIGTYPE_p_FbcVisitor) - Method in class org.sbml.libsbml.FbcModelPlugin
 
acceptFbc(SWIGTYPE_p_FbcVisitor) - Method in class org.sbml.libsbml.FluxBound
 
acceptFbc(SWIGTYPE_p_FbcVisitor) - Method in class org.sbml.libsbml.FluxObjective
 
acceptFbc(SWIGTYPE_p_FbcVisitor) - Method in class org.sbml.libsbml.ListOfObjectives
 
acceptFbc(SWIGTYPE_p_FbcVisitor) - Method in class org.sbml.libsbml.Objective
 
add(ASTNode) - Method in class org.sbml.libsbml.ASTNodeList
 
add(CVTerm) - Method in class org.sbml.libsbml.CVTermList
 
add(Date) - Method in class org.sbml.libsbml.DateList
 
add(ModelCreator) - Method in class org.sbml.libsbml.ModelCreatorList
 
add(SBase) - Method in class org.sbml.libsbml.SBaseList
 
add(SBMLNamespaces) - Method in class org.sbml.libsbml.SBMLNamespacesList
 
add(String, String, String, String) - Method in class org.sbml.libsbml.XMLAttributes
Adds an attribute (a name/value pair) to this XMLAttributes object, optionally with a prefix and URI defining a namespace.
add(String, String, String) - Method in class org.sbml.libsbml.XMLAttributes
Adds an attribute (a name/value pair) to this XMLAttributes object, optionally with a prefix and URI defining a namespace.
add(String, String) - Method in class org.sbml.libsbml.XMLAttributes
Adds an attribute (a name/value pair) to this XMLAttributes object, optionally with a prefix and URI defining a namespace.
add(XMLTriple, String) - Method in class org.sbml.libsbml.XMLAttributes
Adds an attribute with the given XMLTriple/value pair to this XMLAttributes set.
add(String, String) - Method in class org.sbml.libsbml.XMLNamespaces
Appends an XML namespace prefix and URI pair to this list of namespace declarations.
add(String) - Method in class org.sbml.libsbml.XMLNamespaces
Appends an XML namespace prefix and URI pair to this list of namespace declarations.
addAdditionalDir(String) - Method in class org.sbml.libsbml.SBMLFileResolver
 
addAdditionalGraphicalObject(GraphicalObject) - Method in class org.sbml.libsbml.Layout
 
addArgument(String) - Method in class org.sbml.libsbml.SBMLExternalValidator
Adds the given argument to the list of additional arguments
addAssociation(Association) - Method in class org.sbml.libsbml.Association
 
addAttr(String, String, String, String) - Method in class org.sbml.libsbml.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.libsbml.XMLToken
Adds an attribute to the attribute set in this XMLToken optionally with a prefix and URI defining a namespace.
addAttr(String, String) - Method in class org.sbml.libsbml.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.libsbml.XMLToken
Adds an attribute with the given XMLTriple/value pair to the attribute set in this XMLToken.
addChild(ASTNode) - Method in class org.sbml.libsbml.ASTNode
Adds the given node as a child of this ASTNode.
addChild(XMLNode) - Method in class org.sbml.libsbml.XMLNode
Adds a copy of node as a child of this XMLNode.
addCompartment(Compartment) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Compartment object to this Model.
addCompartmentGlyph(CompartmentGlyph) - Method in class org.sbml.libsbml.Layout
 
addCompartmentType(CompartmentType) - Method in class org.sbml.libsbml.Model
Adds a copy of the given CompartmentType object to this Model.
addConstraint(Constraint) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Constraint object to this Model.
addConverter(SBMLConverter) - Method in class org.sbml.libsbml.SBMLConverterRegistry
Adds the given converter to the registry of SBML converters.
addCreator(ModelCreator) - Method in class org.sbml.libsbml.ModelHistory
Adds a copy of a ModelCreator object to the list of 'model creator' values stored in this ModelHistory object.
addCurveSegment(LineSegment) - Method in class org.sbml.libsbml.Curve
 
addCVTerm(CVTerm, boolean) - Method in class org.sbml.libsbml.SBase
Adds a copy of the given CVTerm object to this SBML object.
addCVTerm(CVTerm) - Method in class org.sbml.libsbml.SBase
Adds a copy of the given CVTerm object to this SBML object.
addDeletion(Deletion) - Method in class org.sbml.libsbml.Submodel
 
addEvent(Event) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Event object to this Model.
addEventAssignment(EventAssignment) - Method in class org.sbml.libsbml.Event
Appends a copy of the given EventAssignment to this Event.
addExtension(SBMLExtension) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Add the given SBMLExtension to this SBMLExtensionRegistry.
addExternalModelDefinition(ExternalModelDefinition) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
addFluxBound(FluxBound) - Method in class org.sbml.libsbml.FbcModelPlugin
 
addFluxObjective(FluxObjective) - Method in class org.sbml.libsbml.Objective
 
addFunctionDefinition(FunctionDefinition) - Method in class org.sbml.libsbml.Model
Adds a copy of the given FunctionDefinition object to this Model.
addGene(String) - Method in class org.sbml.libsbml.Association
 
addGeneAssociation(GeneAssociation) - Method in class org.sbml.libsbml.FbcModelPlugin
 
addGeneralGlyph(GeneralGlyph) - Method in class org.sbml.libsbml.Layout
 
addInitialAssignment(InitialAssignment) - Method in class org.sbml.libsbml.Model
Adds a copy of the given InitialAssignment object to this Model.
addL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
adds all L2 Extension namespaces to the namespace list.
addLayout(Layout) - Method in class org.sbml.libsbml.LayoutModelPlugin
 
addLocalParameter(LocalParameter) - Method in class org.sbml.libsbml.KineticLaw
Adds a copy of the given LocalParameter object to the list of local parameters in this KineticLaw.
addModelDefinition(ModelDefinition) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
addModifiedDate(Date) - Method in class org.sbml.libsbml.ModelHistory
Adds a copy of a Date object to the list of 'modified date' values stored in this ModelHistory object.
addModifier(ModifierSpeciesReference) - Method in class org.sbml.libsbml.Reaction
Adds a given ModifierSpeciesReference object as a product in this Reaction.
addNamespace(String, String) - Method in class org.sbml.libsbml.SBMLNamespaces
Add an XML namespace (a pair of URI and prefix) to the set of namespaces within this SBMLNamespaces object.
addNamespace(String, String) - Method in class org.sbml.libsbml.XMLToken
Appends an XML namespace prefix and URI pair to this XMLToken.
addNamespace(String) - Method in class org.sbml.libsbml.XMLToken
Appends an XML namespace prefix and URI pair to this XMLToken.
addNamespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBMLNamespaces
Add the given XML namespaces list to the set of namespaces within this SBMLNamespaces object.
addObjective(Objective) - Method in class org.sbml.libsbml.FbcModelPlugin
 
addOption(ConversionOption) - Method in class org.sbml.libsbml.ConversionProperties
Adds a copy of the given option to this properties object.
addOption(String, String, int, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, String, int) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, String, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, boolean, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, boolean) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, double, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, double) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, float, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, float) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, int, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, int) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addPackageNamespace(String, long, String) - Method in class org.sbml.libsbml.SBMLNamespaces
Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object.
addPackageNamespace(String, long) - Method in class org.sbml.libsbml.SBMLNamespaces
Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object.
addPackageNamespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBMLNamespaces
Add the XML namespaces of package extensions in the given XMLNamespace object to the set of namespaces within this SBMLNamespaces object (Non-package XML namespaces are not added by this function).
addParameter(Parameter) - Method in class org.sbml.libsbml.KineticLaw
Adds a copy of the given Parameter object to the list of local parameters in this KineticLaw.
addParameter(Parameter) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Parameter object to this Model.
addPort(Port) - Method in class org.sbml.libsbml.CompModelPlugin
 
addProduct(SpeciesReference) - Method in class org.sbml.libsbml.Reaction
Adds a given SpeciesReference object as a product in this Reaction.
addReactant(SpeciesReference) - Method in class org.sbml.libsbml.Reaction
Adds a given SpeciesReference object as a reactant in this Reaction.
addReaction(Reaction) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Reaction object to this Model.
addReactionGlyph(ReactionGlyph) - Method in class org.sbml.libsbml.Layout
 
addReferenceGlyph(ReferenceGlyph) - Method in class org.sbml.libsbml.GeneralGlyph
 
addReplacedElement(ReplacedElement) - Method in class org.sbml.libsbml.CompSBasePlugin
 
addResolver(SBMLResolver) - Method in class org.sbml.libsbml.SBMLResolverRegistry
 
addResource(String) - Method in class org.sbml.libsbml.CVTerm
Adds a resource reference to this CVTerm object.
addRule(Rule) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Rule object to this Model.
addSemanticsAnnotation(XMLNode) - Method in class org.sbml.libsbml.ASTNode
Adds the given XMLNode as a semantic annotation of this ASTNode.
addSpecies(Species) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Species object to this Model.
addSpeciesGlyph(SpeciesGlyph) - Method in class org.sbml.libsbml.Layout
 
addSpeciesReferenceGlyph(SpeciesReferenceGlyph) - Method in class org.sbml.libsbml.ReactionGlyph
 
addSpeciesType(SpeciesType) - Method in class org.sbml.libsbml.Model
Adds a copy of the given SpeciesType object to this Model.
addSubGlyph(GraphicalObject) - Method in class org.sbml.libsbml.GeneralGlyph
 
addSubmodel(Submodel) - Method in class org.sbml.libsbml.CompModelPlugin
 
addTextGlyph(TextGlyph) - Method in class org.sbml.libsbml.Layout
 
addUnit(Unit) - Method in class org.sbml.libsbml.UnitDefinition
Adds a copy of the given Unit to this UnitDefinition.
addUnitDefinition(UnitDefinition) - Method in class org.sbml.libsbml.Model
Adds a copy of the given UnitDefinition object to this Model.
AlgebraicRule - Class in org.sbml.libsbml
Implementation of SBML's AlgebraicRule construct.
AlgebraicRule(long, long) - Constructor for class org.sbml.libsbml.AlgebraicRule
Creates a new AlgebraicRule using the given SBML level and version values.
AlgebraicRule(SBMLNamespaces) - Constructor for class org.sbml.libsbml.AlgebraicRule
Creates a new AlgebraicRule using the given SBMLNamespaces object sbmlns.
AllChecksON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnAlgRule - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnAssignRule - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnConstraint - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnDelay - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnEventAssignment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnFunc - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnInitialAssign - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfComps - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfConstraints - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfEventAssign - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfEvents - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfFuncs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfInitAssign - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfLocalParam - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfMods - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfParams - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfReactions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfRules - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfSpeciesRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfUnitDefs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnLocalParameter - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnModifier - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnParameter - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnPriority - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnRateRule - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnSBML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnSpeciesReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnTrigger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnUnit - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnUnitDefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AND_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AnnotationNotElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AnnotationNotesNotAllowedLevel1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
append(SBase) - Method in class org.sbml.libsbml.ListOf
Adds item to the end of this ListOf.
append(String) - Method in class org.sbml.libsbml.XMLToken
Appends characters to this XML text content.
appendAndOwn(SBase) - Method in class org.sbml.libsbml.ListOf
Adds item to the end of this ListOf.
appendAnnotation(XMLNode) - Method in class org.sbml.libsbml.Model
Appends annotation content to any existing content in the 'annotation' subelement of this object.
appendAnnotation(String) - Method in class org.sbml.libsbml.Model
Appends annotation content to any existing content in the 'annotation' subelement of this object.
appendAnnotation(XMLNode) - Method in class org.sbml.libsbml.SBase
Appends the given annotation to the 'annotation' subelement of this object.
appendAnnotation(String) - Method in class org.sbml.libsbml.SBase
Appends the given annotation to the 'annotation' subelement of this object.
appendAnnotation(XMLNode) - Method in class org.sbml.libsbml.SpeciesReference
Appends annotation content to any existing content in the 'annotation' subelement of this object.
appendAnnotation(String) - Method in class org.sbml.libsbml.SpeciesReference
Appends annotation content to any existing content in the 'annotation' subelement of this object.
appendFrom(ListOf) - Method in class org.sbml.libsbml.ListOf
Adds a clone of all items in the provided ListOf to this object.
appendFrom(Model) - Method in class org.sbml.libsbml.Model
Takes the contents of the passed-in Model, makes copies of everything, and appends those copies to the appropriate places in this Model.
appendNotes(XMLNode) - Method in class org.sbml.libsbml.SBase
Appends the given notes to the 'notes' subelement of this object.
appendNotes(String) - Method in class org.sbml.libsbml.SBase
Appends the given notes to the 'notes' subelement of this object.
ApplyCiMustBeModelComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ApplyCiMustBeUserFunction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
areEquivalent(Unit, Unit) - Static method in class org.sbml.libsbml.Unit
Predicate returning true if Unit objects are equivalent.
areEquivalent(UnitDefinition, UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if two UnitDefinition objects are equivalent.
areIdentical(Unit, Unit) - Static method in class org.sbml.libsbml.Unit
Predicate returning true if two Unit objects are identical.
areIdentical(UnitDefinition, UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if two UnitDefinition objects are identical.
ArgsToEqNeedSameType - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AssignmentRule - Class in org.sbml.libsbml
Implementation of SBML's AssignmentRule construct.
AssignmentRule(long, long) - Constructor for class org.sbml.libsbml.AssignmentRule
Creates a new AssignmentRule using the given SBML level and version values.
AssignmentRule(SBMLNamespaces) - Constructor for class org.sbml.libsbml.AssignmentRule
Creates a new AssignmentRule using the given SBMLNamespaces object sbmlns.
AssignmentToConstantEntity - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AssignRuleCompartmentMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AssignRuleParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AssignRuleSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AssignRuleStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Association - Class in org.sbml.libsbml
 
Association(long, long, long) - Constructor for class org.sbml.libsbml.Association
 
Association(long, long) - Constructor for class org.sbml.libsbml.Association
 
Association(long) - Constructor for class org.sbml.libsbml.Association
 
Association() - Constructor for class org.sbml.libsbml.Association
 
Association(XMLNode, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.Association
 
Association(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.Association
 
Association(Association) - Constructor for class org.sbml.libsbml.Association
 
AST_CONSTANT_E - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_CONSTANT_FALSE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_CONSTANT_PI - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_CONSTANT_TRUE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_DIVIDE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ABS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCOS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCOSH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCOT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCOTH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCSC - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCSCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCSEC - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCSECH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCSIN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCSINH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCTAN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCTANH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_CEILING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_COS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_COSH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_COT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_COTH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_CSC - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_CSCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_DELAY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_EXP - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_FACTORIAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_FLOOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_LN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_LOG - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_PIECEWISE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_POWER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ROOT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_SEC - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_SECH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_SIN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_SINH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_TAN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_TANH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_INTEGER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LAMBDA - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LOGICAL_AND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LOGICAL_NOT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LOGICAL_OR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LOGICAL_XOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_MINUS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_NAME - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_NAME_AVOGADRO - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_NAME_TIME - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_PLUS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_POWER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RATIONAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_REAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_REAL_E - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_EQ - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_GEQ - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_GT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_LEQ - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_LT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_NEQ - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TIMES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ASTNode - Class in org.sbml.libsbml
Abstract Syntax Tree (AST) representation of a mathematical expression.
ASTNode(int) - Constructor for class org.sbml.libsbml.ASTNode
Creates and returns a new ASTNode.
ASTNode() - Constructor for class org.sbml.libsbml.ASTNode
Creates and returns a new ASTNode.
ASTNode(ASTNode) - Constructor for class org.sbml.libsbml.ASTNode
Copy constructor; creates a deep copy of the given ASTNode.
ASTNodeList - Class in org.sbml.libsbml
 
ASTNodeList() - Constructor for class org.sbml.libsbml.ASTNodeList
 
AvogadroNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

B

BadCsymbolDefinitionURLValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadlyFormedXML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadMathML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadMathMLNodeType - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadProcessingInstruction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLAttributeValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLComment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLDecl - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLDeclLocation - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLDOCTYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLDocumentStructure - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLIDRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLIDValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLPrefix - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLPrefixValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BIOLOGICAL_QUALIFIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BooleanOpsNeedBooleanArgs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BothAmountAndConcentrationSet - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BothStoichiometryAndMath - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BoundingBox - Class in org.sbml.libsbml
 
BoundingBox(long, long, long) - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox(long, long) - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox(long) - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox() - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox(BoundingBox) - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox(LayoutPkgNamespaces, String, double, double, double, double) - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox(LayoutPkgNamespaces, String, double, double, double, double, double, double) - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox(LayoutPkgNamespaces, String, Point, Dimensions) - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox(XMLNode, long) - Constructor for class org.sbml.libsbml.BoundingBox
 
BoundingBox(XMLNode) - Constructor for class org.sbml.libsbml.BoundingBox
 
BQB_ENCODES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_HAS_PART - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_HAS_PROPERTY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_HAS_VERSION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_DESCRIBED_BY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_ENCODED_BY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_HOMOLOG_TO - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_PART_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_PROPERTY_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_VERSION_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_OCCURS_IN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQM_IS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQM_IS_DERIVED_FROM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQM_IS_DESCRIBED_BY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQM_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

C

CannotConvertToL1V1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
canonicalize() - Method in class org.sbml.libsbml.ASTNode
Converts this ASTNode to a canonical form and returns true if successful, false otherwise.
CelsiusNoLongerValid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
cerr - Static variable in class org.sbml.libsbml.libsbml
Stream handle for low-level C++ standard error stream.
CERR - Static variable in class org.sbml.libsbml.OStream
 
checkConsistency() - Method in class org.sbml.libsbml.SBMLDocument
Performs consistency checking and validation on this SBML document.
checkInternalConsistency() - Method in class org.sbml.libsbml.SBMLDocument
Performs consistency checking on libSBML's internal representation of an SBML Model.
checkL1Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 1 and can be converted to Level 1.
checkL2v1Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 1 and can be converted to Level 2 Version 1.
checkL2v2Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 2 and can be converted to Level 2 Version 2.
checkL2v3Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 3 and can be converted to Level 2 Version 3.
checkL2v4Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 4 and can be converted to Level 2 Version 4.
checkL3v1Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 3 Version 1 and can be converted to Level 3 Version 1.
checkTerm(String) - Static method in class org.sbml.libsbml.SBO
Checks the format of the given SBO identifier string.
checkTerm(int) - Static method in class org.sbml.libsbml.SBO
Checks the format of the given SBO identifier, given in the form of the integer portion alone.
CircularRuleDependency - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
clear(boolean) - Method in class org.sbml.libsbml.ListOf
Removes all items in this ListOf object.
clear() - Method in class org.sbml.libsbml.ListOf
Removes all items in this ListOf object.
clear() - Method in class org.sbml.libsbml.XMLAttributes
Clears (deletes) all attributes in this XMLAttributes object.
clear() - Method in class org.sbml.libsbml.XMLNamespaces
Clears (deletes) all XML namespace declarations in this XMLNamespaces object.
clearAdditionalDirs() - Method in class org.sbml.libsbml.SBMLFileResolver
 
clearArguments() - Method in class org.sbml.libsbml.SBMLExternalValidator
Clear all additional arguments
clearAssociations() - Method in class org.sbml.libsbml.Association
 
clearAttributes() - Method in class org.sbml.libsbml.XMLToken
Clears (deletes) all attributes in this XMLToken.
clearFailures() - Method in class org.sbml.libsbml.SBMLValidator
Clears this validator's list of failures.
clearInstantiation() - Method in class org.sbml.libsbml.Submodel
 
clearLog() - Method in class org.sbml.libsbml.XMLErrorLog
Deletes all errors from this log.
clearNamespaces() - Method in class org.sbml.libsbml.XMLToken
Clears (deletes) all XML namespace declarations in the XMLNamespaces of this XMLToken.
clearReferencedElement() - Method in class org.sbml.libsbml.SBaseRef
 
clearReplacedElements() - Method in class org.sbml.libsbml.CompSBasePlugin
 
clog - Static variable in class org.sbml.libsbml.libsbml
Stream handle for low-level C++ standard logging stream.
CLOG - Static variable in class org.sbml.libsbml.OStream
 
cloneObject() - Method in class org.sbml.libsbml.AlgebraicRule
Creates and returns a deep copy of this Rule.
cloneObject() - Method in class org.sbml.libsbml.AssignmentRule
Creates and returns a deep copy of this Rule.
cloneObject() - Method in class org.sbml.libsbml.Association
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.BoundingBox
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.Compartment
Creates and returns a deep copy of this Compartment object.
cloneObject() - Method in class org.sbml.libsbml.CompartmentGlyph
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.CompartmentType
Creates and returns a deep copy of this CompartmentType.
cloneObject() - Method in class org.sbml.libsbml.CompModelPlugin
Creates and returns a deep copy of this SBasePlugin object.
cloneObject() - Method in class org.sbml.libsbml.CompPkgNamespaces
Creates and returns a deep copy of this SBMLNamespaces.
cloneObject() - Method in class org.sbml.libsbml.CompSBasePlugin
Creates and returns a deep copy of this SBasePlugin object.
cloneObject() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Creates and returns a deep copy of this SBMLDocumentPlugin object.
cloneObject() - Method in class org.sbml.libsbml.Constraint
Creates and returns a deep copy of this Constraint.
cloneObject() - Method in class org.sbml.libsbml.ConversionOption
Creates and returns a deep copy of this ConversionOption object.
cloneObject() - Method in class org.sbml.libsbml.ConversionProperties
Creates and returns a deep copy of this ConversionProperties object.
cloneObject() - Method in class org.sbml.libsbml.CubicBezier
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.Curve
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.CVTerm
Creates and returns a deep copy of this CVTerm object.
cloneObject() - Method in class org.sbml.libsbml.Date
Returns a copy of this Date.
cloneObject() - Method in class org.sbml.libsbml.Delay
Creates and returns a deep copy of this Delay.
cloneObject() - Method in class org.sbml.libsbml.Deletion
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.Dimensions
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.Event
Creates and returns a deep copy of this Event.
cloneObject() - Method in class org.sbml.libsbml.EventAssignment
Creates and returns a deep copy of this EventAssignment.
cloneObject() - Method in class org.sbml.libsbml.ExternalModelDefinition
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.FbcModelPlugin
Creates and returns a deep copy of this SBasePlugin object.
cloneObject() - Method in class org.sbml.libsbml.FbcPkgNamespaces
Creates and returns a deep copy of this SBMLNamespaces.
cloneObject() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Creates and returns a deep copy of this SBasePlugin object.
cloneObject() - Method in class org.sbml.libsbml.FluxBound
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.FluxObjective
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.FunctionDefinition
Creates and returns a deep copy of this FunctionDefinition.
cloneObject() - Method in class org.sbml.libsbml.GeneAssociation
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.GeneralGlyph
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.GraphicalObject
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.InitialAssignment
Creates and returns a deep copy of this InitialAssignment.
cloneObject() - Method in class org.sbml.libsbml.KineticLaw
Creates and returns a deep copy of this KineticLaw object.
cloneObject() - Method in class org.sbml.libsbml.Layout
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.LayoutModelPlugin
Creates and returns a deep copy of this SBasePlugin object.
cloneObject() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
Creates and returns a deep copy of this SBMLNamespaces.
cloneObject() - Method in class org.sbml.libsbml.LayoutSpeciesReferencePlugin
Creates and returns a deep copy of this SBasePlugin object.
cloneObject() - Method in class org.sbml.libsbml.LineSegment
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.ListOf
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfCompartments
Creates and returns a deep copy of this ListOfCompartments instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Creates and returns a deep copy of this ListOfCompartmentTypes instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfConstraints
Creates and returns a deep copy of this ListOfConstraints instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfDeletions
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfEventAssignments
Creates and returns a deep copy of this ListOfEventAssignments.
cloneObject() - Method in class org.sbml.libsbml.ListOfEvents
Creates and returns a deep copy of this ListOfEvents.
cloneObject() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfFluxBounds
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Creates and returns a deep copy of this ListOfFunctionDefinitions instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfGeneAssociations
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfInitialAssignments
Creates and returns a deep copy of this ListOfInitialAssignments instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfLayouts
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfLineSegments
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfLocalParameters
Creates and returns a deep copy of this ListOfLocalParameters object.
cloneObject() - Method in class org.sbml.libsbml.ListOfModelDefinitions
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfObjectives
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfParameters
Creates and returns a deep copy of this ListOfParameters instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfPorts
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfReactions
Creates and returns a deep copy of this ListOfReactions instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfReplacedElements
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfRules
Creates and returns a deep copy of this ListOfRules instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfSpecies
Creates and returns a deep copy of this ListOfSpeciess instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Creates and returns a deep copy of this ListOfSpeciesReferences instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Creates and returns a deep copy of this ListOfSpeciesTypes instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfSubmodels
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfTextGlyphs
Creates and returns a deep copy of this ListOf.
cloneObject() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Creates and returns a deep copy of this ListOfUnitDefinitions instance.
cloneObject() - Method in class org.sbml.libsbml.ListOfUnits
Creates and returns a deep copy of this ListOfUnits.
cloneObject() - Method in class org.sbml.libsbml.LocalParameter
Creates and returns a deep copy of this LocalParameter.
cloneObject() - Method in class org.sbml.libsbml.Model
Creates and returns a deep copy of this Model object.
cloneObject() - Method in class org.sbml.libsbml.ModelCreator
Creates and returns a copy of this ModelCreator.
cloneObject() - Method in class org.sbml.libsbml.ModelDefinition
Creates and returns a deep copy of this Model object.
cloneObject() - Method in class org.sbml.libsbml.ModelHistory
Creates and returns a copy of this ModelHistory object
cloneObject() - Method in class org.sbml.libsbml.ModifierSpeciesReference
Creates and returns a deep copy of this ModifierSpeciesReference instance.
cloneObject() - Method in class org.sbml.libsbml.Objective
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.Parameter
Creates and returns a deep copy of this Parameter.
cloneObject() - Method in class org.sbml.libsbml.Point
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.Port
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.Priority
Creates and returns a deep copy of this Priority.
cloneObject() - Method in class org.sbml.libsbml.RateRule
Creates and returns a deep copy of this Rule.
cloneObject() - Method in class org.sbml.libsbml.Reaction
Creates and returns a deep copy of this Reaction.
cloneObject() - Method in class org.sbml.libsbml.ReactionGlyph
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.ReferenceGlyph
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.ReplacedBy
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.ReplacedElement
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.Rule
Creates and returns a deep copy of this Rule.
cloneObject() - Method in class org.sbml.libsbml.SBase
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.SBasePlugin
Creates and returns a deep copy of this SBasePlugin object.
cloneObject() - Method in class org.sbml.libsbml.SBaseRef
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.SBMLConverter
Creates and returns a deep copy of this SBMLConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLDocument
Creates and returns a deep copy of this SBMLDocument.
cloneObject() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Creates and returns a deep copy of this SBMLDocumentPlugin object.
cloneObject() - Method in class org.sbml.libsbml.SBMLExternalValidator
Creates and returns a deep copy of this converter.
cloneObject() - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Creates and returns a deep copy of this SBMLFunctionDefinitionConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
Creates and returns a deep copy of this SBMLInitialAssignmentConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Creates and returns a deep copy of this SBMLConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLNamespaces
Creates and returns a deep copy of this SBMLNamespaces.
cloneObject() - Method in class org.sbml.libsbml.SBMLRuleConverter
Creates and returns a deep copy of this SBMLLevelVersionConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
Creates and returns a deep copy of this SBMLStripPackageConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLUnitsConverter
Creates and returns a deep copy of this SBMLConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLValidator
Creates and returns a deep copy of this SBMLValidator.
cloneObject() - Method in class org.sbml.libsbml.Species
Creates and returns a deep copy of this Species object.
cloneObject() - Method in class org.sbml.libsbml.SpeciesGlyph
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.SpeciesReference
Creates and returns a deep copy of this SpeciesReference instance.
cloneObject() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.SpeciesType
Creates and returns a deep copy of this SpeciesType.
cloneObject() - Method in class org.sbml.libsbml.StoichiometryMath
Creates and returns a deep copy of this StoichiometryMath object.
cloneObject() - Method in class org.sbml.libsbml.Submodel
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.TextGlyph
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.Trigger
Creates and returns a deep copy of this Trigger.
cloneObject() - Method in class org.sbml.libsbml.Unit
Creates and returns a deep copy of this Unit.
cloneObject() - Method in class org.sbml.libsbml.UnitDefinition
Creates and returns a deep copy of this UnitDefinition.
cloneObject() - Method in class org.sbml.libsbml.XMLAttributes
Creates and returns a deep copy of this XMLAttributes set.
cloneObject() - Method in class org.sbml.libsbml.XMLNamespaces
Creates and returns a deep copy of this XMLNamespaces list.
cloneObject() - Method in class org.sbml.libsbml.XMLNode
Creates and returns a deep copy of this XMLNode.
cloneObject() - Method in class org.sbml.libsbml.XMLToken
Creates and returns a deep copy of this XMLToken.
cloneObject() - Method in class org.sbml.libsbml.XMLTriple
Creates and returns a deep copy of this XMLTriple set.
close() - Method in class org.sbml.libsbml.OFStream
Closes the file currently associated with this stream object.
CNV_TYPE_BOOL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CNV_TYPE_DOUBLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CNV_TYPE_INT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CNV_TYPE_SINGLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CNV_TYPE_STRING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
combine(UnitDefinition, UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Combines two UnitDefinition objects into a single UnitDefinition.
Compartment - Class in org.sbml.libsbml
Implementation of SBML's Compartment construct.
Compartment(long, long) - Constructor for class org.sbml.libsbml.Compartment
Creates a new Compartment using the given SBML level and version values.
Compartment(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Compartment
Creates a new Compartment using the given SBMLNamespaces object sbmlns.
Compartment(Compartment) - Constructor for class org.sbml.libsbml.Compartment
Copy constructor; creates a copy of a Compartment.
CompartmentGlyph - Class in org.sbml.libsbml
 
CompartmentGlyph(long, long, long) - Constructor for class org.sbml.libsbml.CompartmentGlyph
 
CompartmentGlyph(long, long) - Constructor for class org.sbml.libsbml.CompartmentGlyph
 
CompartmentGlyph(long) - Constructor for class org.sbml.libsbml.CompartmentGlyph
 
CompartmentGlyph() - Constructor for class org.sbml.libsbml.CompartmentGlyph
 
CompartmentGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.CompartmentGlyph
 
CompartmentGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.CompartmentGlyph
 
CompartmentGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.CompartmentGlyph
 
CompartmentGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.CompartmentGlyph
 
CompartmentGlyph(XMLNode) - Constructor for class org.sbml.libsbml.CompartmentGlyph
 
CompartmentGlyph(CompartmentGlyph) - Constructor for class org.sbml.libsbml.CompartmentGlyph
 
CompartmentNotOnL1Reaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompartmentOnReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompartmentShouldHaveSize - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompartmentType - Class in org.sbml.libsbml
Implementation of SBML's Level 2's CompartmentType construct.
CompartmentType(long, long) - Constructor for class org.sbml.libsbml.CompartmentType
Creates a new CompartmentType using the given SBML level and version values.
CompartmentType(SBMLNamespaces) - Constructor for class org.sbml.libsbml.CompartmentType
Creates a new CompartmentType using the given SBMLNamespaces object sbmlns.
CompartmentType(CompartmentType) - Constructor for class org.sbml.libsbml.CompartmentType
Copy constructor; creates a copy of this CompartmentType.
CompartmentTypeNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompartmentTypeNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompBase - Class in org.sbml.libsbml
 
CompExtension - Class in org.sbml.libsbml
 
CompExtension() - Constructor for class org.sbml.libsbml.CompExtension
 
CompExtension(CompExtension) - Constructor for class org.sbml.libsbml.CompExtension
 
CompModelPlugin - Class in org.sbml.libsbml
 
CompModelPlugin(String, String, CompPkgNamespaces) - Constructor for class org.sbml.libsbml.CompModelPlugin
 
CompModelPlugin(CompModelPlugin) - Constructor for class org.sbml.libsbml.CompModelPlugin
 
CompPkgNamespaces - Class in org.sbml.libsbml
Class to store level, version and namespace information of SBML extension package.
CompPkgNamespaces(long, long, long, String) - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPkgNamespaces(long, long, long) - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPkgNamespaces(long, long) - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPkgNamespaces(long) - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPkgNamespaces() - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPkgNamespaces(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.CompPkgNamespaces
Copy constructor; creates a copy of a SBMLExtensionNamespaces.
CompSBasePlugin - Class in org.sbml.libsbml
 
CompSBasePlugin(String, String, CompPkgNamespaces) - Constructor for class org.sbml.libsbml.CompSBasePlugin
 
CompSBasePlugin(CompSBasePlugin) - Constructor for class org.sbml.libsbml.CompSBasePlugin
 
CompSBMLDocumentPlugin - Class in org.sbml.libsbml
 
CompSBMLDocumentPlugin(String, String, CompPkgNamespaces) - Constructor for class org.sbml.libsbml.CompSBMLDocumentPlugin
 
