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

G

gamma - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to elemental rotation of an object about the Z coordinate axis

geneProduct - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

GeneProduct - Class in org.sbml.jsbml.ext.fbc

Defines a single gene product.

GeneProduct() - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct

Creates a new GeneProduct instance.

GeneProduct(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct

Creates a new GeneProduct instance.

GeneProduct(String) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct

Creates a new GeneProduct instance.

GeneProduct(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct

Creates a new GeneProduct instance.

GeneProduct(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct

Creates a new GeneProduct instance.

GeneProduct(GeneProduct) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct

Creates a new GeneProduct instance.

geneProductAssociation - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

GeneProductAssociation - Class in org.sbml.jsbml.ext.fbc

Contains a single Association.

GeneProductAssociation() - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation

Creates a new GeneProductAssociation instance.

GeneProductAssociation(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation

Creates a new GeneProductAssociation instance.

GeneProductAssociation(String) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation

Creates a new GeneProductAssociation instance.

GeneProductAssociation(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation

Creates a new GeneProductAssociation instance.

GeneProductAssociation(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation

Creates a new GeneProductAssociation instance.

GeneProductAssociation(GeneProductAssociation) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation

Creates a new GeneProductAssociation instance.

GeneProductConstraints - Class in org.sbml.jsbml.validator.offline.constraints

GeneProductConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints

geneProductIdentifier - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

GeneProductRef - Class in org.sbml.jsbml.ext.fbc

References a GeneProduct.

GeneProductRef() - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef

Creates a new GeneProductRef instance.

GeneProductRef(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef

Creates a new GeneProductRef instance.

GeneProductRef(String) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef

Creates a new GeneProductRef instance.

GeneProductRef(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef

Creates a new GeneProductRef instance.

GeneProductRef(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef

Creates a new GeneProductRef instance.

GeneProductRef(GeneProductRef) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef

Creates a new GeneProductRef instance.

geneProductReference - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

geneProteinAssociation - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

Deprecated.

GENERAL_CONSISTENCY - org.sbml.jsbml.SBMLException.Category

Category of errors that can occur while validating general SBML constructs.

GENERAL_CONSISTENCY - org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY

Correctness and consistency of specific SBML language constructs.

generalGlyph - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

GeneralGlyph - Class in org.sbml.jsbml.ext.layout

The GeneralGlyph is used to facilitate the representation of elements other than Compartment, Species and Reaction and thus can be used for the display of relationships of Rule or elements defined by other SBML packages.

GeneralGlyph() - Constructor for class org.sbml.jsbml.ext.layout.GeneralGlyph

GeneralGlyph(int, int) - Constructor for class org.sbml.jsbml.ext.layout.GeneralGlyph

Creates a new instance of GeneralGlyph.

GeneralGlyph(String) - Constructor for class org.sbml.jsbml.ext.layout.GeneralGlyph

Creates a new instance of GeneralGlyph.

GeneralGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.GeneralGlyph

Creates a new instance of GeneralGlyph.

GeneralGlyph(GeneralGlyph) - Constructor for class org.sbml.jsbml.ext.layout.GeneralGlyph

Creates a new instance of GeneralGlyph cloned from the given element.

GENERALGLYPH - org.sbml.jsbml.ext.render.Style.Type

GeneralGlyphConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the GeneralGlyph class.

GeneralGlyphConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GeneralGlyphConstraints

generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParser

Generate ParseException.

generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2

Generate ParseException.

generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3

Generate ParseException.

generateParseException() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2

Generate ParseException.

generateParseException() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser

Generate ParseException.

generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParser

Generate ParseException.

generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2

Generate ParseException.

generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3

Generate ParseException.

generateParseException() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2

Generate ParseException.

generateSubModel(Model, String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel

Generates a sub-model containing the elements passed as argument and all the necessary dependencies.

generateSubModel(Model, String[], String[], String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel

Generates a sub-model containing the elements passed as argument and all the necessary dependencies.

geometry - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

Geometry - Class in org.sbml.jsbml.ext.render.director

Geometry - Class in org.sbml.jsbml.ext.spatial

Geometry() - Constructor for class org.sbml.jsbml.ext.render.director.Geometry

Geometry() - Constructor for class org.sbml.jsbml.ext.spatial.Geometry

Geometry(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.Geometry

Geometry(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.Geometry

Geometry(Geometry) - Constructor for class org.sbml.jsbml.ext.spatial.Geometry

GeometryConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the Geometry class.

GeometryConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GeometryConstraints

geometryDefinition - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

GeometryDefinition - Class in org.sbml.jsbml.ext.spatial

GeometryDefinition() - Constructor for class org.sbml.jsbml.ext.spatial.GeometryDefinition

GeometryDefinition(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.GeometryDefinition

GeometryDefinition(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.GeometryDefinition

GeometryDefinition(GeometryDefinition) - Constructor for class org.sbml.jsbml.ext.spatial.GeometryDefinition

GeometryDefinitionConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the GeometryDefinition class.

GeometryDefinitionConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GeometryDefinitionConstraints

GeometryKind - Enum in org.sbml.jsbml.ext.spatial

This enum type was created following the specifications defined in Spatial Package v0.90.

geq(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode

Creates an ASTNode representing greater or equal for the two given nodes.

geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

geq(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

Greater equal.

geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML

geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler

geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

geq(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Creates an ASTRelationalOperatorNode representing greater or equal for the two given nodes.

geq(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

Greater equal.

geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler

geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

get(int) - Method in class org.sbml.jsbml.ListOf

Returns the element at the specified position in this list or null if the index is negative or too big.

get(String) - Method in class org.sbml.jsbml.ListOf

Gets the list element which has the id 'id'.

getAbout() - Method in class org.sbml.jsbml.Annotation

Returns the about String of this object.

getAbsoluteSourceURI() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Finds the absolute URI of the source-file specified: If the source is specified through a relative path, will try to use the containing SBMLDocument's SBMLDocument.getLocationURI() to turn it into an absolute URI in the current context.

getAbsoluteSourceURI(URI) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Finds the absolute URI of the source-file specified: If the source is specified through a relative path, will try to use the given absoluteContainingURI to turn it into an absolute URI in the current context.

getAbsoluteValue() - Method in class org.sbml.jsbml.ext.render.RelAbsVector

getActivator() - Static method in class org.sbml.jsbml.SBO

getActiveObjective() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Gets the activeObjective.

getActiveObjective() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives

Returns the value of activeObjective

getActiveObjectiveInstance() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

getActiveObjectiveInstance() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives

Returns the active Objective.

getAdditionalGraphicalObject(int) - Method in class org.sbml.jsbml.ext.layout.Layout

getAdditionalGraphicalObjectCount() - Method in class org.sbml.jsbml.ext.layout.Layout

getAddWhiskers() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Returns the value of addWhiskers

getAdjacentDomains(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the Geometry.listOfAdjacentDomains at the given index.

getAdjacentDomains(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the listOfAdjacentDomains, with the given id.

getAdjacentDomainsCount() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of AdjacentDomainss in this Geometry.

getAlgorithm() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

getAllDeclaredNamespaces(SBase) - Static method in class org.sbml.jsbml.AbstractSBase

Returns a map of all the declared namespaces in the SBML tree, visible to the given SBase.

getAllostericActivator() - Static method in class org.sbml.jsbml.SBO

Describes an activator (ligand) which binds at a site other than the active site, resulting in a conformational change, enhancing the activity of the enzyme.

getAllostericInhibitor() - Static method in class org.sbml.jsbml.SBO

An inhibitor whose binding to an enzyme results in a conformational change, resulting in a loss of enzymatic activity.

getAllowsChildren() - Method in class org.sbml.jsbml.AbstractMathContainer

getAllowsChildren() - Method in class org.sbml.jsbml.AbstractSBase

getAllowsChildren() - Method in class org.sbml.jsbml.Annotation

getAllowsChildren() - Method in class org.sbml.jsbml.ASTNode

getAllowsChildren() - Method in class org.sbml.jsbml.Creator

getAllowsChildren() - Method in class org.sbml.jsbml.CVTerm

getAllowsChildren() - Method in class org.sbml.jsbml.Event

getAllowsChildren() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

getAllowsChildren() - Method in class org.sbml.jsbml.ext.comp.Submodel

getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getAllowsChildren() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation

getAllowsChildren() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

getAllowsChildren() - Method in class org.sbml.jsbml.ext.groups.Group

getAllowsChildren() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject

getAllowsChildren() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

getAllowsChildren() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.GradientBase

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.GradientStop

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.Image

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.LineEnding

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.Polygon

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.Rectangle

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RelAbsVector

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RenderCurve

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.Style

getAllowsChildren() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.CSGObject

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.CSGTransformation

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.Domain

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.Geometry

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.SampledField

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.History

getAllowsChildren() - Method in class org.sbml.jsbml.ListOf

getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTBoolean

getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTFunction

getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTNumber

getAllowsChildren() - Method in class org.sbml.jsbml.math.ASTUnknown

getAllowsChildren() - Method in class org.sbml.jsbml.Model

getAllowsChildren() - Method in class org.sbml.jsbml.Reaction

getAllowsChildren() - Method in class org.sbml.jsbml.SBMLDocument

getAllowsChildren() - Method in class org.sbml.jsbml.SpeciesReference

getAllowsChildren() - Method in class org.sbml.jsbml.UnitDefinition

getAllowsChildren() - Method in class org.sbml.jsbml.util.TreeNodeAdapter

getAllowsChildren() - Method in class org.sbml.jsbml.xml.XMLNode

getAndReplacement() - Method in class org.sbml.jsbml.util.compilers.ConfigurableLogicalFormulaCompiler

Gets the String that will be used to replace ' and ' (the mathML <and> element) in the boolean expressions.

getAndReplacement() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise

Gets the String that will be used to replace ' and ' (the mathML <and> element) in the boolean expressions.

getAnnotation() - Method in class org.sbml.jsbml.AbstractSBase

getAnnotation() - Method in interface org.sbml.jsbml.SBase

Returns the content of the 'annotation' sub-element of this object as an Annotation instance.

getAnnotationBuilder() - Method in class org.sbml.jsbml.Annotation

Deprecated.

getAnnotationString() - Method in class org.sbml.jsbml.AbstractSBase

Returns the Annotation of this SBML object as a String.

getAnnotationString() - Method in interface org.sbml.jsbml.SBase

Returns the content of the 'annotation' sub-element of this object as a String.

getAntisenseRNA() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id for antisense RNA.

getApplyToAll() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Returns the value of applyToAll

getAreaUnits() - Method in class org.sbml.jsbml.Model

Returns the area units ID of this Model.

getAreaUnitsInstance() - Method in class org.sbml.jsbml.Model

Returns the UnitDefinition instance which has the Model.areaUnitsID of this Model as id.

getArgument(int) - Method in class org.sbml.jsbml.FunctionDefinition

Get the nth argument to this function.

getArgument(String) - Method in class org.sbml.jsbml.FunctionDefinition

Get the argument named name to this FunctionDefinition.

getArgumentCount() - Method in class org.sbml.jsbml.FunctionDefinition

Get the number of arguments (bound variables) taken by this FunctionDefinition.

getArrayData() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Returns the value of SpatialPoints.arrayData.

getArrayDataLength() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Returns the value of arrayDataLength.

getArrayDimension() - Method in class org.sbml.jsbml.ext.arrays.Dimension

Returns the value of arrayDimension

getArrayDimension() - Method in class org.sbml.jsbml.ext.arrays.Index

Returns the value of arrayDimension

getAssignmentRuleByVariable(String) - Method in class org.sbml.jsbml.Model

Searches for the first instance of AssignmentRule within this Model's Model.listOfRules, whose variable attribute is set to the value passed to this method.

getAssociatedSpecies() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct

Returns the value of GeneProduct.associatedSpecies.

getAssociation() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation

Returns the value of GeneProductAssociation.association.

getAssociation() - Static method in class org.sbml.jsbml.SBO

Interaction between several biochemical entities that results in the formation of a non-covalent complex

getAssociation(int) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

Gets an element from the LogicalOperator.listOfAssociations at the given index.