CompSBMLDocumentPlugin(CompSBMLDocumentPlugin) - Constructor for class org.sbml.libsbml.CompSBMLDocumentPlugin
 
connectToChild() - Method in class org.sbml.libsbml.CompModelPlugin
 
connectToChild() - Method in class org.sbml.libsbml.CompSBasePlugin
 
connectToChild() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
ConstantNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConstantSpeciesNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Constraint - Class in org.sbml.libsbml
Implementation of SBML's Constraint construct.
Constraint(long, long) - Constructor for class org.sbml.libsbml.Constraint
Creates a new Constraint using the given SBML level and version values.
Constraint(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Constraint
Creates a new Constraint using the given SBMLNamespaces object sbmlns.
Constraint(Constraint) - Constructor for class org.sbml.libsbml.Constraint
Copy constructor; creates a copy of this Constraint.
ConstraintContainsDOCTYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConstraintContainsXMLDecl - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConstraintMathNotBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConstraintNotInXHTMLNamespace - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConstraintNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
contains(long) - Method in class org.sbml.libsbml.SBMLErrorLog
Returns true if SBMLErrorLog contains an errorId
containsUndeclaredUnits() - Method in class org.sbml.libsbml.Delay
Predicate returning true if the 'math' expression in this Delay instance contains parameters with undeclared units or literal numbers.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.EventAssignment
Predicate returning true if the math expression of this EventAssignment contains literal numbers or parameters with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if the math expression of this InitialAssignment contains parameters/numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.KineticLaw
Predicate returning true if the math expression of this KineticLaw contains parameters/numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.Rule
Predicate returning true if the math expression of this Rule contains parameters/numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.StoichiometryMath
Predicate returning true if the math expression of this StoichiometryMath object contains literal numbers or parameters with undeclared units.
containsUri(String) - Method in class org.sbml.libsbml.XMLNamespaces
Tests whether the given uri is contained in this set of namespaces.
ConversionFactorMustConstant - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConversionFactorNotInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConversionFactorOnSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConversionOption - Class in org.sbml.libsbml
Class of object that encapsulates a conversion option.
ConversionOption(String, String, int, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption.
ConversionOption(String, String, int) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption.
ConversionOption(String, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption.
ConversionOption(String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption.
ConversionOption(String, String, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for string-type options.
ConversionOption(String, boolean, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for Boolean-type options.
ConversionOption(String, boolean) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for Boolean-type options.
ConversionOption(String, double, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for double-type options.
ConversionOption(String, double) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for double-type options.
ConversionOption(String, float, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for float-type options.
ConversionOption(String, float) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for float-type options.
ConversionOption(String, int, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for integer-type options.
ConversionOption(String, int) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for integer-type options.
ConversionOption(ConversionOption) - Constructor for class org.sbml.libsbml.ConversionOption
Copy constructor; creates a copy of an ConversionOption object.
ConversionProperties - Class in org.sbml.libsbml
Class of object that encapsulates the properties of an SBML converter.
ConversionProperties(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ConversionProperties
Constructor that initializes the conversion properties with a specific SBML target namespace.
ConversionProperties() - Constructor for class org.sbml.libsbml.ConversionProperties
Constructor that initializes the conversion properties with a specific SBML target namespace.
ConversionProperties(ConversionProperties) - Constructor for class org.sbml.libsbml.ConversionProperties
Copy constructor.
convert() - Method in class org.sbml.libsbml.SBMLConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Replaces invocations of each user-defined function with an in-line copy, similar to macro expansion.
convert() - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLRuleConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLUnitsConverter
Perform the conversion.
convertStringToXMLNode(String, XMLNamespaces) - Static method in class org.sbml.libsbml.XMLNode
Returns an XMLNode which is derived from a string containing XML content.
convertStringToXMLNode(String) - Static method in class org.sbml.libsbml.XMLNode
Returns an XMLNode which is derived from a string containing XML content.
convertTimeAndExtent() - Method in class org.sbml.libsbml.Submodel
 
convertToSI(Unit) - Static method in class org.sbml.libsbml.Unit
Returns a UnitDefinition object containing the given unit converted to the appropriate SI unit.
convertToSI(UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Convert a given UnitDefinition into a new UnitDefinition object that uses SI units.
convertXMLNodeToString(XMLNode) - Static method in class org.sbml.libsbml.XMLNode
Returns a string representation of a given XMLNode.
cout - Static variable in class org.sbml.libsbml.libsbml
Stream handle for low-level C++ standard output stream.
COUT - Static variable in class org.sbml.libsbml.OStream
 
createAdditionalGraphicalObject() - Method in class org.sbml.libsbml.Layout
 
createAlgebraicRule() - Method in class org.sbml.libsbml.Model
Creates a new AlgebraicRule inside this Model and returns it.
createAnd() - Method in class org.sbml.libsbml.Association
 
createAnnotation() - Static method in class org.sbml.libsbml.RDFAnnotationParser
Creates a blank annotation and returns its root XMLNode object.
createAssignmentRule() - Method in class org.sbml.libsbml.Model
Creates a new AssignmentRule inside this Model and returns it.
createAssociation() - Method in class org.sbml.libsbml.GeneAssociation
 
createCompartment() - Method in class org.sbml.libsbml.Model
Creates a new Compartment inside this Model and returns it.
createCompartmentGlyph() - Method in class org.sbml.libsbml.Layout
 
createCompartmentType() - Method in class org.sbml.libsbml.Model
Creates a new CompartmentType inside this Model and returns it.
createConstraint() - Method in class org.sbml.libsbml.Model
Creates a new Constraint inside this Model and returns it.
createCubicBezier() - Method in class org.sbml.libsbml.Curve
 
createCubicBezier() - Method in class org.sbml.libsbml.GeneralGlyph
 
createCubicBezier() - Method in class org.sbml.libsbml.Layout
 
createCubicBezier() - Method in class org.sbml.libsbml.ReactionGlyph
 
createCubicBezier() - Method in class org.sbml.libsbml.ReferenceGlyph
 
createCubicBezier() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
createCVTerms(SBase) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Takes a list of CVTerm objects and creates a the RDF 'Description' element.
createDelay() - Method in class org.sbml.libsbml.Event
Creates a new, empty Delay, adds it to this Event and returns the Delay.
createDelay() - Method in class org.sbml.libsbml.Model
Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.
createDeletion() - Method in class org.sbml.libsbml.Submodel
 
createEvent() - Method in class org.sbml.libsbml.Model
Creates a new Event inside this Model and returns it.
createEventAssignment() - Method in class org.sbml.libsbml.Event
Creates a new, empty EventAssignment, adds it to this Event's list of event assignments and returns the EventAssignment.
createEventAssignment() - Method in class org.sbml.libsbml.Model
Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.
createExternalModelDefinition() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
createFluxBound() - Method in class org.sbml.libsbml.FbcModelPlugin
 
createFluxObjective() - Method in class org.sbml.libsbml.Objective
 
createFunctionDefinition() - Method in class org.sbml.libsbml.Model
Creates a new FunctionDefinition inside this Model and returns it.
createGene(String) - Method in class org.sbml.libsbml.Association
 
createGene() - Method in class org.sbml.libsbml.Association
 
createGeneAssociation() - Method in class org.sbml.libsbml.FbcModelPlugin
 
createGeneralGlyph() - Method in class org.sbml.libsbml.Layout
 
createInitialAssignment() - Method in class org.sbml.libsbml.Model
Creates a new InitialAssignment inside this Model and returns it.
createKineticLaw() - Method in class org.sbml.libsbml.Model
Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.
createKineticLaw() - Method in class org.sbml.libsbml.Reaction
Creates a new KineticLaw object, installs it as this Reaction's 'kineticLaw' subelement, and returns it.
createKineticLawLocalParameter() - Method in class org.sbml.libsbml.Model
Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
createKineticLawParameter() - Method in class org.sbml.libsbml.Model
Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
createLayout() - Method in class org.sbml.libsbml.LayoutModelPlugin
 
createLineSegment() - Method in class org.sbml.libsbml.Curve
 
createLineSegment() - Method in class org.sbml.libsbml.GeneralGlyph
 
createLineSegment() - Method in class org.sbml.libsbml.Layout
 
createLineSegment() - Method in class org.sbml.libsbml.ReactionGlyph
 
createLineSegment() - Method in class org.sbml.libsbml.ReferenceGlyph
 
createLineSegment() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
createLocalParameter() - Method in class org.sbml.libsbml.KineticLaw
Creates a new LocalParameter object, adds it to this KineticLaw's list of local parameters, and returns the LocalParameter object created.
createModel(String) - Method in class org.sbml.libsbml.SBMLDocument
Creates a new Model inside this SBMLDocument, and returns a pointer to it.
createModel() - Method in class org.sbml.libsbml.SBMLDocument
Creates a new Model inside this SBMLDocument, and returns a pointer to it.
createModelDefinition() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
createModifier() - Method in class org.sbml.libsbml.Model
Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it.
createModifier() - Method in class org.sbml.libsbml.Reaction
Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it.
createObject(XMLInputStream) - Method in class org.sbml.libsbml.CompModelPlugin
 
createObject(XMLInputStream) - Method in class org.sbml.libsbml.CompSBasePlugin
 
createObject(XMLInputStream) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
createObject(XMLInputStream) - Method in class org.sbml.libsbml.FbcModelPlugin
 
createObjective() - Method in class org.sbml.libsbml.FbcModelPlugin
 
createOr() - Method in class org.sbml.libsbml.Association
 
createParameter() - Method in class org.sbml.libsbml.KineticLaw
Creates a new Parameter object, adds it to this KineticLaw's list of local parameters, and returns the Parameter object created.
createParameter() - Method in class org.sbml.libsbml.Model
Creates a new Parameter inside this Model and returns it.
createPort() - Method in class org.sbml.libsbml.CompModelPlugin
 
createPriority() - Method in class org.sbml.libsbml.Event
(SBML Level 3 only) Creates a new, empty Priority, adds it to this Event and returns the Priority.
createProduct() - Method in class org.sbml.libsbml.Model
Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.
createProduct() - Method in class org.sbml.libsbml.Reaction
Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it.
createRateRule() - Method in class org.sbml.libsbml.Model
Creates a new RateRule inside this Model and returns it.
createRDFAnnotation() - Static method in class org.sbml.libsbml.RDFAnnotationParser
Creates a blank RDF element suitable for use in SBML annotations.
createReactant() - Method in class org.sbml.libsbml.Model
Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
createReactant() - Method in class org.sbml.libsbml.Reaction
Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it.
createReaction() - Method in class org.sbml.libsbml.Model
Creates a new Reaction inside this Model and returns it.
createReactionGlyph() - Method in class org.sbml.libsbml.Layout
 
createReferenceGlyph() - Method in class org.sbml.libsbml.GeneralGlyph
 
createReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
 
createReplacedElement() - Method in class org.sbml.libsbml.CompSBasePlugin
 
createSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
 
createSpecies() - Method in class org.sbml.libsbml.Model
Creates a new Species inside this Model and returns it.
createSpeciesGlyph() - Method in class org.sbml.libsbml.Layout
 
createSpeciesReferenceGlyph() - Method in class org.sbml.libsbml.Layout
 
createSpeciesReferenceGlyph() - Method in class org.sbml.libsbml.ReactionGlyph
 
createSpeciesType() - Method in class org.sbml.libsbml.Model
Creates a new SpeciesType inside this Model and returns it.
createStoichiometryMath() - Method in class org.sbml.libsbml.SpeciesReference
Creates a new, empty StoichiometryMath object, adds it to this SpeciesReference, and returns it.
createSubmodel() - Method in class org.sbml.libsbml.CompModelPlugin
 
createTextGlyph() - Method in class org.sbml.libsbml.Layout
 
createTrigger() - Method in class org.sbml.libsbml.Event
Creates a new, empty Trigger, adds it to this Event and returns the Trigger.
createTrigger() - Method in class org.sbml.libsbml.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.libsbml.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.libsbml.UnitDefinition
Creates a new and empty Unit, adds it to this UnitDefinition's list of units, and returns it.
createUnitDefinition() - Method in class org.sbml.libsbml.Model
Creates a new UnitDefinition inside this Model and returns it.
CubicBezier - Class in org.sbml.libsbml
 
CubicBezier(long, long, long) - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier(long, long) - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier(long) - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier() - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier(LayoutPkgNamespaces, double, double, double, double) - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier(LayoutPkgNamespaces, double, double, double, double, double, double) - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier(CubicBezier) - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier(LayoutPkgNamespaces, Point, Point) - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier(LayoutPkgNamespaces, Point, Point, Point, Point) - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier(XMLNode, long) - Constructor for class org.sbml.libsbml.CubicBezier
 
CubicBezier(XMLNode) - Constructor for class org.sbml.libsbml.CubicBezier
 
Curve - Class in org.sbml.libsbml
 
Curve(long, long, long) - Constructor for class org.sbml.libsbml.Curve
 
Curve(long, long) - Constructor for class org.sbml.libsbml.Curve
 
Curve(long) - Constructor for class org.sbml.libsbml.Curve
 
Curve() - Constructor for class org.sbml.libsbml.Curve
 
Curve(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.Curve
 
Curve(XMLNode, long) - Constructor for class org.sbml.libsbml.Curve
 
Curve(XMLNode) - Constructor for class org.sbml.libsbml.Curve
 
Curve(Curve) - Constructor for class org.sbml.libsbml.Curve
 
CVTerm - Class in org.sbml.libsbml
Representation of MIRIAM-compliant controlled vocabulary annotation.
CVTerm(int) - Constructor for class org.sbml.libsbml.CVTerm
Creates an empty CVTerm, optionally with the given qualifier type.
CVTerm() - Constructor for class org.sbml.libsbml.CVTerm
Creates an empty CVTerm, optionally with the given qualifier type.
CVTerm(XMLNode) - Constructor for class org.sbml.libsbml.CVTerm
Creates a new CVTerm from the given XMLNode.
CVTerm(CVTerm) - Constructor for class org.sbml.libsbml.CVTerm
Copy constructor; creates a copy of a CVTerm object.
CVTermList - Class in org.sbml.libsbml
 
CVTermList() - Constructor for class org.sbml.libsbml.CVTermList
 

D

DanglingUnitSIdRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Date - Class in org.sbml.libsbml
Representation of MIRIAM-compliant dates used in ModelHistory.
Date(long, long, long, long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date() - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(String) - Constructor for class org.sbml.libsbml.Date
Creates a Date object from a string expressing a date and time value.
Date(Date) - Constructor for class org.sbml.libsbml.Date
Copy constructor; creates a copy of this Date.
DateList - Class in org.sbml.libsbml
 
DateList() - Constructor for class org.sbml.libsbml.DateList
 
deepCopy() - Method in class org.sbml.libsbml.ASTNode
Creates a recursive copy of this node and all its children.
Delay - Class in org.sbml.libsbml
Implementation of SBML's Delay construct for Event.
Delay(long, long) - Constructor for class org.sbml.libsbml.Delay
Creates a new Delay using the given SBML level and version values.
Delay(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Delay
Creates a new Delay using the given SBMLNamespaces object sbmlns.
Delay(Delay) - Constructor for class org.sbml.libsbml.Delay
Copy constructor; creates a copy of this Delay.
DelayNeedsValuesFromTriggerTime - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DelayUnitsNotTime - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
delete() - Method in class org.sbml.libsbml.AlgebraicRule
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.AssignmentRule
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Association
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ASTNode
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ASTNodeList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.BoundingBox
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Compartment
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompartmentGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompartmentType
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompBase
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompExtension
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompModelPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompPkgNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompSBasePlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Constraint
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ConversionOption
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ConversionProperties
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CubicBezier
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Curve
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CVTerm
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CVTermList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Date
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.DateList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Delay
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Deletion
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Dimensions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Event
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.EventAssignment
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ExternalModelDefinition
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcExtension
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcModelPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcPkgNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FluxBound
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FluxObjective
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FunctionDefinition
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GeneAssociation
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GeneralGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GraphicalObject
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.InitialAssignment
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.KineticLaw
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.L3ParserSettings
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Layout
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LayoutExtension
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LayoutModelPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LayoutSpeciesReferencePlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LineSegment
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOf
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfCompartments
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfConstraints
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfDeletions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfEventAssignments
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfEvents
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfFluxBounds
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfGeneAssociations
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfInitialAssignments
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfLayouts
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfLineSegments
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfLocalParameters
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfModelDefinitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfObjectives
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfParameters
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfPorts
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfReactions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfReplacedElements
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfRules
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSpecies
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSubmodels
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfTextGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfUnits
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LocalParameter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Model
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ModelCreator
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ModelCreatorList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ModelDefinition
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ModelHistory
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ModifierSpeciesReference
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Objective
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.OFStream
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.OStream
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.OStringStream
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Parameter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Point
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Port
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Priority
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RateRule
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RDFAnnotationParser
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Reaction
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ReactionGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ReferenceGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ReplacedBy
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ReplacedElement
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Replacing
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Rule
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBase
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBaseList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBasePlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBaseRef
Explicitly deletes the underlying native object.
delete() - Method in exception org.sbml.libsbml.SBMLConstructorException
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLConverterRegistry
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLDocument
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLError
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLErrorLog
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLExtensionException
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLExternalValidator
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLFileResolver
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLNamespacesList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLReader
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLResolver
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLResolverRegistry
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLRuleConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLUnitsConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLUri
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLValidator
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLWriter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBO
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Species
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SpeciesGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SpeciesReference
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SpeciesType
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.StoichiometryMath
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Submodel
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SyntaxChecker
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.TextGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Trigger
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Unit
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.UnitDefinition
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLAttributes
Explicitly deletes the underlying native object.
delete() - Method in exception org.sbml.libsbml.XMLConstructorException
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLError
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLErrorLog
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLNode
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLToken
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLTriple
Explicitly deletes the underlying native object.
deleteLayoutAnnotation(XMLNode) - Static method in class org.sbml.libsbml.libsbml
 
deleteLayoutIdAnnotation(XMLNode) - Static method in class org.sbml.libsbml.libsbml
 
deleteRDFAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Deletes any SBML MIRIAM RDF annotation found in the given XMLNode tree and returns any remaining annotation content.
deleteRDFCVTermAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Deletes any SBML MIRIAM RDF 'CVTerm' annotation found in the given XMLNode tree and returns any remaining annotation content.
deleteRDFHistoryAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Deletes any SBML MIRIAM RDF 'History' annotation found in the given XMLNode tree and returns any remaining annotation content.
Deletion - Class in org.sbml.libsbml
 
Deletion(long, long, long) - Constructor for class org.sbml.libsbml.Deletion
 
Deletion(long, long) - Constructor for class org.sbml.libsbml.Deletion
 
Deletion(long) - Constructor for class org.sbml.libsbml.Deletion
 
Deletion() - Constructor for class org.sbml.libsbml.Deletion
 
Deletion(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.Deletion
 
Deletion(Deletion) - Constructor for class org.sbml.libsbml.Deletion
 
depth() - Method in class org.sbml.libsbml.BoundingBox
 
depth() - Method in class org.sbml.libsbml.Dimensions
 
Dimensions - Class in org.sbml.libsbml
 
Dimensions(long, long, long) - Constructor for class org.sbml.libsbml.Dimensions
 
Dimensions(long, long) - Constructor for class org.sbml.libsbml.Dimensions
 
Dimensions(long) - Constructor for class org.sbml.libsbml.Dimensions
 
Dimensions() - Constructor for class org.sbml.libsbml.Dimensions
 
Dimensions(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.Dimensions
 
Dimensions(Dimensions) - Constructor for class org.sbml.libsbml.Dimensions
 
Dimensions(LayoutPkgNamespaces, double, double, double) - Constructor for class org.sbml.libsbml.Dimensions
 
Dimensions(LayoutPkgNamespaces, double, double) - Constructor for class org.sbml.libsbml.Dimensions
 
Dimensions(XMLNode, long) - Constructor for class org.sbml.libsbml.Dimensions
 
Dimensions(XMLNode) - Constructor for class org.sbml.libsbml.Dimensions
 
disablePackage(String, String) - Method in class org.sbml.libsbml.SBase
Disables the given SBML Level 3 package
disablePackage(String) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Disables the package with the given URI / name.
disablePackages(SWIGTYPE_p_std__vectorT_std__string_t) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Disables all packages with the given URI / name.
disableUnusedPackages(SBMLDocument) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Goes through all extensions in the list of plugins of the given document and disables all plugins that are not being used.
DisallowedDefinitionURLUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DisallowedMathMLEncodingUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DisallowedMathMLSymbol - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DisallowedMathTypeAttributeUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DisallowedMathTypeAttributeValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DisallowedMathUnitsUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.CompExtension
 
DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.FbcExtension
 
DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.LayoutExtension
SBMLExtension derived classes must override this method
DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.CompExtension
 
DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.FbcExtension
 
DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.LayoutExtension
 
DuplicateAnnotationInvalidInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateAnnotationInvalidInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateAnnotationInvalidInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateAnnotationInvalidInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateAnnotationNamespaces - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateComponentId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateLocalParameterId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateMetaId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateUnitDefinitionId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateXMLAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

E

EmptyListElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EmptyListInKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EmptyListInReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EmptyListOfUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EmptyUnitListElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
enableDefaultNS(String, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Set/unset default namespace to each top-level element defined in the given package extension.
enableL2NamespaceForDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Enables all extensions that support serialization / deserialization with SBML Annotations.
enablePackage(String, String, boolean) - Method in class org.sbml.libsbml.SBase
Enables or disables the given SBML Level 3 package
enablePackage(String) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Enables the package with the given URI / name.
enablePackages(SWIGTYPE_p_std__vectorT_std__string_t) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Enables all packages with the given URI / name.
endl() - Method in class org.sbml.libsbml.OStream
Writes an end-of-line character on this tream.
equals(Object) - Method in class org.sbml.libsbml.ASTNode
Equality comparison method for ASTNode.
equals(Object) - Method in class org.sbml.libsbml.CVTerm
Equality comparison method for CVTerm.
equals(Object) - Method in class org.sbml.libsbml.Date
Equality comparison method for Date.
equals(Object) - Method in class org.sbml.libsbml.ModelCreator
Equality comparison method for ModelCreator.
equals(Object) - Method in class org.sbml.libsbml.ModelHistory
Equality comparison method for ModelHistory.
equals(Object) - Method in class org.sbml.libsbml.SBase
Equality comparison method for SBase.
equals(Object) - Method in class org.sbml.libsbml.SBMLNamespaces
Equality comparison method for SBMLNamespaces.
equals(Object) - Method in class org.sbml.libsbml.SBMLReader
Equality comparison method for SBMLReader.
equals(Object) - Method in class org.sbml.libsbml.SBMLWriter
Equality comparison method for SBMLWriter.
equals(Object) - Method in class org.sbml.libsbml.XMLAttributes
Equality comparison method for XMLAttributes.
equals(Object) - Method in class org.sbml.libsbml.XMLError
Equality comparison method for XMLError.
equals(Object) - Method in class org.sbml.libsbml.XMLErrorLog
Equality comparison method for XMLErrorLog.
equals(Object) - Method in class org.sbml.libsbml.XMLNamespaces
Equality comparison method for XMLNamespaces.
equals(Object) - Method in class org.sbml.libsbml.XMLNode
Equality comparison method for XMLNode.
equals(Object) - Method in class org.sbml.libsbml.XMLToken
Equality comparison method for XMLToken.
equals(Object) - Method in class org.sbml.libsbml.XMLTriple
Equality comparison method for XMLTriple.
Event - Class in org.sbml.libsbml
Implementation of SBML's Event construct.
Event(long, long) - Constructor for class org.sbml.libsbml.Event
Creates a new Event using the given SBML level and version values.
Event(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Event
Creates a new Event using the given SBMLNamespaces object sbmlns.
Event(Event) - Constructor for class org.sbml.libsbml.Event
Copy constructor; creates a copy of this Event.
EventAndAssignmentRuleForId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventAssignCompartmentMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventAssignment - Class in org.sbml.libsbml
Implementation of SBML's EventAssignment construct for Event.
EventAssignment(long, long) - Constructor for class org.sbml.libsbml.EventAssignment
Creates a new EventAssignment using the given SBML level and version values.
EventAssignment(SBMLNamespaces) - Constructor for class org.sbml.libsbml.EventAssignment
Creates a new EventAssignment using the given SBMLNamespaces object sbmlns.
EventAssignment(EventAssignment) - Constructor for class org.sbml.libsbml.EventAssignment
Copy constructor; creates a copy of this EventAssignment.
EventAssignmentForConstantEntity - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventAssignParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventAssignSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventAssignStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
expandFunctionDefinitions() - Method in class org.sbml.libsbml.SBMLDocument
Removes FunctionDefinition constructs from the document and expands any instances of their use within <math> elements.
expandInitialAssignments() - Method in class org.sbml.libsbml.SBMLDocument
Removes InitialAssignment constructs from the document and replaces them with appropriate values.
ExtentUnitsNotSubstance - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ExternalModelDefinition - Class in org.sbml.libsbml
 
ExternalModelDefinition(long, long, long) - Constructor for class org.sbml.libsbml.ExternalModelDefinition
 
ExternalModelDefinition(long, long) - Constructor for class org.sbml.libsbml.ExternalModelDefinition
 
ExternalModelDefinition(long) - Constructor for class org.sbml.libsbml.ExternalModelDefinition
 
ExternalModelDefinition() - Constructor for class org.sbml.libsbml.ExternalModelDefinition
 
ExternalModelDefinition(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ExternalModelDefinition
 
ExternalModelDefinition(ExternalModelDefinition) - Constructor for class org.sbml.libsbml.ExternalModelDefinition
 

F

FailedMathMLReadOfDouble - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FailedMathMLReadOfExponential - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FailedMathMLReadOfInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FailedMathMLReadOfRational - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcExtension - Class in org.sbml.libsbml
 
FbcExtension() - Constructor for class org.sbml.libsbml.FbcExtension
 
FbcExtension(FbcExtension) - Constructor for class org.sbml.libsbml.FbcExtension
 
FbcModelPlugin - Class in org.sbml.libsbml
 
FbcModelPlugin(String, String, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcModelPlugin
 
FbcModelPlugin(FbcModelPlugin) - Constructor for class org.sbml.libsbml.FbcModelPlugin
 
FbcPkgNamespaces - Class in org.sbml.libsbml
Class to store level, version and namespace information of SBML extension package.
FbcPkgNamespaces(long, long, long, String) - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcPkgNamespaces(long, long, long) - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcPkgNamespaces(long, long) - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcPkgNamespaces(long) - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcPkgNamespaces() - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcPkgNamespaces(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
Copy constructor; creates a copy of a SBMLExtensionNamespaces.
FbcSpeciesPlugin - Class in org.sbml.libsbml
 
FbcSpeciesPlugin(String, String, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcSpeciesPlugin
 
FbcSpeciesPlugin(FbcSpeciesPlugin) - Constructor for class org.sbml.libsbml.FbcSpeciesPlugin
 
FluxBound - Class in org.sbml.libsbml
 
FluxBound(long, long, long) - Constructor for class org.sbml.libsbml.FluxBound
 
FluxBound(long, long) - Constructor for class org.sbml.libsbml.FluxBound
 
FluxBound(long) - Constructor for class org.sbml.libsbml.FluxBound
 
FluxBound() - Constructor for class org.sbml.libsbml.FluxBound
 
FluxBound(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FluxBound
 
FluxBound(FluxBound) - Constructor for class org.sbml.libsbml.FluxBound
 
FLUXBOUND_OPERATION_EQUAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FLUXBOUND_OPERATION_GREATER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FLUXBOUND_OPERATION_GREATER_EQUAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FLUXBOUND_OPERATION_LESS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FLUXBOUND_OPERATION_LESS_EQUAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FLUXBOUND_OPERATION_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FluxObjective - Class in org.sbml.libsbml
 
FluxObjective(long, long, long) - Constructor for class org.sbml.libsbml.FluxObjective
 
FluxObjective(long, long) - Constructor for class org.sbml.libsbml.FluxObjective
 
FluxObjective(long) - Constructor for class org.sbml.libsbml.FluxObjective
 
FluxObjective() - Constructor for class org.sbml.libsbml.FluxObjective
 
FluxObjective(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FluxObjective
 
FluxObjective(FluxObjective) - Constructor for class org.sbml.libsbml.FluxObjective
 
FormulaInLevel1KL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
formulaToString(ASTNode) - Static method in class org.sbml.libsbml.libsbml
Converts an AST to a string representation of a formula using a syntax basically derived from SBML Level 1.
freeName() - Method in class org.sbml.libsbml.ASTNode
Frees the name of this ASTNode and sets it to null.
FuncDefNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FunctionDefinition - Class in org.sbml.libsbml
Implementation of SBML's FunctionDefinition construct.
FunctionDefinition(long, long) - Constructor for class org.sbml.libsbml.FunctionDefinition
Creates a new FunctionDefinition using the given SBML level and version values.
FunctionDefinition(SBMLNamespaces) - Constructor for class org.sbml.libsbml.FunctionDefinition
Creates a new FunctionDefinition using the given SBMLNamespaces object sbmlns.
FunctionDefinition(FunctionDefinition) - Constructor for class org.sbml.libsbml.FunctionDefinition
Copy constructor; creates a copy of this FunctionDefinition.
FunctionDefMathNotLambda - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

G

GENE_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GeneAssociation - Class in org.sbml.libsbml
 
GeneAssociation(long, long, long) - Constructor for class org.sbml.libsbml.GeneAssociation
 
GeneAssociation(long, long) - Constructor for class org.sbml.libsbml.GeneAssociation
 
GeneAssociation(long) - Constructor for class org.sbml.libsbml.GeneAssociation
 
GeneAssociation() - Constructor for class org.sbml.libsbml.GeneAssociation
 
GeneAssociation(XMLNode, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneAssociation
 
GeneAssociation(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneAssociation
 
GeneAssociation(GeneAssociation) - Constructor for class org.sbml.libsbml.GeneAssociation
 
GeneralGlyph - Class in org.sbml.libsbml
 
GeneralGlyph(long, long, long) - Constructor for class org.sbml.libsbml.GeneralGlyph
 
GeneralGlyph(long, long) - Constructor for class org.sbml.libsbml.GeneralGlyph
 
GeneralGlyph(long) - Constructor for class org.sbml.libsbml.GeneralGlyph
 
GeneralGlyph() - Constructor for class org.sbml.libsbml.GeneralGlyph
 
GeneralGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneralGlyph
 
GeneralGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.GeneralGlyph
 
GeneralGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.GeneralGlyph
 
GeneralGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.GeneralGlyph
 
GeneralGlyph(XMLNode) - Constructor for class org.sbml.libsbml.GeneralGlyph
 
GeneralGlyph(GeneralGlyph) - Constructor for class org.sbml.libsbml.GeneralGlyph
 
GeneralWarningNotSpecified - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
get(long) - Method in class org.sbml.libsbml.ASTNodeList
 
get(long) - Method in class org.sbml.libsbml.CVTermList
 
get(long) - Method in class org.sbml.libsbml.DateList
 
get(long) - Method in class org.sbml.libsbml.ListOf
Get an item from the list.
get(long) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfCompartments
get(String) - Method in class org.sbml.libsbml.ListOfCompartments
Get a Compartment from the ListOfCompartments based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
get(String) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Get a CompartmentType from the ListOfCompartmentTypes based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfConstraints
get(long) - Method in class org.sbml.libsbml.ListOfDeletions
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfDeletions
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfEventAssignments
get(String) - Method in class org.sbml.libsbml.ListOfEventAssignments
Get a EventAssignment from the ListOfEventAssignments based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfEvents
Get a Event from the ListOfEvents.
get(String) - Method in class org.sbml.libsbml.ListOfEvents
Get a Event from the ListOfEvents based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfFluxBounds
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfFluxBounds
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfFluxObjectives
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfFluxObjectives
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
get(String) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Get a FunctionDefinition from the ListOfFunctionDefinitions based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfGeneAssociations
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfGeneAssociations
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfInitialAssignments
get(String) - Method in class org.sbml.libsbml.ListOfInitialAssignments
Get a InitialAssignment from the ListOfInitialAssignments based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfLayouts
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfLayouts
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfLineSegments
Get an item from the list.
get(long) - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the LocalParameter object located at position n within this ListOfLocalParameters instance.
get(String) - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the first LocalParameter object matching the given identifier.
get(long) - Method in class org.sbml.libsbml.ListOfModelDefinitions
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfModelDefinitions
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfObjectives
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfObjectives
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfParameters
Returns the Parameter object located at position n within this ListOfParameters instance.
get(String) - Method in class org.sbml.libsbml.ListOfParameters
Returns the first Parameter object matching the given identifier.
get(long) - Method in class org.sbml.libsbml.ListOfPorts
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfPorts
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfReactions
Get a Reaction from the ListOfReactions.
get(String) - Method in class org.sbml.libsbml.ListOfReactions
Get a Reaction from the ListOfReactions based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfReplacedElements
Get an item from the list.
get(long) - Method in class org.sbml.libsbml.ListOfRules
Get a Rule from the ListOfRules.
get(String) - Method in class org.sbml.libsbml.ListOfRules
Get a Rule from the ListOfRules based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfSpecies
Get a Species from the ListOfSpecies.
get(String) - Method in class org.sbml.libsbml.ListOfSpecies
Get a Species from the ListOfSpecies based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
get(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Get a SpeciesReference from the ListOfSpeciesReferences based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
get(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Get a SpeciesType from the ListOfSpeciesTypes based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfSubmodels
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfSubmodels
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfTextGlyphs
Get an item from the list.
get(String) - Method in class org.sbml.libsbml.ListOfTextGlyphs
Get an item from the list based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
get(String) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Get a UnitDefinition from the ListOfUnitDefinitions based on its identifier.
get(long) - Method in class org.sbml.libsbml.ListOfUnits
Get a Unit from the ListOfUnits.
get(long) - Method in class org.sbml.libsbml.ModelCreatorList
 
get(long) - Method in class org.sbml.libsbml.SBaseList
 
get(long) - Method in class org.sbml.libsbml.SBMLNamespacesList
 
get_ostream() - Method in class org.sbml.libsbml.OStream
Returns the stream object.
getActiveObjective() - Method in class org.sbml.libsbml.FbcModelPlugin
 
getActiveObjective() - Method in class org.sbml.libsbml.ListOfObjectives
 
getActiveObjectiveId() - Method in class org.sbml.libsbml.FbcModelPlugin
 
getAdditionalGraphicalObject(long) - Method in class org.sbml.libsbml.Layout
 
getAdditionalGraphicalObject(String) - Method in class org.sbml.libsbml.Layout
 
getAncestorOfType(int, String) - Method in class org.sbml.libsbml.SBase
Returns the first ancestor object that has the given SBML type code.
getAncestorOfType(int) - Method in class org.sbml.libsbml.SBase
Returns the first ancestor object that has the given SBML type code.
getAnnotation() - Method in class org.sbml.libsbml.SBase
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
getAnnotationString() - Method in class org.sbml.libsbml.SBase
Returns the content of the 'annotation' subelement of this object as a character string.
getAreaUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'areaUnits' attribute of this Model.
getArgument(long) - Method in class org.sbml.libsbml.FunctionDefinition
Get the nth argument to this function.
getArgument(String) - Method in class org.sbml.libsbml.FunctionDefinition
Get the argument named name to this FunctionDefinition.
getArgument(long) - Method in class org.sbml.libsbml.SBMLExternalValidator
Returns the argument for the given index.
getAssociation() - Method in class org.sbml.libsbml.GeneAssociation
 
getAttributes() - Method in class org.sbml.libsbml.XMLToken
Returns the attributes of this element.
getAttributesLength() - Method in class org.sbml.libsbml.XMLToken
Return the number of attributes in the attributes set.
getAttrIndex(String, String) - Method in class org.sbml.libsbml.XMLToken
Return the index of an attribute with the given local name and namespace URI.
getAttrIndex(String) - Method in class org.sbml.libsbml.XMLToken
Return the index of an attribute with the given local name and namespace URI.
getAttrIndex(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
Return the index of an attribute with the given XMLTriple.
getAttrName(int) - Method in class org.sbml.libsbml.XMLToken
Return the local name of an attribute in the attributes set in this XMLToken (by position).
getAttrPrefix(int) - Method in class org.sbml.libsbml.XMLToken
Return the prefix of an attribute in the attribute set in this XMLToken (by position).
getAttrPrefixedName(int) - Method in class org.sbml.libsbml.XMLToken
Return the prefixed name of an attribute in the attribute set in this XMLToken (by position).
getAttrURI(int) - Method in class org.sbml.libsbml.XMLToken
Return the namespace URI of an attribute in the attribute set in this XMLToken (by position).
getAttrValue(int) - Method in class org.sbml.libsbml.XMLToken
Return the value of an attribute in the attribute set in this XMLToken (by position).
getAttrValue(String, String) - Method in class org.sbml.libsbml.XMLToken
Return a value of an attribute with the given local name and namespace URI.
getAttrValue(String) - Method in class org.sbml.libsbml.XMLToken
Return a value of an attribute with the given local name and namespace URI.
getAttrValue(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
Return a value of an attribute with the given XMLTriple.
getBasePoint1() - Method in class org.sbml.libsbml.CubicBezier
 
getBasePoint2() - Method in class org.sbml.libsbml.CubicBezier
 
getBiologicalQualifierType() - Method in class org.sbml.libsbml.CVTerm
Returns the biological qualifier type of this CVTerm object.
getBody() - Method in class org.sbml.libsbml.FunctionDefinition
Get the mathematical expression that is the body of this FunctionDefinition object.
getBoolValue() - Method in class org.sbml.libsbml.ConversionOption
Returns the value of this option as a Boolean.
getBoolValue(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the value of the given option as a Boolean.
getBoundaryCondition() - Method in class org.sbml.libsbml.Species
Get the value of the 'boundaryCondition' attribute.
getBoundingBox() - Method in class org.sbml.libsbml.GraphicalObject
 
getCategory() - Method in class org.sbml.libsbml.XMLError
Returns the category of this error.
getCategoryAsString() - Method in class org.sbml.libsbml.XMLError
Returns a string describing the category of this error.
getCharacter() - Method in class org.sbml.libsbml.ASTNode
Get the value of this node as a single character.
getCharacters() - Method in class org.sbml.libsbml.XMLToken
Returns the text of this element.
getCharge() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
 
getCharge() - Method in class org.sbml.libsbml.Species
Get the value of the 'charge' attribute.
getChemicalFormula() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
 
getChild(long) - Method in class org.sbml.libsbml.ASTNode
Get a child of this node according to its index number.
getChild(long) - Method in class org.sbml.libsbml.XMLNode
Returns the nth child of this XMLNode.
getChild(String) - Method in class org.sbml.libsbml.XMLNode
Returns the first child of this XMLNode with the corresponding name.
getClassName() - Method in class org.sbml.libsbml.ASTNode
Get the class of this ASTNode.
getCoefficient() - Method in class org.sbml.libsbml.FluxObjective
 
getColumn() - Method in class org.sbml.libsbml.SBase
Returns the column number on which this object first appears in the XML representation of the SBML document.
getColumn() - Method in class org.sbml.libsbml.XMLError
Returns the column number in the XML input near where the error, warning or other diagnostic occurred.
getColumn() - Method in class org.sbml.libsbml.XMLToken
Returns the column at which this XMLToken occurred in the input document or data stream.
getCompartment(long) - Method in class org.sbml.libsbml.Model
Get the nth Compartment object in this Model.
getCompartment(String) - Method in class org.sbml.libsbml.Model
Get a Compartment object based on its identifier.
getCompartment() - Method in class org.sbml.libsbml.Reaction
(SBML Level 3 only) Returns the value of the 'compartment' attribute on the Reaction.
getCompartment() - Method in class org.sbml.libsbml.Species
Get the compartment in which this species is located.
getCompartmentGlyph(long) - Method in class org.sbml.libsbml.Layout
 
getCompartmentGlyph(String) - Method in class org.sbml.libsbml.Layout
 
getCompartmentId() - Method in class org.sbml.libsbml.CompartmentGlyph
 
getCompartmentType() - Method in class org.sbml.libsbml.Compartment
Get the value of the 'compartmentType' attribute of this Compartment object.
getCompartmentType(long) - Method in class org.sbml.libsbml.Model
Get the nth CompartmentType object in this Model.
getCompartmentType(String) - Method in class org.sbml.libsbml.Model
Get a CompartmentType object based on its identifier.
getConstant() - Method in class org.sbml.libsbml.Compartment
Get the value of the 'constant' attribute of this Compartment.
getConstant() - Method in class org.sbml.libsbml.Parameter
Gets the value of the 'constant' attribute of this Parameter instance.
getConstant() - Method in class org.sbml.libsbml.Species
Get the value of the 'constant' attribute.
getConstant() - Method in class org.sbml.libsbml.SpeciesReference
Get the value of the 'constant' attribute.
getConstraint(long) - Method in class org.sbml.libsbml.Model
Get the nth Constraint object in this Model.
getConversionFactor() - Method in class org.sbml.libsbml.Model
Returns the value of the 'conversionFactor' attribute of this Model.
getConversionFactor() - Method in class org.sbml.libsbml.ReplacedElement
 
getConversionFactor() - Method in class org.sbml.libsbml.Species
Get the value of the 'conversionFactor' attribute.
getConverterByIndex(int) - Method in class org.sbml.libsbml.SBMLConverterRegistry
Returns the converter with the given index number.
getConverterFor(ConversionProperties) - Method in class org.sbml.libsbml.SBMLConverterRegistry
Returns the converter that best matches the given configuration properties.
getCreatedDate() - Method in class org.sbml.libsbml.ModelHistory
Returns the 'creation date' portion of this ModelHistory object.
getCreator(long) - Method in class org.sbml.libsbml.ModelHistory
Get the nth ModelCreator object stored in this ModelHistory object.
getCurve() - Method in class org.sbml.libsbml.GeneralGlyph
 
getCurve() - Method in class org.sbml.libsbml.ReactionGlyph
 
getCurve() - Method in class org.sbml.libsbml.ReferenceGlyph
 
getCurve() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
getCurveSegment(long) - Method in class org.sbml.libsbml.Curve
 
getCVTerm(long) - Method in class org.sbml.libsbml.SBase
Returns the nth CVTerm in the list of CVTerms of this SBML object.
getCVTerms() - Method in class org.sbml.libsbml.SBase
Returns a list of CVTerm objects in the annotations of this SBML object.
getDateAsString() - Method in class org.sbml.libsbml.Date
Returns the current Date value in text-string form.
getDay() - Method in class org.sbml.libsbml.Date
Returns the day from this Date.
getDefaultL3ParserSettings() - Static method in class org.sbml.libsbml.libsbml
Returns a copy of the default parser settings used by libsbml.parseL3Formula(String formula).
getDefaultLevel() - Static method in class org.sbml.libsbml.CompExtension
 
getDefaultLevel() - Static method in class org.sbml.libsbml.FbcExtension
 
getDefaultLevel() - Static method in class org.sbml.libsbml.LayoutExtension
 
getDefaultLevel() - Static method in class org.sbml.libsbml.SBMLDocument
The default SBML Level of new SBMLDocument objects.
getDefaultPackageVersion() - Static method in class org.sbml.libsbml.CompExtension
 
getDefaultPackageVersion() - Static method in class org.sbml.libsbml.FbcExtension
 
getDefaultPackageVersion() - Static method in class org.sbml.libsbml.LayoutExtension
 
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLRuleConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLUnitsConverter
Returns the default properties of this converter.
getDefaultVersion() - Static method in class org.sbml.libsbml.CompExtension
 
getDefaultVersion() - Static method in class org.sbml.libsbml.FbcExtension
 
getDefaultVersion() - Static method in class org.sbml.libsbml.LayoutExtension
 
getDefaultVersion() - Static method in class org.sbml.libsbml.SBMLDocument
The default Version of new SBMLDocument objects.
getDefinitionURL() - Method in class org.sbml.libsbml.ASTNode
Gets the MathML definitionURL attribute value.
getDelay() - Method in class org.sbml.libsbml.Event
Get the assignment delay portion of this Event, if there is one.
getDeletion() - Method in class org.sbml.libsbml.ReplacedElement
 
getDeletion(long) - Method in class org.sbml.libsbml.Submodel
 
getDeletion(String) - Method in class org.sbml.libsbml.Submodel
 
getDenominator() - Method in class org.sbml.libsbml.ASTNode
Get the value of the denominator of this node.
getDenominator() - Method in class org.sbml.libsbml.SpeciesReference
Get the value of the 'denominator' attribute, for the case of a rational-numbered stoichiometry or a model in SBML Level 1.
getDepth() - Method in class org.sbml.libsbml.Dimensions
 
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Compartment
Constructs and returns a UnitDefinition that corresponds to the units of this Compartment's designated size.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Delay
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this Delay.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.EventAssignment
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this EventAssignment.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.InitialAssignment
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this InitialAssignment.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.KineticLaw
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this KineticLaw.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.LocalParameter
Constructs and returns a UnitDefinition that corresponds to the units of this LocalParameter's value.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Parameter
Constructs and returns a UnitDefinition that corresponds to the units of this Parameter's value.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Rule
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this Rule.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Species
Constructs and returns a UnitDefinition that corresponds to the units of this Species' amount or concentration.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.StoichiometryMath
Calculates and returns a UnitDefinition object that expresses the units returned by the math expression in this StoichiometryMath object.
getDescription() - Method in class org.sbml.libsbml.ConversionOption
Returns the description string for this option.
getDescription(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the description string for a given option in this properties object.
getDimensions() - Method in class org.sbml.libsbml.BoundingBox
 
getDimensions() - Method in class org.sbml.libsbml.Layout
 
getDivider() - Method in class org.sbml.libsbml.CompModelPlugin
 
getDocument() - Method in class org.sbml.libsbml.SBMLConverter
Returns the SBML document that is the subject of the conversions.
getDocument() - Method in class org.sbml.libsbml.SBMLValidator
Returns the current SBML document in use by this validator.
getDoubleValue() - Method in class org.sbml.libsbml.ConversionOption
Returns the value of this option as a double.
getDoubleValue(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the value of the given option as a double.
getElementByMetaId(String) - Method in class org.sbml.libsbml.CompModelPlugin
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.CompSBasePlugin
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Event
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.KineticLaw
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.ListOf
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Model
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Objective
Returns the first child element it can find with a specific 'metaid' attribute value, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Reaction
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.SBase
Returns the first child element it can find with a specific 'metaid' attribute value, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.SBasePlugin
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.SBaseRef
Returns the first child element it can find with a specific 'metaid' attribute value, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Submodel
Returns the first child element it can find with a specific 'metaid' attribute value, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.UnitDefinition
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.CompModelPlugin
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.CompSBasePlugin
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Event
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.KineticLaw
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOf
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfEventAssignments
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfInitialAssignments
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfPorts
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfRules
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Model
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Objective
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Reaction
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.SBase
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.SBasePlugin
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.SBaseRef
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Submodel
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.UnitDefinition
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementName() - Method in class org.sbml.libsbml.Association
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.BoundingBox
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Compartment
Returns the XML element name of this object, which for Compartment, is always 'compartment'.
getElementName() - Method in class org.sbml.libsbml.CompartmentGlyph
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.CompartmentType
Returns the XML element name of this object, which for CompartmentType, is always 'compartmentType'.
getElementName() - Method in class org.sbml.libsbml.Constraint
Returns the XML element name of this object, which for Constraint, is always 'constraint'.
getElementName() - Method in class org.sbml.libsbml.CubicBezier
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Curve
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Delay
Returns the XML element name of this object, which for Delay, is always 'delay'.
getElementName() - Method in class org.sbml.libsbml.Deletion
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Dimensions
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Event
Returns the XML element name of this object, which for Event, is always 'event'.
getElementName() - Method in class org.sbml.libsbml.EventAssignment
Returns the XML element name of this object, which for EventAssignment, is always 'eventAssignment'.
getElementName() - Method in class org.sbml.libsbml.ExternalModelDefinition
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.FluxBound
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.FluxObjective
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.FunctionDefinition
Returns the XML element name of this object, which for FunctionDefinition, is always 'functionDefinition'.
getElementName() - Method in class org.sbml.libsbml.GeneAssociation
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.GeneralGlyph
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.GraphicalObject
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.InitialAssignment
Returns the XML element name of this object, which for InitialAssignment, is always 'initialAssignment'.
getElementName() - Method in class org.sbml.libsbml.KineticLaw
Returns the XML element name of this object, which for Species, is always 'kineticLaw'.
getElementName() - Method in class org.sbml.libsbml.Layout
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.LineSegment
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOf
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfCompartments
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfConstraints
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfDeletions
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfEventAssignments
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfEvents
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfFluxBounds
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfGeneAssociations
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfInitialAssignments
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfLayouts
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfLineSegments
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfModelDefinitions
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfObjectives
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfParameters
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfPorts
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfReactions
Returns the XML element name of this object
getElementName() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfReplacedElements
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfRules
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfSpecies
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfSubmodels
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfTextGlyphs
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfUnits
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.LocalParameter
Returns the XML element name of this object, which for LocalParameter, is always 'localParameter'.
getElementName() - Method in class org.sbml.libsbml.Model
Returns the XML element name of this object, which for Model, is always 'model'.
getElementName() - Method in class org.sbml.libsbml.ModelDefinition
Returns the XML element name of this object, which for Model, is always 'model'.
getElementName() - Method in class org.sbml.libsbml.ModifierSpeciesReference
Returns the XML element name of this object, which for Species, is always 'modifierSpeciesReference'.
getElementName() - Method in class org.sbml.libsbml.Objective
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Parameter
Returns the XML element name of this object, which for Parameter, is always 'parameter'.
getElementName() - Method in class org.sbml.libsbml.Point
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Port
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Priority
Returns the XML element name of this object, which for Priority, is always 'priority'.
getElementName() - Method in class org.sbml.libsbml.Reaction
Returns the XML element name of this object, which for Reaction, is always 'reaction'.
getElementName() - Method in class org.sbml.libsbml.ReactionGlyph
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ReplacedBy
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ReplacedElement
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Rule
Returns the XML element name of this object
getElementName() - Method in class org.sbml.libsbml.SBase
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.SBaseRef
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.SBMLDocument
Returns the XML element name of this object, which for SBMLDocument, is always 'sbml'.
getElementName() - Method in class org.sbml.libsbml.Species
Returns the XML element name of this object, which for Species, is always 'species'.
getElementName() - Method in class org.sbml.libsbml.SpeciesGlyph
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.SpeciesReference
Returns the XML element name of this object, which for SpeciesReference, is always 'speciesReference'.
getElementName() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.SpeciesType
Returns the XML element name of this object, which for SpeciesType, is always 'compartmentType'.
getElementName() - Method in class org.sbml.libsbml.StoichiometryMath
Returns the XML element name of this object, which for StoichiometryMath, is always 'stoichiometryMath'.
getElementName() - Method in class org.sbml.libsbml.Submodel
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.TextGlyph
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Trigger
Returns the XML element name of this object, which for Trigger, is always 'trigger'.
getElementName() - Method in class org.sbml.libsbml.Unit
Returns the XML element name of this object, which for Unit, is always 'unit'.
getElementName() - Method in class org.sbml.libsbml.UnitDefinition
Returns the XML element name of this object, which for UnitDefinition, is always 'unitDefinition'.
getElementNamespace() - Method in class org.sbml.libsbml.SBasePlugin
Returns the XML namespace (URI) of the package extension of this plugin object.
getEmail() - Method in class org.sbml.libsbml.ModelCreator
Returns the 'email' stored in this ModelCreator object.
getEnd() - Method in class org.sbml.libsbml.LineSegment
 
getError(long) - Method in class org.sbml.libsbml.SBMLDocument
Returns the nth error or warning encountered during parsing, consistency checking, or attempted translation of this model.
getError(long) - Method in class org.sbml.libsbml.SBMLErrorLog
Returns the nth SBMLError object in this log.
getError(long) - Method in class org.sbml.libsbml.XMLErrorLog
Returns the nth XMLError object in this log.
getErrorId() - Method in class org.sbml.libsbml.XMLError
Returns the identifier of this error.
getErrorIdOffset() - Method in class org.sbml.libsbml.XMLError
Returns a copy of the message string associated with the given predefined XMLError code.
getErrorLog() - Method in class org.sbml.libsbml.SBMLDocument
Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model.
getErrorLog() - Method in class org.sbml.libsbml.SBMLValidator
Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model.
getEvent(long) - Method in class org.sbml.libsbml.Model
Get the nth Event object in this Model.
getEvent(String) - Method in class org.sbml.libsbml.Model
Get an Event object based on its identifier.
getEventAssignment(long) - Method in class org.sbml.libsbml.Event
Return a specific EventAssignment object of this Event.
getEventAssignment(String) - Method in class org.sbml.libsbml.Event
Return the event assignment indicated by the given variable.
getExponent() - Method in class org.sbml.libsbml.ASTNode
Get the exponent value of this ASTNode.
getExponent() - Method in class org.sbml.libsbml.Unit
Returns the value of the 'exponent' attribute of this unit.
getExponentAsDouble() - Method in class org.sbml.libsbml.Unit
Returns the value of the 'exponent' attribute of this unit.
getExtension(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns an SBMLExtension object with the given package URI or package name (string).
getExtentConversionFactor() - Method in class org.sbml.libsbml.Submodel
 
getExtentUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'extentUnits' attribute of this Model.
getExternalModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
getExternalModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
getFailure(long) - Method in class org.sbml.libsbml.SBMLValidator
Returns the failure object at index n in this validator's list of failures logged during the last run.
getFamilyName() - Method in class org.sbml.libsbml.ModelCreator
Returns the 'family name' stored in this ModelCreator object.
getFast() - Method in class org.sbml.libsbml.Reaction
Returns the value of the 'fast' attribute of this Reaction.
getFloatValue() - Method in class org.sbml.libsbml.ConversionOption
Returns the value of this option as a float.
getFloatValue(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the value of the given option as a float.
getFluxBound(long) - Method in class org.sbml.libsbml.FbcModelPlugin
 
getFluxBound(String) - Method in class org.sbml.libsbml.FbcModelPlugin
 
getFluxBoundOperation() - Method in class org.sbml.libsbml.FluxBound
 
getFluxBoundsForReaction(String) - Method in class org.sbml.libsbml.FbcModelPlugin
 
getFluxObjective(long) - Method in class org.sbml.libsbml.Objective
 
getFluxObjective(String) - Method in class org.sbml.libsbml.Objective
 
getFormula() - Method in class org.sbml.libsbml.KineticLaw
Returns the mathematical formula for this KineticLaw object and return it as as a text string.
getFormula() - Method in class org.sbml.libsbml.Rule
Returns the mathematical expression of this Rule in text-string form.
getFunctionDefinition(long) - Method in class org.sbml.libsbml.Model
Get the nth FunctionDefinitions object in this Model.
getFunctionDefinition(String) - Method in class org.sbml.libsbml.Model
Get a FunctionDefinition object based on its identifier.
getGeneAssociation(long) - Method in class org.sbml.libsbml.FbcModelPlugin
 
getGeneAssociation(String) - Method in class org.sbml.libsbml.FbcModelPlugin
 
getGeneralGlyph(long) - Method in class org.sbml.libsbml.Layout
 
getGeneralGlyph(String) - Method in class org.sbml.libsbml.Layout
 
getGivenName() - Method in class org.sbml.libsbml.ModelCreator
Returns the 'given name' stored in this ModelCreator object.
getGlyphId() - Method in class org.sbml.libsbml.ReferenceGlyph
 
getGraphicalObjectId() - Method in class org.sbml.libsbml.TextGlyph
 
getHasOnlySubstanceUnits() - Method in class org.sbml.libsbml.Species
Get the value of the 'hasOnlySubstanceUnits' attribute.
getHeight() - Method in class org.sbml.libsbml.Dimensions
 
getHost() - Method in class org.sbml.libsbml.SBMLUri
 
getHour() - Method in class org.sbml.libsbml.Date
Returns the hour from this Date.
getHoursOffset() - Method in class org.sbml.libsbml.Date
Returns the hours of the time zone offset from this Date.
getId() - Method in class org.sbml.libsbml.ASTNode
Get the id of this ASTNode.
getId() - Method in class org.sbml.libsbml.Compartment
Returns the value of the 'id' attribute of this Compartment object.
getId() - Method in class org.sbml.libsbml.CompartmentType
Returns the value of the 'id' attribute of this CompartmentType.
getId() - Method in class org.sbml.libsbml.Event
Returns the value of the 'id' attribute of this Event.
getId() - Method in class org.sbml.libsbml.FunctionDefinition
Returns the value of the 'id' attribute of this FunctionDefinition.
getId() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if all the required elements for this InitialAssignment object have been set.
getId() - Method in class org.sbml.libsbml.Model
Returns the value of the 'id' attribute of this Model.
getId() - Method in class org.sbml.libsbml.Parameter
Returns the value of the 'id' attribute of this Parameter.
getId() - Method in class org.sbml.libsbml.Reaction
Returns the value of the 'id' attribute of this Reaction.
getId() - Method in class org.sbml.libsbml.Rule
Renames all the UnitSIdRef attributes on this element
getId() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Returns the value of the 'id' attribute of this SimpleSpeciesReference.
getId() - Method in class org.sbml.libsbml.Species
Returns the value of the 'id' attribute of this Species object.
getId() - Method in class org.sbml.libsbml.SpeciesType
Returns the value of the 'id' attribute of this SpeciesType.
getId() - Method in class org.sbml.libsbml.UnitDefinition
Returns the value of the 'id' attribute of this UnitDefinition.
getIdRef() - Method in class org.sbml.libsbml.SBaseRef
 
getIndex(String) - Method in class org.sbml.libsbml.XMLAttributes
Return the index of an attribute with the given name.
getIndex(String, String) - Method in class org.sbml.libsbml.XMLAttributes
Return the index of an attribute with the given local name and namespace URI.
getIndex(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
Return the index of an attribute with the given XMLTriple.
getIndex(String) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the index of an XML namespace declaration by URI.
getIndex(String) - Method in class org.sbml.libsbml.XMLNode
Return the index of the first child of this XMLNode with the given name.
getIndexByPrefix(String) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the index of an XML namespace declaration by prefix.
getIndexForReferenceGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
 
getIndexForSpeciesReferenceGlyph(String) - Method in class org.sbml.libsbml.ReactionGlyph
 
getIndexForSubGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
 
getInitialAmount() - Method in class org.sbml.libsbml.Species
Get the value of the 'initialAmount' attribute.
getInitialAssignment(long) - Method in class org.sbml.libsbml.Model
Get the nth InitialAssignment object in this Model.
getInitialAssignment(String) - Method in class org.sbml.libsbml.Model
Get an InitialAssignment object based on the symbol to which it assigns a value.
getInitialConcentration() - Method in class org.sbml.libsbml.Species
Get the value of the 'initialConcentration' attribute.
getInitialValue() - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Get the value of the 'initialValue' attribute of this Trigger.
getInstance() - Static method in class org.sbml.libsbml.SBMLConverterRegistry
Returns the singleton instance for the converter registry.
getInstance() - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns an instance (singleton) of the SBMLExtensionRegistry class.
getInstance() - Static method in class org.sbml.libsbml.SBMLResolverRegistry
 
getInstantiation() - Method in class org.sbml.libsbml.Submodel
 
getInteger() - Method in class org.sbml.libsbml.ASTNode
Get the value of this node as an integer.
getIntValue() - Method in class org.sbml.libsbml.ConversionOption
Returns the value of this option as an integer.
getIntValue(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the value of the given option as an integer.
getIsSetListOfFluxObjectives() - Method in class org.sbml.libsbml.Objective
 
getItemTypeCode() - Method in class org.sbml.libsbml.ListOf
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartments
Returns the libSBML type code for the objects contained in this ListOf (i.e., Compartment objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Returns the libSBML type code for the objects contained in this ListOf (i.e., CompartmentType objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfConstraints
Returns the libSBML type code for the objects contained in this ListOf (i.e., Constraint objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfDeletions
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfEventAssignments
Returns the libSBML type code for the objects contained in this ListOf (i.e., EventAssignment objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfEvents
Returns the libSBML type code for the objects contained in this ListOf (i.e., Event objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFluxBounds
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Returns the libSBML type code for the objects contained in this ListOf (i.e., FunctionDefinition objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGeneAssociations
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfInitialAssignments
Returns the libSBML type code for the objects contained in this ListOf (i.e., InitialAssignment objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLayouts
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLineSegments
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the libSBML type code for the objects contained in this ListOf (i.e., LocalParameter objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfModelDefinitions
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfObjectives
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfParameters
Returns the libSBML type code for the objects contained in this ListOf (i.e., Parameter objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfPorts
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReactions
Returns the libSBML type code for the objects contained in this ListOf (i.e., Reaction objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReplacedElements
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfRules
Returns the libSBML type code for the objects contained in this ListOf (i.e., Rule objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpecies
Returns the libSBML type code for the objects contained in this ListOf (i.e., Species objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Returns the libSBML type code for the objects contained in this ListOf (i.e., SpeciesReference objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Returns the libSBML type code for the objects contained in this ListOf (i.e., SpeciesType objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSubmodels
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfTextGlyphs
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Returns the libSBML type code for the objects contained in this ListOf (i.e., UnitDefinition objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfUnits
Returns the libSBML type code for the objects contained in this ListOf (i.e., Unit objects, if the list is non-empty).
getKey() - Method in class org.sbml.libsbml.ConversionOption
Returns the key for this option.
getKind() - Method in class org.sbml.libsbml.Unit
Returns the 'kind' of Unit this is.
getKineticLaw() - Method in class org.sbml.libsbml.Reaction
Returns the KineticLaw object contained in this Reaction.
getL1TypeCode() - Method in class org.sbml.libsbml.Rule
Returns the SBML Level 1 type code for this Rule object.
getLastParseL3Error() - Static method in class org.sbml.libsbml.libsbml
Returns the last error reported by the parser.
getLayout(long) - Method in class org.sbml.libsbml.LayoutModelPlugin
 
getLayout(String) - Method in class org.sbml.libsbml.LayoutModelPlugin
 
getLeftChild() - Method in class org.sbml.libsbml.ASTNode
Get the left child of this node.
getLength() - Method in class org.sbml.libsbml.XMLAttributes
Return the number of attributes in the set.
getLength() - Method in class org.sbml.libsbml.XMLNamespaces
Returns the total number of URI-and-prefix pairs stored in this particular XMLNamespaces instance.
getLengthUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'lengthUnits' attribute of this Model.
getLevel() - Method in class org.sbml.libsbml.SBase
Returns the SBML Level of the SBMLDocument object containing this object.
getLevel() - Method in class org.sbml.libsbml.SBasePlugin
Returns the SBML level of the package extension of this plugin object.
getLevel() - Method in class org.sbml.libsbml.SBMLNamespaces
Get the SBML Level of this SBMLNamespaces object.
getLibSBMLDottedVersion() - Static method in class org.sbml.libsbml.libsbml
Returns the version number of this copy of libSBML as a string.
getLibSBMLVersion() - Static method in class org.sbml.libsbml.libsbml
Returns the version number of this copy of libSBML as an integer.
getLibSBMLVersionString() - Static method in class org.sbml.libsbml.libsbml
Returns the version number of this copy of libSBML as a string without periods.
getLine() - Method in class org.sbml.libsbml.SBase
Returns the line number on which this object first appears in the XML representation of the SBML document.
getLine() - Method in class org.sbml.libsbml.XMLError
Returns the line number in the XML input near where the error, warning or other diagnostic occurred.
getLine() - Method in class org.sbml.libsbml.XMLToken
Returns the line at which this XMLToken occurred in the input document or data stream.
getListCreators() - Method in class org.sbml.libsbml.ModelHistory
Returns the list of ModelCreator objects stored in this ModelHistory object.
getListModifiedDates() - Method in class org.sbml.libsbml.ModelHistory
Returns the list of 'modified date' values (as Date objects) stored in this ModelHistory object.
getListOfAdditionalGraphicalObjects() - Method in class org.sbml.libsbml.Layout
 
getListOfAllElements() - Method in class org.sbml.libsbml.SBase
 
getListOfAllElements() - Method in class org.sbml.libsbml.SBasePlugin
 
getListOfAllElementsFromPlugins() - Method in class org.sbml.libsbml.SBase
 
getListOfAllInstantiatedElements() - Method in class org.sbml.libsbml.Submodel
 
getListOfCompartmentGlyphs() - Method in class org.sbml.libsbml.Layout
 
getListOfCompartments() - Method in class org.sbml.libsbml.Model
Get the ListOfCompartments object in this Model.
getListOfCompartmentTypes() - Method in class org.sbml.libsbml.Model
Get the ListOfCompartmentTypes object in this Model.
getListOfConstraints() - Method in class org.sbml.libsbml.Model
Get the ListOfConstraints object in this Model.
getListOfCurveSegments() - Method in class org.sbml.libsbml.Curve
 
getListOfDeletions() - Method in class org.sbml.libsbml.Submodel
 
getListOfEventAssignments() - Method in class org.sbml.libsbml.Event
Returns the list of event assignments for this Event.
getListOfEvents() - Method in class org.sbml.libsbml.Model
Get the ListOfEvents object in this Model.
getListOfExternalModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
getListOfFluxBounds() - Method in class org.sbml.libsbml.FbcModelPlugin
 
getListOfFluxObjectives() - Method in class org.sbml.libsbml.Objective
 
getListOfFunctionDefinitions() - Method in class org.sbml.libsbml.Model
Get the ListOfFunctionDefinitions object in this Model.
getListOfGeneAssociations() - Method in class org.sbml.libsbml.FbcModelPlugin
 
getListOfInitialAssignments() - Method in class org.sbml.libsbml.Model
Get the ListOfInitialAssignments object in this Model.
getListOfLayouts() - Method in class org.sbml.libsbml.LayoutModelPlugin
 
getListOfLocalParameters() - Method in class org.sbml.libsbml.KineticLaw
Returns the list of local parameters in this KineticLaw object.
getListOfModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
getListOfModifiers() - Method in class org.sbml.libsbml.Reaction
Returns the list of modifiers in this Reaction object.
getListOfNodes() - Method in class org.sbml.libsbml.ASTNode
 
getListOfObjectives() - Method in class org.sbml.libsbml.FbcModelPlugin
 
getListOfParameters() - Method in class org.sbml.libsbml.KineticLaw
Returns the list of local parameters in this KineticLaw object.
getListOfParameters() - Method in class org.sbml.libsbml.Model
Get the ListOfParameters object in this Model.
getListOfPorts() - Method in class org.sbml.libsbml.CompModelPlugin
 
getListOfProducts() - Method in class org.sbml.libsbml.Reaction
Returns the list of products in this Reaction object.
getListOfReactants() - Method in class org.sbml.libsbml.Reaction
Returns the list of reactants in this Reaction object.
getListOfReactionGlyphs() - Method in class org.sbml.libsbml.Layout
 
getListOfReactions() - Method in class org.sbml.libsbml.Model
Get the ListOfReactions object in this Model.
getListOfReferenceGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
 
getListOfReplacedElements() - Method in class org.sbml.libsbml.CompSBasePlugin
 
getListOfRules() - Method in class org.sbml.libsbml.Model
Get the ListOfRules object in this Model.
getListOfSpecies() - Method in class org.sbml.libsbml.Model
Get the ListOfSpecies object in this Model.
getListOfSpeciesGlyphs() - Method in class org.sbml.libsbml.Layout
 
getListOfSpeciesReferenceGlyphs() - Method in class org.sbml.libsbml.ReactionGlyph
 
getListOfSpeciesTypes() - Method in class org.sbml.libsbml.Model
Get the ListOfSpeciesTypes object in this Model.
getListOfSubGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
 
getListOfSubmodels() - Method in class org.sbml.libsbml.CompModelPlugin
 
getListOfTextGlyphs() - Method in class org.sbml.libsbml.Layout
 
getListOfUnitDefinitions() - Method in class org.sbml.libsbml.Model
Get the ListOfUnitDefinitions object in this Model.
getListOfUnits() - Method in class org.sbml.libsbml.UnitDefinition
Returns the list of Units for this UnitDefinition instance.
getLocalParameter(long) - Method in class org.sbml.libsbml.KineticLaw
Returns the nth LocalParameter object in the list of local parameters in this KineticLaw instance.
getLocalParameter(String) - Method in class org.sbml.libsbml.KineticLaw
Returns a local parameter based on its identifier.
getLocationURI() - Method in class org.sbml.libsbml.SBMLDocument
Get the location of this SBMLDocument.
getMantissa() - Method in class org.sbml.libsbml.ASTNode
Get the mantissa value of this node.
getMath() - Method in class org.sbml.libsbml.Constraint
Get the mathematical expression of this Constraint
getMath() - Method in class org.sbml.libsbml.Delay
Get the mathematical formula for the delay and return it as an AST.
getMath() - Method in class org.sbml.libsbml.EventAssignment
Get the mathematical expression in this EventAssignment's 'math' subelement.
getMath() - Method in class org.sbml.libsbml.FunctionDefinition
Get the mathematical formula of this FunctionDefinition.
getMath() - Method in class org.sbml.libsbml.InitialAssignment
Get the mathematical formula of this InitialAssignment.
getMath() - Method in class org.sbml.libsbml.KineticLaw
Returns the mathematical formula for this KineticLaw object and return it as as an AST.
getMath() - Method in class org.sbml.libsbml.Priority
Get the mathematical formula for the priority and return it as an AST.
getMath() - Method in class org.sbml.libsbml.Rule
Get the mathematical formula of this Rule as an ASTNode tree.
getMath() - Method in class org.sbml.libsbml.StoichiometryMath
Retrieves the mathematical formula within this StoichiometryMath and return it as an AST.
getMath() - Method in class org.sbml.libsbml.Trigger
Get the mathematical formula for the trigger and return it as an AST.
getMd5() - Method in class org.sbml.libsbml.ExternalModelDefinition
 
getMessage() - Method in class org.sbml.libsbml.Constraint
Get the message, if any, associated with this Constraint
getMessage() - Method in class org.sbml.libsbml.XMLError
Returns the message text of this error.
getMessageString() - Method in class org.sbml.libsbml.Constraint
Get the message string, if any, associated with this Constraint
getMetaId() - Method in class org.sbml.libsbml.SBase
Returns the value of the 'metaid' attribute of this object.
getMetaIdRef() - Method in class org.sbml.libsbml.GraphicalObject
 
getMetaIdRef() - Method in class org.sbml.libsbml.SBaseRef
 
getMinute() - Method in class org.sbml.libsbml.Date
Returns the minute from this Date.
getMinutesOffset() - Method in class org.sbml.libsbml.Date
Returns the minutes of the time zone offset from this Date.
getModel(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
getModel() - Method in class org.sbml.libsbml.L3ParserSettings
Returns the Model object referenced by this L3ParserSettings object.
getModel() - Method in class org.sbml.libsbml.SBase
Returns the Model object in which the current object is located.
getModel() - Method in class org.sbml.libsbml.SBMLDocument
Returns the Model object stored in this SBMLDocument.
getModel() - Method in class org.sbml.libsbml.SBMLValidator
Returns the Model object stored in the SBMLDocument.
getModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
getModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
getModelHistory() - Method in class org.sbml.libsbml.SBase
Returns the ModelHistory object, if any, attached to this object.
getModelQualifierType() - Method in class org.sbml.libsbml.CVTerm
Returns the model qualifier type of this CVTerm object.
getModelRef() - Method in class org.sbml.libsbml.ExternalModelDefinition
 
getModelRef() - Method in class org.sbml.libsbml.Submodel
 
getModifiedDate() - Method in class org.sbml.libsbml.ModelHistory
Returns the 'modified date' portion of this ModelHistory object.
getModifiedDate(long) - Method in class org.sbml.libsbml.ModelHistory
Get the nth Date object in the list of 'modified date' values stored in this ModelHistory object.
getModifier(long) - Method in class org.sbml.libsbml.Reaction
Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of this Reaction.
getModifier(String) - Method in class org.sbml.libsbml.Reaction
Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction.
getMonth() - Method in class org.sbml.libsbml.Date
Returns the month from this Date.
getMultiplier() - Method in class org.sbml.libsbml.Unit
Returns the value of the 'multiplier' attribute of this Unit.
getName() - Method in class org.sbml.libsbml.ASTNode
Get the value of this node as a string.
getName() - Method in class org.sbml.libsbml.Compartment
Returns the value of the 'name' attribute of this Compartment object.
getName() - Method in class org.sbml.libsbml.CompartmentType
Returns the value of the 'name' attribute of this CompartmentType.
getName() - Method in class org.sbml.libsbml.Event
Returns the value of the 'name' attribute of this Event.
getName() - Method in class org.sbml.libsbml.FunctionDefinition
Returns the value of the 'name' attribute of this FunctionDefinition.
getName() - Method in class org.sbml.libsbml.Model
Returns the value of the 'name' attribute of this Model.
getName() - Method in class org.sbml.libsbml.Parameter
Returns the value of the 'name' attribute of this Parameter.
getName() - Method in class org.sbml.libsbml.Reaction
Returns the value of the 'name' attribute of this Reaction.
getName() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Returns the value of the 'name' attribute of this SimpleSpeciesReference.
getName() - Method in class org.sbml.libsbml.Species
Returns the value of the 'name' attribute of this Species object.
getName() - Method in class org.sbml.libsbml.SpeciesType
Returns the value of the 'name' attribute of this SpeciesType.
getName() - Method in class org.sbml.libsbml.UnitDefinition
Returns the value of the 'name' attribute of this UnitDefinition.
getName(int) - Method in class org.sbml.libsbml.XMLAttributes
Return the local name of an attribute in this XMLAttributes set (by position).
getName() - Method in class org.sbml.libsbml.XMLToken
Returns the (unqualified) name of this XML element.
getName() - Method in class org.sbml.libsbml.XMLTriple
Returns the name portion of this XMLTriple.
getNamespaceIndex(String) - Method in class org.sbml.libsbml.XMLToken
Look up the index of an XML namespace declaration by URI.
getNamespaceIndexByPrefix(String) - Method in class org.sbml.libsbml.XMLToken
Look up the index of an XML namespace declaration by prefix.
getNamespacePrefix(int) - Method in class org.sbml.libsbml.XMLToken
Look up the prefix of an XML namespace declaration by position.
getNamespacePrefix(String) - Method in class org.sbml.libsbml.XMLToken
Look up the prefix of an XML namespace declaration by its URI.
getNamespaces() - Method in class org.sbml.libsbml.SBase
Returns a list of the XML Namespaces declared on this SBML document.
getNamespaces() - Method in class org.sbml.libsbml.SBMLDocument
Returns a list of XML Namespaces associated with the XML content of this SBML document.
getNamespaces() - Method in class org.sbml.libsbml.SBMLNamespaces
Get the XML namespaces list for this SBMLNamespaces object.
getNamespaces() - Method in class org.sbml.libsbml.XMLToken
Returns the XML namespace declarations for this XML element.
getNamespacesLength() - Method in class org.sbml.libsbml.XMLToken
Returns the number of XML namespaces stored in the XMLNamespaces of this XMLToken.
getNamespaceURI(int) - Method in class org.sbml.libsbml.XMLToken
Look up the URI of an XML namespace declaration by its position.
getNamespaceURI(String) - Method in class org.sbml.libsbml.XMLToken
Look up the URI of an XML namespace declaration by its prefix.
getNamespaceURI() - Method in class org.sbml.libsbml.XMLToken
Look up the URI of an XML namespace declaration by its prefix.
getNotes() - Method in class org.sbml.libsbml.SBase
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
getNotesString() - Method in class org.sbml.libsbml.SBase
Returns the content of the 'notes' subelement of this object as a string.
getNumAdditionalGraphicalObjects() - Method in class org.sbml.libsbml.Layout
 
getNumArguments() - Method in class org.sbml.libsbml.FunctionDefinition
Get the number of arguments (bound variables) taken by this FunctionDefinition.
getNumArguments() - Method in class org.sbml.libsbml.SBMLExternalValidator
 
getNumAssociations() - Method in class org.sbml.libsbml.Association
 
getNumAttributes() - Method in class org.sbml.libsbml.XMLAttributes
Return the number of attributes in the set.
getNumChildren() - Method in class org.sbml.libsbml.ASTNode
Get the number of children that this node has.
getNumChildren() - Method in class org.sbml.libsbml.XMLNode
Returns the number of children for this XMLNode.
getNumCompartmentGlyphs() - Method in class org.sbml.libsbml.Layout
 
getNumCompartments() - Method in class org.sbml.libsbml.Model
Get the number of Compartment objects in this Model.
getNumCompartmentTypes() - Method in class org.sbml.libsbml.Model
Get the number of CompartmentType objects in this Model.
getNumConstraints() - Method in class org.sbml.libsbml.Model
Get the number of Constraint objects in this Model.
getNumConverters() - Method in class org.sbml.libsbml.SBMLConverterRegistry
Returns the number of converters known by the registry.
getNumCreators() - Method in class org.sbml.libsbml.ModelHistory
Get the number of ModelCreator objects stored in this ModelHistory object.
getNumCurveSegments() - Method in class org.sbml.libsbml.Curve
 
getNumCVTerms() - Method in class org.sbml.libsbml.SBase
Returns the number of CVTerm objects in the annotations of this SBML object.
getNumDeletions() - Method in class org.sbml.libsbml.Submodel
 
getNumerator() - Method in class org.sbml.libsbml.ASTNode
Get the value of the numerator of this node.
getNumErrors() - Method in class org.sbml.libsbml.SBMLDocument
Returns the number of errors or warnings encountered during parsing, consistency checking, or attempted translation of this model.
getNumErrors(long) - Method in class org.sbml.libsbml.SBMLDocument
Returns the number of errors or warnings encountered with the given severity during parsing, consistency checking, or attempted translation of this model.
getNumErrors() - Method in class org.sbml.libsbml.XMLErrorLog
Returns the number of errors that have been logged.
getNumEventAssignments() - Method in class org.sbml.libsbml.Event
Returns the number of EventAssignment objects attached to this Event.
getNumEvents() - Method in class org.sbml.libsbml.Model
Get the number of Event objects in this Model.
getNumExtension(SBaseExtensionPoint) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns the number of SBMLExtension with the given extension point.
getNumExternalModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
getNumFailsWithSeverity(long) - Method in class org.sbml.libsbml.SBMLErrorLog
Returns the number of errors that have been logged with the given severity code.
getNumFailures() - Method in class org.sbml.libsbml.SBMLValidator
Returns the number of failures encountered in the last validation run.
getNumFluxBounds() - Method in class org.sbml.libsbml.FbcModelPlugin
 
getNumFluxObjectives() - Method in class org.sbml.libsbml.Objective
 
getNumFunctionDefinitions() - Method in class org.sbml.libsbml.Model
Get the number of FunctionDefinition objects in this Model.
getNumGeneAssociations() - Method in class org.sbml.libsbml.FbcModelPlugin
 
getNumGeneralGlyphs() - Method in class org.sbml.libsbml.Layout
 
getNumInitialAssignments() - Method in class org.sbml.libsbml.Model
Get the number of InitialAssignment objects in this Model.
getNumLayouts() - Method in class org.sbml.libsbml.LayoutModelPlugin
 
getNumLocalParameters() - Method in class org.sbml.libsbml.KineticLaw
Returns the number of local parameters in this KineticLaw instance.
getNumModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
getNumModifiedDates() - Method in class org.sbml.libsbml.ModelHistory
Get the number of Date objects in this ModelHistory object's list of 'modified dates'.
getNumModifiers() - Method in class org.sbml.libsbml.Reaction
Returns the number of modifier species in this Reaction.
getNumNamespaces() - Method in class org.sbml.libsbml.XMLNamespaces
Returns the total number of URI-and-prefix pairs stored in this particular XMLNamespaces instance.
getNumObjectives() - Method in class org.sbml.libsbml.FbcModelPlugin
 
getNumParameters() - Method in class org.sbml.libsbml.KineticLaw
Returns the number of local parameters in this KineticLaw instance.
getNumParameters() - Method in class org.sbml.libsbml.Model
Get the number of Parameter objects in this Model.
getNumPlugins() - Method in class org.sbml.libsbml.SBase
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
getNumPorts() - Method in class org.sbml.libsbml.CompModelPlugin
 
getNumProducts() - Method in class org.sbml.libsbml.Reaction
Returns the number of product species in this Reaction.
getNumReactants() - Method in class org.sbml.libsbml.Reaction
Returns the number of reactant species in this Reaction.
getNumReactionGlyphs() - Method in class org.sbml.libsbml.Layout
 
getNumReactions() - Method in class org.sbml.libsbml.Model
Get the number of Reaction objects in this Model.
getNumReferenceGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
 
getNumReferents() - Method in class org.sbml.libsbml.ReplacedElement
 
getNumReferents() - Method in class org.sbml.libsbml.SBaseRef
 
getNumRegisteredPackages() - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns the number of registered packages.
getNumReplacedElements() - Method in class org.sbml.libsbml.CompSBasePlugin
 