getAssociationCount() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

Returns the number of Associations in this LogicalOperator.

getAttributes() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML

getAttributes() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the attributes of this element.

getAttributesLength() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the number of attributes in the attributes set.

getAttrIndex(String) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the index of an attribute with the given local name.

getAttrIndex(String, String) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the index of an attribute with the given local name and namespace URI.

getAttrIndex(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the index of an attribute with the given XMLTriple.

getAttrName(int) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the local name of an attribute in the attributes set in this XMLToken (by position).

getAttrPrefix(int) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the prefix of an attribute in the attribute set in this XMLToken (by position).

getAttrPrefixedName(int) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the prefixed name of an attribute in the attribute set in this XMLToken (by position).

getAttrURI(int) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the namespace URI of an attribute in the attribute set in this XMLToken (by position).

getAttrValue(int) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the value of an attribute in the attribute set in this XMLToken (by position).

getAttrValue(String) - Method in class org.sbml.jsbml.xml.XMLToken

Returns a value of an attribute with the given local name.

getAttrValue(String, String) - Method in class org.sbml.jsbml.xml.XMLToken

Returns a value of an attribute with the given local name and namespace URI.

getAttrValue(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLToken

Returns a value of an attribute with the given XMLTriple.

getAvogadro(int, int) - Static method in class org.sbml.jsbml.util.Maths

Returns the avogadro value corresponding to the given SBML level and version.

getBackgroundColor() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getBase() - Method in class org.sbml.jsbml.math.ASTLogarithmNode

Return the base of this ASTLogarithmNode

getBasePoint1() - Method in class org.sbml.jsbml.ext.layout.CubicBezier

getBasePoint2() - Method in class org.sbml.jsbml.ext.layout.CubicBezier

getBasis() - Method in class org.sbml.jsbml.math.ASTPowerNode

Get the basis of this ASTPowerNode

getBeginColumn() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Get token beginning column number.

getBeginColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Get token beginning column number.

getBeginLine() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Get token beginning line number.

getBeginLine() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Get token beginning line number.

getBindingActivator() - Static method in class org.sbml.jsbml.SBO

An essential activator that affects the apparent value of the Michaelis constant(s).

getBindingSite1() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Returns the value of InSpeciesTypeBond.bindingSite1.

getBindingSite2() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Returns the value of InSpeciesTypeBond.bindingSite2.

getBindingStatus() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Returns the value of OutwardBindingSite.bindingStatus.

getBiochemicalReaction() - Static method in class org.sbml.jsbml.SBO

An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants.

getBiologicalQualifierFor(String) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier

getBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm

Returns the CVTerm.Qualifier for this CVTerm, only if it if of type CVTerm.Type.BIOLOGICAL_QUALIFIER, null otherwise.

getBody() - Method in class org.sbml.jsbml.FunctionDefinition

Get the mathematical expression that is the body of this FunctionDefinition object.

getBoundaryCondition() - Method in class org.sbml.jsbml.Species

Returns the boundaryCondition Boolean of this Species.

getBoundaryDomainType() - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

Returns the value of boundaryDomainType

getBoundaryMaximum() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

Returns the value of boundaryMaximum

getBoundaryMinimum() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

Returns the value of boundaryMinimum

getBoundingBox() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject

getBoundingBox() - Method in interface org.sbml.jsbml.ext.layout.IBoundingBox

Returns the BoundingBox.

getBoundingBox() - Method in class org.sbml.jsbml.ext.render.LineEnding

getBuilder() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

getBundle(String) - Static method in class org.sbml.jsbml.util.ResourceManager

Loads the ResourceBundle with the given name for the default Locale.

getBundle(String, Locale) - Static method in class org.sbml.jsbml.util.ResourceManager

Loads the ResourceBundle with the given name for the given Locale.

getBundleString(ResourceBundle, String) - Static method in class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory

Gets the String corresponding to the given key in the bundle, returns null if the key is not found.

getBvarCount() - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode

Get the number of bvar elements in this ASTLambdaFunctionNode

getBytesFromResourceLocation(String) - Method in class org.sbml.jsbml.resources.Resource

Gets the byte data from a file at the given resource location.

getCalculatedStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference

This method computes the fraction of the stoichiometry and the denominator.

getCaseSensitive() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3

Returns the case sensitivity of the parser, for the mathml elements.

getCatalysis() - Static method in class org.sbml.jsbml.SBO

Modification of the velocity of a reaction by lowering the energy of the transition state.

getCatalyst() - Static method in class org.sbml.jsbml.SBO

Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed.

getCatalyticActivator() - Static method in class org.sbml.jsbml.SBO

getCategory() - Method in exception org.sbml.jsbml.SBMLError

Returns the category of the SBMLError

getCategory() - Method in exception org.sbml.jsbml.SBMLException

getCategory() - Method in class org.sbml.jsbml.util.Detail

getCategory() - Method in class org.sbml.jsbml.validator.offline.constraints.CategoryConstraintGroup

Returns the SBMLValidator.CHECK_CATEGORY this ConstraintGroup is linked to.

getCBOTerm() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

Returns the value of CBO

getChangedBy() - Method in class org.sbml.jsbml.ext.req.ChangedMath

Returns the value of changedBy

getCharacter() - Method in class org.sbml.jsbml.ASTNode

Gets the value of this node as a single character.

getCharacters() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML

getCharacters() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the text of this element.

getCharge() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

Returns the value of FBCSpeciesPlugin.charge.

getCharge() - Method in class org.sbml.jsbml.Species

Deprecated.

getCheckCategories() - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Returns all the enabled check categories.

getChemicalFormula() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

Returns the value of FBCSpeciesPlugin.chemicalFormula.

getChild() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode

Get the child of this node

getChild(int) - Method in class org.sbml.jsbml.ASTNode

Gets a child of this node according to an index number.

getChild(int) - Method in class org.sbml.jsbml.xml.XMLNode

Returns the child XMLNode at index childIndex.

getChildAt(int) - Method in class org.sbml.jsbml.AbstractMathContainer

getChildAt(int) - Method in class org.sbml.jsbml.AbstractSBase

getChildAt(int) - Method in class org.sbml.jsbml.Annotation

getChildAt(int) - Method in class org.sbml.jsbml.ASTNode

getChildAt(int) - Method in class org.sbml.jsbml.Constraint

getChildAt(int) - Method in class org.sbml.jsbml.Creator

getChildAt(int) - Method in class org.sbml.jsbml.CVTerm

getChildAt(int) - Method in class org.sbml.jsbml.Event

getChildAt(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.comp.SBaseRef

getChildAt(int) - Method in class org.sbml.jsbml.ext.comp.Submodel

getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getChildAt(int) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation

getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

getChildAt(int) - Method in class org.sbml.jsbml.ext.fbc.Objective

getChildAt(int) - Method in class org.sbml.jsbml.ext.groups.Group

getChildAt(int) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.BoundingBox

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.CubicBezier

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.Curve

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.GraphicalObject

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.Layout

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.LineSegment

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph

getChildAt(int) - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

getChildAt(int) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.qual.Transition

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.GradientBase

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.GradientStop

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.Image

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.LineEnding

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.Polygon

The listOfElements and listOfCurveSegments will take the indices 0 and 1, or 0 (if only one is set).

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.Rectangle

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RelAbsVector

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderCurve

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderGroup

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.Style

getChildAt(int) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CSGObject

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.CSGTransformation

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.Domain

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.ParameterType

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

getChildAt(int) - Method in class org.sbml.jsbml.History

getChildAt(int) - Method in class org.sbml.jsbml.KineticLaw

getChildAt(int) - Method in class org.sbml.jsbml.ListOf

getChildAt(int) - Method in class org.sbml.jsbml.math.AbstractASTNode

getChildAt(int) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode

getChildAt(int) - Method in class org.sbml.jsbml.math.ASTBoolean

getChildAt(int) - Method in class org.sbml.jsbml.math.ASTFunction

getChildAt(int) - Method in class org.sbml.jsbml.math.ASTNumber

getChildAt(int) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode

getChildAt(int) - Method in class org.sbml.jsbml.math.ASTUnknown

getChildAt(int) - Method in class org.sbml.jsbml.Model

getChildAt(int) - Method in class org.sbml.jsbml.Reaction

getChildAt(int) - Method in class org.sbml.jsbml.SBMLDocument

getChildAt(int) - Method in class org.sbml.jsbml.SpeciesReference

getChildAt(int) - Method in class org.sbml.jsbml.UnitDefinition

getChildAt(int) - Method in class org.sbml.jsbml.util.TreeNodeAdapter

getChildAt(int) - Method in class org.sbml.jsbml.xml.XMLNode

getChildCount() - Method in class org.sbml.jsbml.AbstractMathContainer

getChildCount() - Method in class org.sbml.jsbml.AbstractSBase

getChildCount() - Method in class org.sbml.jsbml.Annotation

getChildCount() - Method in class org.sbml.jsbml.ASTNode

getChildCount() - Method in class org.sbml.jsbml.Constraint

getChildCount() - Method in class org.sbml.jsbml.Creator

getChildCount() - Method in class org.sbml.jsbml.CVTerm

getChildCount() - Method in class org.sbml.jsbml.Event

getChildCount() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

getChildCount() - Method in class org.sbml.jsbml.ext.comp.Submodel

getChildCount() - Method in class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

getChildCount() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

getChildCount() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getChildCount() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation

getChildCount() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

getChildCount() - Method in class org.sbml.jsbml.ext.fbc.Objective

getChildCount() - Method in class org.sbml.jsbml.ext.groups.Group

getChildCount() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.layout.BoundingBox

getChildCount() - Method in class org.sbml.jsbml.ext.layout.CubicBezier

getChildCount() - Method in class org.sbml.jsbml.ext.layout.Curve

getChildCount() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph

getChildCount() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject

getChildCount() - Method in class org.sbml.jsbml.ext.layout.Layout

getChildCount() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.layout.LineSegment

getChildCount() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

getChildCount() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph

getChildCount() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

getChildCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

getChildCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

getChildCount() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.qual.Transition

getChildCount() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

getChildCount() - Method in class org.sbml.jsbml.ext.render.GradientBase

getChildCount() - Method in class org.sbml.jsbml.ext.render.GradientStop

getChildCount() - Method in class org.sbml.jsbml.ext.render.Image

getChildCount() - Method in class org.sbml.jsbml.ext.render.LineEnding

getChildCount() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

getChildCount() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getChildCount() - Method in class org.sbml.jsbml.ext.render.Polygon

getChildCount() - Method in class org.sbml.jsbml.ext.render.Rectangle

getChildCount() - Method in class org.sbml.jsbml.ext.render.RelAbsVector

getChildCount() - Method in class org.sbml.jsbml.ext.render.RenderCurve

getChildCount() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getChildCount() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getChildCount() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.render.Style

getChildCount() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.CSGObject

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.CSGTransformation

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.Domain

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.Geometry

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.SampledField

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

getChildCount() - Method in class org.sbml.jsbml.History

getChildCount() - Method in class org.sbml.jsbml.KineticLaw

getChildCount() - Method in class org.sbml.jsbml.ListOf

getChildCount() - Method in class org.sbml.jsbml.math.ASTBoolean

getChildCount() - Method in class org.sbml.jsbml.math.ASTFunction

getChildCount() - Method in class org.sbml.jsbml.math.ASTNumber

getChildCount() - Method in class org.sbml.jsbml.math.ASTUnknown

getChildCount() - Method in class org.sbml.jsbml.Model

getChildCount() - Method in class org.sbml.jsbml.Reaction

getChildCount() - Method in class org.sbml.jsbml.SBMLDocument

getChildCount() - Method in class org.sbml.jsbml.SpeciesReference

getChildCount() - Method in class org.sbml.jsbml.UnitDefinition

getChildCount() - Method in class org.sbml.jsbml.util.TreeNodeAdapter

getChildCount() - Method in class org.sbml.jsbml.xml.XMLNode

getChildElement(String, String) - Method in class org.sbml.jsbml.xml.XMLNode

Gets the first direct child element of this XMLNode with the given local name and namespace.

getChildElements(String, String) - Method in class org.sbml.jsbml.xml.XMLNode

Gets all the direct children of this XMLNode with the given local name and namespace.

getChildren() - Method in class org.sbml.jsbml.ASTNode

Returns the list of children of the current ASTNode.

getChildren() - Method in class org.sbml.jsbml.math.ASTFunction

Returns the list of children of the current ASTFunction.

getChildren() - Method in class org.sbml.jsbml.ontology.Term

Returns a set of all the children Term.

getClassName() - Method in class org.sbml.jsbml.ASTNode

Returns the class name of the mathML element represented by this ASTNode.

getCode() - Method in exception org.sbml.jsbml.SBMLError

Returns the code of this SBMLError.

getCode() - Method in exception org.sbml.jsbml.SBMLException

getCoefficient() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective

Returns the value of coefficient

getColorDefinition(String) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getColorDefinitionCount() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getColumn() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Deprecated.

getColumn() - Method in exception org.sbml.jsbml.SBMLError

Returns the column where this SBMLError happened.

getColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Deprecated.

getColumn() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the column at which this XMLToken occurred in the input document or data stream.

getCompartment() - Method in interface org.sbml.jsbml.CompartmentalizedSBase

Returns the value of the referenced compartment.

getCompartment() - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph

getCompartment() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

getCompartment() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

getCompartment() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

getCompartment() - Method in class org.sbml.jsbml.Reaction

Only available if Level >= 3.

getCompartment() - Static method in class org.sbml.jsbml.SBO

Physical compartment.

getCompartment() - Method in class org.sbml.jsbml.Species

getCompartment(int) - Method in class org.sbml.jsbml.Model

Gets the n^th Compartment instance of the listOfCompartments.

getCompartment(String) - Method in class org.sbml.jsbml.Model

Gets the Compartment of the listOfCompartments which has 'id' as id.

getCompartmentCount() - Method in class org.sbml.jsbml.Model

Returns the number of Compartments of this Model.

getCompartmentGlyph(int) - Method in class org.sbml.jsbml.ext.layout.Layout

Gets an element from the listOfCompartmentGlyphs at the given index.

getCompartmentGlyph(String) - Method in class org.sbml.jsbml.ext.layout.Layout

Gets an element from the listOfCompartmentGlyphs, with the given id.

getCompartmentGlyphCount() - Method in class org.sbml.jsbml.ext.layout.Layout

Returns the number of CompartmentGlyphs of this Layout.

getCompartmentInstance() - Method in interface org.sbml.jsbml.CompartmentalizedSBase

Returns the Compartment that is referenced by this SBase.

getCompartmentInstance() - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph

getCompartmentInstance() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

getCompartmentInstance() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

getCompartmentInstance() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

getCompartmentInstance() - Method in class org.sbml.jsbml.Reaction

getCompartmentInstance() - Method in class org.sbml.jsbml.Species

getCompartmentMapping() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

Returns the value of compartmentMapping

getCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Returns the value of MultiSimpleSpeciesReferencePlugin.compartmentReference.

getCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Returns the value of SpeciesTypeInstance.compartmentReference.

getCompartmentReference(int) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Gets an element from the MultiCompartmentPlugin.listOfCompartmentReferences at the given index.

getCompartmentReference(String) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Gets an element from the listOfCompartmentReferences, with the given id.

getCompartmentReferenceCount() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the number of CompartmentReferences in this MultiCompartmentPlugin.

getCompartmentType() - Method in class org.sbml.jsbml.Compartment

Deprecated.

Only defined in SBML Level 2 Versions 2 through 4.

getCompartmentType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the value of MultiCompartmentPlugin.compartmentType.

getCompartmentType(int) - Method in class org.sbml.jsbml.Model

Deprecated.

Only valid in SBML Level 2 for Versions 2 through 4.

getCompartmentType(String) - Method in class org.sbml.jsbml.Model

Deprecated.

Only valid in SBML Level 2 for Versions 2 through 4.

getCompartmentTypeCount() - Method in class org.sbml.jsbml.Model

Deprecated.

using CompartmentType is not recommended, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.

getCompartmentTypeInstance() - Method in class org.sbml.jsbml.Compartment

Deprecated.

getCompetitiveInhibitor() - Static method in class org.sbml.jsbml.SBO

Substance that decreases the probability of a chemical reaction, without itself being consumed or transformed by the reaction, by stericaly hindering the interaction between reactants.

getComplementA() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Returns the value of complementA

getComplementB() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Returns the value of complementB

getCompleteInhibitor() - Static method in class org.sbml.jsbml.SBO

getComplex() - Static method in class org.sbml.jsbml.SBO

getComplexAssembly() - Static method in class org.sbml.jsbml.SBO

Interaction between several biochemical entities that results in the formation of a non-covalent complex Also known as non-covalent binding

getComponent() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Returns the value of OutwardBindingSite.component.

getComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the value of SpeciesFeature.component.

getComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Returns the value of SpeciesTypeComponentIndex.component.

getComponent() - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature

Returns the value of SubListOfSpeciesFeature.component.

getComponents() - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent

Returns the value of components

getComponentsLength() - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent

Returns the value of componentsLength

getCompression() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Returns the value of compression.

getCompression() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of compression

getCompression() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Returns the value of compression.

getConservationLaw() - Static method in class org.sbml.jsbml.SBO

getConstant() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

getConstant() - Method in class org.sbml.jsbml.SpeciesReference

getConstant() - Method in class org.sbml.jsbml.Symbol

getConstant() - Method in interface org.sbml.jsbml.Variable

getConstantAvogadro(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

getConstantAvogadro(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

getConstantAvogadro(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

getConstantAvogadro(String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

Creates an ASTNode2Value that represent's Avogadro's number.

getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

getConstantAvogadro(String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

Creates an ASTNodeValue that represent's Avogadro's number.

getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

getConstantE() - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

getConstantE() - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

getConstantE() - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

getConstantE() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

getConstantE() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

getConstantE() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

getConstantE() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

getConstantE() - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler

getConstantE() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

getConstantE() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

getConstantE() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

getConstantE() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

getConstantE() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

getConstantE() - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler

getConstantE() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

getConstantE() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

getConstantFalse() - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

getConstantFalse() - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

getConstantFalse() - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

getConstantFalse() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

getConstantFalse() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

getConstantFalse() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

getConstantFalse() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

getConstantPi() - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

getConstantPi() - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

getConstantPi() - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

getConstantPi() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

getConstantPi() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

getConstantPi() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

getConstantPi() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

getConstantPi() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

getConstantPi() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

getConstantPi() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

getConstantPi() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

getConstantPi() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

getConstantPi() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

getConstantPi() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

getConstantTrue() - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

getConstantTrue() - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

getConstantTrue() - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

getConstantTrue() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

getConstantTrue() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

getConstantTrue() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

getConstantTrue() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

getConstraint(int) - Method in class org.sbml.jsbml.Model

Gets the n^th Constraint object in this Model.

getConstraintCount() - Method in class org.sbml.jsbml.Model

Returns the number of Constraints of this Model.

getConstraints() - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup

Returns the members of the group.

getConstraintsCount() - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup

Returns the number of constraints in this group

getConstraintsForAttribute(Class<?>, String, int, int, Set<Class<?>>, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory

Returns all constraints necessary to validate the attribute of the specified class.

getConstraintsForAttribute(Class<?>, String, int, int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory

Returns all constraints necessary to validate the attribute of the specified class.

getConstraintsForClass(Class<?>, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory

Gets all the constraints for one class.

getConstraintsForClass(Class<?>, SBMLValidator.CHECK_CATEGORY[], int, int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory

Gets all the constraints for one class and some SBMLValidator.CHECK_CATEGORYs.

getConstraintType() - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Gets the Class on which the root constraint is typed.

getConsumption() - Static method in class org.sbml.jsbml.SBO

Decrease in amount of a material or conceptual entity.

getContinuousFramework() - Static method in class org.sbml.jsbml.SBO

getConversion() - Static method in class org.sbml.jsbml.SBO

Biochemical reaction that results in the modification of some covalent bonds.

getConversionFactor() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Returns the value of conversionFactor

getConversionFactor() - Method in class org.sbml.jsbml.Model

Returns the conversionFactor ID of this Model.

getConversionFactor() - Method in class org.sbml.jsbml.Species

Returns the conversionFactor of this Species.

getConversionFactorInstance() - Method in class org.sbml.jsbml.Model

Returns the Parameter instance which has the conversionFactorID of this Model as id.

getConversionFactorInstance() - Method in class org.sbml.jsbml.Species

Returns the conversionFactor of this Species as a Parameter instance.

getCoord1() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Returns the value of coord1

getCoord2() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Returns the value of coord2

getCoord3() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

Returns the value of coord3

getCoordinate() - Method in class org.sbml.jsbml.ext.render.RelAbsVector

Produces a string of the format "a" or "r%" or "a+r%" or "a-r%" as specified in the render-documentation.

getCoordinate() - Method in class org.sbml.jsbml.ext.spatial.AdvectionCoefficient

Returns the value of coordinate

getCoordinate() - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference

Deprecated.

getCoordinateBoundary() - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

Returns the value of coordinateBoundary

getCoordinateComponent(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the Geometry.listOfCoordinateComponents at the given index.

getCoordinateComponent(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the listOfCoordinateComponents, with the given id.

getCoordinateComponentCount() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of CoordinateComponents in this Geometry.

getCoordinateReference1() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Returns the value of coordinateReference1

getCoordinateReference2() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Returns the value of coordinateReference2

getCoordinateSystem() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the value of coordinateSystem

getCreatedDate() - Method in class org.sbml.jsbml.History

Returns the createdDate from the History.

getCreator(int) - Method in class org.sbml.jsbml.History

Get the nth Creator object in this History.

getCreatorCount() - Method in class org.sbml.jsbml.History

Get the number of Creator objects in this History.

getCSGNode() - Method in class org.sbml.jsbml.ext.spatial.CSGObject

Returns the value of csgNode

getCSGNode() - Method in class org.sbml.jsbml.ext.spatial.CSGTransformation

Returns the value of csgNode

getCSGObjectCount() - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

Returns the number of CSGObjects in this CSGeometry.

getCsgObjectRef() - Method in class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive

Returns the value of csgObjectRef

getCurve() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph

Gets the Curve.

getCurve() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

getCurve() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph

getCurve() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

getCurveSegment(int) - Method in class org.sbml.jsbml.ext.layout.Curve

getCurveSegment(int) - Method in interface org.sbml.jsbml.ext.layout.ICurve

getCurveSegment(int) - Method in class org.sbml.jsbml.ext.render.Polygon

Gets an element from the Polygon.listOfCurveSegments at the given index.

getCurveSegment(int) - Method in class org.sbml.jsbml.ext.render.RenderCurve

Gets an element from the RenderCurve.listOfCurveSegments at the given index.

getCurveSegmentCount() - Method in class org.sbml.jsbml.ext.layout.Curve

getCurveSegmentCount() - Method in interface org.sbml.jsbml.ext.layout.ICurve

getCurveSegmentCount() - Method in class org.sbml.jsbml.ext.render.Polygon

Returns the number of CurveSegments in this RenderCurve.

getCurveSegmentCount() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns the number of CurveSegments in this RenderCurve.

getCVTerm(int) - Method in class org.sbml.jsbml.AbstractSBase

getCVTerm(int) - Method in class org.sbml.jsbml.Annotation

Returns the CVTerm at the ith position in the list of CVTerms.

getCVTerm(int) - Method in interface org.sbml.jsbml.SBase

Returns the CVTerm instance at the position 'index' in the list of CVTerms of this object.

getCVTermCount() - Method in class org.sbml.jsbml.AbstractSBase

getCVTermCount() - Method in class org.sbml.jsbml.Annotation

Gives the number of CVTerms in this Annotation.

getCVTermCount() - Method in interface org.sbml.jsbml.SBase

Returns the number of CVTerms of this SBase.

getCVTerms() - Method in class org.sbml.jsbml.AbstractSBase

getCVTerms() - Method in interface org.sbml.jsbml.SBase

Returns the list of CVTerms of this object.

getCx() - Method in class org.sbml.jsbml.ext.render.Ellipse

getCx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getCy() - Method in class org.sbml.jsbml.ext.render.Ellipse

getCy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getCz() - Method in class org.sbml.jsbml.ext.render.Ellipse

getCz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getData() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of data

getDataString() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of data

getDataType() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Returns the value of dataType.