getNumResolvers() - Method in class org.sbml.libsbml.SBMLResolverRegistry
 
getNumResources() - Method in class org.sbml.libsbml.CVTerm
Returns the number of resources for this CVTerm object.
getNumRules() - Method in class org.sbml.libsbml.Model
Get the number of Rule objects in this Model.
getNumSemanticsAnnotations() - Method in class org.sbml.libsbml.ASTNode
Get the number of semantic annotation elements inside this node.
getNumSpecies() - Method in class org.sbml.libsbml.Model
Get the number of Specie objects in this Model.
getNumSpeciesGlyphs() - Method in class org.sbml.libsbml.Layout
 
getNumSpeciesReferenceGlyphs() - Method in class org.sbml.libsbml.ReactionGlyph
 
getNumSpeciesTypes() - Method in class org.sbml.libsbml.Model
Get the number of SpeciesType objects in this Model.
getNumSpeciesWithBoundaryCondition() - Method in class org.sbml.libsbml.Model
Get the number of Species in this Model having their 'boundaryCondition' attribute value set to true.
getNumSubGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
 
getNumSubmodels() - Method in class org.sbml.libsbml.CompModelPlugin
 
getNumTextGlyphs() - Method in class org.sbml.libsbml.Layout
 
getNumUnitDefinitions() - Method in class org.sbml.libsbml.Model
Get the number of UnitDefinition objects in this Model.
getNumUnits() - Method in class org.sbml.libsbml.UnitDefinition
Returns the number of Unit objects contained within this UnitDefinition.
getObjective(long) - Method in class org.sbml.libsbml.FbcModelPlugin
 
getObjective(String) - Method in class org.sbml.libsbml.FbcModelPlugin
 
getObjectiveType() - Method in class org.sbml.libsbml.Objective
 
getOffset() - Method in class org.sbml.libsbml.Unit
Returns the value of the 'offset' attribute of this Unit.
getOperation() - Method in class org.sbml.libsbml.FluxBound
 
getOperatorName() - Method in class org.sbml.libsbml.ASTNode
Get the value of this operator node as a string.
getOption(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the ConversionOption object for a given key.
getOrganisation() - Method in class org.sbml.libsbml.ModelCreator
(Alternate spelling) Returns the 'organization' stored in this ModelCreator object.
getOrganization() - Method in class org.sbml.libsbml.ModelCreator
Returns the 'organization' stored in this ModelCreator object.
getOriginOfTextId() - Method in class org.sbml.libsbml.TextGlyph
 
getOutputFileName() - Method in class org.sbml.libsbml.SBMLExternalValidator
 
getOutside() - Method in class org.sbml.libsbml.Compartment
Get the identifier, if any, of the compartment that is designated as being outside of this one.
getPackage() - Method in class org.sbml.libsbml.XMLError
Returns a copy of the message string associated with the given predefined XMLError code.
getPackageName() - Method in class org.sbml.libsbml.CompBase
Returns the name of the SBML Level 3 package in which this element is defined.
getPackageName() - Static method in class org.sbml.libsbml.CompExtension
 
getPackageName() - Method in class org.sbml.libsbml.CompPkgNamespaces
Returns the name of the main package for this namespace.
getPackageName() - Static method in class org.sbml.libsbml.FbcExtension
 
getPackageName() - Method in class org.sbml.libsbml.FbcPkgNamespaces
Returns the name of the main package for this namespace.
getPackageName() - Static method in class org.sbml.libsbml.LayoutExtension
 
getPackageName() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
Returns the name of the main package for this namespace.
getPackageName() - Method in class org.sbml.libsbml.SBase
Returns the name of the SBML Level 3 package in which this element is defined.
getPackageName() - Method in class org.sbml.libsbml.SBasePlugin
Returns the package name of this plugin object.
getPackageName() - Method in class org.sbml.libsbml.SBMLNamespaces
Returns the name of the main package for this namespace.
getPackageRequired(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns the required attribute of the given package extension.
getPackageURI() - Method in class org.sbml.libsbml.CompBase
 
getPackageVersion() - Method in class org.sbml.libsbml.CompBase
Returns the Version of the SBML Level 3 package to which this element belongs to.
getPackageVersion() - Method in class org.sbml.libsbml.CompPkgNamespaces
 
getPackageVersion() - Method in class org.sbml.libsbml.FbcPkgNamespaces
 
getPackageVersion() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
 
getPackageVersion() - Method in class org.sbml.libsbml.SBase
Returns the Version of the SBML Level 3 package to which this element belongs to.
getPackageVersion() - Method in class org.sbml.libsbml.SBasePlugin
Returns the package version of the package extension of this plugin object.
getParameter(long) - Method in class org.sbml.libsbml.KineticLaw
Returns the nth Parameter object in the list of local parameters in this KineticLaw instance.
getParameter(String) - Method in class org.sbml.libsbml.KineticLaw
Returns a local parameter based on its identifier.
getParameter(long) - Method in class org.sbml.libsbml.Model
Get the nth Parameter object in this Model.
getParameter(String) - Method in class org.sbml.libsbml.Model
Get a Parameter object based on its identifier.
getParentModel(SBase) - Static method in class org.sbml.libsbml.CompBase
 
getParentSBMLObject() - Method in class org.sbml.libsbml.ASTNode
Returns the parent SBML object.
getParentSBMLObject() - Method in class org.sbml.libsbml.SBase
Returns the parent SBML object containing this object.
getParentSBMLObject() - Method in class org.sbml.libsbml.SBasePlugin
Returns the parent SBase object to which this plugin object connected.
getParseAvogadroCsymbol() - Method in class org.sbml.libsbml.L3ParserSettings
Returns true if the current settings are oriented towards handling avogadro for SBML Level 3.
getParseCollapseMinus() - Method in class org.sbml.libsbml.L3ParserSettings
Returns a flag indicating the current behavior set for handling multiple unary minuses in formulas.
getParseLog() - Method in class org.sbml.libsbml.L3ParserSettings
Returns the current setting indicating what to do with formulas containing the function log with one argument.
getParseUnits() - Method in class org.sbml.libsbml.L3ParserSettings
Returns if the current settings allow units in text-string mathematical formulas.
getPath() - Method in class org.sbml.libsbml.SBMLUri
 
getPersistent() - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Get the value of the 'persistent' attribute of this Trigger.
getPlugin(String) - Method in class org.sbml.libsbml.SBase
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
getPlugin(long) - Method in class org.sbml.libsbml.SBase
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
getPort(long) - Method in class org.sbml.libsbml.CompModelPlugin
 
getPort(String) - Method in class org.sbml.libsbml.CompModelPlugin
 
getPortRef() - Method in class org.sbml.libsbml.SBaseRef
 
getPosition() - Method in class org.sbml.libsbml.BoundingBox
 
getPrecedence() - Method in class org.sbml.libsbml.ASTNode
Get the precedence of this node in the infix math syntax of SBML Level 1.
getPrefix() - Method in class org.sbml.libsbml.SBasePlugin
Returns the prefix of the package extension of this plugin object.
getPrefix(int) - Method in class org.sbml.libsbml.XMLAttributes
Return the prefix of an attribute in this XMLAttributes set (by position).
getPrefix(int) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the prefix of an XML namespace declaration by its position.
getPrefix(String) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the prefix of an XML namespace declaration by its URI.
getPrefix() - Method in class org.sbml.libsbml.XMLToken
Returns the namespace prefix of this XML element.
getPrefix() - Method in class org.sbml.libsbml.XMLTriple
Returns the prefix portion of this XMLTriple.
getPrefixedName(int) - Method in class org.sbml.libsbml.XMLAttributes
Return the prefixed name of an attribute in this XMLAttributes set (by position).
getPrefixedName() - Method in class org.sbml.libsbml.XMLTriple
Returns the prefixed name from this XMLTriple.
getPriority() - Method in class org.sbml.libsbml.Event
(SBML Level 3 only) Get the event priority portion of this Event.
getProduct(long) - Method in class org.sbml.libsbml.Reaction
Returns the nth product species (as a SpeciesReference object) in the list of products in this Reaction.
getProduct(String) - Method in class org.sbml.libsbml.Reaction
Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction.
getProgram() - Method in class org.sbml.libsbml.SBMLExternalValidator
 
getProperties() - Method in class org.sbml.libsbml.SBMLConverter
Returns the current properties in effect for this converter.
getQualifierType() - Method in class org.sbml.libsbml.CVTerm
Returns the qualifier type of this CVTerm object.
getQuery() - Method in class org.sbml.libsbml.SBMLUri
 
getReactant(long) - Method in class org.sbml.libsbml.Reaction
Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reaction.
getReactant(String) - Method in class org.sbml.libsbml.Reaction
Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction.
getReaction() - Method in class org.sbml.libsbml.FluxBound
 
getReaction() - Method in class org.sbml.libsbml.FluxObjective
 
getReaction() - Method in class org.sbml.libsbml.GeneAssociation
 
getReaction(long) - Method in class org.sbml.libsbml.Model
Get the nth Reaction object in this Model.
getReaction(String) - Method in class org.sbml.libsbml.Model
Get a Reaction object based on its identifier.
getReactionGlyph(long) - Method in class org.sbml.libsbml.Layout
 
getReactionGlyph(String) - Method in class org.sbml.libsbml.Layout
 
getReactionId() - Method in class org.sbml.libsbml.ReactionGlyph
 
getReal() - Method in class org.sbml.libsbml.ASTNode
Get the real-numbered value of this node.
getReference() - Method in class org.sbml.libsbml.Association
 
getReferencedElement() - Method in class org.sbml.libsbml.SBaseRef
 
getReferencedElementFrom(Model) - Method in class org.sbml.libsbml.ReplacedElement
 
getReferencedElementFrom(Model) - Method in class org.sbml.libsbml.SBaseRef
 
getReferencedModel() - Method in class org.sbml.libsbml.ExternalModelDefinition
 
getReferenceGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
 
getReferenceId() - Method in class org.sbml.libsbml.GeneralGlyph
 
getReferenceId() - Method in class org.sbml.libsbml.ReferenceGlyph
 
getRegisteredPackageName(long) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns the registered package name at the given index
getReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
 
getReplacedElement(long) - Method in class org.sbml.libsbml.CompSBasePlugin
 
getRequired() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Returns the bool value of 'required' attribute of corresponding package in SBMLDocument element.
getResolverByIndex(int) - Method in class org.sbml.libsbml.SBMLResolverRegistry
 
getResourceBiologicalQualifier(String) - Method in class org.sbml.libsbml.SBase
Returns the MIRIAM biological qualifier associated with the given resource.
getResourceModelQualifier(String) - Method in class org.sbml.libsbml.SBase
Returns the MIRIAM model qualifier associated with the given resource.
getResources() - Method in class org.sbml.libsbml.CVTerm
Returns the resource references for this CVTerm object.
getResourceURI(long) - Method in class org.sbml.libsbml.CVTerm
Returns the value of the nth resource for this CVTerm object.
getReversible() - Method in class org.sbml.libsbml.Reaction
Returns the value of the 'reversible' attribute on the Reaction as a boolean value.
getRightChild() - Method in class org.sbml.libsbml.ASTNode
Get the right child of this node.
getRole() - Method in class org.sbml.libsbml.ReferenceGlyph
 
getRole() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
getRoleString() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
getRule(long) - Method in class org.sbml.libsbml.Model
Get the nth Rule object in this Model.
getRule(String) - Method in class org.sbml.libsbml.Model
Get a Rule object based on the variable to which it assigns a value.
getSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
 
getSBMLDocument() - Method in class org.sbml.libsbml.SBase
Returns the SBMLDocument object containing this object instance.
getSBMLDocument() - Method in class org.sbml.libsbml.SBasePlugin
Returns the parent SBMLDocument of this plugin object.
getSBMLErrMsg() - Method in exception org.sbml.libsbml.SBMLConstructorException
Returns the message associated with this SBML exception.
getSBMLFileName() - Method in class org.sbml.libsbml.SBMLExternalValidator
 
getSBMLNamespaceURI(long, long) - Static method in class org.sbml.libsbml.SBMLNamespaces
Returns a string representing the SBML XML namespace for the given level and version of SBML.
getSBOTerm() - Method in class org.sbml.libsbml.SBase
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
getSBOTermAsURL() - Method in class org.sbml.libsbml.SBase
Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.
getSBOTermID() - Method in class org.sbml.libsbml.SBase
Returns the string representation of the 'sboTerm' attribute of this object.
getScale() - Method in class org.sbml.libsbml.Unit
Returns the value of the 'scale' attribute of this unit.
getScheme() - Method in class org.sbml.libsbml.SBMLUri
 
getSecond() - Method in class org.sbml.libsbml.Date
Returns the seconds from this Date.
getSemanticsAnnotation(long) - Method in class org.sbml.libsbml.ASTNode
Get the nth semantic annotation of this node.
getSeverity() - Method in class org.sbml.libsbml.XMLError
Returns the severity of this error.
getSeverityAsString() - Method in class org.sbml.libsbml.XMLError
Returns a string describing the severity level of this error.
getShortMessage() - Method in class org.sbml.libsbml.XMLError
Returns a brief message for this error.
getSignOffset() - Method in class org.sbml.libsbml.Date
Returns the sign of the time zone offset from this Date.
getSize() - Method in class org.sbml.libsbml.ASTNodeList
 
getSize() - Method in class org.sbml.libsbml.Compartment
Get the size of this Compartment.
getSize() - Method in class org.sbml.libsbml.CVTermList
 
getSize() - Method in class org.sbml.libsbml.DateList
 
getSize() - Method in class org.sbml.libsbml.ModelCreatorList
 
getSize() - Method in class org.sbml.libsbml.SBaseList
 
getSize() - Method in class org.sbml.libsbml.SBMLNamespacesList
 
getSource() - Method in class org.sbml.libsbml.ExternalModelDefinition
 
getSpatialDimensions() - Method in class org.sbml.libsbml.Compartment
Get the number of spatial dimensions of this Compartment object.
getSpatialDimensionsAsDouble() - Method in class org.sbml.libsbml.Compartment
Get the number of spatial dimensions of this Compartment object as a double.
getSpatialSizeUnits() - Method in class org.sbml.libsbml.Species
Get the value of the 'spatialSizeUnits' attribute.
getSpecies(long) - Method in class org.sbml.libsbml.Model
Get the nth Species object in this Model.
getSpecies(String) - Method in class org.sbml.libsbml.Model
Get a Species object based on its identifier.
getSpecies() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Get the value of the 'species' attribute.
getSpeciesGlyph(long) - Method in class org.sbml.libsbml.Layout
 
getSpeciesGlyph(String) - Method in class org.sbml.libsbml.Layout
 
getSpeciesGlyphId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
getSpeciesId() - Method in class org.sbml.libsbml.SpeciesGlyph
 
getSpeciesReference(String) - Method in class org.sbml.libsbml.Model
Get a SpeciesReference object based on its identifier.
getSpeciesReferenceGlyph(long) - Method in class org.sbml.libsbml.ReactionGlyph
 
getSpeciesReferenceId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
getSpeciesType(long) - Method in class org.sbml.libsbml.Model
Get the nth SpeciesType object in this Model.
getSpeciesType(String) - Method in class org.sbml.libsbml.Model
Get a SpeciesType object based on its identifier.
getSpeciesType() - Method in class org.sbml.libsbml.Species
Get the type of this Species object object.
getStandardMessage(int) - Static method in class org.sbml.libsbml.XMLError
Returns a copy of the message string associated with the given predefined XMLError code.
getStart() - Method in class org.sbml.libsbml.LineSegment
 
getStoichiometry() - Method in class org.sbml.libsbml.SpeciesReference
Get the value of the 'stoichiometry' attribute.
getStoichiometryMath() - Method in class org.sbml.libsbml.SpeciesReference
Get the content of the 'stoichiometryMath' subelement as an ASTNode tree.
getStyle() - Method in class org.sbml.libsbml.ASTNode
Get the style of this ASTNode.
getSubGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
 
getSubmodel(long) - Method in class org.sbml.libsbml.CompModelPlugin
 
getSubmodel(String) - Method in class org.sbml.libsbml.CompModelPlugin
 
getSubmodelRef() - Method in class org.sbml.libsbml.Replacing
 
getSubstanceConversionFactor() - Method in class org.sbml.libsbml.Submodel
 
getSubstanceUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Returns the value of the 'substanceUnits' attribute of this KineticLaw object.
getSubstanceUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'substanceUnits' attribute of this Model.
getSubstanceUnits() - Method in class org.sbml.libsbml.Species
Get the value of the 'substanceUnits' attribute.
getSupportedNamespaces() - Static method in class org.sbml.libsbml.SBMLNamespaces
Returns a list of all supported SBMLNamespaces in this version of libsbml.
getSymbol() - Method in class org.sbml.libsbml.InitialAssignment
Get the value of the 'symbol' attribute of this InitialAssignment.
getTargetLevel() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Returns the target SBML Level for the conversion.
getTargetNamespaces() - Method in class org.sbml.libsbml.ConversionProperties
Returns the current target SBML namespace.
getTargetNamespaces() - Method in class org.sbml.libsbml.SBMLConverter
Returns the target SBML namespaces of the currently set properties.
getTargetVersion() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Returns the target SBML Version for the conversion.
getText() - Method in class org.sbml.libsbml.TextGlyph
 
getTextGlyph(long) - Method in class org.sbml.libsbml.Layout
 
getTextGlyph(String) - Method in class org.sbml.libsbml.Layout
 
getTimeConversionFactor() - Method in class org.sbml.libsbml.Submodel
 
getTimeUnits() - Method in class org.sbml.libsbml.Event
Get the value of the 'timeUnits' attribute of this Event, if it has one.
getTimeUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Returns the value of the 'timeUnits' attribute of this KineticLaw object.
getTimeUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'timeUnits' attribute of this Model.
getTrigger() - Method in class org.sbml.libsbml.Event
Get the event trigger portion of this Event.
getType() - Method in class org.sbml.libsbml.Association
 
getType() - Method in class org.sbml.libsbml.ASTNode
Get the type of this ASTNode.
getType() - Method in class org.sbml.libsbml.ConversionOption
Returns the type of this option
getType(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the type of a given option in this properties object.
getType() - Method in class org.sbml.libsbml.Objective
 
getType() - Method in class org.sbml.libsbml.Rule
Get the type of rule this is.
getTypeCode() - Method in class org.sbml.libsbml.Association
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.BoundingBox
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.Compartment
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.CompartmentGlyph
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.CompartmentType
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Constraint
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.CubicBezier
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.Curve
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.Delay
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Deletion
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.Dimensions
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.Event
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.EventAssignment
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.ExternalModelDefinition
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.FluxBound
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.FluxObjective
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.FunctionDefinition
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.GeneAssociation
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.GeneralGlyph
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.GraphicalObject
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.InitialAssignment
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.KineticLaw
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Layout
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.LineSegment
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.ListOf
Returns the libSBML type code for this object, namely, SBML_LIST_OF.
getTypeCode() - Method in class org.sbml.libsbml.ListOfCompartments
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfConstraints
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfEventAssignments
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfEvents
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfInitialAssignments
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfParameters
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfReactions
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfRules
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfSpecies
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfUnits
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.LocalParameter
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Model
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ModelDefinition
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ModifierSpeciesReference
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Objective
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.Parameter
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Point
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.Port
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.Priority
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Reaction
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ReactionGlyph
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.ReplacedBy
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.ReplacedElement
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.Rule
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.SBase
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.SBaseRef
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.SBMLDocument
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Species
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.SpeciesGlyph
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.SpeciesReference
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.SpeciesType
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.StoichiometryMath
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Submodel
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.TextGlyph
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.Trigger
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Unit
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.UnitDefinition
Returns the libSBML type code for this object instance.
getUnit(long) - Method in class org.sbml.libsbml.UnitDefinition
Returns a specific Unit instance belonging to this UnitDefinition.
getUnitDefinition(long) - Method in class org.sbml.libsbml.Model
Get the nth UnitDefinition object in this Model.
getUnitDefinition(String) - Method in class org.sbml.libsbml.Model
Get a UnitDefinition based on its identifier.
getUnitRef() - Method in class org.sbml.libsbml.SBaseRef
 
getUnits() - Method in class org.sbml.libsbml.ASTNode
Get the units of this ASTNode.
getUnits() - Method in class org.sbml.libsbml.Compartment
Get the units of this compartment's size.
getUnits() - Method in class org.sbml.libsbml.Parameter
Gets the units defined for this Parameter.
getUnits() - Method in class org.sbml.libsbml.Rule
Returns the units for the mathematical formula of this Rule.
getUnits() - Method in class org.sbml.libsbml.Species
Get the value of the 'units' attribute.
getURI() - Method in class org.sbml.libsbml.CompPkgNamespaces
Returns a string representing the SBML XML namespace of this object.
getURI() - Method in class org.sbml.libsbml.FbcPkgNamespaces
Returns a string representing the SBML XML namespace of this object.
getURI() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
Returns a string representing the SBML XML namespace of this object.
getURI() - Method in class org.sbml.libsbml.SBasePlugin
Gets the URI to which this element belongs to.
getURI() - Method in class org.sbml.libsbml.SBMLNamespaces
Returns a string representing the SBML XML namespace of this object.
getUri() - Method in class org.sbml.libsbml.SBMLUri
 
getURI(int) - Method in class org.sbml.libsbml.XMLAttributes
Return the namespace URI of an attribute in this XMLAttributes set (by position).
getURI(int) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the URI of an XML namespace declaration by its position.
getURI(String) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the URI of an XML namespace declaration by its prefix.
getURI() - Method in class org.sbml.libsbml.XMLNamespaces
Look up the URI of an XML namespace declaration by its prefix.
getURI() - Method in class org.sbml.libsbml.XMLToken
Returns the namespace URI of this XML element.
getURI() - Method in class org.sbml.libsbml.XMLTriple
Returns the URI portion of this XMLTriple.
getUseValuesFromTriggerTime() - Method in class org.sbml.libsbml.Event
Get the value of the 'useValuesFromTriggerTime' attribute of this Event.
getValidityFlag() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Returns the flag indicating whether the conversion has been set to 'strict'.
getValue() - Method in class org.sbml.libsbml.ConversionOption
Returns the value of this option.
getValue(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the value of the given option as a string.
getValue() - Method in class org.sbml.libsbml.FluxBound
 
getValue() - Method in class org.sbml.libsbml.Parameter
Gets the numerical value of this Parameter.
getValue(int) - Method in class org.sbml.libsbml.XMLAttributes
Return the value of an attribute in this XMLAttributes set (by position).
getValue(String) - Method in class org.sbml.libsbml.XMLAttributes
Return an attribute's value by name.
getValue(String, String) - Method in class org.sbml.libsbml.XMLAttributes
Return a value of an attribute with the given local name and namespace URI.
getValue(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
Return a value of an attribute with the given XMLTriple.
getVariable() - Method in class org.sbml.libsbml.EventAssignment
Get the value of this EventAssignment's 'variable' attribute.
getVariable() - Method in class org.sbml.libsbml.Rule
Get the value of the 'variable' attribute of this Rule object.
getVersion() - Method in class org.sbml.libsbml.SBase
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
getVersion() - Method in class org.sbml.libsbml.SBasePlugin
Returns the SBML version of the package extension of this plugin object.
getVersion() - Method in class org.sbml.libsbml.SBMLNamespaces
Get the SBML Version of this SBMLNamespaces object.
getVolume() - Method in class org.sbml.libsbml.Compartment
Get the volume of this Compartment.
getVolumeUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'volumeUnits' attribute of this Model.
getWidth() - Method in class org.sbml.libsbml.Dimensions
 
getXmlnsL2() - Static method in class org.sbml.libsbml.LayoutExtension
 
getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.CompExtension
 
getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.FbcExtension
 
getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.LayoutExtension
 
getXmlnsXSI() - Static method in class org.sbml.libsbml.LayoutExtension
 
getXOffset() - Method in class org.sbml.libsbml.Point
 
getYear() - Method in class org.sbml.libsbml.Date
Returns the year from this Date.
getYOffset() - Method in class org.sbml.libsbml.Point
 
getZOffset() - Method in class org.sbml.libsbml.Point
 
GlobalUnitsNotDeclared - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GraphicalObject - Class in org.sbml.libsbml
 
GraphicalObject(long, long, long) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(long, long) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(long) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject() - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(LayoutPkgNamespaces, String, double, double, double, double) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(LayoutPkgNamespaces, String, double, double, double, double, double, double) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(LayoutPkgNamespaces, String, Point, Dimensions) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(LayoutPkgNamespaces, String, BoundingBox) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(XMLNode, long) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(XMLNode) - Constructor for class org.sbml.libsbml.GraphicalObject
 
GraphicalObject(GraphicalObject) - Constructor for class org.sbml.libsbml.GraphicalObject
 

H

hasAttr(int) - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether an attribute with the given index exists in the attribute set in this XMLToken.
hasAttr(String, String) - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether an attribute with the given local name and namespace URI exists in the attribute set in this XMLToken.
hasAttr(String) - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether an attribute with the given local name and namespace URI exists in the attribute set in this XMLToken.
hasAttr(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether an attribute with the given XML triple exists in the attribute set in this XMLToken
hasAttribute(int) - Method in class org.sbml.libsbml.XMLAttributes
Predicate returning true or false depending on whether an attribute with the given index exists in this XMLAttributes.
hasAttribute(String, String) - Method in class org.sbml.libsbml.XMLAttributes
Predicate returning true or false depending on whether an attribute with the given local name and namespace URI exists in this XMLAttributes.
hasAttribute(String) - Method in class org.sbml.libsbml.XMLAttributes
Predicate returning true or false depending on whether an attribute with the given local name and namespace URI exists in this XMLAttributes.
hasAttribute(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
Predicate returning true or false depending on whether an attribute with the given XML triple exists in this XMLAttributes.
hasBzip2() - Static method in class org.sbml.libsbml.SBMLReader
Static method; returns true if this copy of libSBML supports bzip2 format compression.
hasBzip2() - Static method in class org.sbml.libsbml.SBMLWriter
Predicate returning true if this copy of libSBML has been linked with the bzip2 library.
hasChild(String) - Method in class org.sbml.libsbml.XMLNode
Return a boolean indicating whether this XMLNode has a child with the given name.
hasCorrectNumberArguments() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true or false depending on whether this ASTNode has the correct number of children for it's type.
hasExpectedXHTMLSyntax(XMLNode, SBMLNamespaces) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true or false depending on whether the given XMLNode object contains valid XHTML content.
hasExpectedXHTMLSyntax(XMLNode) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true or false depending on whether the given XMLNode object contains valid XHTML content.
hashCode() - Method in class org.sbml.libsbml.ASTNode
Returns a hashcode for this ASTNode object.
hashCode() - Method in class org.sbml.libsbml.CVTerm
Returns a hashcode for this CVTerm object.
hashCode() - Method in class org.sbml.libsbml.Date
Returns a hashcode for this Date object.
hashCode() - Method in class org.sbml.libsbml.ModelCreator
Returns a hashcode for this ModelCreator object.
hashCode() - Method in class org.sbml.libsbml.ModelHistory
Returns a hashcode for this ModelHistory object.
hashCode() - Method in class org.sbml.libsbml.SBase
Returns a hashcode for this SBase object.
hashCode() - Method in class org.sbml.libsbml.SBMLNamespaces
Returns a hashcode for this SBMLNamespaces object.
hashCode() - Method in class org.sbml.libsbml.SBMLReader
Returns a hashcode for this SBMLReader object.
hashCode() - Method in class org.sbml.libsbml.SBMLWriter
Returns a hashcode for this SBMLWriter object.
hashCode() - Method in class org.sbml.libsbml.XMLAttributes
Returns a hashcode for this XMLAttributes object.
hashCode() - Method in class org.sbml.libsbml.XMLError
Returns a hashcode for this XMLError object.
hashCode() - Method in class org.sbml.libsbml.XMLErrorLog
Returns a hashcode for this XMLErrorLog object.
hashCode() - Method in class org.sbml.libsbml.XMLNamespaces
Returns a hashcode for this XMLNamespaces object.
hashCode() - Method in class org.sbml.libsbml.XMLNode
Returns a hashcode for this XMLNode object.
hashCode() - Method in class org.sbml.libsbml.XMLToken
Returns a hashcode for this XMLToken object.
hashCode() - Method in class org.sbml.libsbml.XMLTriple
Returns a hashcode for this XMLTriple object.
hasNamespaceNS(String, String) - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether an XML Namespace with the given uri/prefix pair is contained in the XMLNamespaces ofthis XMLToken.
hasNamespacePrefix(String) - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether an XML Namespace with the given prefix is contained in the XMLNamespaces of this XMLToken.
hasNamespaceURI(String) - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether an XML Namespace with the given URI is contained in the XMLNamespaces of this XMLToken.
hasNS(String, String) - Method in class org.sbml.libsbml.XMLNamespaces
Predicate returning true or false depending on whether an XML Namespace with the given URI and prefix pair is contained in this XMLNamespaces list.
HasOnlySubsNoSpatialUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
HasOnlySubstanceUnitsNotinL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
HasOnlySubsUnitsNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
hasOption(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns true if this properties object contains an option with the given key.
hasPrefix(String) - Method in class org.sbml.libsbml.XMLNamespaces
Predicate returning true or false depending on whether an XML Namespace with the given prefix is contained in this XMLNamespaces list.
hasRequiredAttributes() - Method in class org.sbml.libsbml.AlgebraicRule
Predicate returning true if all the required attributes for this AlgebraicRule object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.AssignmentRule
Predicate returning true if all the required attributes for this AssignmentRule object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if all the required attributes for this Compartment object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.CompartmentType
Predicate returning true if all the required attributes for this CompartmentType object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.CVTerm
Predicate returning true if all the required elements for this CVTerm object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Event
Predicate returning true if all the required attributes for this Event object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.EventAssignment
Predicate returning true if all the required attributes for this EventAssignment object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if all the required attributes for this FunctionDefinition object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if all the required attributes for this InitialAssignment object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.KineticLaw
Predicate returning true if all the required attributes for this KineticLaw object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.LocalParameter
Predicate returning true if all the required attributes for this LocalParameter object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true if all the required elements for this ModelCreator object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.ModelHistory
Predicate returning true if all the required elements for this ModelHistory object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.ModifierSpeciesReference
Predicate returning true if all the required attributes for this ModifierSpeciesReference object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if all the required attributes for this Parameter object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.RateRule
Predicate returning true if all the required attributes for this RateRule object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if all the required attributes for this Reaction object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Rule
Predicate returning true if all the required attributes for this Rule object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Species
Predicate returning true if all the required attributes for this Species object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.SpeciesReference
Predicate returning true if all the required attributes for this SpeciesReference object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.SpeciesType
Predicate returning true if all the required attributes for this SpeciesType object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Trigger
Predicate returning true if all the required attributes for this Trigger object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Unit
Predicate returning true if all the required attributes for this Unit object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if all the required attributes for this UnitDefinition object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Constraint
Predicate returning true if all the required elements for this Constraint object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Delay
Predicate returning true if all the required elements for this Delay object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Event
Predicate returning true if all the required elements for this Event object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.EventAssignment
Predicate returning true if all the required elements for this EventAssignment object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.FbcModelPlugin
 
hasRequiredElements() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if all the required elements for this FunctionDefinition object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if all the required elements for this InitialAssignment object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.KineticLaw
Predicate returning true if all the required elements for this KineticLaw object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Model
Predicate returning true if all the required elements for this Model object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Priority
Predicate returning true if all the required elements for this Priority object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Rule
Predicate returning true if all the required elements for this Rule object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.StoichiometryMath
Predicate returning true if all the required elements for this StoichiometryMath object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Trigger
Predicate returning true if all the required elements for this Trigger object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if all the required elements for this UnitDefinition object have been set.
hasTargetNamespaces() - Method in class org.sbml.libsbml.ConversionProperties
Returns true if the target SBML namespace has been set.
hasUnits() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node or any of its children nodes have the attribute sbml:units.
hasURI(String) - Method in class org.sbml.libsbml.XMLNamespaces
Predicate returning true or false depending on whether an XML Namespace with the given URI is contained in this XMLNamespaces list.
hasValidLevelVersionNamespaceCombination() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.
hasZlib() - Static method in class org.sbml.libsbml.SBMLReader
Static method; returns true if this copy of libSBML supports gzip and zip format compression.
hasZlib() - Static method in class org.sbml.libsbml.SBMLWriter
Predicate returning true if this copy of libSBML has been linked with the zlib library.
height() - Method in class org.sbml.libsbml.BoundingBox
 
height() - Method in class org.sbml.libsbml.Dimensions
 

I

IdCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IdCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IdNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InconsistentArgUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InconsistentArgUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InconsistentExponUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InconsistentKineticLawUnitsL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InconsistentPowerUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectCompartmentSpatialDimensions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectOrderInConstraint - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectOrderInEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectOrderInKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectOrderInModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectOrderInReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
init() - Static method in class org.sbml.libsbml.CompExtension
 
init() - Static method in class org.sbml.libsbml.FbcExtension
 
init() - Static method in class org.sbml.libsbml.LayoutExtension
 
init() - Static method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
 
init() - Static method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
 
init() - Static method in class org.sbml.libsbml.SBMLLevelVersionConverter
 
init() - Static method in class org.sbml.libsbml.SBMLRuleConverter
 
init() - Static method in class org.sbml.libsbml.SBMLStripPackageConverter
 
init() - Static method in class org.sbml.libsbml.SBMLUnitsConverter
 
InitAssignCompartmenMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitAssignmentAndRuleForSameId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitAssignParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitAssignSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitAssignStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
initDefaults() - Method in class org.sbml.libsbml.BoundingBox
 
initDefaults() - Method in class org.sbml.libsbml.Compartment
Initializes the fields of this Compartment object to 'typical' default values.
initDefaults() - Method in class org.sbml.libsbml.CompartmentGlyph
 
initDefaults() - Method in class org.sbml.libsbml.CubicBezier
 
initDefaults() - Method in class org.sbml.libsbml.Curve
 
initDefaults() - Method in class org.sbml.libsbml.Dimensions
 
initDefaults() - Method in class org.sbml.libsbml.GeneralGlyph
 
initDefaults() - Method in class org.sbml.libsbml.GraphicalObject
 
initDefaults() - Method in class org.sbml.libsbml.Layout
 
initDefaults() - Method in class org.sbml.libsbml.LineSegment
 
initDefaults() - Method in class org.sbml.libsbml.Parameter
Initializes the fields of this Parameter object to 'typical' defaults values.
initDefaults() - Method in class org.sbml.libsbml.Point
 
initDefaults() - Method in class org.sbml.libsbml.Reaction
Initializes the fields of this Reaction object to 'typical' default values.
initDefaults() - Method in class org.sbml.libsbml.ReactionGlyph
 
initDefaults() - Method in class org.sbml.libsbml.ReferenceGlyph
 
initDefaults() - Method in class org.sbml.libsbml.Species
Initializes the fields of this Species object to 'typical' defaults values.
initDefaults() - Method in class org.sbml.libsbml.SpeciesGlyph
 
initDefaults() - Method in class org.sbml.libsbml.SpeciesReference
Initializes the fields of this SpeciesReference object to 'typical' default values.
initDefaults() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
initDefaults() - Method in class org.sbml.libsbml.TextGlyph
 
initDefaults() - Method in class org.sbml.libsbml.Unit
Initializes the fields of this Unit object to 'typical' default values.
InitialAssignment - Class in org.sbml.libsbml
Implementation of SBML's InitialAssignment construct.
InitialAssignment(long, long) - Constructor for class org.sbml.libsbml.InitialAssignment
Creates a new InitialAssignment using the given SBML level and version values.
InitialAssignment(SBMLNamespaces) - Constructor for class org.sbml.libsbml.InitialAssignment
Creates a new InitialAssignment using the given SBMLNamespaces object sbmlns.
InitialAssignment(InitialAssignment) - Constructor for class org.sbml.libsbml.InitialAssignment
Copy constructor; creates a copy of this InitialAssignment.
InitialAssignNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitialValueFalseEventNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitialValueNotBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
insert(int, SBase) - Method in class org.sbml.libsbml.ListOf
Inserts the item at the given position of this ListOf
insertAndOwn(int, SBase) - Method in class org.sbml.libsbml.ListOf
Inserts the item at the given position of this ListOf
insertChild(long, ASTNode) - Method in class org.sbml.libsbml.ASTNode
Insert the given ASTNode at point n in the list of children of this ASTNode.
insertChild(long, XMLNode) - Method in class org.sbml.libsbml.XMLNode
Inserts a copy of the given node as the nth child of this XMLNode.
instantiate() - Method in class org.sbml.libsbml.Submodel
 