getDataType() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of dataType

getDataType() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

Returns the value of dataType.

getDataType(ASTNode) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

Returns the data type of an ASTNode.

getDeclaredNamespaces() - Method in class org.sbml.jsbml.AbstractSBase

getDeclaredNamespaces() - Method in class org.sbml.jsbml.Annotation

getDeclaredNamespaces() - Method in interface org.sbml.jsbml.SBase

Returns all the namespaces declared on this object.

getDefaultIndentChar() - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter

Returns the default symbol to be used to indent new elements in the XML representation of SBML data structures.

getDefaultIndentCount() - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter

Returns the default number of indent symbols to be concatenated at the beginning of a new block in an XML representation of SBML data structures.

getDefaultLevel() - Method in class org.sbml.jsbml.SBMLDocument

Returns the default SBML Level of new SBMLDocument objects.

getDefaultPossibleEnzymes() - Static method in class org.sbml.jsbml.SBO

Creates and returns a list of molecule types accepted as an enzyme by default.

getDefaultValue(String) - Method in class org.sbml.jsbml.ext.render.DefaultValues

getDefaultValues() - Method in class org.sbml.jsbml.ext.render.DefaultValues

getDefaultValues() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Returns the value of ListOfRenderInformation.defaultValues.

getDefaultVersion() - Method in class org.sbml.jsbml.SBMLDocument

Returns the default Version of new SBMLDocument objects.

getDefinedSpecies(Reaction) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

getDefinition() - Method in class org.sbml.jsbml.ontology.Term

Returns the definition of this Term, which is stored in the corresponding OBO file under the key def.

getDefinitionURIavogadro() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getDefinitionURIdelay() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getDefinitionURItime() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getDefinitionURL() - Method in class org.sbml.jsbml.ASTNode

Returns the definitionURL

getDefinitionURL() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the value of UncertParameter.definitionURL.

getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode

Returns the definitionURL of the MathML element represented by this ASTCiFunctionNode

getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiNumberNode

getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode

getDefinitionURL() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode

Returns the definitionURL of the MathML element represented by this ASTCSymbolBaseNode

getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode

getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode

getDegradation() - Static method in class org.sbml.jsbml.SBO

Complete disappearance of a physical entity.

getDelay() - Method in class org.sbml.jsbml.Event

getDelayCount() - Method in class org.sbml.jsbml.Model

Returns the number of Delays of this Model.

getDeletion() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Returns the value of deletion

getDeletionCount() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns the number of Deletion objects in this Submodel.

getDenominator() - Method in class org.sbml.jsbml.ASTNode

Gets the value of the denominator of this node.

getDenominator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode

Get the denominator value of this node.

getDenominator() - Method in class org.sbml.jsbml.SpeciesReference

Deprecated.

Use for Level 1 only.

getDepth() - Method in class org.sbml.jsbml.ext.layout.Dimensions

getDerivedExtendUnitDefinition(Model) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

Returns the extend UnitDefinition for the given Model.

getDerivedSubstanceUnitDefinition() - Method in class org.sbml.jsbml.Species

Returns the derived species substance units, never dividing by the compartment units.

getDerivedSubstanceUnitDefinition(Model) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

Returns the substance UnitDefinition for the given Model.

getDerivedSubstanceUnitDefinition(Species) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

Returns the substance only derived UnitDefinition for the given Species.

getDerivedTimeUnitDefinition(Model) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

Returns the time UnitDefinition for the given Model.

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.AbstractMathContainer

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Compartment

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Event

Deprecated.

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.ext.arrays.Dimension

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.ext.qual.Input

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.ext.qual.Output

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Reaction

getDerivedUnitDefinition() - Method in interface org.sbml.jsbml.SBaseWithDerivedUnit

Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model.

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.Species

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.SpeciesReference

getDerivedUnitDefinition(ValidationContext, SBaseWithDerivedUnit) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

Returns the derived UnitDefinition for the given SBaseWithDerivedUnit.

getDerivedUnits() - Method in class org.sbml.jsbml.AbstractMathContainer

getDerivedUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit

getDerivedUnits() - Method in class org.sbml.jsbml.Event

Deprecated.

getDerivedUnits() - Method in class org.sbml.jsbml.ext.arrays.Dimension

getDerivedUnits() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getDerivedUnits() - Method in class org.sbml.jsbml.ext.qual.Input

getDerivedUnits() - Method in class org.sbml.jsbml.ext.qual.Output

getDerivedUnits() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

getDerivedUnits() - Method in class org.sbml.jsbml.Reaction

getDerivedUnits() - Method in interface org.sbml.jsbml.SBaseWithDerivedUnit

Derives the unit of this quantity.

getDerivedUnits() - Method in class org.sbml.jsbml.Species

Derives the unit of this Species.

getDerivedUnits() - Method in class org.sbml.jsbml.SpeciesReference

getDerivedVariable() - Method in class org.sbml.jsbml.AlgebraicRule

Provides a convenient way to obtain the variable whose amount is determined by this rule.

getDetail() - Method in exception org.sbml.jsbml.SBMLError

getDimension(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Gets an element from the listOfDimensions at the given index.

getDimension(String) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Gets an element from the listOfDimensions, with the given id.

getDimensionByArrayDimension(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Gets an element from the listOfDimensions at the given arrayDimension.

getDimensionCount() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the number of Dimensions in this ArraysSBasePlugin.

getDimensions() - Method in class org.sbml.jsbml.ext.layout.BoundingBox

getDimensions() - Method in class org.sbml.jsbml.ext.layout.Layout

getDimensionSizes(Model, ArraysSBasePlugin) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Maps a dimension id to the size of the dimension object.

getDiscreteFramework() - Static method in class org.sbml.jsbml.SBO

getDissociation() - Static method in class org.sbml.jsbml.SBO

Transformation of a non-covalent complex that results in the formation of several independent biochemical entities.

getDistinctAttribute() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Deprecated.

Returns the value of distinctAttribute

getDNA() - Static method in class org.sbml.jsbml.SBO

Polymer composed of nucleotides containing deoxyribose and linked by phosphodiester bonds.

getDNASegment() - Static method in class org.sbml.jsbml.SBO

Fragment or region of a DNA macromolecule.

getDocument() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

getDomain(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the Geometry.listOfDomains at the given index.

getDomain(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the listOfDomains, with the given id.

getDomain1() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

Returns the value of domain1

getDomain2() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

Returns the value of domain2

getDomainCount() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of Domains in this Geometry.

getDomainType() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

Returns the value of domainType

getDomainType() - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping

Returns the value of domainType

getDomainType() - Method in class org.sbml.jsbml.ext.spatial.CSGObject

Returns the value of domainType

getDomainType() - Method in class org.sbml.jsbml.ext.spatial.Domain

Returns the value of domainType

getDomainType() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Returns the value of domain

getDomainType() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

Returns the value of domainType

getDomainType(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the Geometry.listOfDomainTypes at the given index.

getDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the listOfDomainTypes, with the given id.

getDomainTypeCount() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of DomainTypes in this Geometry.

getDomainTypeInstance() - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping

getDrug() - Static method in class org.sbml.jsbml.SBO

getElement(int) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Gets an element from the listOfElements at the given index.

getElement(String) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Gets an element from the listOfElements, with the given id.

getElementByMetaId(String) - Method in class org.sbml.jsbml.AbstractSBase

getElementByMetaId(String) - Method in interface org.sbml.jsbml.SBase

Returns the first child element found that has the given metaid.

getElementByMetaId(String) - Method in class org.sbml.jsbml.SBMLDocument

Returns the SBase with the given metaid in this SBMLDocument or null if no such SBase is found.

getElementBySId(String) - Method in class org.sbml.jsbml.AbstractSBase

getElementBySId(String) - Method in class org.sbml.jsbml.Model

Returns an SBase element of the model that has the given 'id' as id or null if no element is found.

getElementBySId(String) - Method in interface org.sbml.jsbml.SBase

Returns the first child element found that has the given id.

getElementCount() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the number of Transformation2Ds in this RenderGroup.

getElementName() - Method in class org.sbml.jsbml.AbstractSBase

getElementName() - Method in class org.sbml.jsbml.AssignmentRule

getElementName() - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives

getElementName() - Method in class org.sbml.jsbml.ext.layout.Point

getElementName() - Method in class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

getElementName() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

getElementName() - Method in class org.sbml.jsbml.ext.render.GradientStop

getElementName() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getElementName() - Method in class org.sbml.jsbml.ext.render.LocalStyle

getElementName() - Method in class org.sbml.jsbml.ext.render.RenderCurve

getElementName() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getElementName() - Method in class org.sbml.jsbml.ext.render.RenderPoint

getElementName() - Method in class org.sbml.jsbml.ext.spatial.Boundary

Returns the value of the XML element name.

getElementName() - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

getElementName() - Method in class org.sbml.jsbml.ext.spatial.CSGObject

getElementName() - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive

getElementName() - Method in class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive

getElementName() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

getElementName() - Method in class org.sbml.jsbml.ext.spatial.CSGScale

getElementName() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

getElementName() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

getElementName() - Method in class org.sbml.jsbml.ListOf

getElementName() - Method in class org.sbml.jsbml.LocalParameter

getElementName() - Method in interface org.sbml.jsbml.SBase

Returns the XML element name of this object.

getElementName() - Method in class org.sbml.jsbml.SBMLDocument

getElementName() - Method in class org.sbml.jsbml.Species

getElementName() - Method in class org.sbml.jsbml.SpeciesReference

getElementName() - Method in class org.sbml.jsbml.util.ListOfWithName

Deprecated.

getElementNameEquivalent() - Method in enum org.sbml.jsbml.CVTerm.Qualifier

Returns a name corresponding to this Qualifier Object.

getElementNameEquivalent() - Method in enum org.sbml.jsbml.CVTerm.Type

Returns a name corresponding to this Type of qualifier Object.

getElementNameEquivalentToQualifier(CVTerm.Qualifier) - Static method in class org.sbml.jsbml.Annotation

Returns a String which represents the given CVTerm.Qualifier.

getElementNamespace() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin

getElementNamespace() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

getElementNamespace() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getElementNamespace() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

Returns the XML namespace (URI) of the package extension of this plugin object.

getElementNamespace() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getElementNamespace() - Method in interface org.sbml.jsbml.ext.SBasePlugin

Returns the XML namespace (URI) of the package extension of this plugin object.

getEmail() - Method in class org.sbml.jsbml.Creator

Returns the email from the Creator.

getEmptySet() - Static method in class org.sbml.jsbml.SBO

Empty set is used to represent the source of a creation process or the result of a degradation process.

getEnabledPackageNamespace(String) - Method in class org.sbml.jsbml.SBMLDocument

Return the package namespace enabled on this SBMLDocument or null if the package is not enabled.

getEncoding() - Method in class org.sbml.jsbml.ASTNode

Returns the encoding of the mathML element represented by this ASTNode.

getEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode

getEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode

getEncoding() - Method in interface org.sbml.jsbml.math.ASTCSymbolNode

Returns the encoding of the MathML element represented by this ASTCSymbolNode

getEncoding() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode

getEnd() - Method in class org.sbml.jsbml.ext.layout.CurveSegment

Returns the End Point of this CurveSegment.

getEnd() - Method in class org.sbml.jsbml.ext.layout.LineSegment

getEndColumn() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Get token end column number.

getEndColumn() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Get token end column number.

getEndHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns the value of endHead

getEndHead() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getEndLine() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Get token end line number.

getEndLine() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Get token end line number.

getEnthalpyChange() - Static method in class org.sbml.jsbml.SBO

Change in enthalpy observed in the constituents of a thermodynamic system when undergoing a transformation or chemical reaction.

getEntity() - Static method in class org.sbml.jsbml.SBO

getEntropyChange() - Static method in class org.sbml.jsbml.SBO

The increase or decrease of the entropy of a system.

getEnzymaticCatalysis() - Static method in class org.sbml.jsbml.SBO

getEquilibriumConstant() - Static method in class org.sbml.jsbml.SBO

Quantity characterizing a chemical equilibrium in a chemical reaction, which is a useful tool to determine the concentration of various reactants or products in a system where chemical equilibrium occurs.

getError(int) - Method in class org.sbml.jsbml.SBMLDocument

Returns the i^th error or warning encountered during consistency checking.

getError(long) - Method in class org.sbml.jsbml.SBMLErrorLog

Returns the nth SBMLError object in this log.

getErrorCode() - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraint

getErrorCode() - Method in interface org.sbml.jsbml.validator.offline.constraints.AnyConstraint

Returns the error code from this constraint.

getErrorCount() - Method in class org.sbml.jsbml.SBMLDocument

Returns the number of errors or warnings encountered during consistency checking.

getErrorCount() - Method in class org.sbml.jsbml.SBMLErrorLog

Returns the number of errors that have been logged.

getErrorId() - Method in exception org.sbml.jsbml.xml.XMLException

getErrorLog() - Method in class org.sbml.jsbml.SBMLDocument

Returns a collection of all SBMLErrors reflecting problems in the overall data structure of this SBMLDocument.

getErrorLog() - Method in class org.sbml.jsbml.validator.offline.LoggingValidationContext

Gets the SBMLErrorLog of this context.

getErrorsBySeverity(SBMLError.SEVERITY) - Method in class org.sbml.jsbml.SBMLErrorLog

getEssentialActivator() - Static method in class org.sbml.jsbml.SBO

getEvent() - Static method in class org.sbml.jsbml.SBO

getEvent(int) - Method in class org.sbml.jsbml.Model

Gets the n^th Event object in this Model.

getEvent(String) - Method in class org.sbml.jsbml.Model

Gets the Event which as the given id as id.

getEventAssignment(int) - Method in class org.sbml.jsbml.Event

Gets an element from the listOfEventAssignments at the given index.

getEventAssignment(String) - Method in class org.sbml.jsbml.Event

Gets an element from the listOfEventAssignments, with the given id.

getEventAssignmentCount() - Method in class org.sbml.jsbml.Event

Returns the number of EventAssignments in this Event.

getEventAssignmentCount() - Method in class org.sbml.jsbml.Model

Returns the number of EventAssignments of this Model.

getEventCount() - Method in class org.sbml.jsbml.Model

Returns the number of Events of this Model.

getExcerpt() - Method in exception org.sbml.jsbml.SBMLError

Returns a fragment of the original XML file that induced the error.

getExponent() - Method in class org.sbml.jsbml.ASTNode

Gets the exponent value of this ASTNode.

getExponent() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode

Get the exponent value of this node.

getExponent() - Method in class org.sbml.jsbml.math.ASTPowerNode

Get the exponent of this ASTPowerNode

getExponent() - Method in class org.sbml.jsbml.Unit

getExponentAsDouble() - Method in class org.sbml.jsbml.Unit

Deprecated.

use Unit.getExponent()

getExtendedASTNode() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin

getExtendedASTNode() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

Returns the object that is extended by this plug-in.

getExtendedSBase() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

getExtendedSBase() - Method in interface org.sbml.jsbml.ext.SBasePlugin

Returns the SBase object that is extended by this plug-in.

getExtendedSBase() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

getExtendedSBase() - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin

getExtendedSBase() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

getExtendedSBase() - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

getExtendedSBase() - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

getExtension(String) - Method in class org.sbml.jsbml.AbstractSBase

getExtension(String) - Method in class org.sbml.jsbml.ASTNode

Returns the ASTNodePlugin object which matches this package name or URI.

getExtension(String) - Method in interface org.sbml.jsbml.SBase

Returns the SBasePlugin extension object which matches this package name or URI.

getExtensionCount() - Method in class org.sbml.jsbml.AbstractSBase

getExtensionCount() - Method in class org.sbml.jsbml.ASTNode

Returns the number of ASTNodePlugins of this ASTNode.

getExtensionCount() - Method in interface org.sbml.jsbml.SBase

Returns the number of SBasePlugins of this SBase.

getExtensionPackages() - Method in class org.sbml.jsbml.AbstractSBase

getExtensionPackages() - Method in class org.sbml.jsbml.ASTNode

Returns the map containing all the ASTNodePlugin extension objects of this ASTNode.

getExtensionPackages() - Method in interface org.sbml.jsbml.SBase

Returns the map containing all the SBasePlugin extension objects of this SBase.

getExtentConversionFactor() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns the value of extentConversionFactor

getExtentUnits() - Method in class org.sbml.jsbml.Model

Returns the extent units ID of this Model.

getExtentUnitsInstance() - Method in class org.sbml.jsbml.Model

Returns the UnitDefinition instance which has the extent units ID of this Model as id.

getExternalModelDefinition(int) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the n-th ExternalModelDefinition object in this CompSBMLDocumentPlugin.

getExternalModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns a ExternalModelDefinition element that has the given 'id' within this CompSBMLDocumentPlugin or null if no such element can be found.

getExternalModelDefinitionCount() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the number of ExternalModelDefinition objects in this CompSBMLDocumentPlugin.

getFamilyName() - Method in class org.sbml.jsbml.Creator

Returns the familyName from the Creator.

getFast() - Method in class org.sbml.jsbml.Reaction

Deprecated.

getFieldCount() - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Returns the number of values in this ArraysCompiler.

getFill() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

getFillRule() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

getFilters() - Method in class org.sbml.jsbml.util.filters.AndFilter

getFirst() - Method in class org.sbml.jsbml.ListOf

Returns the first element in this list.

getFirstElementIndex(XMLNode) - Static method in class org.sbml.jsbml.AbstractSBase

Return the index of the first child of type 'Element' for the given XMLNode.

getFluxBound(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Deprecated.

Only defined in FBC version 1.

getFluxBoundCount() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Deprecated.

Only defined in FBC version 1.

getFluxObjectiveCount() - Method in class org.sbml.jsbml.ext.fbc.Objective

getFontFamily() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

getFontFamily() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getFontFamily() - Method in class org.sbml.jsbml.ext.render.Text

getFontSize() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

getFontSize() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getFontSize() - Method in class org.sbml.jsbml.ext.render.Text

getFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the value of fontStyleItalic

getFontWeightBold() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the value of fontWeightBold

getFormats(String) - Method in class org.sbml.jsbml.util.XMLResourceBundleControl

getFormula() - Method in class org.sbml.jsbml.AbstractMathContainer

Deprecated.

getFormula() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Deprecated.

getFormula() - Method in interface org.sbml.jsbml.MathContainer

Deprecated.

As this is part of SBML Level 1, it is strongly recommended not to work with the String representation of a formula, but to deal with a more flexible ASTNode.

getForwardTransformation() - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation

Returns the value of forwardTransformation

getFullAnnotation() - Method in class org.sbml.jsbml.Annotation

getFullAnnotationString() - Method in class org.sbml.jsbml.Annotation

getFunctionalCompartment() - Static method in class org.sbml.jsbml.SBO

getFunctionalEntity() - Static method in class org.sbml.jsbml.SBO

getFunctionDefinition(int) - Method in class org.sbml.jsbml.Model

Gets the n^th FunctionDefinition instance of the listOfFunctionDefinitions.

getFunctionDefinition(String) - Method in class org.sbml.jsbml.Model

Returns the FunctionDefinition of the Model.listOfFunctionDefinitions which has 'id' as id.

getFunctionDefinitionCount() - Method in class org.sbml.jsbml.Model

Returns the number of FunctionDefinitions of this Model.

getFunctionTermCount() - Method in class org.sbml.jsbml.ext.qual.Transition

getFunctionType() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

Returns the value of functionType

getFx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getFy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getFz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getGene() - Static method in class org.sbml.jsbml.SBO

A gene is an informational molecule segment.

getGeneCodingRegion() - Static method in class org.sbml.jsbml.SBO

getGeneProduct() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef

Returns the value of GeneProductRef.geneProduct.

getGeneProduct(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Gets an element from the FBCModelPlugin.listOfGeneProducts at the given index.

getGeneProduct(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Gets an element from the listOfGeneProducts, with the given id.

getGeneProductAssociation() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

Returns the value of FBCReactionPlugin.geneProductAssociation.

getGeneProductCount() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Returns the number of GeneProducts in this FBCModelPlugin.

getGeneProductInstance() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef

Returns the GeneProduct referenced by this GeneProductRef.

getGeneric() - Static method in class org.sbml.jsbml.SBO

getGeneticInteraction() - Static method in class org.sbml.jsbml.SBO

A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone.

getGeometry() - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin

Returns the value of geometry

getGeometryDefinition() - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

Returns the value of geometryDefinition

getGeometryDefinition(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the Geometry.listOfGeometryDefinitions at the given index.

getGeometryDefinition(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the listOfGeometryDefinitions, with the given id.

getGeometryDefinitionCount() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of GeometryDefinitions in this Geometry.

getGeometryInstance() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

Returns the Geometry instance.

getGibbsFreeEnergyChange() - Static method in class org.sbml.jsbml.SBO

The increase or decrease of the Gibbs free energy of a system.

getGivenName() - Method in class org.sbml.jsbml.Creator

Returns the givenName from the Creator.

getGlyph() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph

getGraphicalObject() - Method in class org.sbml.jsbml.ext.layout.TextGlyph

getGraphicalObjectInstance() - Method in class org.sbml.jsbml.ext.layout.TextGlyph

Direct access to the GraphicalObject linked to this TextGlyph.

getGroup() - Method in class org.sbml.jsbml.ext.render.LineEnding

getGroup() - Method in class org.sbml.jsbml.ext.render.Style

getGroup(int) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Returns the n-th Group object in this GroupsModelPlugin.

getGroup(String) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Gets the Group that has the given id.

getGroupCount() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Returns the number of Groups of this GroupsModelPlugin.

getHashMap() - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Gets the validation objects HashMap.

getHasOnlySubstanceUnits() - Method in class org.sbml.jsbml.Species

Returns the hasOnlySubstanceUnits Boolean of this Species.

getHeight() - Method in class org.sbml.jsbml.ext.layout.Dimensions

getHeight() - Method in class org.sbml.jsbml.ext.render.Image

getHeight() - Method in class org.sbml.jsbml.ext.render.Rectangle

getHillEquation() - Static method in class org.sbml.jsbml.SBO

getHistory() - Method in class org.sbml.jsbml.AbstractSBase

getHistory() - Method in class org.sbml.jsbml.Annotation

Returns the History of the Annotation.

getHistory() - Method in interface org.sbml.jsbml.SBase

Returns the History instance of this object.

getHref() - Method in class org.sbml.jsbml.ext.render.Image

getId() - Method in class org.sbml.jsbml.AbstractSBase

getId() - Method in class org.sbml.jsbml.ASTNode

Returns the id of the mathML element represented by this ASTNode.

getId() - Method in class org.sbml.jsbml.math.AbstractASTNode

getId() - Method in interface org.sbml.jsbml.math.ASTNode2

Get the id of this node

getId() - Method in class org.sbml.jsbml.math.ASTUnknown

getId() - Method in interface org.sbml.jsbml.NamedSBase

Returns the id of the element if it is set, an empty string otherwise.

getId() - Method in class org.sbml.jsbml.ontology.Term

Returns the SBO identifier of this Term, for instance: SBO:0000031.

getId() - Method in interface org.sbml.jsbml.SBase

Returns the id of the element if it is set, an empty string otherwise.

getId() - Method in class org.sbml.jsbml.util.filters.AssignmentVariableFilter

getId() - Method in class org.sbml.jsbml.util.filters.IdFilter

Returns the id that will be searched for by the filter.

getId() - Method in class org.sbml.jsbml.util.filters.NameFilter

Returns the id.

getId() - Method in class org.sbml.jsbml.util.filters.SIdFilter

Returns the id that will be searched for by the filter.

getIdenticalAttribute() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Deprecated.

Returns the value of identicalAttribute

getIDList() - Method in class org.sbml.jsbml.ext.render.LocalStyle

getIdOrName(SBase) - Static method in class org.sbml.jsbml.util.SBMLtools

getIdRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns the value of idRef

getIdRef() - Method in class org.sbml.jsbml.ext.dyn.DynElement

Returns the value of idRef

getIdRef() - Method in class org.sbml.jsbml.ext.groups.Member

Returns the value of idRef

GetImage() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Get token literal value.