IntegerSpatialDimensions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InternalXMLParserError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
intToString(int) - Static method in class org.sbml.libsbml.SBO
Returns the integer as a correctly formatted SBO identifier string.
Invalid1DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Invalid2DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Invalid3DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidAfterXMLContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidApplyCiInLambda - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidAreaRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidAssignRuleVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidCharInXML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidCiInLambda - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidCompartmentSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidCompartmentTypeRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidCompartmentTypeSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidConstraintContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidConstraintSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidDelaySBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidEventAssignmentSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidEventAssignmentVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidEventSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidFunctionDefReturnType - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidFunctionDefSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidInitAssignSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidInitAssignSymbol - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidKineticLawSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidL1CompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidLengthRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidMathElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidMetaidSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidModelSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidModifiersList - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidNamespaceOnSBML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidNameSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidNoArgsPassedToFunctionDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidNotesContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidParameterSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidParameterUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidRateRuleVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidReactantsProductsList - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidReactionSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidRuleOrdering - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidRuleSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSBMLLevelVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSBOTermSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesCompartmentRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesReferenceSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesSusbstanceUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesTypeRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesTypeSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSubstanceRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidTargetLevelVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidTimeRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidTriggerSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidUnitDefId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidUnitIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidUnitKind - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidUnitsValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidVolumeRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidXMLConstruct - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
is_open() - Method in class org.sbml.libsbml.OFStream
Returns true if this stream object is currently associated with a file.
isAlgebraic() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is an AlgebraicRule.
isAmpere() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind ampere.
isAssignment() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is an AssignmentRule.
isAttributesEmpty() - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether the attribute set in this XMLToken set is empty.
isAvogadro() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node is the special symbol avogadro. The predicate returns false (zero) otherwise.
isAvogadro() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind avogadro.
isBecquerel() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind becquerel
isBoolean() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node has a boolean type (a logical operator, a relational operator, or the constants true or false).
isBuiltIn(String, long) - Static method in class org.sbml.libsbml.Unit
Predicate to test whether a given string is the name of a predefined SBML unit.
isCandela() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind candela
isCelsius() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind Celsius
isCompartmentVolume() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is an CompartmentVolumeRule or equivalent.
isConservationLaw(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isConstant() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node represents a MathML constant (e.g., true, Pi).
isContinuousFramework(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isCoulomb() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind coulomb
isDimensionless() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind dimensionless.
isDiscreteFramework(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isElement() - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether this XMLToken is an XML element.
isEmpty() - Method in class org.sbml.libsbml.XMLAttributes
Predicate returning true or false depending on whether this XMLAttributes set is empty.
isEmpty() - Method in class org.sbml.libsbml.XMLNamespaces
Predicate returning true or false depending on whether this XMLNamespaces list is empty.
isEmpty() - Method in class org.sbml.libsbml.XMLTriple
Predicate returning true or false depending on whether this XMLTriple is empty.
isEnabled(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Checks if the extension with the given URI is enabled (true) or disabled (false)
isEnabledDefaultNS(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns true if a default namespace is added to each top-level element defined in the given package extension, otherwise returns false.
isEnd() - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether this XMLToken is an XML end element.
isEndFor(XMLToken) - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether this XMLToken is an XML end element for the given start element.
isEntity(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isEOF() - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether this XMLToken is an end of file marker.
isError() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error is a significant error.
isEvent(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isFarad() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind farad
isFatal() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error is a fatal run-time error.
isFunction() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node represents a MathML function (e.g., abs()), or an SBML Level 1 function, or a user-defined function.
isFunctionalCompartment(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isFunctionalEntity(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isGram() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind gram
isGray() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind gray
isHenry() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind henry
isHertz() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind hertz
isIgnoredPackage(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns true if the given package extension is one of an ignored packages, otherwise returns false.
isInfinity() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node represents the special IEEE 754 value infinity, false (zero) otherwise.
isInfo() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error object is for information purposes only.
isInteger() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node contains an integer value, false (zero) otherwise.
isInteraction(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isInternal() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error resulted from an internal program error.
isItem() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind item
isJoule() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind joule
isKatal() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind katal
isKelvin() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind kelvin
isKilogram() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind kilogram
isKineticConstant(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isLambda() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node is a MathML <lambda>, false (zero) otherwise.
isLitre() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind litre
isLog10() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node represents a log10 function, false (zero) otherwise.
isLogical() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node is a MathML logical operator (i.e., and, or, not, xor).
isLogicalFramework(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isLumen() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind lumen
isLux() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind lux
isMaterialEntity(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isMathematicalExpression(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isMetadataRepresentation(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isMetre() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind metre
isModellingFramework(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isModifier(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isModifier() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Predicate returning true if this is a ModifierSpeciesReference.
isMole() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind mole
isName() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node is a user-defined variable name in SBML L1, L2 (MathML), or the special symbols delay or time. The predicate returns false (zero) otherwise.
isNamespacesEmpty() - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether the XMLNamespaces of this XMLToken is empty.
isNaN() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node represents the special IEEE 754 value 'not a number' (NaN), false (zero) otherwise.
isNegInfinity() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node represents the special IEEE 754 value 'negative infinity', false (zero) otherwise.
isNewton() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind newton
isNumber() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node contains a number, false (zero) otherwise.
isObselete(long) - Static method in class org.sbml.libsbml.SBO
Predicate for checking whether the given term is obsolete.
isOccurringEntityRepresentation(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isOhm() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind ohm
isOperator() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node is a mathematical operator, meaning, +, -, *, / or ^ (power).
isPackageEnabled(String) - Method in class org.sbml.libsbml.SBase
Predicate returning true if the given SBML Level 3 package is enabled with this object.
isPackageEnabled(String) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
 
isPackageURIEnabled(String) - Method in class org.sbml.libsbml.SBase
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.
isParameter() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is an ParameterRule or equivalent.
isParticipant(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isParticipantRole(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isPascal() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind pascal
isPhysicalEntityRepresentation(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isPhysicalParticipant(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isPiecewise() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node is the MathML <piecewise> construct, false (zero) otherwise.
isPopulatedListFormulaUnitsData() - Method in class org.sbml.libsbml.Model
Predicate returning true if the list of FormulaUnitsData is populated.
isProduct(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isQuantitativeParameter(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isRadian() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind radian
isRate() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is a RateRule (SBML Levels 2–3) or has a 'type' attribute value of 'rate' (SBML Level 1).
isRateLaw(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isRational() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node represents a rational number, false (zero) otherwise.
isReactant(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isReal() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node can represent a real number, false (zero) otherwise.
isRegistered(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Checks if the extension with the given URI is registered (true) or not (false)
isRelational() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node is a MathML relational operator, meaning ==, >=, >, <, and !=.
isSBMLNamespace(String) - Static method in class org.sbml.libsbml.SBMLNamespaces
Predicate returning true if the given URL is one of SBML XML namespaces.
isScalar() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is an AssignmentRule (SBML Levels 2–3) or has a 'type' attribute value of 'scalar' (SBML Level 1).
isSecond() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind second
isSetActiveObjective() - Method in class org.sbml.libsbml.ListOfObjectives
 
isSetAnnotation() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's 'annotation' subelement exists and has content.
isSetAreaUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'areaUnits' attribute is set.
isSetAssociation() - Method in class org.sbml.libsbml.GeneAssociation
 
isSetBody() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if the body of this FunctionDefinition has set.
isSetBoundaryCondition() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'boundaryCondition' attribute is set.
isSetCharge() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
 
isSetCharge() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'charge' attribute is set.
isSetChemicalFormula() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
 
isSetClass() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node has the mathml attribute class.
isSetCoefficient() - Method in class org.sbml.libsbml.FluxObjective
 
isSetCompartment() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if this Reaction's 'compartment' attribute is set.
isSetCompartment() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'compartment' attribute is set.
isSetCompartmentId() - Method in class org.sbml.libsbml.CompartmentGlyph
 
isSetCompartmentType() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment's 'compartmentType' attribute is set.
isSetConstant() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment's 'constant' attribute is set.
isSetConstant() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if the 'constant' attribute of this Parameter is set.
isSetConstant() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'constant' attribute is set.
isSetConstant() - Method in class org.sbml.libsbml.SpeciesReference
Predicate returning true if this SpeciesReference's 'constant' attribute is set
isSetConversionFactor() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'conversionFactor' attribute is set.
isSetConversionFactor() - Method in class org.sbml.libsbml.ReplacedElement
 
isSetConversionFactor() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'conversionFactor' attribute is set.
isSetCreatedDate() - Method in class org.sbml.libsbml.ModelHistory
Predicate returning true or false depending on whether this ModelHistory's 'creation date' is set.
isSetCurve() - Method in class org.sbml.libsbml.GeneralGlyph
 
isSetCurve() - Method in class org.sbml.libsbml.ReactionGlyph
 
isSetCurve() - Method in class org.sbml.libsbml.ReferenceGlyph
 
isSetCurve() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
isSetDelay() - Method in class org.sbml.libsbml.Event
Predicate for testing whether the delay for this Event is set.
isSetDeletion() - Method in class org.sbml.libsbml.ReplacedElement
 
isSetEmail() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true or false depending on whether this ModelCreator's 'email' part is set.
isSetExponent() - Method in class org.sbml.libsbml.Unit
Predicate to test whether the 'exponent' attribute of this Unit is set.
isSetExtentConversionFactor() - Method in class org.sbml.libsbml.Submodel
 
isSetExtentUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'extentUnits' attribute is set.
isSetFamilyName() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true or false depending on whether this ModelCreator's 'family name' part is set.
isSetFast() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if the value of the 'fast' attribute on this Reaction.
isSetFormula() - Method in class org.sbml.libsbml.KineticLaw
Predicate returning true if this KineticLaw's 'formula' attribute is set.
isSetFormula() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule's mathematical expression is set.
isSetGivenName() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true or false depending on whether this ModelCreator's 'given name' part is set.
isSetGlyphId() - Method in class org.sbml.libsbml.ReferenceGlyph
 
isSetGraphicalObjectId() - Method in class org.sbml.libsbml.TextGlyph
 
isSetHasOnlySubstanceUnits() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'hasOnlySubstanceUnits' attribute is set.
isSetId() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node has the mathml attribute id.
isSetId() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.CompartmentType
Predicate returning true if this CompartmentType's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Event
Predicate returning true if this Event's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if this FunctionDefinition's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if this Parameter's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if this Reaction's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Predicate returning true if this SimpleSpeciesReference's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.SpeciesType
Predicate returning true if this SpeciesType's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if this UnitDefinition's 'id' attribute is set.
isSetIdRef() - Method in class org.sbml.libsbml.SBaseRef
 
isSetInitialAmount() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'initialAmount' attribute is set.
isSetInitialConcentration() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'initialConcentration' attribute is set.
isSetInitialValue() - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Predicate to test whether the 'initialValue' attribute for this trigger is set.
isSetKind() - Method in class org.sbml.libsbml.Unit
Predicate to test whether the 'kind' attribute of this Unit is set.
isSetKineticLaw() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if this Reaction contains a kinetic law object.
isSetLengthUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'lengthUnits' attribute is set.
isSetMath() - Method in class org.sbml.libsbml.Constraint
Predicate returning true if a mathematical formula is defined for this Constraint.
isSetMath() - Method in class org.sbml.libsbml.Delay
Predicate to test whether the formula for this delay is set.
isSetMath() - Method in class org.sbml.libsbml.EventAssignment
Predicate for testing whether the 'math' subelement of this EventAssignment is set.
isSetMath() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if this FunctionDefinition's 'math' subelement contains a value.
isSetMath() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if this InitialAssignment's 'math' subelement contains a value.
isSetMath() - Method in class org.sbml.libsbml.KineticLaw
Predicate returning true if this Kinetic's 'math' subelement is set.
isSetMath() - Method in class org.sbml.libsbml.Priority
Predicate to test whether the formula for this delay is set.
isSetMath() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule's mathematical expression is set.
isSetMath() - Method in class org.sbml.libsbml.StoichiometryMath
Predicate to test whether the math for this StoichiometryMath object is set.
isSetMath() - Method in class org.sbml.libsbml.Trigger
Predicate to test whether the math for this trigger is set.
isSetMd5() - Method in class org.sbml.libsbml.ExternalModelDefinition
 
isSetMessage() - Method in class org.sbml.libsbml.Constraint
Predicate returning true if a message is defined for this Constraint.
isSetMetaId() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's 'metaid' attribute is set.
isSetMetaIdRef() - Method in class org.sbml.libsbml.GraphicalObject
 
isSetMetaIdRef() - Method in class org.sbml.libsbml.SBaseRef
 
isSetModelHistory() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object has a ModelHistory object attached to it.
isSetModelRef() - Method in class org.sbml.libsbml.ExternalModelDefinition
 
isSetModelRef() - Method in class org.sbml.libsbml.Submodel
 
isSetModifiedDate() - Method in class org.sbml.libsbml.ModelHistory
Predicate returning true or false depending on whether this ModelHistory's 'modified date' is set.
isSetMultiplier() - Method in class org.sbml.libsbml.Unit
Predicate to test whether the 'multiplier' attribute of this Unit is set.
isSetName() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.CompartmentType
Predicate returning true if this CompartmentType's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Event
Predicate returning true if this Event's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if this FunctionDefinition's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if this Parameter's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if this Reaction's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Predicate returning true if this SimpleSpeciesReference's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.SpeciesType
Predicate returning true if this SpeciesType's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if this UnitDefinition's 'name' attribute is set.
isSetNotes() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's 'notes' subelement exists and has content.
isSetOperation() - Method in class org.sbml.libsbml.FluxBound
 
isSetOrganisation() - Method in class org.sbml.libsbml.ModelCreator
(Alternate spelling) Predicate returning true or false depending on whether this ModelCreator's 'organization' part is set.
isSetOrganization() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true or false depending on whether this ModelCreator's 'organization' part is set.
isSetOriginOfTextId() - Method in class org.sbml.libsbml.TextGlyph
 
isSetOutside() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment's 'outside' attribute is set.
isSetPackageRequired(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns true if the required attribute of the given package extension is defined, otherwise returns false.
isSetPersistent() - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Predicate to test whether the 'persistent' attribute for this trigger is set.
isSetPortRef() - Method in class org.sbml.libsbml.SBaseRef
 
isSetPriority() - Method in class org.sbml.libsbml.Event
(SBML Level 3 only) Predicate for testing whether the priority for this Event is set.
isSetReaction() - Method in class org.sbml.libsbml.FluxBound
 
isSetReaction() - Method in class org.sbml.libsbml.FluxObjective
 
isSetReaction() - Method in class org.sbml.libsbml.GeneAssociation
 
isSetReactionId() - Method in class org.sbml.libsbml.ReactionGlyph
 
isSetReference() - Method in class org.sbml.libsbml.Association
 
isSetReferenceId() - Method in class org.sbml.libsbml.GeneralGlyph
 
isSetReferenceId() - Method in class org.sbml.libsbml.ReferenceGlyph
 
isSetReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
 
isSetRequired() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Predicate returning true or false depending on whether this SBMLDocumentPlugin's 'required' attribute has been set.
isSetReversible() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if this Reaction's 'reversible' attribute is set.
isSetRole() - Method in class org.sbml.libsbml.ReferenceGlyph
 
isSetRole() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
isSetSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
 
isSetSBOTerm() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's 'sboTerm' attribute is set.
isSetScale() - Method in class org.sbml.libsbml.Unit
Predicate to test whether the 'scale' attribute of this Unit is set.
isSetSize() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment's 'size' attribute is set.
isSetSource() - Method in class org.sbml.libsbml.ExternalModelDefinition
 
isSetSpatialDimensions() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment's 'spatialDimensions' attribute is set.
isSetSpatialSizeUnits() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'spatialSizeUnits' attribute is set.
isSetSpecies() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Predicate returning true if this SimpleSpeciesReference's 'species' attribute is set.
isSetSpeciesGlyphId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
isSetSpeciesId() - Method in class org.sbml.libsbml.SpeciesGlyph
 
isSetSpeciesReferenceId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
isSetSpeciesType() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'speciesType' attribute is set.
isSetStoichiometry() - Method in class org.sbml.libsbml.SpeciesReference
Predicate returning true if this SpeciesReference's 'stoichiometry' attribute is set.
isSetStoichiometryMath() - Method in class org.sbml.libsbml.SpeciesReference
Predicate returning true if this SpeciesReference's 'stoichiometryMath' subelement is set
isSetStyle() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node has the mathml attribute style.
isSetSubmodelRef() - Method in class org.sbml.libsbml.Replacing
 
isSetSubstanceConversionFactor() - Method in class org.sbml.libsbml.Submodel
 
isSetSubstanceUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Predicate returning true if this SpeciesReference's 'substanceUnits' attribute is set.
isSetSubstanceUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'substanceUnits' attribute is set.
isSetSubstanceUnits() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'substanceUnits' attribute is set.
isSetSymbol() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if this InitialAssignment's 'symbol' attribute is set.
isSetText() - Method in class org.sbml.libsbml.TextGlyph
 
isSetTimeConversionFactor() - Method in class org.sbml.libsbml.Submodel
 
isSetTimeUnits() - Method in class org.sbml.libsbml.Event
Predicate for testing whether the 'timeUnits' attribute of this Event is set.
isSetTimeUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Predicate returning true if this SpeciesReference's 'timeUnits' attribute is set.
isSetTimeUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'timeUnits' attribute is set.
isSetTrigger() - Method in class org.sbml.libsbml.Event
Predicate for testing whether the trigger for this Event is set.
isSetType() - Method in class org.sbml.libsbml.Association
 
isSetType() - Method in class org.sbml.libsbml.Objective
 
isSetUnitRef() - Method in class org.sbml.libsbml.SBaseRef
 
isSetUnits() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node has the attribute sbml:units.
isSetUnits() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment's 'units' attribute is set.
isSetUnits() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if the 'units' attribute of this Parameter is set.
isSetUnits() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule's 'units' attribute is set.
isSetUnits() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'units' attribute is set.
isSetUseValuesFromTriggerTime() - Method in class org.sbml.libsbml.Event
Predicate for testing whether the 'useValuesFromTriggerTime' attribute of this Event is set.
isSetValue() - Method in class org.sbml.libsbml.FluxBound
 
isSetValue() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if the 'value' attribute of this Parameter is set.
isSetVariable() - Method in class org.sbml.libsbml.EventAssignment
Predicate for testing whether the attribute 'variable' of this EventAssignment is set.
isSetVariable() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule's 'variable' attribute is set.
isSetVolume() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment's 'volume' attribute is set.
isSetVolumeUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'volumeUnits' attribute is set.
isSiemens() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind siemens
isSievert() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind sievert
isSpeciesConcentration() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is a SpeciesConcentrationRule or equivalent.
isSqrt() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node represents a square root function, false (zero) otherwise.
isStart() - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether this XMLToken is an XML start element.
isSteadyStateExpression(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isSteradian() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind steradian
isSystem() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error was generated by the operating system.
isSystemsDescriptionParameter(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTesla() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind tesla
isText() - Method in class org.sbml.libsbml.XMLToken
Predicate returning true or false depending on whether this XMLToken is an XML text element.
isUMinus() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node is a unary minus operator, false (zero) otherwise.
isUnitKind(String, long, long) - Static method in class org.sbml.libsbml.Unit
Predicate to test whether a given string is the name of a valid base unit in SBML (such as 'gram' or 'mole').
isUnknown() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node has an unknown type.
isUPlus() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node is a unary plus operator, false (zero) otherwise.
isValid() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error resulted from a problem or whether it was logged as an unknown error.
isValidCombination() - Method in class org.sbml.libsbml.SBMLNamespaces
Predicate returning true if the given set of namespaces represent a valid set
isValidSBMLSId(String) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true true or false depending on whether the argument string conforms to the syntax of SBML identifiers.
isValidUnitSId(String) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true or false depending on whether the argument string conforms to the syntax of SBML unit identifiers.
isValidXMLID(String) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true or false depending on whether the argument string conforms to the XML data type ID.
isVariantOfArea() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'area'.
isVariantOfDimensionless() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the unit 'dimensionless'.
isVariantOfLength() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'length'.
isVariantOfMass() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'mass'.
isVariantOfSubstance() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'substance'.
isVariantOfSubstancePerTime() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit 'substance' divided by the predefined unit 'time'.
isVariantOfTime() - Method in class org.sbml.libsbml.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.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'volume'.
isVolt() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind volt
isWarning() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error object is a warning.
isWatt() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind watt
isWeber() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind weber
isWellFormedASTNode() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true or false depending on whether this ASTNode is well-formed.
isXML() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error resulted from a problem in the XML input (e.g., an XML syntax error).

K

KineticLaw - Class in org.sbml.libsbml
Implementation of SBML's KineticLaw construct.
KineticLaw(long, long) - Constructor for class org.sbml.libsbml.KineticLaw
Creates a new KineticLaw using the given SBML level and version values.
KineticLaw(SBMLNamespaces) - Constructor for class org.sbml.libsbml.KineticLaw
Creates a new KineticLaw using the given SBMLNamespaces object sbmlns.
KineticLaw(KineticLaw) - Constructor for class org.sbml.libsbml.KineticLaw
Copy constructor; creates a copy of this KineticLaw.
KineticLawNotSubstancePerTime - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
KineticLawParametersAreLocalOnly - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

L

L1V1CompartmentVolumeReqd - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3AreaUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3ConversionFactorOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3ExtentUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3LengthUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3NotSchemaConformant - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3NotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_AVOGADRO_IS_CSYMBOL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_AVOGADRO_IS_NAME - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_COLLAPSE_UNARY_MINUS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_EXPAND_UNARY_MINUS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_NO_UNITS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_PARSE_LOG_AS_ERROR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_PARSE_LOG_AS_LN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_PARSE_LOG_AS_LOG10 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_PARSE_UNITS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3PackageOnLowerSBML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3ParserSettings - Class in org.sbml.libsbml
A helper class for controlling the behavior of the text-string formula parser.
L3ParserSettings() - Constructor for class org.sbml.libsbml.L3ParserSettings
Creates a new L3ParserSettings object with default values.
L3ParserSettings(Model, int, boolean, boolean, boolean) - Constructor for class org.sbml.libsbml.L3ParserSettings
Creates a new L3ParserSettings object with specific values for all possible settings.
L3SpatialDimensionsUnset - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3SubstanceUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3TimeUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3VolumeUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LambdaOnlyAllowedInFunctionDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Layout - Class in org.sbml.libsbml
 
Layout(long, long, long) - Constructor for class org.sbml.libsbml.Layout
 
Layout(long, long) - Constructor for class org.sbml.libsbml.Layout
 
Layout(long) - Constructor for class org.sbml.libsbml.Layout
 
Layout() - Constructor for class org.sbml.libsbml.Layout
 
Layout(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.Layout
 
Layout(LayoutPkgNamespaces, String, Dimensions) - Constructor for class org.sbml.libsbml.Layout
 
Layout(XMLNode, long) - Constructor for class org.sbml.libsbml.Layout
 
Layout(XMLNode) - Constructor for class org.sbml.libsbml.Layout
 
Layout(Layout) - Constructor for class org.sbml.libsbml.Layout
 
LayoutExtension - Class in org.sbml.libsbml
 
LayoutExtension() - Constructor for class org.sbml.libsbml.LayoutExtension
 
LayoutExtension(LayoutExtension) - Constructor for class org.sbml.libsbml.LayoutExtension
 
LayoutModelPlugin - Class in org.sbml.libsbml
 
LayoutModelPlugin(String, String, LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.LayoutModelPlugin
 
LayoutModelPlugin(LayoutModelPlugin) - Constructor for class org.sbml.libsbml.LayoutModelPlugin
 
LayoutPkgNamespaces - Class in org.sbml.libsbml
Class to store level, version and namespace information of SBML extension package.
LayoutPkgNamespaces(long, long, long, String) - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPkgNamespaces(long, long, long) - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPkgNamespaces(long, long) - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPkgNamespaces(long) - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPkgNamespaces() - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPkgNamespaces(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
Copy constructor; creates a copy of a SBMLExtensionNamespaces.
LayoutSpeciesReferencePlugin - Class in org.sbml.libsbml
 
LayoutSpeciesReferencePlugin(String, String, LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.LayoutSpeciesReferencePlugin
 
LayoutSpeciesReferencePlugin(LayoutSpeciesReferencePlugin) - Constructor for class org.sbml.libsbml.LayoutSpeciesReferencePlugin
 
LevelPositiveInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
libsbml - Class in org.sbml.libsbml
Wrapper class for global methods and constants defined by libSBML.
LIBSBML_ANNOTATION_NAME_NOT_FOUND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_ANNOTATION_NS_NOT_FOUND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_GENERAL_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_IDENTIFIER_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_INTERNAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_INTERNAL_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_MATHML_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_MODELING_PRACTICE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_OVERDETERMINED_MODEL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L1_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L2V1_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L2V2_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L2V3_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L2V4_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L3V1_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBO_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SYSTEM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_UNITS_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_XML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CONV_CONVERSION_NOT_AVAILABLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CONV_INVALID_SRC_DOCUMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CONV_INVALID_TARGET_NAMESPACE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CONV_PKG_CONSIDERED_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CONV_PKG_CONVERSION_NOT_AVAILABLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_DOTTED_VERSION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_DUPLICATE_ANNOTATION_NS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_DUPLICATE_OBJECT_ID - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_INDEX_EXCEEDS_SIZE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_INVALID_ATTRIBUTE_VALUE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_INVALID_OBJECT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_INVALID_XML_OPERATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_LEVEL_MISMATCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_NAMESPACES_MISMATCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_OPERATION_FAILED - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_OPERATION_SUCCESS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_CONFLICT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_CONFLICTED_VERSION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_DISABLED - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_UNKNOWN_VERSION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_VERSION_MISMATCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_ERROR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_FATAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_GENERAL_WARNING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_INFO - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_NOT_APPLICABLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_SCHEMA_ERROR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_WARNING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_UNEXPECTED_ATTRIBUTE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_VERSION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_VERSION_MISMATCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_VERSION_STRING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LibSBMLAdditionalCodesLowerBound - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
libsbmlConstants - Interface in org.sbml.libsbml
 
LineSegment - Class in org.sbml.libsbml
 
LineSegment(long, long, long) - Constructor for class org.sbml.libsbml.LineSegment
 
LineSegment(long, long) - Constructor for class org.sbml.libsbml.LineSegment
 
LineSegment(long) - Constructor for class org.sbml.libsbml.LineSegment
 
LineSegment() - Constructor for class org.sbml.libsbml.LineSegment
 
LineSegment(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.LineSegment
 
LineSegment(LayoutPkgNamespaces, double, double, double, double) - Constructor for class org.sbml.libsbml.LineSegment
 
LineSegment(LineSegment) - Constructor for class org.sbml.libsbml.LineSegment
 
LineSegment(LayoutPkgNamespaces, double, double, double, double, double, double) - Constructor for class org.sbml.libsbml.LineSegment
 
LineSegment(LayoutPkgNamespaces, Point, Point) - Constructor for class org.sbml.libsbml.LineSegment
 
LineSegment(XMLNode, long) - Constructor for class org.sbml.libsbml.LineSegment
 
LineSegment(XMLNode) - Constructor for class org.sbml.libsbml.LineSegment
 
ListOf - Class in org.sbml.libsbml
Parent class for the various SBML 'ListOfXYZ' classes.
ListOf(long, long) - Constructor for class org.sbml.libsbml.ListOf
Creates a new ListOf object.
ListOf(long) - Constructor for class org.sbml.libsbml.ListOf
Creates a new ListOf object.
ListOf() - Constructor for class org.sbml.libsbml.ListOf
Creates a new ListOf object.
ListOf(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOf
Creates a new ListOf with SBMLNamespaces object.
ListOf(ListOf) - Constructor for class org.sbml.libsbml.ListOf
Copy constructor; creates a copy of this ListOf.
ListOfCompartmentGlyphs - Class in org.sbml.libsbml
 
ListOfCompartmentGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfCompartmentGlyphs
 
ListOfCompartmentGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfCompartmentGlyphs
 
ListOfCompartmentGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfCompartmentGlyphs
 
ListOfCompartmentGlyphs() - Constructor for class org.sbml.libsbml.ListOfCompartmentGlyphs
 
ListOfCompartmentGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfCompartmentGlyphs
 
ListOfCompartments - Class in org.sbml.libsbml
Implementation of SBML Level 2's ListOfCompartments construct.
ListOfCompartments(long, long) - Constructor for class org.sbml.libsbml.ListOfCompartments
Creates a new ListOfCompartments object.
ListOfCompartments(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfCompartments
Creates a new ListOfCompartments object.
ListOfCompartmentTypes - Class in org.sbml.libsbml
Implementation of SBML's ListOfCompartmentTypes construct.
ListOfCompartmentTypes(long, long) - Constructor for class org.sbml.libsbml.ListOfCompartmentTypes
Creates a new ListOfCompartmentTypes object.
ListOfCompartmentTypes(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfCompartmentTypes
Creates a new ListOfCompartmentTypes object.
ListOfConstraints - Class in org.sbml.libsbml
Implementation of SBML's ListOfConstraints construct.
ListOfConstraints(long, long) - Constructor for class org.sbml.libsbml.ListOfConstraints
Creates a new ListOfConstraints object.
ListOfConstraints(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfConstraints
Creates a new ListOfConstraints object.
ListOfDeletions - Class in org.sbml.libsbml
 
ListOfDeletions(long, long, long) - Constructor for class org.sbml.libsbml.ListOfDeletions
 
ListOfDeletions(long, long) - Constructor for class org.sbml.libsbml.ListOfDeletions
 
ListOfDeletions(long) - Constructor for class org.sbml.libsbml.ListOfDeletions
 
ListOfDeletions() - Constructor for class org.sbml.libsbml.ListOfDeletions
 
ListOfDeletions(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfDeletions
 
ListOfEventAssignments - Class in org.sbml.libsbml
Implementation of SBML's ListOfEventAssignments construct.
ListOfEventAssignments(long, long) - Constructor for class org.sbml.libsbml.ListOfEventAssignments
Creates a new ListOfEventAssignments object.
ListOfEventAssignments(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfEventAssignments
Creates a new ListOfEventAssignments object.
ListOfEvents - Class in org.sbml.libsbml
Implementation of SBML's ListOfEvents construct.
ListOfEvents(long, long) - Constructor for class org.sbml.libsbml.ListOfEvents
Creates a new ListOfEvents object.
ListOfEvents(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfEvents
Creates a new ListOfEvents object.
ListOfExternalModelDefinitions - Class in org.sbml.libsbml
 
ListOfExternalModelDefinitions(long, long, long) - Constructor for class org.sbml.libsbml.ListOfExternalModelDefinitions
 
ListOfExternalModelDefinitions(long, long) - Constructor for class org.sbml.libsbml.ListOfExternalModelDefinitions
 
ListOfExternalModelDefinitions(long) - Constructor for class org.sbml.libsbml.ListOfExternalModelDefinitions
 
ListOfExternalModelDefinitions() - Constructor for class org.sbml.libsbml.ListOfExternalModelDefinitions
 
ListOfExternalModelDefinitions(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfExternalModelDefinitions
 
ListOfFluxBounds - Class in org.sbml.libsbml
 
ListOfFluxBounds(long, long, long) - Constructor for class org.sbml.libsbml.ListOfFluxBounds
 
ListOfFluxBounds(long, long) - Constructor for class org.sbml.libsbml.ListOfFluxBounds
 
ListOfFluxBounds(long) - Constructor for class org.sbml.libsbml.ListOfFluxBounds
 
ListOfFluxBounds() - Constructor for class org.sbml.libsbml.ListOfFluxBounds
 
ListOfFluxBounds(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfFluxBounds
 
ListOfFluxObjectives - Class in org.sbml.libsbml
 
ListOfFluxObjectives(long, long, long) - Constructor for class org.sbml.libsbml.ListOfFluxObjectives
 
ListOfFluxObjectives(long, long) - Constructor for class org.sbml.libsbml.ListOfFluxObjectives
 
ListOfFluxObjectives(long) - Constructor for class org.sbml.libsbml.ListOfFluxObjectives
 
ListOfFluxObjectives() - Constructor for class org.sbml.libsbml.ListOfFluxObjectives
 
ListOfFluxObjectives(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfFluxObjectives
 
ListOfFunctionDefinitions - Class in org.sbml.libsbml
Implementation of SBML's ListOfFunctionDefinitions construct.
ListOfFunctionDefinitions(long, long) - Constructor for class org.sbml.libsbml.ListOfFunctionDefinitions
Creates a new ListOfFunctionDefinitions object.
ListOfFunctionDefinitions(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfFunctionDefinitions
Creates a new ListOfFunctionDefinitions object.
ListOfGeneAssociations - Class in org.sbml.libsbml
 
ListOfGeneAssociations(long, long, long) - Constructor for class org.sbml.libsbml.ListOfGeneAssociations
 
ListOfGeneAssociations(long, long) - Constructor for class org.sbml.libsbml.ListOfGeneAssociations
 
ListOfGeneAssociations(long) - Constructor for class org.sbml.libsbml.ListOfGeneAssociations
 
ListOfGeneAssociations() - Constructor for class org.sbml.libsbml.ListOfGeneAssociations
 
ListOfGeneAssociations(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfGeneAssociations
 
ListOfGraphicalObjects - Class in org.sbml.libsbml
 
ListOfGraphicalObjects(long, long, long) - Constructor for class org.sbml.libsbml.ListOfGraphicalObjects
 
ListOfGraphicalObjects(long, long) - Constructor for class org.sbml.libsbml.ListOfGraphicalObjects
 
ListOfGraphicalObjects(long) - Constructor for class org.sbml.libsbml.ListOfGraphicalObjects
 
ListOfGraphicalObjects() - Constructor for class org.sbml.libsbml.ListOfGraphicalObjects
 
ListOfGraphicalObjects(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfGraphicalObjects
 
ListOfInitialAssignments - Class in org.sbml.libsbml
Implementation of SBML's ListOfInitialAssignments construct.
ListOfInitialAssignments(long, long) - Constructor for class org.sbml.libsbml.ListOfInitialAssignments
Creates a new ListOfInitialAssignments object.
ListOfInitialAssignments(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfInitialAssignments
Creates a new ListOfInitialAssignments object.
ListOfLayouts - Class in org.sbml.libsbml
 
ListOfLayouts(long, long, long) - Constructor for class org.sbml.libsbml.ListOfLayouts
 
ListOfLayouts(long, long) - Constructor for class org.sbml.libsbml.ListOfLayouts
 
ListOfLayouts(long) - Constructor for class org.sbml.libsbml.ListOfLayouts
 
ListOfLayouts() - Constructor for class org.sbml.libsbml.ListOfLayouts
 
ListOfLayouts(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfLayouts
 
ListOfLineSegments - Class in org.sbml.libsbml
 
ListOfLineSegments(long, long, long) - Constructor for class org.sbml.libsbml.ListOfLineSegments
 
ListOfLineSegments(long, long) - Constructor for class org.sbml.libsbml.ListOfLineSegments
 
ListOfLineSegments(long) - Constructor for class org.sbml.libsbml.ListOfLineSegments
 
ListOfLineSegments() - Constructor for class org.sbml.libsbml.ListOfLineSegments
 
ListOfLineSegments(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfLineSegments
 
ListOfLocalParameters - Class in org.sbml.libsbml
Implementation of SBML Level 3's ListOfLocalParameters construct.
ListOfLocalParameters(long, long) - Constructor for class org.sbml.libsbml.ListOfLocalParameters
Creates a new ListOfLocalParameters object.
ListOfLocalParameters(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfLocalParameters
Creates a new ListOfLocalParameters object.
ListOfModelDefinitions - Class in org.sbml.libsbml
 
ListOfModelDefinitions(long, long, long) - Constructor for class org.sbml.libsbml.ListOfModelDefinitions
 
ListOfModelDefinitions(long, long) - Constructor for class org.sbml.libsbml.ListOfModelDefinitions
 
ListOfModelDefinitions(long) - Constructor for class org.sbml.libsbml.ListOfModelDefinitions
 
ListOfModelDefinitions() - Constructor for class org.sbml.libsbml.ListOfModelDefinitions
 
ListOfModelDefinitions(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfModelDefinitions
 
ListOfObjectives - Class in org.sbml.libsbml
 
ListOfObjectives(long, long, long) - Constructor for class org.sbml.libsbml.ListOfObjectives
 
ListOfObjectives(long, long) - Constructor for class org.sbml.libsbml.ListOfObjectives
 
ListOfObjectives(long) - Constructor for class org.sbml.libsbml.ListOfObjectives
 
ListOfObjectives() - Constructor for class org.sbml.libsbml.ListOfObjectives
 
ListOfObjectives(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfObjectives
 
ListOfParameters - Class in org.sbml.libsbml
Implementation of SBML's ListOfParameters construct.
ListOfParameters(long, long) - Constructor for class org.sbml.libsbml.ListOfParameters
Creates a new ListOfParameters object.
ListOfParameters(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfParameters
Creates a new ListOfParameters object.
ListOfPorts - Class in org.sbml.libsbml
 
ListOfPorts(long, long, long) - Constructor for class org.sbml.libsbml.ListOfPorts
 
ListOfPorts(long, long) - Constructor for class org.sbml.libsbml.ListOfPorts
 
ListOfPorts(long) - Constructor for class org.sbml.libsbml.ListOfPorts
 
ListOfPorts() - Constructor for class org.sbml.libsbml.ListOfPorts
 
ListOfPorts(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfPorts
 
ListOfReactionGlyphs - Class in org.sbml.libsbml
 
ListOfReactionGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfReactionGlyphs
 
ListOfReactionGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfReactionGlyphs
 
ListOfReactionGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfReactionGlyphs
 
ListOfReactionGlyphs() - Constructor for class org.sbml.libsbml.ListOfReactionGlyphs
 
ListOfReactionGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfReactionGlyphs
 
ListOfReactions - Class in org.sbml.libsbml
Implementation of SBML's ListOfReactions construct.
ListOfReactions(long, long) - Constructor for class org.sbml.libsbml.ListOfReactions
Creates a new ListOfReactions object.
ListOfReactions(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfReactions
Creates a new ListOfReactions object.
ListOfReferenceGlyphs - Class in org.sbml.libsbml
 
ListOfReferenceGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfReferenceGlyphs
 
ListOfReferenceGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfReferenceGlyphs
 
ListOfReferenceGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfReferenceGlyphs
 
ListOfReferenceGlyphs() - Constructor for class org.sbml.libsbml.ListOfReferenceGlyphs
 
ListOfReferenceGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfReferenceGlyphs
 
ListOfReplacedElements - Class in org.sbml.libsbml
 
ListOfReplacedElements(long, long, long) - Constructor for class org.sbml.libsbml.ListOfReplacedElements
 
ListOfReplacedElements(long, long) - Constructor for class org.sbml.libsbml.ListOfReplacedElements
 
ListOfReplacedElements(long) - Constructor for class org.sbml.libsbml.ListOfReplacedElements
 
ListOfReplacedElements() - Constructor for class org.sbml.libsbml.ListOfReplacedElements
 
ListOfReplacedElements(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfReplacedElements
 
ListOfRules - Class in org.sbml.libsbml
Implementation of SBML's ListOfRules construct.
ListOfRules(long, long) - Constructor for class org.sbml.libsbml.ListOfRules
Creates a new ListOfRules object.
ListOfRules(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfRules
Creates a new ListOfRules object.
ListOfSpecies - Class in org.sbml.libsbml
Implementation of SBML Level 2's ListOfSpecies construct.
ListOfSpecies(long, long) - Constructor for class org.sbml.libsbml.ListOfSpecies
Creates a new ListOfSpecies object.
ListOfSpecies(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfSpecies
Creates a new ListOfSpecies object.
ListOfSpeciesGlyphs - Class in org.sbml.libsbml
 
ListOfSpeciesGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesGlyphs
 
ListOfSpeciesGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesGlyphs
 
ListOfSpeciesGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfSpeciesGlyphs
 