GetImage() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Get token literal value.

getIndent() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getIndent() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser

Returns the indent

getIndentationChar() - Method in class org.sbml.jsbml.SBMLWriter

Gives the symbol that is used to indent the SBML output for a better structure and to improve human-readability.

getIndentationChar() - Method in class org.sbml.jsbml.xml.stax.SBMLWriter

Gives the symbol that is used to indent the SBML output for a better structure and to improve human-readability.

getIndentationCount() - Method in class org.sbml.jsbml.SBMLWriter

Gives the number of indent symbols that are inserted in a line to better structure the SBML output.

getIndentationCount() - Method in class org.sbml.jsbml.xml.stax.SBMLWriter

Gives the number of indent symbols that are inserted in a line to better structure the SBML output.

getIndentifyingParent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Returns the value of SpeciesTypeComponentIndex.identifyingParent.

getIndenting() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getIndenting() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser

Returns true if indenting

getIndex(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Gets an element from the listOfIndices at the given index.

getIndex(int, String) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Gets an element from the listOfIndices based on array dimension and referenced attribute.

getIndex(String) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns the index of an attribute with the given name.

getIndex(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces

Gets the index of an XML namespace declaration by URI.

getIndex(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns the index of an attribute with the given local name and namespace URI.

getIndex(TreeNode) - Method in class org.sbml.jsbml.AbstractTreeNode

getIndex(TreeNode) - Method in class org.sbml.jsbml.math.ASTUnknown

getIndex(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns the index of an attribute with the given XMLTriple.

getIndexByPrefix(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces

Gets the index of an XML namespace declaration by prefix.

getIndexCount() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the number of Indexs in this ArraysSBasePlugin.

getInhibition() - Static method in class org.sbml.jsbml.SBO

Negative modulation of the execution of a process.

getInhibitor() - Static method in class org.sbml.jsbml.SBO

Substance that decreases the probability of a chemical reaction without itself being consumed or transformed by the reaction.

getInitialAmount() - Method in class org.sbml.jsbml.Species

Returns the initialAmount of this Species.

getInitialAssignment(int) - Method in class org.sbml.jsbml.Model

Gets the n^th InitialAssignment object in this Model.

getInitialAssignment(String) - Method in class org.sbml.jsbml.Model

Deprecated.

Since L3V2, every SBase can have an id. Use either Model.getInitialAssignmentById(String) or Model.getInitialAssignmentBySymbol(String)

getInitialAssignmentById(String) - Method in class org.sbml.jsbml.Model

Returns the InitialAssignment of the Model.listOfInitialAssignments whose id attribute, has the given id as identifier.

getInitialAssignmentBySymbol(String) - Method in class org.sbml.jsbml.Model

Returns the InitialAssignment of the Model.listOfInitialAssignments whose symbol attribute, i.e., whose Variable has the given variable as identifier.

getInitialAssignmentCount() - Method in class org.sbml.jsbml.Model

Returns the number of InitialAssignments of this Model.

getInitialConcentration() - Method in class org.sbml.jsbml.Species

Returns the initialConcentration of this Species.

getInitialLevel() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

getInitialValue() - Method in class org.sbml.jsbml.Trigger

getInputCount() - Method in class org.sbml.jsbml.ext.qual.Transition

getInSpeciesTypeBond(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Gets an element from the MultiSpeciesType.listOfInSpeciesTypeBonds at the given index.

getInSpeciesTypeBond(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Gets an element from the listOfInSpeciesTypeBonds, with the given id.

getInSpeciesTypeBondCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the number of InSpeciesTypeBonds in this MultiSpeciesType.

getInstance() - Static method in class org.sbml.jsbml.math.ASTUnknown

getInstance() - Static method in class org.sbml.jsbml.resources.Resource

getInstance() - Static method in class org.sbml.jsbml.util.JAXPFacade

Creates and returns a new JAXPFacade.

getInstance() - Static method in class org.sbml.jsbml.validator.offline.factory.ConstraintFactory

Returns the ConstraintFactory singleton instance.

getInstance(String) - Static method in class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration

Gets a ConstraintDeclaration corresponding to the given class name.

getInteger() - Method in class org.sbml.jsbml.ASTNode

Gets the value of this node as an integer.

getInteger() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode

Get the integer value of this node.

getInteraction() - Static method in class org.sbml.jsbml.SBO

getInterpolation() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of interpolation type

getInterpolationType() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of interpolation type

getIon() - Static method in class org.sbml.jsbml.SBO

getIonChannel() - Static method in class org.sbml.jsbml.SBO

getIonicStrength() - Static method in class org.sbml.jsbml.SBO

A combined (weighted) measure of the concentration of all electrolytes present in a solution.

getIrreversibleInhibitor() - Static method in class org.sbml.jsbml.SBO

An inhibitor which binds irreversibly with the enzyme such that it cannot be removed, and abolishes enzymatic function.

getIsActive() - Method in class org.sbml.jsbml.ext.spatial.GeometryDefinition

Returns the value of isActive

getIsLocal() - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

Returns the value of isLocal

getIsType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the value of MultiCompartmentPlugin.isType.

getJSBMLDottedVersion() - Static method in class org.sbml.jsbml.JSBML

Returns the JSBML version as a string of the form '1.2.3'.

getJSBMLVersion() - Static method in class org.sbml.jsbml.JSBML

Returns the JSBML version as an integer: version 1.2.3 becomes 123.

getJSBMLVersionString() - Static method in class org.sbml.jsbml.JSBML

Returns the JSBML version as a string: version 1.2.3 becomes '123'.

getKey() - Method in class org.sbml.jsbml.util.Pair

getKeys() - Method in class org.sbml.jsbml.validator.offline.i18n.fr.SBMLErrorPostMessage_fr

getKeys() - Method in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorMessage

getKeys() - Method in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPostMessage

getKeys() - Method in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPreMessage_en_EN_L2V1

getKeys() - Method in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPreMessage_en_EN_L3V1

getKeys() - Method in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPreMessage

getKeys() - Method in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorShortMessage

getKind() - Method in class org.sbml.jsbml.ext.groups.Group

getKind() - Method in class org.sbml.jsbml.Unit

getKineticConstant() - Static method in class org.sbml.jsbml.SBO

getKineticLaw() - Method in class org.sbml.jsbml.Reaction

getKineticLawCount() - Method in class org.sbml.jsbml.Model

Returns the number of KineticLaws of this Model.

getL() - Method in class org.sbml.jsbml.util.ValuePair

getLabel() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct

Returns the value of GeneProduct.label

getLang() - Method in class org.sbml.jsbml.util.Message

getLast() - Method in class org.sbml.jsbml.ListOf

Returns the last element in this list.

getLayout() - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

getLayout() - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

getLayout(int) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getLayoutCount() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

Returns the number of Layouts of this LayoutModelPlugin.

getLayoutIndex() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

getLeftChild() - Method in class org.sbml.jsbml.ASTNode

Gets the left child of this node.

getLeftChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode

Get the left child of this ASTBinaryFunctionNode

getLength() - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns the number of attributes in the set.

getLength() - Method in class org.sbml.jsbml.xml.XMLNamespaces

Returns the total number of URI-and-prefix pairs stored in this particular XMLNamespaces instance.

getLengthUnits() - Method in class org.sbml.jsbml.Model

Returns the length units ID of this Model.

getLengthUnitsInstance() - Method in class org.sbml.jsbml.Model

Returns the length units of this Model as a UnitDefinition.

getLevel() - Method in class org.sbml.jsbml.AbstractSBase

getLevel() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin

getLevel() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

getLevel() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

Returns the SBML level of this plugin object.

getLevel() - Method in interface org.sbml.jsbml.ext.SBasePlugin

Returns the SBML level of this plugin object.

getLevel() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

Returns the level of the SBML document that was the basis to create this ASTNode2Value.

getLevel() - Method in interface org.sbml.jsbml.SBase

Returns the SBML Level of the overall SBML document.

getLevel() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3

Returns the SBML Level.

getLevel() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

Returns the level of the SBML document that was the basis to create this ASTNodeValue.

getLevel() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

getLevel() - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Returns the used level of SBML

getLevelAndVersion() - Method in class org.sbml.jsbml.AbstractSBase

getLevelAndVersion() - Method in interface org.sbml.jsbml.SBase

Returns the Level and Version combination of this SBase.

getLevelAndVersion() - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Returns the SBML level and version of the ValidationContext.

getLine() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Deprecated.

getLine() - Method in exception org.sbml.jsbml.SBMLError

Returns the line where this SBMLError happened.

getLine() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Deprecated.

getLine() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the line at which this XMLToken occurred in the input document or data stream.

getLineWidth() - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNnode

getLineWidth() - Method in interface org.sbml.jsbml.ext.render.director.SBGNNode

getListOfAdditionalGraphicalObjects() - Method in class org.sbml.jsbml.ext.layout.Layout

getListOfAdjacentDomains() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the listOfAdjacentDomains.

getListOfAnalyticVolumes() - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry

Returns the listOfAnalyticVolumes.

getListOfAssociations() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

Returns the LogicalOperator.listOfAssociations.

getListOfChangedMaths() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin

Returns the listOfChangedMaths.

getListOfColorDefinitions() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getListOfCompartmentGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout

getListOfCompartmentReferences() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the MultiCompartmentPlugin.listOfCompartmentReferences.

getListOfCompartments() - Method in class org.sbml.jsbml.Model

Returns the listOfCompartments of this Model.

getListOfCompartmentTypes() - Method in class org.sbml.jsbml.Model

Deprecated.

Only valid in SBML Level 2 for Versions 2 through 4.

getListOfConstraints() - Method in class org.sbml.jsbml.Model

Returns the listOfConstraints of this Model.

getListOfCoordinateComponents() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the listOfCoordinateComponents.

getListOfCount() - Method in class org.sbml.jsbml.Model

Returns the number of ListOfs of this Model.

getListOfCreators() - Method in class org.sbml.jsbml.History

Get the list of Creator objects in this History.

getListOfCSGNodes() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Returns the listOfCSGNodes.

getListOfCSGObjects() - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

Returns the listOfCSGObjects.

getListOfCurveSegments() - Method in class org.sbml.jsbml.ext.layout.Curve

getListOfCurveSegments() - Method in interface org.sbml.jsbml.ext.layout.ICurve

getListOfCurveSegments() - Method in class org.sbml.jsbml.ext.render.Polygon

Returns the Polygon.listOfCurveSegments.

getListOfCurveSegments() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns the RenderCurve.listOfCurveSegments.

getListOfCVTerms() - Method in class org.sbml.jsbml.Annotation

Returns the list of CVTerms.

getListOfDeletions() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns the listOfDeletions.

getListOfDimensions() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the listOfDimensions.

getListOfDomains() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the listOfDomains.

getListOfDomainTypes() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the listOfDomainTypes.

getListOfDynElements() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Returns the value of listOfDynElements

getListOfElements() - Method in class org.sbml.jsbml.ext.render.Polygon

getListOfElements() - Method in class org.sbml.jsbml.ext.render.RenderCurve

getListOfElements() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the listOfElements.

getListOfErrors() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysConstraint

Gets the listOfErrors after checking the model.

getListOfErrors() - Method in class org.sbml.jsbml.SBMLDocument

Returns a collection of all SBMLErrors reflecting problems in the overall data structure of this SBMLDocument.

getListOfEventAssignments() - Method in class org.sbml.jsbml.Event

Returns the listOfEventAssignments.

getListOfEvents() - Method in class org.sbml.jsbml.Model

Returns the listOfEvents of this Model.

getListOfExternalModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the listOfExternalModelDefinitions.

getListOfFluxBounds() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Deprecated.