ListOfSpeciesGlyphs() - Constructor for class org.sbml.libsbml.ListOfSpeciesGlyphs
 
ListOfSpeciesGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfSpeciesGlyphs
 
ListOfSpeciesReferenceGlyphs - Class in org.sbml.libsbml
 
ListOfSpeciesReferenceGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
 
ListOfSpeciesReferenceGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
 
ListOfSpeciesReferenceGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
 
ListOfSpeciesReferenceGlyphs() - Constructor for class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
 
ListOfSpeciesReferenceGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
 
ListOfSpeciesReferences - Class in org.sbml.libsbml
Implementation of SBML's ListOfSpeciesReferences construct.
ListOfSpeciesReferences(long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferences
Creates a new, empty ListOfSpeciesReferences object.
ListOfSpeciesReferences(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferences
Creates a new ListOfSpeciesReferences object.
ListOfSpeciesTypes - Class in org.sbml.libsbml
Implementation of SBML's ListOfSpeciesTypes construct.
ListOfSpeciesTypes(long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesTypes
Creates a new ListOfSpeciesTypes object.
ListOfSpeciesTypes(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfSpeciesTypes
Creates a new ListOfSpeciesTypes object.
ListOfSubmodels - Class in org.sbml.libsbml
 
ListOfSubmodels(long, long, long) - Constructor for class org.sbml.libsbml.ListOfSubmodels
 
ListOfSubmodels(long, long) - Constructor for class org.sbml.libsbml.ListOfSubmodels
 
ListOfSubmodels(long) - Constructor for class org.sbml.libsbml.ListOfSubmodels
 
ListOfSubmodels() - Constructor for class org.sbml.libsbml.ListOfSubmodels
 
ListOfSubmodels(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfSubmodels
 
ListOfTextGlyphs - Class in org.sbml.libsbml
 
ListOfTextGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfTextGlyphs
 
ListOfTextGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfTextGlyphs
 
ListOfTextGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfTextGlyphs
 
ListOfTextGlyphs() - Constructor for class org.sbml.libsbml.ListOfTextGlyphs
 
ListOfTextGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfTextGlyphs
 
ListOfUnitDefinitions - Class in org.sbml.libsbml
Implementation of SBML's ListOfUnitDefinitions construct.
ListOfUnitDefinitions(long, long) - Constructor for class org.sbml.libsbml.ListOfUnitDefinitions
Creates a new ListOfUnitDefinitions object.
ListOfUnitDefinitions(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfUnitDefinitions
Creates a new ListOfUnitDefinitions object.
ListOfUnits - Class in org.sbml.libsbml
Implementation of SBML's ListOfUnits construct.
ListOfUnits(long, long) - Constructor for class org.sbml.libsbml.ListOfUnits
Creates a new ListOfUnits object.
ListOfUnits(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfUnits
Creates a new ListOfUnits object.
LocalParameter - Class in org.sbml.libsbml
Implementation of SBML Level 3's LocalParameter construct.
LocalParameter(long, long) - Constructor for class org.sbml.libsbml.LocalParameter
Creates a new LocalParameter object with the given SBML level and version values.
LocalParameter(SBMLNamespaces) - Constructor for class org.sbml.libsbml.LocalParameter
Creates a new LocalParameter object with the given SBMLNamespaces object sbmlns.
LocalParameter(LocalParameter) - Constructor for class org.sbml.libsbml.LocalParameter
Copy constructor; creates a copy of a given LocalParameter object.
LocalParameter(Parameter) - Constructor for class org.sbml.libsbml.LocalParameter
Copy constructor; creates a LocalParameter object by copying the attributes of a given Parameter object.
LocalParameterShadowsId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
logFailure(SBMLError) - Method in class org.sbml.libsbml.SBMLValidator
Adds the given failure to this list of Validators failures.
logInvalidId(String, String) - Method in class org.sbml.libsbml.CompSBasePlugin
 

M

matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLConverter
Predicate returning true if this converter's properties matches a given set of configuration properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Predicate returning true if this converter's properties matches a given set of configuration properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLRuleConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLStripPackageConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLUnitsConverter
Predicate returning true if this converter's properties matches a given set of configuration properties.
matchesRequiredSBMLNamespacesForAddition(SBase) - Method in class org.sbml.libsbml.SBase
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.
matchesSBMLNamespaces(SBase) - Method in class org.sbml.libsbml.SBase
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.
MathCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MathCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MathResultMustBeNumeric - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
merge(Unit, Unit) - Static method in class org.sbml.libsbml.Unit
Merges two Unit objects with the same 'kind' attribute value into a single Unit.
MetaIdNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingAnnotationNamespace - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingEventAssignment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingOrInconsistentLevel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingOrInconsistentVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingSpeciesCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingTriggerInEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingXMLAttributeValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingXMLDecl - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingXMLElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingXMLEncoding - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingXMLRequiredAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Model - Class in org.sbml.libsbml
Implementation of SBML's Model construct.
Model(long, long) - Constructor for class org.sbml.libsbml.Model
Creates a new Model using the given SBML level and version values.
Model(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Model
Creates a new Model using the given SBMLNamespaces object sbmlns.
Model(Model) - Constructor for class org.sbml.libsbml.Model
Copy constructor; creates a (deep) copy of the given Model object.
MODEL_QUALIFIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ModelCreator - Class in org.sbml.libsbml
Representation of MIRIAM-compliant model creator data used in ModelHistory.
ModelCreator() - Constructor for class org.sbml.libsbml.ModelCreator
Creates a new ModelCreator object.
ModelCreator(XMLNode) - Constructor for class org.sbml.libsbml.ModelCreator
Creates a new ModelCreator from an XMLNode.
ModelCreator(ModelCreator) - Constructor for class org.sbml.libsbml.ModelCreator
Copy constructor; creates a copy of the ModelCreator.
ModelCreatorList - Class in org.sbml.libsbml
 
ModelCreatorList() - Constructor for class org.sbml.libsbml.ModelCreatorList
 
ModelDefinition - Class in org.sbml.libsbml
 
ModelDefinition(long, long, long) - Constructor for class org.sbml.libsbml.ModelDefinition
 
ModelDefinition(long, long) - Constructor for class org.sbml.libsbml.ModelDefinition
 
ModelDefinition(long) - Constructor for class org.sbml.libsbml.ModelDefinition
 
ModelDefinition() - Constructor for class org.sbml.libsbml.ModelDefinition
 
ModelDefinition(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ModelDefinition
 
ModelDefinition(Model) - Constructor for class org.sbml.libsbml.ModelDefinition
 
ModelHistory - Class in org.sbml.libsbml
Representation of MIRIAM-compliant model history data.
ModelHistory() - Constructor for class org.sbml.libsbml.ModelHistory
Creates a new ModelHistory object.
ModelHistory(ModelHistory) - Constructor for class org.sbml.libsbml.ModelHistory
Copy constructor; creates a copy of this ModelHistory object.
ModelSBOBranchChangedBeyondL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ModelSBOBranchChangedBeyondL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ModelSBOBranchChangedInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ModelSBOBranchChangedInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ModifierSpeciesReference - Class in org.sbml.libsbml
Implementation of SBML's ModifierSpeciesReference construct.
ModifierSpeciesReference(long, long) - Constructor for class org.sbml.libsbml.ModifierSpeciesReference
Creates a new ModifierSpeciesReference using the given SBML level and version values.
ModifierSpeciesReference(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ModifierSpeciesReference
Creates a new ModifierSpeciesReference using the given SBMLNamespaces object sbmlns.
MultipleAnnotations - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MultipleAssignmentOrRateRules - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MultipleEventAssignmentsForId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MultipleInitAssignments - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MultiplierNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MultSpeciesSameTypeInCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

N

NameNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NeedCompartmentIfHaveSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoBodyInFunctionDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoCompartmentOutsideInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoCompartmentTypeInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoCompartmentTypeInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoCompartmentTypeInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoConcentrationInZeroD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoConstraintsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoConstraintsInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoDelayedEventAssignmentInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoDelayedEventAssignmentInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoDelayedEventAssignmentInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoEventsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoEventTimeUnitsInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoEventTimeUnitsInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoEventTimeUnitsInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoFancyStoichiometryMathInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoFunctionDefinitionsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoIdOnSpeciesReferenceInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoInitialAssignmentsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoInitialAssignmentsInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawSubstanceUnitsInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawSubstanceUnitsInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawSubstanceUnitsInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawSubstanceUnitsInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawTimeUnitsInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawTimeUnitsInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawTimeUnitsInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawTimeUnitsInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NonBoundarySpeciesAssignedAndUsed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NonConstantLocalParameter - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NonConstantSpeciesUsed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoNon3DCompartmentsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoNonIntegerStoichiometryInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NonPersistentNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoReactantsOrProducts - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSBOTermsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSBOTermsInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpatialUnitsInZeroD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesSpatialSizeUnitsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesSpatialSizeUnitsInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesSpatialSizeUnitsInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesSpatialSizeUnitsInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesTypeInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesTypeInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesTypesInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoStoichiometryMathInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NotesContainsDOCTYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NotesContainsXMLDecl - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NotesNotInXHTMLNamespace - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoTimeSymbolInFunctionDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NotSchemaConformant - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NotUTF8 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitMultipliersOrOffsetsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitOffsetInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitOffsetInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitOffsetInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitOffsetInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitsOnCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NumericOpsNeedNumericArgs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

O

Objective - Class in org.sbml.libsbml
 
Objective(long, long, long) - Constructor for class org.sbml.libsbml.Objective
 
Objective(long, long) - Constructor for class org.sbml.libsbml.Objective
 
Objective(long) - Constructor for class org.sbml.libsbml.Objective
 
Objective() - Constructor for class org.sbml.libsbml.Objective
 
Objective(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.Objective
 
Objective(Objective) - Constructor for class org.sbml.libsbml.Objective
 
OBJECTIVE_TYPE_MAXIMIZE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OBJECTIVE_TYPE_MINIMIZE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OBJECTIVE_TYPE_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ObseleteSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OffsetNoLongerValid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OffsetNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OFStream - Class in org.sbml.libsbml
Wrapper class for the C++ standard file stream ofstream.
OFStream(String, boolean) - Constructor for class org.sbml.libsbml.OFStream
Creates a new OFStream object for a file.
OFStream(String) - Constructor for class org.sbml.libsbml.OFStream
Creates a new OFStream object for a file.
OneDimensionalCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneListOfEventAssignmentsPerEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneListOfPerKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneListOfUnitsPerUnitDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathElementPerConstraint - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathElementPerFunc - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathElementPerInitialAssign - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathElementPerRule - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathPerDelay - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathPerEventAssignment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathPerKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathPerPriority - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathPerTrigger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMessageElementPerConstraint - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneOfEachListOf - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneSubElementPerReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyCompartmentsInListOfCompartments - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyConstraintsInListOfConstraints - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyEventAssignInListOfEventAssign - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyEventsInListOfEvents - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyFuncDefsInListOfFuncDefs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyInitAssignsInListOfInitAssigns - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyLocalParamsInListOfLocalParams - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyOneDelayPerEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyOneNotesElementAllowed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyOnePriorityPerEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyParametersInListOfParameters - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyReactionsInListOfReactions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyRulesInListOfRules - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlySpeciesInListOfSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyUnitDefsInListOfUnitDefs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyUnitsInListOfUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
open(String, boolean) - Method in class org.sbml.libsbml.OFStream
Opens a file and associates this stream object with it.
open(String) - Method in class org.sbml.libsbml.OFStream
Opens a file and associates this stream object with it.
OpsNeedCorrectNumberOfArgs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OR_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
org.sbml.libsbml - package org.sbml.libsbml
 
OStream - Class in org.sbml.libsbml
Wrapper class for the C++ standard streams cout, cerr, and clog.
OStream(int) - Constructor for class org.sbml.libsbml.OStream
Creates a new OStream object with one of standard output stream objects.
OStream() - Constructor for class org.sbml.libsbml.OStream
Creates a new OStream object with one of standard output stream objects.
OStringStream - Class in org.sbml.libsbml
Wrapper class for the C++ standard stream ostringstream.
OStringStream() - Constructor for class org.sbml.libsbml.OStringStream
Creates a new OStringStream object
OverdeterCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OverdeterCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OverdeterminedSystem - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

P

PackageConversionNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PackageNSMustMatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PackageRequiredShouldBeFalse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Parameter - Class in org.sbml.libsbml
Implementation of SBML's Parameter construct.
Parameter(long, long) - Constructor for class org.sbml.libsbml.Parameter
Creates a new Parameter using the given SBML level and version values.
Parameter(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Parameter
Creates a new Parameter using the given SBMLNamespaces object sbmlns.
Parameter(Parameter) - Constructor for class org.sbml.libsbml.Parameter
Copy constructor; creates a copy of a Parameter.
ParameterShouldHaveUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ParameterUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
parseCVTerms(SBase) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Takes a list of CVTerm objects and creates a complete SBML annotation around it.
parseFormula(String) - Static method in class org.sbml.libsbml.libsbml
Parses the given SBML formula and returns a representation of it as an Abstract Syntax Tree (AST).
parseInfixAssociation(String) - Static method in class org.sbml.libsbml.Association
 
parseL3Formula(String) - Static method in class org.sbml.libsbml.libsbml
Parses the given mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
parseL3FormulaWithModel(String, Model) - Static method in class org.sbml.libsbml.libsbml
Parses the given mathematical formula using specific a specific Model to resolve symbols, and returns an Abstract Syntax Tree (AST) representation of the result.
parseL3FormulaWithSettings(String, L3ParserSettings) - Static method in class org.sbml.libsbml.libsbml
Parses the given mathematical formula using specific parser settings and returns an Abstract Syntax Tree (AST) representation of the result.
parseLayoutAnnotation(XMLNode, ListOfLayouts) - Static method in class org.sbml.libsbml.libsbml
 
parseLayoutId(SimpleSpeciesReference) - Static method in class org.sbml.libsbml.libsbml
 
parseLayouts(Model) - Static method in class org.sbml.libsbml.libsbml
 
parseModelHistory(SBase) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Reads the model history and cvTerms stored in obj and creates the XML structure for an SBML annotation representing that metadata if there is a model history stored in obj.
parseOnlyModelHistory(SBase) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Reads the model history stored in obj and creates the XML structure for an SBML annotation representing that history.
parseRDFAnnotation(XMLNode, SWIGTYPE_p_List, String, XMLInputStream) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Parses an annotation (given as an XMLNode tree) into a list of CVTerm objects.
parseRDFAnnotation(XMLNode, SWIGTYPE_p_List, String) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Parses an annotation (given as an XMLNode tree) into a list of CVTerm objects.
parseRDFAnnotation(XMLNode, String, XMLInputStream) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Parses an annotation into a ModelHistory class instance.
parseRDFAnnotation(XMLNode, String) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Parses an annotation into a ModelHistory class instance.
parseRDFAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Parses an annotation into a ModelHistory class instance.
parseRDFAnnotation(XMLNode, CVTermList) - Static method in class org.sbml.libsbml.RDFAnnotationParser
 
parseSpeciesReferenceAnnotation(XMLNode, SimpleSpeciesReference) - Static method in class org.sbml.libsbml.libsbml
 
performDeletion() - Method in class org.sbml.libsbml.SBaseRef
 
performDeletions() - Method in class org.sbml.libsbml.Submodel
 
performReplacement() - Method in class org.sbml.libsbml.ReplacedBy
 
performReplacement() - Method in class org.sbml.libsbml.ReplacedElement
 
performReplacement() - Method in class org.sbml.libsbml.Replacing
 
PersistentNotBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PieceNeedsBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PiecewiseNeedsConsistentTypes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Point - Class in org.sbml.libsbml
 
Point(long, long, long) - Constructor for class org.sbml.libsbml.Point
 
Point(long, long) - Constructor for class org.sbml.libsbml.Point
 
Point(long) - Constructor for class org.sbml.libsbml.Point
 
Point() - Constructor for class org.sbml.libsbml.Point
 
Point(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.Point
 
Point(Point) - Constructor for class org.sbml.libsbml.Point
 
Point(LayoutPkgNamespaces, double, double, double) - Constructor for class org.sbml.libsbml.Point
 
Point(LayoutPkgNamespaces, double, double) - Constructor for class org.sbml.libsbml.Point
 
Point(XMLNode, long) - Constructor for class org.sbml.libsbml.Point
 
Point(XMLNode) - Constructor for class org.sbml.libsbml.Point
 
populateListFormulaUnitsData() - Method in class org.sbml.libsbml.Model
Populates the list of FormulaDataUnits with the units derived for the model.
Port - Class in org.sbml.libsbml
 
Port(long, long, long) - Constructor for class org.sbml.libsbml.Port
 
Port(long, long) - Constructor for class org.sbml.libsbml.Port
 
Port(long) - Constructor for class org.sbml.libsbml.Port
 
Port() - Constructor for class org.sbml.libsbml.Port
 
Port(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.Port
 
Port(Port) - Constructor for class org.sbml.libsbml.Port
 
PracticeCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PracticeCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
prepend(ASTNode) - Method in class org.sbml.libsbml.ASTNodeList
 
prepend(CVTerm) - Method in class org.sbml.libsbml.CVTermList
 
prepend(Date) - Method in class org.sbml.libsbml.DateList
 
prepend(ModelCreator) - Method in class org.sbml.libsbml.ModelCreatorList
 
prepend(SBase) - Method in class org.sbml.libsbml.SBaseList
 
prepend(SBMLNamespaces) - Method in class org.sbml.libsbml.SBMLNamespacesList
 
prependChild(ASTNode) - Method in class org.sbml.libsbml.ASTNode
Adds the given node as a child of this ASTNode.
printErrors(OStream) - Method in class org.sbml.libsbml.SBMLDocument
Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document.
printErrors() - Method in class org.sbml.libsbml.SBMLDocument
Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document.
printErrors(OStream) - Method in class org.sbml.libsbml.XMLErrorLog
Prints all the errors or warnings stored in this error log
printErrors() - Method in class org.sbml.libsbml.XMLErrorLog
Prints all the errors or warnings stored in this error log
printUnits(UnitDefinition, boolean) - Static method in class org.sbml.libsbml.UnitDefinition
Expresses the given definition in a plain-text form.
printUnits(UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Expresses the given definition in a plain-text form.
Priority - Class in org.sbml.libsbml
Implementation of SBML Level 3's Priority construct for Event.
Priority(long, long) - Constructor for class org.sbml.libsbml.Priority
Creates a new Priority object using the given SBML level and version values.
Priority(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Priority
Creates a new Priority object using the given SBMLNamespaces object sbmlns.
Priority(Priority) - Constructor for class org.sbml.libsbml.Priority
Copy constructor; creates a copy of this Priority.
PriorityLostFromL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PriorityUnitsNotDimensionless - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

R

RateRule - Class in org.sbml.libsbml
Implementation of SBML's RateRule construct.
RateRule(long, long) - Constructor for class org.sbml.libsbml.RateRule
Creates a new RateRule using the given SBML level and version values.
RateRule(SBMLNamespaces) - Constructor for class org.sbml.libsbml.RateRule
Creates a new RateRule using the given SBMLNamespaces object sbmlns.
RateRuleCompartmentMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateRuleForConstantEntity - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateRuleParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateRuleSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateRuleStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RDFAboutTagNotMetaid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RDFAnnotationParser - Class in org.sbml.libsbml
Read/write/manipulate RDF annotations stored in SBML annotation elements.
RDFAnnotationParser() - Constructor for class org.sbml.libsbml.RDFAnnotationParser
 
RDFEmptyAboutTag - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RDFMissingAboutTag - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RDFNotCompleteModelHistory - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RDFNotModelHistory - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Reaction - Class in org.sbml.libsbml
Implementation of SBML's Reaction construct.
Reaction(long, long) - Constructor for class org.sbml.libsbml.Reaction
Creates a new Reaction using the given SBML level and version values.
Reaction(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Reaction
Creates a new Reaction using the given SBMLNamespaces object sbmlns.
Reaction(Reaction) - Constructor for class org.sbml.libsbml.Reaction
Copy constructor; creates a copy of this Reaction.
ReactionGlyph - Class in org.sbml.libsbml
 
ReactionGlyph(long, long, long) - Constructor for class org.sbml.libsbml.ReactionGlyph
 
ReactionGlyph(long, long) - Constructor for class org.sbml.libsbml.ReactionGlyph
 
ReactionGlyph(long) - Constructor for class org.sbml.libsbml.ReactionGlyph
 
ReactionGlyph() - Constructor for class org.sbml.libsbml.ReactionGlyph
 
ReactionGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ReactionGlyph
 
ReactionGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.ReactionGlyph
 
ReactionGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.ReactionGlyph
 
ReactionGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.ReactionGlyph
 
ReactionGlyph(XMLNode) - Constructor for class org.sbml.libsbml.ReactionGlyph
 
ReactionGlyph(ReactionGlyph) - Constructor for class org.sbml.libsbml.ReactionGlyph
 
readMathMLFromString(String) - Static method in class org.sbml.libsbml.libsbml
Reads the MathML from the given XML string, constructs a corresponding abstract syntax tree, and returns a pointer to the root of the tree.
readOtherXML(SBase, XMLInputStream) - Method in class org.sbml.libsbml.FbcModelPlugin
 
readSBML(String) - Static method in class org.sbml.libsbml.libsbml
Reads an SBML document from the given file filename.
readSBML(String) - Method in class org.sbml.libsbml.SBMLReader
Reads an SBML document from a file.
readSBMLFromFile(String) - Static method in class org.sbml.libsbml.libsbml
Reads an SBML document from the given file filename.
readSBMLFromFile(String) - Method in class org.sbml.libsbml.SBMLReader
Reads an SBML document from a file.
readSBMLFromString(String) - Static method in class org.sbml.libsbml.libsbml
Reads an SBML document from a string assumed to be in XML format.
readSBMLFromString(String) - Method in class org.sbml.libsbml.SBMLReader
Reads an SBML document from the given XML string.
RecursiveCompartmentContainment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RecursiveFunctionDefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
reduceToBinary() - Method in class org.sbml.libsbml.ASTNode
Reduces this ASTNode to a binary tree.
ReferenceGlyph - Class in org.sbml.libsbml
 
ReferenceGlyph(long, long, long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
 
ReferenceGlyph(long, long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
 
ReferenceGlyph(long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
 
ReferenceGlyph() - Constructor for class org.sbml.libsbml.ReferenceGlyph
 
ReferenceGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ReferenceGlyph
 
ReferenceGlyph(LayoutPkgNamespaces, String, String, String, String) - Constructor for class org.sbml.libsbml.ReferenceGlyph
 
ReferenceGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
 
ReferenceGlyph(XMLNode) - Constructor for class org.sbml.libsbml.ReferenceGlyph
 
ReferenceGlyph(ReferenceGlyph) - Constructor for class org.sbml.libsbml.ReferenceGlyph
 
relativeTo(String) - Method in class org.sbml.libsbml.SBMLUri
 
remove(long) - Method in class org.sbml.libsbml.ASTNodeList
 
remove(long) - Method in class org.sbml.libsbml.CVTermList
 
remove(long) - Method in class org.sbml.libsbml.DateList
 
remove(long) - Method in class org.sbml.libsbml.ListOf
Removes the nth item from this ListOf items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfCompartments
Removes the nth item from this ListOfCompartments items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfCompartments
Removes item in this ListOfCompartments items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Removes the nth item from this ListOfCompartmentTypes items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Removes item in this ListOfCompartmentTypes items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfConstraints
Removes the nth item from this ListOfConstraints items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfDeletions
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfDeletions
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfEventAssignments
Removes the nth item from this ListOfEventAssignments items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfEventAssignments
Removes item in this ListOfEventAssignments items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfEvents
Removes the nth item from this ListOfEvents items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfEvents
Removes item in this ListOfEvents items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfFluxBounds
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfFluxBounds
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfFluxObjectives
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfFluxObjectives
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Removes the nth item from this ListOfFunctionDefinitions items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Removes item in this ListOfFunctionDefinitions items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfGeneAssociations
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfGeneAssociations
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfInitialAssignments
Removes the nth item from this ListOfInitialAssignments items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfInitialAssignments
Removes item in this ListOfInitialAssignments items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfLayouts
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfLayouts
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfLineSegments
Removes the nth item from this ListOf items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfLocalParameters
Removes the nth item from this ListOfLocalParameters, and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfLocalParameters
Removes the first LocalParameter object in this ListOfLocalParameters matching the given identifier, and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfModelDefinitions
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfModelDefinitions
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfObjectives
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfObjectives
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfParameters
Removes the nth item from this ListOfParameters, and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfParameters
Removes the first Parameter object in this ListOfParameters matching the given identifier, and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfPorts
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfPorts
Removes the nth item from this ListOf items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfReactions
Removes the nth item from this ListOfReactions items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfReactions
Removes item in this ListOfReactions items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfReplacedElements
Removes the nth item from this ListOf items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfRules
Removes the nth item from this ListOfRules items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfRules
Removes item in this ListOfRules items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfSpecies
Removes the nth item from this ListOfSpeciess items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfSpecies
Removes item in this ListOfSpeciess items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Removes the nth item from this ListOfSpeciesReferences items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Removes item in this ListOfSpeciesReferences items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Removes the nth item from this ListOfSpeciesTypes items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Removes item in this ListOfSpeciesTypes items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfSubmodels
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfSubmodels
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfTextGlyphs
Removes the nth item from this ListOf items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfTextGlyphs
Removes item in this ListOf items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Removes the nth item from this ListOfUnitDefinitions items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Removes item in this ListOfUnitDefinitions items with the given identifier.
remove(long) - Method in class org.sbml.libsbml.ListOfUnits
Removes the nth item from this ListOfUnits items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ModelCreatorList
 
remove(long) - Method in class org.sbml.libsbml.SBaseList
 
remove(long) - Method in class org.sbml.libsbml.SBMLErrorLog
Removes an error having errorId from the SBMLError list.
remove(long) - Method in class org.sbml.libsbml.SBMLNamespacesList
 
remove(int) - Method in class org.sbml.libsbml.XMLAttributes
Removes an attribute with the given index from this XMLAttributes set.
remove(String, String) - Method in class org.sbml.libsbml.XMLAttributes
Removes an attribute with the given local name and namespace URI from this XMLAttributes set.
remove(String) - Method in class org.sbml.libsbml.XMLAttributes
Removes an attribute with the given local name and namespace URI from this XMLAttributes set.
remove(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
Removes an attribute with the given XMLTriple from this XMLAttributes set.
remove(int) - Method in class org.sbml.libsbml.XMLNamespaces
Removes an XML Namespace stored in the given position of this list.
remove(String) - Method in class org.sbml.libsbml.XMLNamespaces
Removes an XML Namespace with the given prefix.
removeAdditionalGraphicalObject(long) - Method in class org.sbml.libsbml.Layout
 
removeAdditionalGraphicalObject(String) - Method in class org.sbml.libsbml.Layout
 
removeAssociation(int) - Method in class org.sbml.libsbml.Association
 
removeAttr(int) - Method in class org.sbml.libsbml.XMLToken
Removes an attribute with the given index from the attribute set in this XMLToken.
removeAttr(String, String) - Method in class org.sbml.libsbml.XMLToken
Removes an attribute with the given local name and namespace URI from the attribute set in this XMLToken.
removeAttr(String) - Method in class org.sbml.libsbml.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.libsbml.XMLToken
Removes an attribute with the given XMLTriple from the attribute set in this XMLToken.
removeChild(long) - Method in class org.sbml.libsbml.ASTNode
Removes the nth child of this ASTNode object.
removeChild(long) - Method in class org.sbml.libsbml.XMLNode
Removes the nth child of this XMLNode and returns the removed node.
removeChildren() - Method in class org.sbml.libsbml.XMLNode
Removes all children from this node.
removeCompartment(long) - Method in class org.sbml.libsbml.Model
Removes the nth Compartment object from this Model object and returns a pointer to it.
removeCompartment(String) - Method in class org.sbml.libsbml.Model
Removes the Compartment object with the given identifier from this Model object and returns a pointer to it.
removeCompartmentGlyph(long) - Method in class org.sbml.libsbml.Layout
 
removeCompartmentGlyph(String) - Method in class org.sbml.libsbml.Layout
 
removeCompartmentType(long) - Method in class org.sbml.libsbml.Model
Removes the nth CompartmentType object from this Model object and returns a pointer to it.
removeCompartmentType(String) - Method in class org.sbml.libsbml.Model
Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it.
removeConstraint(long) - Method in class org.sbml.libsbml.Model
Removes the nth Constraint object from this Model object and returns a pointer to it.
removeDeletion(long) - Method in class org.sbml.libsbml.Submodel
 
removeDeletion(String) - Method in class org.sbml.libsbml.Submodel
 
removeEvent(long) - Method in class org.sbml.libsbml.Model
Removes the nth Event object from this Model object and returns a pointer to it.
removeEvent(String) - Method in class org.sbml.libsbml.Model
Removes the Event object with the given identifier from this Model object and returns a pointer to it.
removeEventAssignment(long) - Method in class org.sbml.libsbml.Event
Removes the nth EventAssignment object from this Event object and returns a pointer to it.
removeEventAssignment(String) - Method in class org.sbml.libsbml.Event
Removes the EventAssignment object with the given 'variable' attribute from this Event object and returns a pointer to it.
removeExternalModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
removeExternalModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
removeFluxBound(long) - Method in class org.sbml.libsbml.FbcModelPlugin
 
removeFluxBound(String) - Method in class org.sbml.libsbml.FbcModelPlugin
 
removeFluxObjective(long) - Method in class org.sbml.libsbml.Objective
 
removeFluxObjective(String) - Method in class org.sbml.libsbml.Objective
 
removeFromParentAndDelete() - Method in class org.sbml.libsbml.Delay
Finds this Delay's Event parent and calls unsetDelay() on it, indirectly deleting itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.KineticLaw
Finds this KineticLaw's Reaction parent and calls unsetKineticLaw() on it, indirectly deleting itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.ListOf
Because ListOf objects typically live as object children of their parent object and not as pointer children, this function clears itself, but does not attempt to do anything else.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.Model
Finds this Model's parent SBMLDocument and calls setModel(null) on it, indirectly deleting itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.ModelDefinition
Finds this Model's parent SBMLDocument and calls setModel(null) on it, indirectly deleting itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.Priority
Finds this Priority's Event parent and calls unsetPriority() on it, indirectly deleting itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.ReplacedBy
Removes itself from its parent.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.SBase
Removes itself from its parent.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.SBaseRef
Removes itself from its parent.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.StoichiometryMath
Finds this StoichiometryMath's SpeciesReference parent and calls unsetStoichiometryMath() on it, indirectly deleting itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.Trigger
Finds this Trigger's Event parent and calls unsetTrigger() on it, indirectly deleting itself.
removeFunctionDefinition(long) - Method in class org.sbml.libsbml.Model
Removes the nth FunctionDefinition object from this Model object and returns a pointer to it.
removeFunctionDefinition(String) - Method in class org.sbml.libsbml.Model
Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it.
removeGeneAssociation(long) - Method in class org.sbml.libsbml.FbcModelPlugin
 
removeGeneAssociation(String) - Method in class org.sbml.libsbml.FbcModelPlugin
 
removeInitialAssignment(long) - Method in class org.sbml.libsbml.Model
Removes the nth InitialAssignment object from this Model object and returns a pointer to it.
removeInitialAssignment(String) - Method in class org.sbml.libsbml.Model
Removes the InitialAssignment object with the given 'symbol' attribute from this Model object and returns a pointer to it.
removeL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Remove all L2 Extension namespaces from the namespace list.
removeLayout(long) - Method in class org.sbml.libsbml.LayoutModelPlugin
 
removeLocalParameter(long) - Method in class org.sbml.libsbml.KineticLaw
Removes the nth LocalParameter object in the list of local parameters in this KineticLaw instance and returns a pointer to it.
removeLocalParameter(String) - Method in class org.sbml.libsbml.KineticLaw
Removes a LocalParameter object with the given identifier in the list of local parameters in this KineticLaw instance and returns a pointer to it.
removeModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
removeModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
 
removeModifier(long) - Method in class org.sbml.libsbml.Reaction
Removes the nth modifier species (ModifierSpeciesReference object) in the list of modifiers in this Reaction and returns a pointer to it.
removeModifier(String) - Method in class org.sbml.libsbml.Reaction
Removes the modifier species (ModifierSpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.
removeNamespace(String) - Method in class org.sbml.libsbml.SBMLNamespaces
Removes an XML namespace from the set of namespaces within this SBMLNamespaces object.
removeNamespace(int) - Method in class org.sbml.libsbml.XMLToken
Removes an XML Namespace stored in the given position of the XMLNamespaces of this XMLToken.
removeNamespace(String) - Method in class org.sbml.libsbml.XMLToken
Removes an XML Namespace with the given prefix.
removeObjective(long) - Method in class org.sbml.libsbml.FbcModelPlugin
 
removeObjective(String) - Method in class org.sbml.libsbml.FbcModelPlugin
 
removeOption(String) - Method in class org.sbml.libsbml.ConversionProperties
Removes the option with the given key from this properties object.
removePackageNamespace(long, long, String, long) - Method in class org.sbml.libsbml.SBMLNamespaces
Removes an XML namespace of a package extension from the set of namespaces within this SBMLNamespaces object.
removeParameter(long) - Method in class org.sbml.libsbml.KineticLaw
Removes the nth Parameter object in the list of local parameters in this KineticLaw instance and returns a pointer to it.
removeParameter(String) - Method in class org.sbml.libsbml.KineticLaw
Removes a Parameter object with the given identifier in the list of local parameters in this KineticLaw instance and returns a pointer to it.
removeParameter(long) - Method in class org.sbml.libsbml.Model
Removes the nth Parameter object from this Model object and returns a pointer to it.
removeParameter(String) - Method in class org.sbml.libsbml.Model
Removes the Parameter object with the given identifier from this Model object and returns a pointer to it.
removePort(long) - Method in class org.sbml.libsbml.CompModelPlugin
 
removeProduct(long) - Method in class org.sbml.libsbml.Reaction
Removes the nth product species (SpeciesReference object) in the list of products in this Reaction and returns a pointer to it.
removeProduct(String) - Method in class org.sbml.libsbml.Reaction
Removes the product species (SpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.
removeReactant(long) - Method in class org.sbml.libsbml.Reaction
Removes the nth reactant species (SpeciesReference object) in the list of reactants in this Reaction and returns a pointer to it.
removeReactant(String) - Method in class org.sbml.libsbml.Reaction
Removes the reactant species (SpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.
removeReaction(long) - Method in class org.sbml.libsbml.Model
Removes the nth Reaction object from this Model object and returns a pointer to it.
removeReaction(String) - Method in class org.sbml.libsbml.Model
Removes the Reaction object with the given identifier from this Model object and returns a pointer to it.
removeReactionGlyph(long) - Method in class org.sbml.libsbml.Layout
 
removeReactionGlyph(String) - Method in class org.sbml.libsbml.Layout
 
removeReferenceGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
 
removeReferenceGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
 
removeReplacedElement(long) - Method in class org.sbml.libsbml.CompSBasePlugin
 
removeResolver(int) - Method in class org.sbml.libsbml.SBMLResolverRegistry
 
removeResource(String) - Method in class org.sbml.libsbml.CVTerm
Removes a resource URI from the set of resources stored in this CVTerm object.
removeResource(int) - Method in class org.sbml.libsbml.XMLAttributes
Removes an attribute with the given index from this XMLAttributes set.
removeRule(long) - Method in class org.sbml.libsbml.Model
Removes the nth Rule object from this Model object and returns a pointer to it.
removeRule(String) - Method in class org.sbml.libsbml.Model
Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it.
removeScale(Unit) - Static method in class org.sbml.libsbml.Unit
Manipulates the attributes of the Unit to express the unit with the value of the scale attribute reduced to zero.
removeSpecies(long) - Method in class org.sbml.libsbml.Model
Removes the nth Species object from this Model object and returns a pointer to it.
removeSpecies(String) - Method in class org.sbml.libsbml.Model
Removes the Species object with the given identifier from this Model object and returns a pointer to it.
removeSpeciesGlyph(long) - Method in class org.sbml.libsbml.Layout
 
removeSpeciesGlyph(String) - Method in class org.sbml.libsbml.Layout
 
removeSpeciesReferenceGlyph(String) - Method in class org.sbml.libsbml.Layout
 
removeSpeciesReferenceGlyph(long) - Method in class org.sbml.libsbml.ReactionGlyph
 
removeSpeciesReferenceGlyph(String) - Method in class org.sbml.libsbml.ReactionGlyph
 
removeSpeciesType(long) - Method in class org.sbml.libsbml.Model
Removes the nth SpeciesType object from this Model object and returns a pointer to it.
removeSpeciesType(String) - Method in class org.sbml.libsbml.Model
Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it.
removeSubGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
 
removeSubGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
 
removeSubmodel(long) - Method in class org.sbml.libsbml.CompModelPlugin
 
removeTextGlyph(long) - Method in class org.sbml.libsbml.Layout
 
removeTextGlyph(String) - Method in class org.sbml.libsbml.Layout
 
removeTopLevelAnnotationElement(String, String) - Method in class org.sbml.libsbml.SBase
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
removeTopLevelAnnotationElement(String) - Method in class org.sbml.libsbml.SBase
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
removeUnit(long) - Method in class org.sbml.libsbml.UnitDefinition
Removes the nth Unit object from this UnitDefinition object and returns a pointer to it.
removeUnitDefinition(long) - Method in class org.sbml.libsbml.Model
Removes the nth UnitDefinition object from this Model object and returns a pointer to it.
removeUnitDefinition(String) - Method in class org.sbml.libsbml.Model
Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it.
renameMetaIdRefs(String, String) - Method in class org.sbml.libsbml.Port
Renames all the MetaIdRef attributes on this element.
renameMetaIdRefs(String, String) - Method in class org.sbml.libsbml.SBase
Renames all the MetaIdRef attributes on this element.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.AssignmentRule
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ASTNode
Renames all the SIdRef attributes on this node and any child node
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Compartment
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Constraint
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Delay
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.EventAssignment
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.InitialAssignment
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.KineticLaw
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Model
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Port
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Priority
Renames all the SIdRef attributes on this element, including any found in MathML.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.RateRule
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Reaction
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ReplacedElement
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Replacing
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Rule
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SBase
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SBaseRef
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Species
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.StoichiometryMath
Renames all the SIdRef attributes on this element, including any found in MathML
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Submodel
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Trigger
Renames all the SIdRef attributes on this element, including any found in MathML
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.ASTNode
Renames all the UnitSIdRef attributes on this node and any child node.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Compartment
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Constraint
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Delay
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.EventAssignment
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.FunctionDefinition
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.InitialAssignment
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.KineticLaw
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Model
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Parameter
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Port
Renames all the UnitSIdRef attributes on this element.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Priority
Renames all the UnitSIdRef attributes on this element.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Rule
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.SBase
Renames all the UnitSIdRef attributes on this element.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Species
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.StoichiometryMath
Renames all the UnitSIdRef attributes on this element
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Trigger
Renames all the UnitSIdRef attributes on this element
reorder(UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Alphabetically orders the Unit objects within the ListOfUnits of a UnitDefinition.
RepeatedRule10304 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RepeatedRule20611 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
replaceArgument(String, ASTNode) - Method in class org.sbml.libsbml.ASTNode
Replaces occurences of a given name within this ASTNode with the name/value/formula represented by arg.
replaceChild(long, ASTNode) - Method in class org.sbml.libsbml.ASTNode
Replaces the nth child of this ASTNode with the given ASTNode.
ReplacedBy - Class in org.sbml.libsbml
 
ReplacedBy(long, long, long) - Constructor for class org.sbml.libsbml.ReplacedBy
 
ReplacedBy(long, long) - Constructor for class org.sbml.libsbml.ReplacedBy
 
ReplacedBy(long) - Constructor for class org.sbml.libsbml.ReplacedBy
 
ReplacedBy() - Constructor for class org.sbml.libsbml.ReplacedBy
 
ReplacedBy(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ReplacedBy
 
ReplacedBy(ReplacedBy) - Constructor for class org.sbml.libsbml.ReplacedBy
 
ReplacedElement - Class in org.sbml.libsbml
 
ReplacedElement(long, long, long) - Constructor for class org.sbml.libsbml.ReplacedElement
 
ReplacedElement(long, long) - Constructor for class org.sbml.libsbml.ReplacedElement
 
ReplacedElement(long) - Constructor for class org.sbml.libsbml.ReplacedElement
 
ReplacedElement() - Constructor for class org.sbml.libsbml.ReplacedElement
 
ReplacedElement(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ReplacedElement
 
ReplacedElement(ReplacedElement) - Constructor for class org.sbml.libsbml.ReplacedElement
 
replaceElement(SBase, SBase) - Method in class org.sbml.libsbml.Submodel
 
replaceTopLevelAnnotationElement(XMLNode) - Method in class org.sbml.libsbml.SBase
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
replaceTopLevelAnnotationElement(String) - Method in class org.sbml.libsbml.SBase
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
replaceWithAndMaybeDelete(SBase, boolean, ASTNode) - Method in class org.sbml.libsbml.Replacing
 
Replacing - Class in org.sbml.libsbml
 
representsValidDate() - Method in class org.sbml.libsbml.Date
Returns true or false depending on whether this date object represents a valid date and time value.
RequiredPackagePresent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
resetElementNamespace(String) - Method in class org.sbml.libsbml.ListOfLayouts
 
resolve(String, String) - Method in class org.sbml.libsbml.SBMLFileResolver
 
resolve(String) - Method in class org.sbml.libsbml.SBMLFileResolver
 
resolve(String, String) - Method in class org.sbml.libsbml.SBMLResolver
 
resolve(String) - Method in class org.sbml.libsbml.SBMLResolver
 
resolve(String, String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
 
resolve(String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
 
resolveUri(String, String) - Method in class org.sbml.libsbml.SBMLFileResolver
 
resolveUri(String) - Method in class org.sbml.libsbml.SBMLFileResolver
 
resolveUri(String, String) - Method in class org.sbml.libsbml.SBMLResolver
 
resolveUri(String) - Method in class org.sbml.libsbml.SBMLResolver
 
resolveUri(String, String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
 
resolveUri(String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
 
returnsBoolean(Model) - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node returns a boolean type or false (zero) otherwise.
returnsBoolean() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true (non-zero) if this node returns a boolean type or false (zero) otherwise.
Rule - Class in org.sbml.libsbml
Implementation of SBML's Rule construct.
Rule(Rule) - Constructor for class org.sbml.libsbml.Rule
Copy constructor; creates a copy of this Rule.
RULE_TYPE_INVALID - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RULE_TYPE_RATE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RULE_TYPE_SCALAR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

S

saveReferencedElement() - Method in class org.sbml.libsbml.Deletion
 
saveReferencedElement() - Method in class org.sbml.libsbml.Port
 
saveReferencedElement() - Method in class org.sbml.libsbml.Replacing
 
saveReferencedElement() - Method in class org.sbml.libsbml.SBaseRef
 
SBase - Class in org.sbml.libsbml
Implementation of SBase, the base class of most SBML objects.
SBaseList - Class in org.sbml.libsbml
 
SBaseList() - Constructor for class org.sbml.libsbml.SBaseList
 
SBasePlugin - Class in org.sbml.libsbml
Representation of a plug-in object of SBML's package extension.
SBaseRef - Class in org.sbml.libsbml
 
SBaseRef(long, long, long) - Constructor for class org.sbml.libsbml.SBaseRef
 
SBaseRef(long, long) - Constructor for class org.sbml.libsbml.SBaseRef
 
SBaseRef(long) - Constructor for class org.sbml.libsbml.SBaseRef
 
SBaseRef() - Constructor for class org.sbml.libsbml.SBaseRef
 
SBaseRef(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.SBaseRef
 
SBaseRef(SBaseRef) - Constructor for class org.sbml.libsbml.SBaseRef
 
SBML_ALGEBRAIC_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_ASSIGNMENT_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_DELETION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_EXTERNALMODELDEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_MODELDEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_PORT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_REPLACEDBY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_REPLACEDELEMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_SBASEREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_SUBMODEL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMPARTMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMPARTMENT_TYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMPARTMENT_VOLUME_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_CONSTRAINT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_DELAY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_DOCUMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_EVENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_EVENT_ASSIGNMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_FLUXBOUND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_FLUXOBJECTIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_GENEASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_OBJECTIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FUNCTION_DEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_INITIAL_ASSIGNMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_KINETIC_LAW - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_BOUNDINGBOX - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_COMPARTMENTGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_CUBICBEZIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_CURVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_DIMENSIONS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_GENERALGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_GRAPHICALOBJECT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_LAYOUT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_LINESEGMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_POINT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_REACTIONGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_REFERENCEGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_SPECIESGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_SPECIESREFERENCEGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_TEXTGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LIST_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LOCAL_PARAMETER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_MODEL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_MODIFIER_SPECIES_REFERENCE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_PARAMETER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_PARAMETER_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_PRIORITY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RATE_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_REACTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_SPECIES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_SPECIES_CONCENTRATION_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_SPECIES_REFERENCE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_SPECIES_TYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_STOICHIOMETRY_MATH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_TRIGGER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_UNIT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_UNIT_DEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBMLCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBMLCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBMLCodesUpperBound - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBMLConstructorException - Exception in org.sbml.libsbml
Class of exceptions thrown by constructors of some libSBML objects.
SBMLConstructorException(String) - Constructor for exception org.sbml.libsbml.SBMLConstructorException
Exception thrown by libSBML object constructors if something prevents the object from being properly created.
SBMLConstructorException() - Constructor for exception org.sbml.libsbml.SBMLConstructorException
 
SBMLConstructorException(String, String) - Constructor for exception org.sbml.libsbml.SBMLConstructorException
 
SBMLConstructorException(String, SBMLNamespaces) - Constructor for exception org.sbml.libsbml.SBMLConstructorException
 
SBMLConverter - Class in org.sbml.libsbml
Base class for SBML converters.
SBMLConverter() - Constructor for class org.sbml.libsbml.SBMLConverter
Creates a new SBMLConverter object.
SBMLConverter(SBMLConverter) - Constructor for class org.sbml.libsbml.SBMLConverter
Copy constructor; creates a copy of an SBMLConverter object.
SBMLConverterRegistry - Class in org.sbml.libsbml
Registry of all SBML converters.
SBMLDocument - Class in org.sbml.libsbml
Container for an SBML document and interface for global operations on SBML documents.
SBMLDocument(long, long) - Constructor for class org.sbml.libsbml.SBMLDocument
Creates a new SBMLDocument, optionally with given values for the SBML Level and Version.
SBMLDocument(long) - Constructor for class org.sbml.libsbml.SBMLDocument
Creates a new SBMLDocument, optionally with given values for the SBML Level and Version.
SBMLDocument() - Constructor for class org.sbml.libsbml.SBMLDocument
Creates a new SBMLDocument, optionally with given values for the SBML Level and Version.
SBMLDocument(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SBMLDocument
Creates a new SBMLDocument using the given SBMLNamespaces object sbmlns.
SBMLDocument(SBMLDocument) - Constructor for class org.sbml.libsbml.SBMLDocument
Copy constructor; creates a copy of this SBMLDocument.
SBMLDocumentPlugin - Class in org.sbml.libsbml
 
SBMLDocumentPlugin(String, String, SBMLNamespaces) - Constructor for class org.sbml.libsbml.SBMLDocumentPlugin
Constructor
SBMLDocumentPlugin(SBMLDocumentPlugin) - Constructor for class org.sbml.libsbml.SBMLDocumentPlugin
Copy constructor.
SBMLError - Class in org.sbml.libsbml
Representation of errors, warnings and other diagnostics
SBMLError(long, long, long, String, long, long, long, long, String, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long, long, long, long, String) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long, long, long, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long, long, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError() - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(SBMLError) - Constructor for class org.sbml.libsbml.SBMLError
Copy constructor; creates a copy of this SBMLError.
SBMLErrorLog - Class in org.sbml.libsbml
Log of errors and other events encountered during SBML processing.
SBMLExtensionException - Class in org.sbml.libsbml
 
SBMLExtensionException(String) - Constructor for class org.sbml.libsbml.SBMLExtensionException
constructor
SBMLExtensionRegistry - Class in org.sbml.libsbml
 
SBMLExternalValidator - Class in org.sbml.libsbml
 
SBMLExternalValidator() - Constructor for class org.sbml.libsbml.SBMLExternalValidator
Constructor.
SBMLExternalValidator(SBMLExternalValidator) - Constructor for class org.sbml.libsbml.SBMLExternalValidator
Copy constructor.
SBMLFileResolver - Class in org.sbml.libsbml
 
SBMLFileResolver() - Constructor for class org.sbml.libsbml.SBMLFileResolver
 
SBMLFileResolver(SBMLFileResolver) - Constructor for class org.sbml.libsbml.SBMLFileResolver
 
SBMLFunctionDefinitionConverter - Class in org.sbml.libsbml
SBML converter for replacing function definitions.
SBMLFunctionDefinitionConverter() - Constructor for class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Creates a new SBMLFunctionDefinitionConverter object.
SBMLFunctionDefinitionConverter(SBMLFunctionDefinitionConverter) - Constructor for class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Copy constructor; creates a copy of an SBMLFunctionDefinitionConverter object.
SBMLInitialAssignmentConverter - Class in org.sbml.libsbml
SBML converter for replacing initial assignments.
SBMLInitialAssignmentConverter() - Constructor for class org.sbml.libsbml.SBMLInitialAssignmentConverter
Creates a new SBMLInitialAssignmentConverter object.
SBMLInitialAssignmentConverter(SBMLInitialAssignmentConverter) - Constructor for class org.sbml.libsbml.SBMLInitialAssignmentConverter
Copy constructor; creates a copy of an SBMLInitialAssignmentConverter object.
SBMLLevelVersionConverter - Class in org.sbml.libsbml
SBML converter for transforming documents from one Level+Version to another.
SBMLLevelVersionConverter() - Constructor for class org.sbml.libsbml.SBMLLevelVersionConverter
Creates a new SBMLLevelVersionConverter object.
SBMLLevelVersionConverter(SBMLLevelVersionConverter) - Constructor for class org.sbml.libsbml.SBMLLevelVersionConverter
Copy constructor; creates a copy of an SBMLLevelVersionConverter object.
SBMLNamespaceInAnnotation - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBMLNamespaces - Class in org.sbml.libsbml
Class to store SBML level, version and namespace information.
SBMLNamespaces(long, long) - Constructor for class org.sbml.libsbml.SBMLNamespaces
Creates a new SBMLNamespaces object corresponding to the given SBML level and version.
SBMLNamespaces(long) - Constructor for class org.sbml.libsbml.SBMLNamespaces
Creates a new SBMLNamespaces object corresponding to the given SBML level and version.
SBMLNamespaces() - Constructor for class org.sbml.libsbml.SBMLNamespaces
Creates a new SBMLNamespaces object corresponding to the given SBML level and version.
SBMLNamespaces(long, long, String, long, String) - Constructor for class org.sbml.libsbml.SBMLNamespaces
(For Extension)
SBMLNamespaces(long, long, String, long) - Constructor for class org.sbml.libsbml.SBMLNamespaces
(For Extension)
SBMLNamespaces(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SBMLNamespaces
Copy constructor; creates a copy of a SBMLNamespaces.
SBMLNamespacesList - Class in org.sbml.libsbml
 
SBMLNamespacesList() - Constructor for class org.sbml.libsbml.SBMLNamespacesList
 
SBMLReader - Class in org.sbml.libsbml
Methods for reading SBML from files and text strings.
SBMLReader() - Constructor for class org.sbml.libsbml.SBMLReader
Creates a new SBMLReader and returns it.
SBMLResolver - Class in org.sbml.libsbml
 
SBMLResolver() - Constructor for class org.sbml.libsbml.SBMLResolver
 
SBMLResolver(SBMLResolver) - Constructor for class org.sbml.libsbml.SBMLResolver
 
SBMLResolverRegistry - Class in org.sbml.libsbml
 
SBMLRuleConverter - Class in org.sbml.libsbml
SBML converter for reordering rules and assignments in a model.
SBMLRuleConverter() - Constructor for class org.sbml.libsbml.SBMLRuleConverter
Creates a new SBMLLevelVersionConverter object.
SBMLRuleConverter(SBMLRuleConverter) - Constructor for class org.sbml.libsbml.SBMLRuleConverter
Copy constructor; creates a copy of an SBMLLevelVersionConverter object.
SBMLStripPackageConverter - Class in org.sbml.libsbml
SBML converter for removing packages.
SBMLStripPackageConverter() - Constructor for class org.sbml.libsbml.SBMLStripPackageConverter
Creates a new SBMLStripPackageConverter object.
SBMLStripPackageConverter(SBMLStripPackageConverter) - Constructor for class org.sbml.libsbml.SBMLStripPackageConverter
Copy constructor; creates a copy of an SBMLStripPackageConverter object.
SBMLTypeCode_toString(int, String) - Static method in class org.sbml.libsbml.libsbml
This method takes an SBML type code and returns a string representing the code.
SBMLUnitsConverter - Class in org.sbml.libsbml
SBML converter to convert a model's units to SI units.
SBMLUnitsConverter() - Constructor for class org.sbml.libsbml.SBMLUnitsConverter
 
SBMLUnitsConverter(SBMLUnitsConverter) - Constructor for class org.sbml.libsbml.SBMLUnitsConverter
 
SBMLUri - Class in org.sbml.libsbml
 
SBMLUri(String) - Constructor for class org.sbml.libsbml.SBMLUri
 
SBMLUri(SBMLUri) - Constructor for class org.sbml.libsbml.SBMLUri
 
SBMLValidator - Class in org.sbml.libsbml
Base class for SBML validators
SBMLValidator() - Constructor for class org.sbml.libsbml.SBMLValidator
Creates a new SBMLValidator.
SBMLValidator(SBMLValidator) - Constructor for class org.sbml.libsbml.SBMLValidator
Copy constructor; creates a copy of an SBMLValidator object.
SBMLWriter - Class in org.sbml.libsbml
Methods for writing SBML to files and text strings.
SBMLWriter() - Constructor for class org.sbml.libsbml.SBMLWriter
Creates a new SBMLWriter.
SBO - Class in org.sbml.libsbml
Methods for interacting with Systems Biology Ontology terms.
SBO() - Constructor for class org.sbml.libsbml.SBO
 
SBOCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBOCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBOTermNotUniversalInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBOTermNotValidAttributeBeforeL2V2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBOTermNotValidAttributeBeforeL2V3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
setActiveObjective(String) - Method in class org.sbml.libsbml.ListOfObjectives
 
setActiveObjectiveId(String) - Method in class org.sbml.libsbml.FbcModelPlugin
 
setAdditionalDirs(SWIGTYPE_p_std__vectorT_std__string_t) - Method in class org.sbml.libsbml.SBMLFileResolver
 
setAnnotation(XMLNode) - Method in class org.sbml.libsbml.Model
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.
setAnnotation(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.
setAnnotation(XMLNode) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'annotation' subelement of this SBML object.
setAnnotation(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'annotation' subelement of this SBML object.
setAnnotation(XMLNode) - Method in class org.sbml.libsbml.SpeciesReference
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.
setAnnotation(String) - Method in class org.sbml.libsbml.SpeciesReference
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.
setAreaUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'areaUnits' attribute of this Model.
setAssociation(Association) - Method in class org.sbml.libsbml.GeneAssociation
 
setAttributes(XMLAttributes) - Method in class org.sbml.libsbml.XMLToken
Sets an XMLAttributes to this XMLToken.
setBasePoint1(Point) - Method in class org.sbml.libsbml.CubicBezier
 
setBasePoint1(double, double, double) - Method in class org.sbml.libsbml.CubicBezier
 
setBasePoint1(double, double) - Method in class org.sbml.libsbml.CubicBezier
 
setBasePoint2(Point) - Method in class org.sbml.libsbml.CubicBezier
 
setBasePoint2(double, double, double) - Method in class org.sbml.libsbml.CubicBezier
 
setBasePoint2(double, double) - Method in class org.sbml.libsbml.CubicBezier
 
setBiologicalQualifierType(int) - Method in class org.sbml.libsbml.CVTerm
Sets the biology qualifier type of this CVTerm object.
setBiologicalQualifierType(String) - Method in class org.sbml.libsbml.CVTerm
Sets the biology qualifier type code of this CVTerm object.
setBoolValue(boolean) - Method in class org.sbml.libsbml.ConversionOption
Set the value of this option to a given Boolean value.
setBoolValue(String, boolean) - Method in class org.sbml.libsbml.ConversionProperties
Sets the value of the given option to a Boolean.
setBoundaryCondition(boolean) - Method in class org.sbml.libsbml.Species
Sets the 'boundaryCondition' attribute of this Species object.
setBoundingBox(BoundingBox) - Method in class org.sbml.libsbml.GraphicalObject
 
setBounds(double, double, double) - Method in class org.sbml.libsbml.Dimensions
 
setBounds(double, double) - Method in class org.sbml.libsbml.Dimensions
 
setCharacter(char) - Method in class org.sbml.libsbml.ASTNode
Sets the value of this ASTNode to the given character.
setCharge(int) - Method in class org.sbml.libsbml.FbcSpeciesPlugin
 
setCharge(int) - Method in class org.sbml.libsbml.Species
Sets the 'charge' attribute of this Species object.
setChemicalFormula(String) - Method in class org.sbml.libsbml.FbcSpeciesPlugin
 
setClassName(String) - Method in class org.sbml.libsbml.ASTNode
Sets the mathml class of this ASTNode to className.
setCoefficient(double) - Method in class org.sbml.libsbml.FluxObjective
 
setColumn(long) - Method in class org.sbml.libsbml.XMLError
Sets the column number where this error occurred.
setCompartment(String) - Method in class org.sbml.libsbml.Reaction
Sets the value of the 'compartment' attribute of this Reaction.
setCompartment(String) - Method in class org.sbml.libsbml.Species
Sets the 'compartment' attribute of this Species object.
setCompartmentId(String) - Method in class org.sbml.libsbml.CompartmentGlyph
 
setCompartmentType(String) - Method in class org.sbml.libsbml.Compartment
Sets the 'compartmentType' attribute of this Compartment.
setConsistencyChecks(int, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Controls the consistency checks that are performed when SBMLDocument.checkConsistency() is called.
setConsistencyChecksForConversion(int, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Controls the consistency checks that are performed when SBMLDocument.setLevelAndVersion(long lev, long ver, boolean strict) is called.
setConstant(boolean) - Method in class org.sbml.libsbml.Compartment
Sets the value of the 'constant' attribute of this Compartment.
setConstant(boolean) - Method in class org.sbml.libsbml.Parameter
Sets the 'constant' attribute of this Parameter to the given boolean flag.
setConstant(boolean) - Method in class org.sbml.libsbml.Species
Sets the 'constant' attribute of this Species object.
setConstant(boolean) - Method in class org.sbml.libsbml.SpeciesReference
Sets the 'constant' attribute of this SpeciesReference to the given boolean flag.
setConversionFactor(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'conversionFactor' attribute of this Model.
setConversionFactor(String) - Method in class org.sbml.libsbml.ReplacedElement
 
setConversionFactor(String) - Method in class org.sbml.libsbml.Species
Sets the value of the 'conversionFactor' attribute of this Species object.
setCreatedDate(Date) - Method in class org.sbml.libsbml.ModelHistory
Sets the creation date of this ModelHistory object.
setCurve(Curve) - Method in class org.sbml.libsbml.GeneralGlyph
 
setCurve(Curve) - Method in class org.sbml.libsbml.ReactionGlyph
 
setCurve(Curve) - Method in class org.sbml.libsbml.ReferenceGlyph
 
setCurve(Curve) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
setDateAsString(String) - Method in class org.sbml.libsbml.Date
Sets the value of this Date object using a date and time value expressed as a text string.
setDay(long) - Method in class org.sbml.libsbml.Date
Sets the value of the day of this Date object.
setDelay(Delay) - Method in class org.sbml.libsbml.Event
Sets the delay definition of this Event to a copy of the given Delay object instance.
setDeletion(String) - Method in class org.sbml.libsbml.ReplacedElement
 
setDenominator(int) - Method in class org.sbml.libsbml.SpeciesReference
Set the value of the 'denominator' attribute, for the case of a rational-numbered stoichiometry or a model in SBML Level 1.
setDepth(double) - Method in class org.sbml.libsbml.BoundingBox
 
setDepth(double) - Method in class org.sbml.libsbml.Dimensions
 
setDescription(String) - Method in class org.sbml.libsbml.ConversionOption
Sets the description text for this option.
setDimensions(Dimensions) - Method in class org.sbml.libsbml.BoundingBox
 
setDimensions(Dimensions) - Method in class org.sbml.libsbml.Layout
 
setDivider(String) - Method in class org.sbml.libsbml.CompModelPlugin
 
setDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLConverter
Sets the current SBML document to the given SBMLDocument object.
setDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLValidator
Sets the current SBML document to the given SBMLDocument object.
setDoubleValue(double) - Method in class org.sbml.libsbml.ConversionOption
Set the value of this option to a given double value.
setDoubleValue(String, double) - Method in class org.sbml.libsbml.ConversionProperties
Sets the value of the given option to a double.
setElementName(String) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
 
setElementName(String) - Method in class org.sbml.libsbml.Point
 
setElementNamespace(String) - Method in class org.sbml.libsbml.SBasePlugin
Sets the XML namespace to which this element belongs to.
setEmail(String) - Method in class org.sbml.libsbml.ModelCreator
Sets the 'email' portion of this ModelCreator object.
setEnabled(String, boolean) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Enable/disable the package with the given uri.
setEnd(Point) - Method in class org.sbml.libsbml.LineSegment
 
setEnd(double, double, double) - Method in class org.sbml.libsbml.LineSegment
 
setEnd(double, double) - Method in class org.sbml.libsbml.LineSegment
 
setEnd() - Method in class org.sbml.libsbml.XMLToken
Declares this XML start element is also an end element.
setEOF() - Method in class org.sbml.libsbml.XMLToken
Declares this XMLToken is an end-of-file (input) marker.
setExponent(int) - Method in class org.sbml.libsbml.Unit
Sets the 'exponent' attribute value of this Unit.
setExponent(double) - Method in class org.sbml.libsbml.Unit
Sets the 'exponent' attribute value of this Unit.
setExtentConversionFactor(String) - Method in class org.sbml.libsbml.Submodel
 
setExtentUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'extentUnits' attribute of this Model.
setFamilyName(String) - Method in class org.sbml.libsbml.ModelCreator
Sets the 'family name' portion of this ModelCreator object.
setFast(boolean) - Method in class org.sbml.libsbml.Reaction
Sets the value of the 'fast' attribute of this Reaction.
setFloatValue(float) - Method in class org.sbml.libsbml.ConversionOption
Set the value of this option to a given float value.
setFloatValue(String, float) - Method in class org.sbml.libsbml.ConversionProperties
Sets the value of the given option to a float.
setFormula(String) - Method in class org.sbml.libsbml.KineticLaw
Sets the mathematical expression of this KineticLaw instance to the given formula.
setFormula(String) - Method in class org.sbml.libsbml.Rule
Sets the 'math' subelement of this Rule to an expression in text-string form.
setGivenName(String) - Method in class org.sbml.libsbml.ModelCreator
Sets the 'given name' portion of this ModelCreator object.
setGlyphId(String) - Method in class org.sbml.libsbml.ReferenceGlyph
 
setGraphicalObjectId(String) - Method in class org.sbml.libsbml.TextGlyph
 
setHasOnlySubstanceUnits(boolean) - Method in class org.sbml.libsbml.Species
Sets the 'hasOnlySubstanceUnits' attribute of this Species object.
setHeight(double) - Method in class org.sbml.libsbml.BoundingBox
 
setHeight(double) - Method in class org.sbml.libsbml.Dimensions
 
setHour(long) - Method in class org.sbml.libsbml.Date
Sets the value of the hour of this Date object.
setHoursOffset(long) - Method in class org.sbml.libsbml.Date
Sets the value of this Date object's time zone hour offset.
setId(String) - Method in class org.sbml.libsbml.ASTNode
Sets the mathml id of this ASTNode to id.
setId(String) - Method in class org.sbml.libsbml.Compartment
Sets the value of the 'id' attribute of this Compartment.
setId(String) - Method in class org.sbml.libsbml.CompartmentType
Sets the value of the 'id' attribute of this CompartmentType.
setId(String) - Method in class org.sbml.libsbml.Event
Sets the value of the 'id' attribute of this Event.
setId(String) - Method in class org.sbml.libsbml.FunctionDefinition
Sets the value of the 'id' attribute of this FunctionDefinition.
setId(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'id' attribute of this Model.
setId(String) - Method in class org.sbml.libsbml.Parameter
Sets the value of the 'id' attribute of this Parameter.
setId(String) - Method in class org.sbml.libsbml.Reaction
Sets the value of the 'id' attribute of this Reaction.
setId(String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
Sets the value of the 'id' attribute of this SimpleSpeciesReference.
setId(String) - Method in class org.sbml.libsbml.Species
Sets the value of the 'id' attribute of this Species object.
setId(String) - Method in class org.sbml.libsbml.SpeciesType
Sets the value of the 'id' attribute of this SpeciesType.
setId(String) - Method in class org.sbml.libsbml.UnitDefinition
Sets the value of the 'id' attribute of this UnitDefinition.
setIdRef(String) - Method in class org.sbml.libsbml.SBaseRef
 
setInitialAmount(double) - Method in class org.sbml.libsbml.Species
Sets the 'initialAmount' attribute of this Species and marks the field as set.
setInitialConcentration(double) - Method in class org.sbml.libsbml.Species
Sets the 'initialConcentration' attribute of this Species and marks the field as set.
setInitialValue(boolean) - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Sets the 'initialValue' attribute of this Trigger instance.
setIntValue(int) - Method in class org.sbml.libsbml.ConversionOption
Set the value of this option to a given int value.
setIntValue(String, int) - Method in class org.sbml.libsbml.ConversionProperties
Sets the value of the given option to an integer.
setKey(String) - Method in class org.sbml.libsbml.ConversionOption
Sets the key for this option.
setKind(int) - Method in class org.sbml.libsbml.Unit
Sets the 'kind' attribute value of this Unit.
setKineticLaw(KineticLaw) - Method in class org.sbml.libsbml.Reaction
Sets the 'kineticLaw' subelement of this Reaction to a copy of the given KineticLaw object.
setL1TypeCode(int) - Method in class org.sbml.libsbml.Rule
Sets the SBML Level 1 type code for this Rule.
setLengthUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'lengthUnits' attribute of this Model.
setLevelAndVersion(long, long, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.
setLevelAndVersion(long, long) - Method in class org.sbml.libsbml.SBMLDocument
Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.
setLine(long) - Method in class org.sbml.libsbml.XMLError
Sets the line number where this error occurred.
setLocationURI(String) - Method in class org.sbml.libsbml.SBMLDocument
Sets the location of this SBMLDocument.
setMath(ASTNode) - Method in class org.sbml.libsbml.Constraint
Sets the mathematical expression of this Constraint to a copy of the AST given as math.
setMath(ASTNode) - Method in class org.sbml.libsbml.Delay
Sets the delay expression of this Delay instance to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.EventAssignment
Sets the 'math' subelement of this EventAssignment to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.FunctionDefinition
Sets the 'math' subelement of this FunctionDefinition to the Abstract Syntax Tree given in math.
setMath(ASTNode) - Method in class org.sbml.libsbml.InitialAssignment
Sets the 'math' subelement of this InitialAssignment.
setMath(ASTNode) - Method in class org.sbml.libsbml.KineticLaw
Sets the mathematical expression of this KineticLaw instance to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.Priority
Sets the math expression of this Priority instance to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.Rule
Sets the 'math' subelement of this Rule to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.StoichiometryMath
Sets the 'math' expression of this StoichiometryMath instance to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.Trigger
Sets the trigger expression of this Trigger instance to a copy of the given ASTNode.
setMd5(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
 
setMessage(XMLNode) - Method in class org.sbml.libsbml.Constraint
Sets the message of this Constraint.
setMetaId(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'metaid' attribute of this object.
setMetaIdRef(String) - Method in class org.sbml.libsbml.GraphicalObject
 
setMetaIdRef(String) - Method in class org.sbml.libsbml.SBaseRef
 
setMinute(long) - Method in class org.sbml.libsbml.Date
Sets the value of the minute of this Date object.
setMinutesOffset(long) - Method in class org.sbml.libsbml.Date
Sets the value of this Date object's time zone minutes offset.
setModel(Model) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the model reference in this L3ParserSettings object.
setModel(Model) - Method in class org.sbml.libsbml.SBMLDocument
Sets the Model for this SBMLDocument to a copy of the given Model.
setModelHistory(ModelHistory) - Method in class org.sbml.libsbml.SBase
Sets the ModelHistory of this object.
setModelQualifierType(int) - Method in class org.sbml.libsbml.CVTerm
Sets the model qualifier type of this CVTerm object.
setModelQualifierType(String) - Method in class org.sbml.libsbml.CVTerm
Sets the model qualifier type code value of this CVTerm object.
setModelRef(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
 
setModelRef(String) - Method in class org.sbml.libsbml.Submodel
 
setModifiedDate(Date) - Method in class org.sbml.libsbml.ModelHistory
Sets the modification date of this ModelHistory object.
setMonth(long) - Method in class org.sbml.libsbml.Date
Sets the value of the month of this Date object.
setMultiplier(double) - Method in class org.sbml.libsbml.Unit
Sets the 'multipler' attribute value of this Unit.
setName(String) - Method in class org.sbml.libsbml.ASTNode
Sets the value of this ASTNode to the given name.
setName(String) - Method in class org.sbml.libsbml.Compartment
Sets the value of the 'name' attribute of this Compartment.
setName(String) - Method in class org.sbml.libsbml.CompartmentType
Sets the value of the 'name' attribute of this CompartmentType.
setName(String) - Method in class org.sbml.libsbml.Event
Sets the value of the 'name' attribute of this Event.
setName(String) - Method in class org.sbml.libsbml.FunctionDefinition
Sets the value of the 'name' attribute of this FunctionDefinition.
setName(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'name' attribute of this Model.
setName(String) - Method in class org.sbml.libsbml.Parameter
Sets the value of the 'name' attribute of this Parameter.
setName(String) - Method in class org.sbml.libsbml.Reaction
Sets the value of the 'name' attribute of this Reaction.
setName(String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
Sets the value of the 'name' attribute of this SimpleSpeciesReference.
setName(String) - Method in class org.sbml.libsbml.Species
Sets the value of the 'name' attribute of this Species object.
setName(String) - Method in class org.sbml.libsbml.SpeciesType
Sets the value of the 'name' attribute of this SpeciesType.
setName(String) - Method in class org.sbml.libsbml.UnitDefinition
Sets the value of the 'name' attribute of this UnitDefinition.
setNamespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBase
Sets the namespaces relevant of this SBML object.
setNamespaces(XMLNamespaces) - Method in class org.sbml.libsbml.XMLToken
Sets an XMLnamespaces to this XML element.
setNotes(XMLNode) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'notes' subelement of this SBML object.
setNotes(String, boolean) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.
setNotes(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.
setOffset(double) - Method in class org.sbml.libsbml.Unit
Sets the 'offset' attribute value of this Unit.
setOffsets(double, double, double) - Method in class org.sbml.libsbml.Point
 
setOffsets(double, double) - Method in class org.sbml.libsbml.Point
 
setOperation(String) - Method in class org.sbml.libsbml.FluxBound
 
setOperation(int) - Method in class org.sbml.libsbml.FluxBound
 
setOrganisation(String) - Method in class org.sbml.libsbml.ModelCreator
(Alternate spelling) Sets the 'organization' portion of this ModelCreator object.
setOrganization(String) - Method in class org.sbml.libsbml.ModelCreator
Sets the 'organization' portion of this ModelCreator object.
setOriginOfTextId(String) - Method in class org.sbml.libsbml.TextGlyph
 
setOutputFileName(String) - Method in class org.sbml.libsbml.SBMLExternalValidator
Sets the output file name
setOutside(String) - Method in class org.sbml.libsbml.Compartment
Sets the 'outside' attribute of this Compartment.
setPackageRequired(String, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Sets the required attribute value of the given package extension.
setParseAvogadroCsymbol(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the parser's behavior in handling the string avogadro in mathematical formulas.
setParseCollapseMinus(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the behavior for handling unary minuses appearing in mathematical formulas.
setParseLog(int) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the behavior for handling log in mathematical formulas.
setParseUnits(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the parser's behavior in handling units associated with numbers in a mathematical formula.
setPersistent(boolean) - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Sets the 'persistent' attribute of this Trigger instance.
setPortRef(String) - Method in class org.sbml.libsbml.Port
 
setPortRef(String) - Method in class org.sbml.libsbml.SBaseRef
 
setPosition(Point) - Method in class org.sbml.libsbml.BoundingBox
 
setPriority(Priority) - Method in class org.sbml.libsbml.Event
(SBML Level 3 only) Sets the priority definition of this Event to a copy of the given Priority object instance.
setProgram(String) - Method in class org.sbml.libsbml.SBMLExternalValidator
Sets the name of the program to run
setProgramName(String) - Method in class org.sbml.libsbml.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.libsbml.SBMLWriter
Sets the version of this program, i.e., the program that is about to write out the SBMLDocument.
setProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLConverter
Sets the configuration properties to be used by this converter.
setQualifierType(int) - Method in class org.sbml.libsbml.CVTerm
Sets the qualifier code of this CVTerm object.
setReaction(String) - Method in class org.sbml.libsbml.FluxBound
 
setReaction(String) - Method in class org.sbml.libsbml.FluxObjective
 
setReaction(String) - Method in class org.sbml.libsbml.GeneAssociation
 
setReactionId(String) - Method in class org.sbml.libsbml.ReactionGlyph
 
setReference(String) - Method in class org.sbml.libsbml.Association
 
setReferenceId(String) - Method in class org.sbml.libsbml.GeneralGlyph
 
setReferenceId(String) - Method in class org.sbml.libsbml.ReferenceGlyph
 
setReplacedBy(ReplacedBy) - Method in class org.sbml.libsbml.CompSBasePlugin
 
setRequired(boolean) - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Sets the bool value of 'required' attribute of corresponding package in SBMLDocument element.
setReversible(boolean) - Method in class org.sbml.libsbml.Reaction
Sets the value of the 'reversible' attribute of this Reaction.
setRole(String) - Method in class org.sbml.libsbml.ReferenceGlyph
 
setRole(String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
setRole(int) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
setSBaseRef(SBaseRef) - Method in class org.sbml.libsbml.SBaseRef
 
setSBMLFileName(String) - Method in class org.sbml.libsbml.SBMLExternalValidator
Sets the filename for the temporary file to be created
setSBOTerm(int) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'sboTerm' attribute.
setSBOTerm(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'sboTerm' attribute by string.
setScale(int) - Method in class org.sbml.libsbml.Unit
Sets the 'scale' attribute value of this Unit.
setSecond(long) - Method in class org.sbml.libsbml.Date
Sets the value of the second of the Date object.
setSignOffset(long) - Method in class org.sbml.libsbml.Date
Sets the value of the sign of the time zone offset of this Date object.
setSize(double) - Method in class org.sbml.libsbml.Compartment
Sets the 'size' attribute (or 'volume' in SBML Level 1) of this Compartment.
setSource(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
 
setSpatialDimensions(long) - Method in class org.sbml.libsbml.Compartment
Sets the 'spatialDimensions' attribute of this Compartment.
setSpatialDimensions(double) - Method in class org.sbml.libsbml.Compartment
Sets the 'spatialDimensions' attribute of this Compartment as a double.
setSpatialSizeUnits(String) - Method in class org.sbml.libsbml.Species
(SBML Level 2 Versions 1–2) Sets the 'spatialSizeUnits' attribute of this Species object.
setSpecies(String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
Sets the 'species' attribute of this SimpleSpeciesReference.
setSpeciesGlyphId(String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
setSpeciesId(String) - Method in class org.sbml.libsbml.SpeciesGlyph
 