Only defined in FBC version 1.

getListOfFluxObjectives() - Method in class org.sbml.jsbml.ext.fbc.Objective

Returns the listOfFluxObjectives

getListOfFunctionDefinitions() - Method in class org.sbml.jsbml.Model

Returns the listOfFunctionDefinitions of this Model.

getListOfFunctionTerms() - Method in class org.sbml.jsbml.ext.qual.Transition

getListOfGeneProducts() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Returns the FBCModelPlugin.listOfGeneProducts.

getListOfGeometryDefinitions() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the listOfGeometryDefinitions.

getListOfGeometryDefinitions() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

Returns the listOfGeometryDefinitions.

getListOfGlobalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

getListOfGradientDefinitions() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getListOfGradientStops() - Method in class org.sbml.jsbml.ext.render.GradientBase

getListOfGroups() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Returns the listOfGroups.

getListOfIndices() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the listOfIndices.

getListOfInitialAssignments() - Method in class org.sbml.jsbml.Model

Returns the listOfInitialAssignments of this Model.

getListOfInputs() - Method in class org.sbml.jsbml.ext.qual.Transition

getListOfInSpeciesTypeBonds() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the MultiSpeciesType.listOfInSpeciesTypeBonds.

getListOfInteriorPoints() - Method in class org.sbml.jsbml.ext.spatial.Domain

Returns the listOfInteriorPoints.

getListOfLayouts() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getListOfLineEndings() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getListOfLocalParameters() - Method in class org.sbml.jsbml.KineticLaw

getListOfLocalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

getListOfLocalStyles() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getListOfMembers() - Method in class org.sbml.jsbml.ext.groups.Group

Returns the Group.listOfMembers.

getListOfModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the listOfModelDefinitions.

getListOfModifiedDates() - Method in class org.sbml.jsbml.History

Get the list of modifiedDate objects in this History.

getListOfModifiers() - Method in class org.sbml.jsbml.Reaction

getListOfNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm

Returns the CVTerm.listOfNestedCVTerms.

getListOfNodes() - Method in class org.sbml.jsbml.ASTNode

Returns the list of children of the current ASTNode.

getListOfNodes() - Method in class org.sbml.jsbml.math.ASTFunction

Returns the list of children of the current ASTFunction.

getListOfNodes(Filter) - Method in class org.sbml.jsbml.ASTNode

Returns the list of children of the current ASTNode that satisfy the given filter.

getListOfNodes(Filter) - Method in class org.sbml.jsbml.math.ASTFunction

Returns the list of children of the current ASTFunction that satisfy the given filter.

getListOfObjectives() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Returns the FBCModelPlugin.listOfObjectives.

getListOfOrdinalMappings() - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry

Returns the listOfOrdinalMappings.

getListOfOutputs() - Method in class org.sbml.jsbml.ext.qual.Transition

getListOfOutwardBindingSites() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the MultiSpeciesPlugin.listOfOutwardBindingSites.

getListOfParameters() - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

use KineticLaw.getListOfLocalParameters()

getListOfParameters() - Method in class org.sbml.jsbml.Model

Returns the Model.listOfParameters of this Model.

getListOfParametricObjects() - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

Returns the listOfParametricObjects.

getListOfPorts() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the listOfPorts.

getListOfPossibleSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues.

getListOfPredefinedUnitDefinitions() - Method in class org.sbml.jsbml.Model

Returns the list of predefined UnitDefinition.

getListOfProducts() - Method in class org.sbml.jsbml.Reaction

getListOfQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getListOfReactants() - Method in class org.sbml.jsbml.Reaction

getListOfReactionGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout

getListOfReactions() - Method in class org.sbml.jsbml.Model

Returns the listOfReactions of this Model.

getListOfReferenceGlyphs() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph

Returns the GeneralGlyph.listOfReferenceGlyphs.

getListOfReplacedElements() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns the listOfReplacedElements

getListOfRules() - Method in class org.sbml.jsbml.Model

Returns the listOfRules of this Model.

getListOfSampledFields() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the listOfSampledFields.

getListOfSampledVolumes() - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

Returns the listOfSampledVolumes.

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.CompParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.DistribParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.DynParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.FBCParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.GroupsParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.LayoutParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.QualParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.ReqParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getListOfSBMLElementsToWrite(Object) - Method in interface org.sbml.jsbml.xml.parsers.WritingParser

Returns the list of children of the objectToWrite.

getListOfSemanticsAnnotations() - Method in class org.sbml.jsbml.ASTNode

Returns the list of semantics annotations of this node.

getListOfSpatialComponents() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Returns the value of listOfSpatialComponents

getListOfSpecies() - Method in class org.sbml.jsbml.Model

Returns the Model.listOfSpecies of this Model.

getListOfSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the MultiSpeciesPlugin.listOfSpeciesFeatures.

getListOfSpeciesFeatureTypes() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the MultiSpeciesType.listOfSpeciesFeatureTypes.

getListOfSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the SpeciesFeature.listOfSpeciesFeatureValues.

getListOfSpeciesGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout

getListOfSpeciesReferenceGlyphs() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

Returns the list of SpeciesReferenceGlyphs.

getListOfSpeciesTypeComponentIndexes() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the MultiSpeciesType.listOfSpeciesTypeComponentIndexes.

getListOfSpeciesTypeComponentMapInProducts() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Returns the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts.

getListOfSpeciesTypeInstances() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the MultiSpeciesType.listOfSpeciesTypeInstances.

getListOfSpeciesTypes() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Returns the listOfSpeciesTypes.

getListOfSpeciesTypes() - Method in class org.sbml.jsbml.Model

Deprecated.

Only valid in SBML Level 2 for Versions 2 through 4.

getListOfStyles() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

getListOfSubGlyphs() - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph

Returns the listOfSubGlyphs.

getListOfSubListOfSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the MultiSpeciesPlugin.listOfSubListOfSpeciesFeatures.

getListOfSubmodels() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the listOfSubmodels.

getListOfTextGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout

getListOfTransitions() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getListOfTreeNodeChangeListeners() - Method in class org.sbml.jsbml.AbstractTreeNode

getListOfTreeNodeChangeListeners() - Method in class org.sbml.jsbml.math.ASTUnknown

getListOfTreeNodeChangeListeners() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Returns all TreeNodeChangeListeners that are assigned to this element.

getListOfUncertainties() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Returns the DistribSBasePlugin.listOfUncertainties.

getListOfUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Returns the Uncertainty.listOfUncertParameters.

getListOfUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the UncertParameter.listOfUncertParameters.

getListOfUnitDefinitions() - Method in class org.sbml.jsbml.Model

Returns the listOfUnitDefinitions of this Model.

getListOfUnits() - Method in class org.sbml.jsbml.UnitDefinition

getLocalParameter(int) - Method in class org.sbml.jsbml.KineticLaw

getLocalParameter(String) - Method in class org.sbml.jsbml.KineticLaw

getLocalParameterCount() - Method in class org.sbml.jsbml.KineticLaw

getLocalParameterCount() - Method in class org.sbml.jsbml.Model

Returns the number of parameters that are contained within kineticLaws in the reactions of this model.

getLocalRenderInformation(int) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

getLocalStyleCount() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getLocationURI() - Method in class org.sbml.jsbml.SBMLDocument

Returns the URI specifying whence this SBMLDocument was read.

getLogBehavior() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3

Returns the parser behavior when encountering the 'log' operator with one argument.

getLogger() - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener

getLogicalFramework() - Static method in class org.sbml.jsbml.SBO

getLowerBound(Map<String, Double>) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Returns the lower bound index from a collection of Dimension objects.

getLowerFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

Returns the value of FBCReactionPlugin.lowerFluxBound.

getLowerFluxBoundInstance() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

getMacromolecule() - Static method in class org.sbml.jsbml.SBO

Returns the SBO term id for macromolecule.

getManager() - Static method in class org.sbml.jsbml.xml.parsers.ParserManager

Returns the ParserManager.

getMantissa() - Method in class org.sbml.jsbml.ASTNode

Gets the mantissa value of this node.

getMantissa() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode

Get the mantissa value of this node.

getMapIdToValue() - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Returns the idToValue Map.

getMatching() - Method in class org.sbml.jsbml.validator.OverdeterminationValidator

Returns the determined matching

getMaterialEntity() - Static method in class org.sbml.jsbml.SBO

getMath() - Method in class org.sbml.jsbml.AbstractMathContainer

getMath() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getMath() - Method in interface org.sbml.jsbml.MathContainer

If MathContainer.isSetMath() returns true, this method returns the ASTNode belonging to this MathContainer.

getMathContainerCount() - Method in class org.sbml.jsbml.Model

Returns the number of elements that can contain math in the Model .

getMathDerivedUnitDefinition(ValidationContext, MathContainer) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools

Returns the derived UnitDefinition for the given MathContainer.

getMathematicalExpression() - Static method in class org.sbml.jsbml.SBO

getMathMLClass() - Method in class org.sbml.jsbml.math.AbstractASTNode

getMathMLClass() - Method in interface org.sbml.jsbml.math.ASTNode2

Returns the class of the MathML element represented by this ASTNode2

getMathMLClass() - Method in class org.sbml.jsbml.math.ASTUnknown

getMathMLString() - Method in class org.sbml.jsbml.AbstractMathContainer

getMathMLString() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getMathMLString() - Method in interface org.sbml.jsbml.MathContainer

If MathContainer.isSetMath() returns true, this method returns the corresponding MathML String, otherwise an empty String will be returned.

getMaxLevel() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

getMaxValue() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

Returns the value of maxValue

getMd5() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Returns the value of md5 or an empty String if it is not set.

getMember(int) - Method in class org.sbml.jsbml.ext.groups.Group

Gets an element from the Group.listOfMembers at the given index.

getMember(String) - Method in class org.sbml.jsbml.ext.groups.Group

Gets an element from the listOfMembers, with the given id.

getMemberCount() - Method in class org.sbml.jsbml.ext.groups.Group

Returns the number of Members of this Group.

getMembersShareType() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

Deprecated.

Returns the value of membersShareType

getMessage() - Method in class org.sbml.jsbml.Constraint

Returns the message of this Constraint.

getMessage() - Method in error org.sbml.jsbml.math.parser.TokenMgrError

You can also modify the body of this method to customize your error messages.

getMessage() - Method in exception org.sbml.jsbml.SBMLError

Returns the message of the SBMLError

getMessage() - Method in error org.sbml.jsbml.text.parser.TokenMgrError

You can also modify the body of this method to customize your error messages.

getMessage() - Method in class org.sbml.jsbml.util.Message

getMessage(Throwable) - Static method in class org.sbml.jsbml.util.StringTools

getMessageInstance() - Method in exception org.sbml.jsbml.SBMLError

Returns the full Message.

getMessageString() - Method in class org.sbml.jsbml.Constraint

Returns the message of this Constraint as an XML String.

getMessengerRNA() - Static method in class org.sbml.jsbml.SBO

getMetaId() - Method in class org.sbml.jsbml.AbstractSBase

getMetaId() - Method in interface org.sbml.jsbml.SBase

Returns the metaid of this element.

getMetaId() - Method in class org.sbml.jsbml.util.filters.MetaIdFilter

Returns the metaid that will be searched for by the filter.

getMetaidRef() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject

Returns the value of metaidRef

getMetaIdRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns the value of metaIdRef

getMetaIdRef() - Method in class org.sbml.jsbml.ext.dyn.DynElement

Returns the value of metaIdRef

getMetaIdRef() - Method in class org.sbml.jsbml.ext.groups.Member

Returns the value of metaIdRef

getMinValue() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

Returns the value of minValue

getModel() - Method in class org.sbml.jsbml.AbstractSBase

getModel() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getModel() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Returns the Model

getModel() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns the Model

getModel() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

getModel() - Method in interface org.sbml.jsbml.SBase

Returns the Model object in which the current SBase is located.

getModel() - Method in class org.sbml.jsbml.SBMLDocument

Returns the model of this SBMLDocument.

getModel() - Method in class org.sbml.jsbml.util.ModelBuilder

getModelDefinition(int) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the n-th ModelDefinition object in this CompSBMLDocumentPlugin.

getModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns a ModelDefinition element that has the given 'id' within this CompSBMLDocumentPlugin or null if no such element can be found.

getModelDefinitionCount() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the number of ModelDefinition objects in this CompSBMLDocumentPlugin.

getModelHistory() - Method in class org.sbml.jsbml.Model

Deprecated.

use SBase.getHistory()

getModellingFramework() - Static method in class org.sbml.jsbml.SBO

getModelOrSubmodel(SBase) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseRefConstraints

getModelQualifierFor(String) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier

getModelQualifierType() - Method in class org.sbml.jsbml.CVTerm

Returns the CVTerm.Qualifier for this CVTerm, only if it if of type CVTerm.Type.MODEL_QUALIFIER, null otherwise.