setSpeciesReferenceId(String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
setSpeciesType(String) - Method in class org.sbml.libsbml.Species
Sets the 'speciesType' attribute of this Species object.
setStart(Point) - Method in class org.sbml.libsbml.LineSegment
 
setStart(double, double, double) - Method in class org.sbml.libsbml.LineSegment
 
setStart(double, double) - Method in class org.sbml.libsbml.LineSegment
 
setStoichiometry(double) - Method in class org.sbml.libsbml.SpeciesReference
Sets the value of the 'stoichiometry' attribute of this SpeciesReference.
setStoichiometryMath(StoichiometryMath) - Method in class org.sbml.libsbml.SpeciesReference
Sets the 'stoichiometryMath' subelement of this SpeciesReference.
setStyle(String) - Method in class org.sbml.libsbml.ASTNode
Sets the mathml style of this ASTNode to style.
setSubmodelRef(String) - Method in class org.sbml.libsbml.Replacing
 
setSubstanceConversionFactor(String) - Method in class org.sbml.libsbml.Submodel
 
setSubstanceUnits(String) - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Sets the 'substanceUnits' attribute of this KineticLaw object to a copy of the identifier given in sid.
setSubstanceUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'substanceUnits' attribute of this Model.
setSubstanceUnits(String) - Method in class org.sbml.libsbml.Species
Sets the 'substanceUnits' attribute of this Species object.
setSymbol(String) - Method in class org.sbml.libsbml.InitialAssignment
Sets the 'symbol' attribute value of this InitialAssignment.
setTargetNamespaces(SBMLNamespaces) - Method in class org.sbml.libsbml.ConversionProperties
Sets the target namespace.
setText(String) - Method in class org.sbml.libsbml.TextGlyph
 
setTimeConversionFactor(String) - Method in class org.sbml.libsbml.Submodel
 
setTimeUnits(String) - Method in class org.sbml.libsbml.Event
Sets the 'timeUnits' attribute of this Event to a copy of sid.
setTimeUnits(String) - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Sets the 'timeUnits' attribute of this KineticLaw object to a copy of the identifier in sid.
setTimeUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'timeUnits' attribute of this Model.
setTrigger(Trigger) - Method in class org.sbml.libsbml.Event
Sets the trigger definition of this Event to a copy of the given Trigger object instance.
setTriple(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
Sets the XMLTripe (name, uri and prefix) of this XML element.
setType(int) - Method in class org.sbml.libsbml.Association
 
setType(int) - Method in class org.sbml.libsbml.ASTNode
Sets the type of this ASTNode to the given type code.
setType(int) - Method in class org.sbml.libsbml.ConversionOption
Sets the type of this option.
setType(String) - Method in class org.sbml.libsbml.Objective
 
setType(int) - Method in class org.sbml.libsbml.Objective
 
setUnitRef(String) - Method in class org.sbml.libsbml.SBaseRef
 
setUnits(String) - Method in class org.sbml.libsbml.ASTNode
Sets the units of this ASTNode to units.
setUnits(String) - Method in class org.sbml.libsbml.Compartment
Sets the 'units' attribute of this Compartment.
setUnits(String) - Method in class org.sbml.libsbml.Parameter
Sets the 'units' attribute of this Parameter to a copy of the given units identifier units.
setUnits(String) - Method in class org.sbml.libsbml.Rule
Sets the units for this Rule.
setUnits(String) - Method in class org.sbml.libsbml.Species
(SBML Level 1 only) Sets the units of this Species object.
setUseValuesFromTriggerTime(boolean) - Method in class org.sbml.libsbml.Event
Sets the 'useValuesFromTriggerTime' attribute of this Event to a value.
setValue(int) - Method in class org.sbml.libsbml.ASTNode
Sets the value of this ASTNode to the given (long) integer and sets the node type to AST_INTEGER.
setValue(int, int) - Method in class org.sbml.libsbml.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.libsbml.ASTNode
Sets the value of this ASTNode to the given real (double) and sets the node type to AST_REAL.
setValue(double, int) - Method in class org.sbml.libsbml.ASTNode
Sets the value of this ASTNode to the given real (double) in two parts: the mantissa and the exponent.
setValue(String) - Method in class org.sbml.libsbml.ConversionOption
Sets the value for this option.
setValue(String, String) - Method in class org.sbml.libsbml.ConversionProperties
Sets the value of the given option to a string.
setValue(double) - Method in class org.sbml.libsbml.FluxBound
 
setValue(double) - Method in class org.sbml.libsbml.Parameter
Sets the 'value' attribute of this Parameter to the given double value and marks the attribute as set.
setVariable(String) - Method in class org.sbml.libsbml.EventAssignment
Sets the attribute 'variable' of this EventAssignment to a copy of the given identifier string.
setVariable(String) - Method in class org.sbml.libsbml.Rule
Sets the 'variable' attribute value of this Rule object.
setVolume(double) - Method in class org.sbml.libsbml.Compartment
Sets the 'volume' attribute (or 'size' in SBML Level 2) of this Compartment.
setVolumeUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'volumeUnits' attribute of this Model.
setWidth(double) - Method in class org.sbml.libsbml.BoundingBox
 
setWidth(double) - Method in class org.sbml.libsbml.Dimensions
 
setX(double) - Method in class org.sbml.libsbml.BoundingBox
 
setX(double) - Method in class org.sbml.libsbml.Point
 
setXOffset(double) - Method in class org.sbml.libsbml.Point
 
setY(double) - Method in class org.sbml.libsbml.BoundingBox
 
setY(double) - Method in class org.sbml.libsbml.Point
 
setYear(long) - Method in class org.sbml.libsbml.Date
Sets the value of the year of this Date object.
setYOffset(double) - Method in class org.sbml.libsbml.Point
 
setZ(double) - Method in class org.sbml.libsbml.BoundingBox
 
setZ(double) - Method in class org.sbml.libsbml.Point
 
setZOffset(double) - Method in class org.sbml.libsbml.Point
 
SimpleSpeciesReference - Class in org.sbml.libsbml
Implementation of SBML's SimpleSpeciesReference construct.
simplify(UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Simplifies the UnitDefinition such that any given kind of Unit object occurs only once in the ListOfUnits.
size() - Method in class org.sbml.libsbml.ListOf
Get the size of this ListOf.
SpatialSizeUnitsNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpatialSizeUnitsRemoved - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpatialUnitsInOneD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpatialUnitsInThreeD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpatialUnitsInTwoD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Species - Class in org.sbml.libsbml
Implementation of SBML's Species construct.
Species(long, long) - Constructor for class org.sbml.libsbml.Species
Creates a new Species using the given SBML level and version values.
Species(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Species
Creates a new Species using the given SBMLNamespaces object sbmlns.
Species(Species) - Constructor for class org.sbml.libsbml.Species
Copy constructor; creates a copy of this Species object.
SPECIES_ROLE_ACTIVATOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_INHIBITOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_MODIFIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_PRODUCT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_SIDEPRODUCT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_SIDESUBSTRATE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_SUBSTRATE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_UNDEFINED - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesCompartmentRequiredInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesGlyph - Class in org.sbml.libsbml
 
SpeciesGlyph(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
 
SpeciesGlyph(long, long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
 
SpeciesGlyph(long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
 
SpeciesGlyph() - Constructor for class org.sbml.libsbml.SpeciesGlyph
 
SpeciesGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesGlyph
 
SpeciesGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.SpeciesGlyph
 
SpeciesGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.SpeciesGlyph
 
SpeciesGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
 
SpeciesGlyph(XMLNode) - Constructor for class org.sbml.libsbml.SpeciesGlyph
 
SpeciesGlyph(SpeciesGlyph) - Constructor for class org.sbml.libsbml.SpeciesGlyph
 
SpeciesInvalidExtentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesReference - Class in org.sbml.libsbml
Implementation of SBML's SpeciesReference construct.
SpeciesReference(long, long) - Constructor for class org.sbml.libsbml.SpeciesReference
Creates a new SpeciesReference using the given SBML level and version values.
SpeciesReference(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SpeciesReference
Creates a new SpeciesReference using the given SBMLNamespaces object sbmlns.
SpeciesReference(SpeciesReference) - Constructor for class org.sbml.libsbml.SpeciesReference
Copy constructor; creates a copy of this SpeciesReference.
SpeciesReferenceGlyph - Class in org.sbml.libsbml
 
SpeciesReferenceGlyph(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
 
SpeciesReferenceGlyph(long, long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
 
SpeciesReferenceGlyph(long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
 
SpeciesReferenceGlyph() - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
 
SpeciesReferenceGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
 
SpeciesReferenceGlyph(LayoutPkgNamespaces, String, String, String, int) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
 
SpeciesReferenceGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
 
SpeciesReferenceGlyph(XMLNode) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
 
SpeciesReferenceGlyph(SpeciesReferenceGlyph) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
 
SpeciesShouldHaveValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesType - Class in org.sbml.libsbml
Implementation of SBML Level 2's SpeciesType construct.
SpeciesType(long, long) - Constructor for class org.sbml.libsbml.SpeciesType
Creates a new SpeciesType using the given SBML level and version values.
SpeciesType(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SpeciesType
Creates a new SpeciesType using the given SBMLNamespaces object sbmlns.
SpeciesType(SpeciesType) - Constructor for class org.sbml.libsbml.SpeciesType
Copy constructor; creates a copy of this SpeciesType.
SpeciesTypeNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesTypeNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StoichiometryMath - Class in org.sbml.libsbml
Implementation of SBML Level 2's StoichiometryMath construct.
StoichiometryMath(long, long) - Constructor for class org.sbml.libsbml.StoichiometryMath
Creates a new StoichiometryMath object using the given SBML level values.
StoichiometryMath(SBMLNamespaces) - Constructor for class org.sbml.libsbml.StoichiometryMath
Creates a new StoichiometryMath object using the given SBMLNamespaces object sbmlns.
StoichiometryMath(StoichiometryMath) - Constructor for class org.sbml.libsbml.StoichiometryMath
Copy constructor; creates a copy of this StoichiometryMath.
StoichiometryMathNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StoichiometryMathNotYetSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
str() - Method in class org.sbml.libsbml.OStringStream
Returns the copy of the string object currently assosiated with this ostringstream buffer.
str(String) - Method in class org.sbml.libsbml.OStringStream
Sets string s to the string object currently assosiated with this stream buffer.
straighten() - Method in class org.sbml.libsbml.CubicBezier
 
StrictSBORequiredInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StrictSBORequiredInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StrictUnitsRequiredInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StrictUnitsRequiredInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StrictUnitsRequiredInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StrictUnitsRequiredInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
stringToInt(String) - Static method in class org.sbml.libsbml.SBO
Returns the string as a correctly formatted SBO integer portion.
Submodel - Class in org.sbml.libsbml
 
Submodel(long, long, long) - Constructor for class org.sbml.libsbml.Submodel
 
Submodel(long, long) - Constructor for class org.sbml.libsbml.Submodel
 
Submodel(long) - Constructor for class org.sbml.libsbml.Submodel
 
Submodel() - Constructor for class org.sbml.libsbml.Submodel
 
Submodel(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.Submodel
 
Submodel(Submodel) - Constructor for class org.sbml.libsbml.Submodel
 
SubstanceUnitsOnSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SubsUnitsAllowedInKL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SubsUnitsNoLongerValid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
swapChildren(ASTNode) - Method in class org.sbml.libsbml.ASTNode
Swap the children of this ASTNode object with the children of the given ASTNode object.
swigReleaseOwnership() - Method in class org.sbml.libsbml.SBMLConverter
 
swigReleaseOwnership() - Method in class org.sbml.libsbml.SBMLValidator
 
swigTakeOwnership() - Method in class org.sbml.libsbml.SBMLConverter
 
swigTakeOwnership() - Method in class org.sbml.libsbml.SBMLValidator
 
SWIGTYPE_p_CompVisitor - Class in org.sbml.libsbml
 
SWIGTYPE_p_FbcVisitor - Class in org.sbml.libsbml
 
SyntaxChecker - Class in org.sbml.libsbml
Methods for checking syntax of SBML identifiers and other strings.
SyntaxChecker() - Constructor for class org.sbml.libsbml.SyntaxChecker
 

T

TextGlyph - Class in org.sbml.libsbml
 
TextGlyph(long, long, long) - Constructor for class org.sbml.libsbml.TextGlyph
 
TextGlyph(long, long) - Constructor for class org.sbml.libsbml.TextGlyph
 
TextGlyph(long) - Constructor for class org.sbml.libsbml.TextGlyph
 
TextGlyph() - Constructor for class org.sbml.libsbml.TextGlyph
 
TextGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.TextGlyph
 
TextGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.TextGlyph
 
TextGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.TextGlyph
 
TextGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.TextGlyph
 
TextGlyph(XMLNode) - Constructor for class org.sbml.libsbml.TextGlyph
 
TextGlyph(TextGlyph) - Constructor for class org.sbml.libsbml.TextGlyph
 
ThreeDimensionalCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
TimeUnitsAllowedInKL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
TimeUnitsEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
TimeUnitsNoLongerValid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
TimeUnitsRemoved - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
toInfix() - Method in class org.sbml.libsbml.Association
 
toSBML() - Method in class org.sbml.libsbml.SBase
Returns a string consisting of a partial SBML corresponding to just this object.
toString() - Method in class org.sbml.libsbml.XMLErrorLog
Writes all errors contained in this log to a string and returns it.
toString() - Method in class org.sbml.libsbml.XMLToken
Prints a string representation of the underlying token stream, for debugging purposes.
toXML() - Method in class org.sbml.libsbml.Association
 
toXML() - Method in class org.sbml.libsbml.BoundingBox
 
toXML() - Method in class org.sbml.libsbml.CompartmentGlyph
 
toXML() - Method in class org.sbml.libsbml.CubicBezier
 
toXML() - Method in class org.sbml.libsbml.Curve
 
toXML() - Method in class org.sbml.libsbml.Dimensions
 
toXML() - Method in class org.sbml.libsbml.GeneAssociation
 
toXML() - Method in class org.sbml.libsbml.GeneralGlyph
 
toXML() - Method in class org.sbml.libsbml.GraphicalObject
 
toXML() - Method in class org.sbml.libsbml.Layout
 
toXML() - Method in class org.sbml.libsbml.LineSegment
 
toXML() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
 
toXML() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
 
toXML() - Method in class org.sbml.libsbml.ListOfLayouts
 
toXML() - Method in class org.sbml.libsbml.ListOfLineSegments
 
toXML() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
 
toXML() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
 
toXML() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
 
toXML() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
 
toXML() - Method in class org.sbml.libsbml.ListOfTextGlyphs
 
toXML(String) - Method in class org.sbml.libsbml.Point
 
toXML() - Method in class org.sbml.libsbml.ReactionGlyph
 
toXML() - Method in class org.sbml.libsbml.ReferenceGlyph
 
toXML() - Method in class org.sbml.libsbml.SpeciesGlyph
 
toXML() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
toXML() - Method in class org.sbml.libsbml.TextGlyph
 
toXMLString() - Method in class org.sbml.libsbml.XMLNode
Returns a string representation of this XMLNode.
Trigger - Class in org.sbml.libsbml
Implementation of SBML's Trigger construct for Event.
Trigger(long, long) - Constructor for class org.sbml.libsbml.Trigger
Creates a new Trigger using the given SBML level and version values.
Trigger(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Trigger
Creates a new Trigger using the given SBMLNamespaces object sbmlns.
Trigger(Trigger) - Constructor for class org.sbml.libsbml.Trigger
Copy constructor; creates a copy of this Trigger.
TriggerMathNotBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
TwoDimensionalCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

U

UnclosedXMLToken - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredExtentUnitsL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredObjectUnitsL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredSpeciesInStoichMath - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredSpeciesRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredTimeUnitsL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndefinedOutsideCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndefinedXMLEntity - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UninterpretableXMLContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Unit - Class in org.sbml.libsbml
Implementation of SBML's Unit construct.
Unit(long, long) - Constructor for class org.sbml.libsbml.Unit
Creates a new Unit using the given SBML level and version values.
Unit(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Unit
Creates a new Unit using the given SBMLNamespaces object sbmlns.
Unit(Unit) - Constructor for class org.sbml.libsbml.Unit
Copy constructor; creates a copy of this Unit.
UNIT_KIND_AMPERE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_AVOGADRO - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_BECQUEREL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_CANDELA - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_CELSIUS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_COULOMB - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_DIMENSIONLESS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_FARAD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_GRAM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_GRAY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_HENRY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_HERTZ - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_INVALID - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_ITEM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_JOULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_KATAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_KELVIN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_KILOGRAM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_LITER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_LITRE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_LUMEN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_LUX - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_METER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_METRE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_MOLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_NEWTON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_OHM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_PASCAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_RADIAN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_SECOND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_SIEMENS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_SIEVERT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_STERADIAN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_TESLA - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_VOLT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_WATT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_WEBER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnitDefinition - Class in org.sbml.libsbml
Implementation of SBML's UnitDefinition construct.
UnitDefinition(long, long) - Constructor for class org.sbml.libsbml.UnitDefinition
Creates a new UnitDefinition using the given SBML level and version values.
UnitDefinition(SBMLNamespaces) - Constructor for class org.sbml.libsbml.UnitDefinition
Creates a new UnitDefinition using the given SBMLNamespaces object sbmlns.
UnitDefinition(UnitDefinition) - Constructor for class org.sbml.libsbml.UnitDefinition
Copy constructor; creates a copy of this UnitDefinition.
UnitKind_equals(int, int) - Static method in class org.sbml.libsbml.libsbml
Tests for logical equality between two given UNIT_KIND_ code values.
UnitKind_forName(String) - Static method in class org.sbml.libsbml.libsbml
Converts a text string naming a kind of unit to its corresponding libSBML UNIT_KIND_ constant/enumeration value.
UnitKind_isValidUnitKindString(String, long, long) - Static method in class org.sbml.libsbml.libsbml
Predicate for testing whether a given string corresponds to a predefined libSBML unit code.
UnitKind_toString(int) - Static method in class org.sbml.libsbml.libsbml
Converts a unit code to a text string equivalent.
UnitsCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnitsCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnitsNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNKNOWN_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNKNOWN_QUALIFIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnknownCoreAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnknownError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnknownPackageAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnrecognisedSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnrecognizedElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnrecognizedXMLElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnrecognizedXMLParserCode - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnrequiredPackagePresent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
unsetActiveObjective() - Method in class org.sbml.libsbml.ListOfObjectives
 
unsetActiveObjectiveId() - Method in class org.sbml.libsbml.FbcModelPlugin
 
unsetAnnotation() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'annotation' subelement of this SBML object.
unsetAreaUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'areaUnits' attribute of this Model.
unsetAssociation() - Method in class org.sbml.libsbml.GeneAssociation
 
unsetCharge() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
 
unsetCharge() - Method in class org.sbml.libsbml.Species
Unsets the 'charge' attribute value of this Species object.
unsetChemicalFormula() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
 
unsetClass() - Method in class org.sbml.libsbml.ASTNode
Unsets the mathml class of this ASTNode.
unsetCoefficient() - Method in class org.sbml.libsbml.FluxObjective
 
unsetCompartment() - Method in class org.sbml.libsbml.Reaction
Unsets the value of the 'compartment' attribute of this Reaction.
unsetCompartmentType() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'compartmentType' attribute of this Compartment.
unsetConversionFactor() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'conversionFactor' attribute of this Model.
unsetConversionFactor() - Method in class org.sbml.libsbml.ReplacedElement
 
unsetConversionFactor() - Method in class org.sbml.libsbml.Species
Unsets the 'conversionFactor' attribute value of this Species object.
unsetCVTerms() - Method in class org.sbml.libsbml.SBase
Clears the list of CVTerm objects attached to this SBML object.
unsetDelay() - Method in class org.sbml.libsbml.Event
Unsets the Delay of this Event.
unsetDeletion() - Method in class org.sbml.libsbml.ReplacedElement
 
unsetEmail() - Method in class org.sbml.libsbml.ModelCreator
Unsets the 'email' portion of this ModelCreator object.
unsetEnd() - Method in class org.sbml.libsbml.XMLToken
Declares this XML start/end element is no longer an end element.
unsetExtentConversionFactor() - Method in class org.sbml.libsbml.Submodel
 
unsetExtentUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'extentUnits' attribute of this Model.
unsetFamilyName() - Method in class org.sbml.libsbml.ModelCreator
Unsets the 'family name' portion of this ModelCreator object.
unsetFast() - Method in class org.sbml.libsbml.Reaction
Unsets the value of the 'fast' attribute of this Reaction.
unsetGivenName() - Method in class org.sbml.libsbml.ModelCreator
Unsets the 'given name' portion of this ModelCreator object.
unsetId() - Method in class org.sbml.libsbml.ASTNode
Unsets the mathml id of this ASTNode.
unsetId() - Method in class org.sbml.libsbml.BoundingBox
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.Deletion
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.Dimensions
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.Event
Unsets the value of the 'id' attribute of this Event.
unsetId() - Method in class org.sbml.libsbml.ExternalModelDefinition
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.FluxBound
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.FluxObjective
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.GeneAssociation
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.GraphicalObject
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.Layout
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'id' attribute of this Model.
unsetId() - Method in class org.sbml.libsbml.Objective
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.Point
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.Port
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Unsets the value of the 'id' attribute of this SimpleSpeciesReference.
unsetId() - Method in class org.sbml.libsbml.Submodel
Unsets the value of the 'id' attribute of this SBML object.
unsetIdRef() - Method in class org.sbml.libsbml.SBaseRef
 
unsetInitialAmount() - Method in class org.sbml.libsbml.Species
Unsets the 'initialAmount' attribute value of this Species object.
unsetInitialConcentration() - Method in class org.sbml.libsbml.Species
Unsets the 'initialConcentration' attribute value of this Species object.
unsetKineticLaw() - Method in class org.sbml.libsbml.Reaction
Unsets the 'kineticLaw' subelement of this Reaction.
unsetLengthUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'lengthUnits' attribute of this Model.
unsetMd5() - Method in class org.sbml.libsbml.ExternalModelDefinition
 
unsetMessage() - Method in class org.sbml.libsbml.Constraint
Unsets the 'message' subelement of this Constraint.
unsetMetaId() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'metaid' attribute of this SBML object.
unsetMetaIdRef() - Method in class org.sbml.libsbml.GraphicalObject
 
unsetMetaIdRef() - Method in class org.sbml.libsbml.SBaseRef
 
unsetModel() - Method in class org.sbml.libsbml.L3ParserSettings
Sets the Model reference in this L3ParserSettings object to null.
unsetModelHistory() - Method in class org.sbml.libsbml.SBase
Unsets the ModelHistory object attached to this object.
unsetModelRef() - Method in class org.sbml.libsbml.ExternalModelDefinition
 
unsetModelRef() - Method in class org.sbml.libsbml.Submodel
 
unsetName() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'name' attribute of this Compartment.
unsetName() - Method in class org.sbml.libsbml.CompartmentType
Unsets the value of the 'name' attribute of this CompartmentType.
unsetName() - Method in class org.sbml.libsbml.Deletion
Unsets the value of the 'name' attribute of this SBML object.
unsetName() - Method in class org.sbml.libsbml.Event
Unsets the value of the 'name' attribute of this Event.
unsetName() - Method in class org.sbml.libsbml.ExternalModelDefinition
Unsets the value of the 'name' attribute of this SBML object.
unsetName() - Method in class org.sbml.libsbml.FluxBound
Unsets the value of the 'name' attribute of this SBML object.
unsetName() - Method in class org.sbml.libsbml.FluxObjective
Unsets the value of the 'name' attribute of this SBML object.
unsetName() - Method in class org.sbml.libsbml.FunctionDefinition
Unsets the value of the 'name' attribute of this FunctionDefinition.
unsetName() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'name' attribute of this Model.
unsetName() - Method in class org.sbml.libsbml.Objective
Unsets the value of the 'name' attribute of this SBML object.
unsetName() - Method in class org.sbml.libsbml.Parameter
Unsets the value of the 'name' attribute of this Parameter.
unsetName() - Method in class org.sbml.libsbml.Port
Unsets the value of the 'name' attribute of this SBML object.
unsetName() - Method in class org.sbml.libsbml.Reaction
Unsets the value of the 'name' attribute of this Reaction.
unsetName() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'name' attribute of this SBML object.
unsetName() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Unsets the value of the 'name' attribute of this SimpleSpeciesReference.
unsetName() - Method in class org.sbml.libsbml.Species
Unsets the value of the 'name' attribute of this Species object.
unsetName() - Method in class org.sbml.libsbml.SpeciesType
Unsets the value of the 'name' attribute of this SpeciesType.
unsetName() - Method in class org.sbml.libsbml.Submodel
Unsets the value of the 'name' attribute of this SBML object.
unsetName() - Method in class org.sbml.libsbml.UnitDefinition
Unsets the value of the 'name' attribute of this UnitDefinition.
unsetNotes() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'notes' subelement of this SBML object.
unsetOperation() - Method in class org.sbml.libsbml.FluxBound
 
unsetOrganisation() - Method in class org.sbml.libsbml.ModelCreator
(Alternate spelling) Unsets the 'organization' portion of this ModelCreator object.
unsetOrganization() - Method in class org.sbml.libsbml.ModelCreator
Unsets the 'organization' portion of this ModelCreator object.
unsetOutside() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'outside' attribute of this Compartment.
unsetPortRef() - Method in class org.sbml.libsbml.SBaseRef
 
unsetPriority() - Method in class org.sbml.libsbml.Event
(SBML Level 3 only) Unsets the Priority of this Event.
unsetReaction() - Method in class org.sbml.libsbml.FluxBound
 
unsetReaction() - Method in class org.sbml.libsbml.FluxObjective
 
unsetReaction() - Method in class org.sbml.libsbml.GeneAssociation
 
unsetReference() - Method in class org.sbml.libsbml.Association
 
unsetReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
 
unsetRequired() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Unsets the value of the 'required' attribute of this SBMLDocumentPlugin.
unsetSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
 
unsetSBOTerm() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'sboTerm' attribute of this SBML object.
unsetSize() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'size' attribute of this Compartment.
unsetSource() - Method in class org.sbml.libsbml.ExternalModelDefinition
 
unsetSpatialDimensions() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'spatialDimensions' attribute of this Compartment.
unsetSpatialSizeUnits() - Method in class org.sbml.libsbml.Species
Unsets the 'spatialSizeUnits' attribute value of this Species object.
unsetSpeciesType() - Method in class org.sbml.libsbml.Species
Unsets the 'speciesType' attribute value of this Species object.
unsetStoichiometry() - Method in class org.sbml.libsbml.SpeciesReference
Unsets the 'stoichiometry' attribute of this SpeciesReference.
unsetStoichiometryMath() - Method in class org.sbml.libsbml.SpeciesReference
Unsets the 'stoichiometryMath' subelement of this SpeciesReference.
unsetStyle() - Method in class org.sbml.libsbml.ASTNode
Unsets the mathml style of this ASTNode.
unsetSubmodelRef() - Method in class org.sbml.libsbml.Replacing
 
unsetSubstanceConversionFactor() - Method in class org.sbml.libsbml.Submodel
 
unsetSubstanceUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Unsets the 'substanceUnits' attribute of this KineticLaw object.
unsetSubstanceUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'substanceUnits' attribute of this Model.
unsetSubstanceUnits() - Method in class org.sbml.libsbml.Species
Unsets the 'substanceUnits' attribute value of this Species object.
unsetTimeConversionFactor() - Method in class org.sbml.libsbml.Submodel
 
unsetTimeUnits() - Method in class org.sbml.libsbml.Event
Unsets the 'timeUnits' attribute of this Event.
unsetTimeUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Unsets the 'timeUnits' attribugte of this KineticLaw object.
unsetTimeUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'timeUnits' attribute of this Model.
unsetTrigger() - Method in class org.sbml.libsbml.Event
Unsets the Trigger of this Event.
unsetType() - Method in class org.sbml.libsbml.Association
 
unsetType() - Method in class org.sbml.libsbml.Objective
 
unsetUnitRef() - Method in class org.sbml.libsbml.SBaseRef
 
unsetUnits() - Method in class org.sbml.libsbml.ASTNode
Unsets the units of this ASTNode.
unsetUnits() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'units' attribute of this Compartment.
unsetUnits() - Method in class org.sbml.libsbml.Parameter
Unsets the 'units' attribute of this Parameter instance.
unsetUnits() - Method in class org.sbml.libsbml.Rule
Unsets the 'units' for this Rule.
unsetUnits() - Method in class org.sbml.libsbml.Species
Unsets the 'units' attribute value of this Species object.
unsetValue() - Method in class org.sbml.libsbml.FluxBound
 
unsetValue() - Method in class org.sbml.libsbml.Parameter
Unsets the 'value' attribute of this Parameter instance.
unsetVolume() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'volume' attribute of this Compartment.
unsetVolumeUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'volumeUnits' attribute of this Model.
UpperUnitBound - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

V

validate() - Method in class org.sbml.libsbml.SBMLExternalValidator
the actual conversion
validate() - Method in class org.sbml.libsbml.SBMLValidator
Runs this validator on the current SBML document.
validate(SBMLDocument) - Method in class org.sbml.libsbml.SBMLValidator
Validates the given SBMLDocument object.
validate(String) - Method in class org.sbml.libsbml.SBMLValidator
Validates the SBML document located at the given filename.
validateSBML() - Method in class org.sbml.libsbml.SBMLDocument
Performs consistency checking and validation on this SBML document.
ValuesFromTriggerTimeNeedDelay - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
VariableNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
VersionPositiveInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
VolumeLitreDefExponentNotOne - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
VolumeMetreDefExponentNot3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

W

width() - Method in class org.sbml.libsbml.BoundingBox
 
width() - Method in class org.sbml.libsbml.Dimensions
 
writeAttributes(XMLOutputStream) - Method in class org.sbml.libsbml.FbcModelPlugin
 
writeMathMLToString(ASTNode) - Static method in class org.sbml.libsbml.libsbml
Writes the given ASTNode (and its children) to a string as MathML, and returns the string.
writeSBML(SBMLDocument, String) - Static method in class org.sbml.libsbml.libsbml
Writes the given SBML document d to the file named by filename.
writeSBML(SBMLDocument, String) - Method in class org.sbml.libsbml.SBMLWriter
Writes the given SBML document to filename.
writeSBML(SBMLDocument, OStream) - Method in class org.sbml.libsbml.SBMLWriter
Writes the given SBML document to the output stream.
writeSBMLToFile(SBMLDocument, String) - Static method in class org.sbml.libsbml.libsbml
Writes the given SBML document d to the file filename.
writeSBMLToFile(SBMLDocument, String) - Method in class org.sbml.libsbml.SBMLWriter
Writes the given SBML document to filename.
writeSBMLToString(SBMLDocument) - Static method in class org.sbml.libsbml.libsbml
Writes the given SBML document d to an in-memory string and returns the string.
writeSBMLToString(SBMLDocument) - Method in class org.sbml.libsbml.SBMLWriter
Writes the given SBML document to an in-memory string and returns a pointer to it.

X

x() - Method in class org.sbml.libsbml.BoundingBox
 
x() - Method in class org.sbml.libsbml.Point
 
XMLAttributes - Class in org.sbml.libsbml
Representation of attributes on an XML node.
XMLAttributes() - Constructor for class org.sbml.libsbml.XMLAttributes
Creates a new empty XMLAttributes set.
XMLAttributes(XMLAttributes) - Constructor for class org.sbml.libsbml.XMLAttributes
Copy constructor; creates a copy of this XMLAttributes set.
XMLAttributeTypeMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLBadColon - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLBadNumber - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLBadUTF8Content - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLConstructorException - Exception in org.sbml.libsbml
Class of exceptions thrown by constructors of some libSBML objects.
XMLConstructorException(String) - Constructor for exception org.sbml.libsbml.XMLConstructorException
 
XMLConstructorException() - Constructor for exception org.sbml.libsbml.XMLConstructorException
 
XMLContentEmpty - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLEmptyValueNotPermitted - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
xmlEquals(XMLNode, boolean) - Method in class org.sbml.libsbml.XMLNode
Compare this XMLNode against another XMLNode returning true if both nodes represent the same XML tree, or false otherwise.
xmlEquals(XMLNode) - Method in class org.sbml.libsbml.XMLNode
Compare this XMLNode against another XMLNode returning true if both nodes represent the same XML tree, or false otherwise.
XMLError - Class in org.sbml.libsbml
Representation of errors, warnings and other diagnostics
XMLError(int, String, long, long, long, long) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int, String, long, long, long) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int, String, long, long) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int, String, long) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int, String) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError() - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(XMLError) - Constructor for class org.sbml.libsbml.XMLError
Copy constructor; creates a copy of this XMLError.
XMLErrorCodesUpperBound - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLErrorLog - Class in org.sbml.libsbml
Log of errors and other events encountered while processing an XML file or data stream.
XMLExpectedQuotedString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLFileOperationError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLFileUnreadable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLFileUnwritable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLNamespaces - Class in org.sbml.libsbml
Representation of XML Namespaces.
XMLNamespaces() - Constructor for class org.sbml.libsbml.XMLNamespaces
Creates a new empty list of XML namespace declarations.
XMLNamespaces(XMLNamespaces) - Constructor for class org.sbml.libsbml.XMLNamespaces
Copy constructor; creates a copy of this XMLNamespaces list.
XMLNetworkAccessError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLNode - Class in org.sbml.libsbml
Representation of a node in an XML document tree.
XMLNode() - Constructor for class org.sbml.libsbml.XMLNode
Creates a new empty XMLNode with no children.
XMLNode(XMLToken) - Constructor for class org.sbml.libsbml.XMLNode
Creates a new XMLNode by copying token.
XMLNode(XMLTriple, XMLAttributes, XMLNamespaces, long, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a new start element XMLNode with the given set of attributes and namespace declarations.
XMLNode(XMLTriple, XMLAttributes, XMLNamespaces, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a new start element XMLNode with the given set of attributes and namespace declarations.
XMLNode(XMLTriple, XMLAttributes, XMLNamespaces) - Constructor for class org.sbml.libsbml.XMLNode
Creates a new start element XMLNode with the given set of attributes and namespace declarations.
XMLNode(XMLTriple, XMLAttributes, long, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a start element XMLNode with the given set of attributes.
XMLNode(XMLTriple, XMLAttributes, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a start element XMLNode with the given set of attributes.
XMLNode(XMLTriple, XMLAttributes) - Constructor for class org.sbml.libsbml.XMLNode
Creates a start element XMLNode with the given set of attributes.
XMLNode(XMLTriple, long, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates an end element XMLNode.
XMLNode(XMLTriple, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates an end element XMLNode.
XMLNode(XMLTriple) - Constructor for class org.sbml.libsbml.XMLNode
Creates an end element XMLNode.
XMLNode(String, long, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a text XMLNode.
XMLNode(String, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a text XMLNode.
XMLNode(String) - Constructor for class org.sbml.libsbml.XMLNode
Creates a text XMLNode.
XMLNode(XMLNode) - Constructor for class org.sbml.libsbml.XMLNode
Copy constructor; creates a copy of this XMLNode.
XMLOutOfMemory - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLTagMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLToken - Class in org.sbml.libsbml
Representation of a token in an XML stream.
XMLToken() - Constructor for class org.sbml.libsbml.XMLToken
Creates a new empty XMLToken.
XMLToken(XMLTriple, XMLAttributes, XMLNamespaces, long, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates a start element XMLToken with the given set of attributes and namespace declarations.
XMLToken(XMLTriple, XMLAttributes, XMLNamespaces, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates a start element XMLToken with the given set of attributes and namespace declarations.
XMLToken(XMLTriple, XMLAttributes, XMLNamespaces) - Constructor for class org.sbml.libsbml.XMLToken
Creates a start element XMLToken with the given set of attributes and namespace declarations.
XMLToken(XMLTriple, XMLAttributes, long, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates a start element XMLToken with the given set of attributes.
XMLToken(XMLTriple, XMLAttributes, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates a start element XMLToken with the given set of attributes.
XMLToken(XMLTriple, XMLAttributes) - Constructor for class org.sbml.libsbml.XMLToken
Creates a start element XMLToken with the given set of attributes.
XMLToken(XMLTriple, long, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates an end element XMLToken.
XMLToken(XMLTriple, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates an end element XMLToken.
XMLToken(XMLTriple) - Constructor for class org.sbml.libsbml.XMLToken
Creates an end element XMLToken.
XMLToken(String, long, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates a text XMLToken.
XMLToken(String, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates a text XMLToken.
XMLToken(String) - Constructor for class org.sbml.libsbml.XMLToken
Creates a text XMLToken.
XMLToken(XMLToken) - Constructor for class org.sbml.libsbml.XMLToken
Copy constructor; creates a copy of this XMLToken.
XMLTranscoderError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLTriple - Class in org.sbml.libsbml
Representation of a qualified XML name.
XMLTriple() - Constructor for class org.sbml.libsbml.XMLTriple
Creates a new, empty XMLTriple.
XMLTriple(String, String, String) - Constructor for class org.sbml.libsbml.XMLTriple
Creates a new XMLTriple with the given name, uri and and prefix.
XMLTriple(String, char) - Constructor for class org.sbml.libsbml.XMLTriple
Creates a new XMLTriple by splitting the given triplet on the separator character sepchar.
XMLTriple(String) - Constructor for class org.sbml.libsbml.XMLTriple
Creates a new XMLTriple by splitting the given triplet on the separator character sepchar.
XMLTriple(XMLTriple) - Constructor for class org.sbml.libsbml.XMLTriple
Copy constructor; creates a copy of this XMLTriple set.
XMLUnexpectedEOF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLUnknownError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

Y

y() - Method in class org.sbml.libsbml.BoundingBox
 
y() - Method in class org.sbml.libsbml.Point
 

Z

z() - Method in class org.sbml.libsbml.BoundingBox
 
z() - Method in class org.sbml.libsbml.Point
 
ZeroDCompartmentContainment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ZeroDimensionalCompartmentConst - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ZeroDimensionalCompartmentSize - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ZeroDimensionalCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
A B C D E F G H I K L M N O P R S T U V W X Y Z 
libSBML
5.8.0


LibSBML, an application programming interface (API) library for SBML.