getModelRef() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Returns the value of modelRef or an empty String if it is not set.

getModelRef() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns the value of modelRef

getModifiedDate() - Method in class org.sbml.jsbml.History

Returns the modifiedDate from the History.

getModifiedDate(int) - Method in class org.sbml.jsbml.History

Get the nth Date object in the list of ModifiedDates in this History.

getModifiedDateCount() - Method in class org.sbml.jsbml.History

Get the number of ModifiedDate objects in this History.

getModifier() - Static method in class org.sbml.jsbml.SBO

Substance that changes the velocity of a process without itself being consumed or transformed by the reaction.

getModifier(int) - Method in class org.sbml.jsbml.Reaction

getModifier(String) - Method in class org.sbml.jsbml.Reaction

Searches the first ModifierSpeciesReference in the Reaction.listOfModifiers of this Reaction with the given identifier.

getModifierCount() - Method in class org.sbml.jsbml.Reaction

getModifierForSpecies(String) - Method in class org.sbml.jsbml.Reaction

Returns the first ModifierSpeciesReference in the Reaction.listOfModifiers of this Reaction whose 'species' attribute points to a Species with the given identifier.

getModifierSpeciesReferenceCount() - Method in class org.sbml.jsbml.Model

Returns the number of ModifierSpeciesReferences in the Model.

getModifierSpeciesReferences() - Method in class org.sbml.jsbml.Model

Returns all ModifierSpeciesReferences, registered in any Reaction.

getModifierUnknownActivity() - Static method in class org.sbml.jsbml.SBO

A modifier whose activity is not known or has not been specified.

getModulation() - Static method in class org.sbml.jsbml.SBO

Modification of the execution of an event or a process.

getMolecularInteraction() - Static method in class org.sbml.jsbml.SBO

Relationship between molecular entities, based on contacts, direct or indirect.

getMultiplier() - Method in class org.sbml.jsbml.Unit

getName() - Method in class org.sbml.jsbml.AbstractSBase

getName() - Method in class org.sbml.jsbml.ASTNode

Gets the name of this node.

getName() - Method in class org.sbml.jsbml.math.ASTCiNumberNode

Deprecated.

getName() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode

getName() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode

Returns the name of the MathML element represented by this ASTCSymbolBaseNode

getName() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode

getName() - Method in class org.sbml.jsbml.math.ASTFunction

Returns the name of the MathML element represented by this ASTFunction

getName() - Method in interface org.sbml.jsbml.NamedSBase

Returns the name of the element if it is set, an empty string otherwise.

getName() - Method in class org.sbml.jsbml.ontology.Term

Returns the name of this Term, i.e., a very short characterization.

getName() - Method in interface org.sbml.jsbml.SBase

Returns the name of the element if it is set, an empty string otherwise.

getName() - Method in enum org.sbml.jsbml.Unit.Kind

Returns the name of this unit kind.

getName() - Method in class org.sbml.jsbml.util.filters.NameFilter

Returns the name.

getName() - Method in class org.sbml.jsbml.util.Option

getName() - Method in class org.sbml.jsbml.validator.offline.constraints.helper.CycleDetectionTreeNode

getName() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML

getName() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the (unqualified) name of this XML element.

getName() - Method in class org.sbml.jsbml.xml.XMLTriple

Returns the name portion of this XMLTriple.

getName(int) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns the local name of an attribute in this XMLAttributes set (by position).

getNamedSBaseCount() - Method in class org.sbml.jsbml.Model

Returns the number of NamedSBases in the Model, so elements that can have a name in SBML L3V1 or below.

getNamedSBaseInstance() - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

Gets the NamedSBase instance corresponding to the reference id.

getNamedSBaseWithDerivedUnitCount() - Method in class org.sbml.jsbml.Model

Returns the number of NamedSBaseWithDerivedUnits in the Model, so elements that can have a name and a derived unit in SBML L3V1 or below.

getNameOrId(SBase) - Static method in class org.sbml.jsbml.util.SBMLtools

getNamespace() - Method in class org.sbml.jsbml.AbstractSBase

getNamespace() - Method in interface org.sbml.jsbml.SBase

Returns the namespace to which this SBase belong to.

getNamespace() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.CompParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.DistribParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.DynParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.FBCParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.GroupsParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.LayoutParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getNamespaceFor(int, int, int) - Method in interface org.sbml.jsbml.xml.parsers.PackageParser

Gets the namespace for this package that correspond to the given SBML level, version and the package version.

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.QualParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.ReqParser

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getNamespaceFor(int, int, int, String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager

Gets the namespace for the given package name that correspond to the SBML level, version and package version.

getNamespaceFrom(int, int) - Static method in class org.sbml.jsbml.JSBML

getNamespaceIndex(String) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the index of an XML namespace declaration by URI.

getNamespaceIndexByPrefix(String) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the index of an XML namespace declaration by prefix.

getNamespacePrefix(int) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the prefix of an XML namespace declaration by position.

getNamespacePrefix(String) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the prefix of an XML namespace declaration by its URI.

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.CompParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.DistribParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.DynParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.FBCParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.GroupsParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.LayoutParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.QualParser

getNamespaces() - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser

Returns a List of all the namespaces that this parser is handling.

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.ReqParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getNamespaces() - Method in interface org.sbml.jsbml.xml.parsers.WritingParser

Returns a List of all the namespaces that this parser is handling

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader

getNamespaces() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the XML namespace declarations for this XML element.

getNamespacesLength() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the number of XML namespaces stored in the XMLNamespaces of this XMLToken.

getNamespaceURI() - Method in enum org.sbml.jsbml.CVTerm.Type

Returns the name space associated to this CVTerm.Type.

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter

Return the namespace URI of the namespace parsed by this class.

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.CompParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.DistribParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.DynParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.FBCParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.GroupsParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser

getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.LayoutParser

getNamespaceURI() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.QualParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.ReqParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the URI of an XML namespace declaration for the empty prefix.

getNamespaceURI(int) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the URI of an XML namespace declaration by its position.

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.arrays.ArraysConstants

Returns the namespace URI associated with the arrays package.

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.comp.CompConstants

Returns a namespace URI corresponding to the given SBML level and version.

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.dyn.DynConstants

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.fbc.FBCConstants

Returns a namespace URI corresponding to the given SBML level and version.

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.groups.GroupsConstants

Returns a namespace URI corresponding to the given SBML level and version.

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.layout.LayoutConstants

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.multi.MultiConstants

Returns a namespace corresponding to the given SBML level and version or null.

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.qual.QualConstants

Returns a namespace URI corresponding to the given level and version.

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.render.RenderConstants

Returns the namespace URI corresponding to the given level and version.

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.spatial.SpatialConstants

getNamespaceURI(int, int, int) - Static method in class org.sbml.jsbml.ext.fbc.FBCConstants

Returns a namespace URI corresponding to the given SBML level and version and package version.

getNamespaceURI(int, int, int) - Static method in class org.sbml.jsbml.ext.req.ReqConstants

Gets the namespace for this package that correspond to the given SBML level, version and the package version.

getNamespaceURI(String) - Method in class org.sbml.jsbml.xml.XMLToken

Returns the URI of an XML namespace declaration by its prefix.

getNecessaryStimulation() - Static method in class org.sbml.jsbml.SBO

Control that is necessary to the execution of a process.

getNegativeInfinity() - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

getNegativeInfinity() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

getNegativeInfinity() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler

getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

getNegativeInfinity() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

getNestedCVTerm(int) - Method in class org.sbml.jsbml.CVTerm

Gets an element from the CVTerm.listOfNestedCVTerms at the given index.

getNestedCVTermCount() - Method in class org.sbml.jsbml.CVTerm

Returns the number of CVTerms in this CVTerm.

getNextObject(ValidationContext, T, int) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.UniqueValidation

Returns the n-th object that should be tested.

getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParser

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.math.parser.FormulaParserTokenManager

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParser

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager

Get the next Token.

getNextToken() - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager

Get the next Token.

getNode() - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

getNonAllostericActivator() - Static method in class org.sbml.jsbml.SBO

Describes an activator (ligand) which binds to the enzyme, which does not result in a conformational change, but which enhances the enzyme's activity.

getNonCompetitiveInhibitor() - Static method in class org.sbml.jsbml.SBO

Substance that decreases the probability of a chemical reaction, without itself being consumed or transformed by the reaction, and without sterically hindering the interaction between reactants.

getNonCovalentComplex() - Static method in class org.sbml.jsbml.SBO

Entity composed of several independant components that are not linked by covalent bonds.

getNonEssentialActivator() - Static method in class org.sbml.jsbml.SBO

An activator which is not necessary for an enzymatic reaction, but whose presence will further increase enzymatic activity.

getNonRDFannotation() - Method in class org.sbml.jsbml.Annotation

Returns the XMLNode containing annotations other than the official RDF annotation, as defined in the SBML specifications.

getNonRDFannotationAsString() - Method in class org.sbml.jsbml.Annotation

Returns the String containing annotations other than RDF annotation.

getNotes() - Method in class org.sbml.jsbml.AbstractSBase

Returns an XMLNode object that represent the notes of this element.

getNotes() - Method in interface org.sbml.jsbml.SBase

Returns the XMLNode containing the notes sub-element of this object.

getNotesString() - Method in class org.sbml.jsbml.AbstractSBase

getNotesString() - Method in interface org.sbml.jsbml.SBase

Returns the notes sub-element of this object as a String.

getNumAdjacentDomains() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of AdjacentDomainss in this Geometry.

getNumArguments() - Method in class org.sbml.jsbml.FunctionDefinition

Get the number of arguments (bound variables) taken by this FunctionDefinition.

getNumAssociations() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

Returns the number of Associations in this LogicalOperator.

getNumber() - Method in class org.sbml.jsbml.math.ASTCnNumberNode

Get the numerical base of MathML element.

getNumbering(long) - Static method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

getNumbering(long) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

getNumberOfNonEmptyChildElement(XMLNode) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser

Returns the number of child XMLNode, excluding text XMLNode that contains only spaces.

getNumChildren() - Method in class org.sbml.jsbml.AbstractTreeNode

Returns the number of child elements of this TreeNode.

getNumCompartmentGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout

Returns the number of CompartmentGlyphs of this Layout.

getNumCompartmentReferences() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the number of CompartmentReferences in this MultiCompartmentPlugin.

getNumCompartments() - Method in class org.sbml.jsbml.Model

Returns the number of Compartments of this Model.

getNumCompartmentTypes() - Method in class org.sbml.jsbml.Model

Deprecated.

getNumConstraints() - Method in class org.sbml.jsbml.Model

Returns the number of Constraints of this Model.

getNumCoordinateComponents() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of CoordinateComponents in this Geometry.

getNumCreators() - Method in class org.sbml.jsbml.History

Get the number of Creator objects in this History.

getNumCSGObjects() - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

Returns the number of CSGObjects in this CSGeometry.

getNumCurveSegments() - Method in class org.sbml.jsbml.ext.render.Polygon

Returns the number of CurveSegments in this RenderCurve.

getNumCurveSegments() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns the number of CurveSegments in this RenderCurve.

getNumCVTerms() - Method in class org.sbml.jsbml.AbstractSBase

getNumCVTerms() - Method in class org.sbml.jsbml.Annotation

Gives the number of CVTerms in this Annotation.

getNumCVTerms() - Method in interface org.sbml.jsbml.SBase

Returns the number of CVTerms of this SBase.

getNumDelays() - Method in class org.sbml.jsbml.Model

Returns the number of Delays of this Model.

getNumDimensions() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the number of Dimensions in this ArraysSBasePlugin.

getNumDomains() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of Domains in this Geometry.

getNumDomainTypes() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of DomainTypes in this Geometry.

getNumElements() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the number of Transformation2Ds in this RenderGroup.

getNumerator() - Method in class org.sbml.jsbml.ASTNode

Gets the value of the numerator of this node.

getNumerator() - Method in class org.sbml.jsbml.math.ASTCnRationalNode

Get the numerator value of this node.

getNumericValue() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Returns the value of PossibleSpeciesFeatureValue.numericValue.

getNumErrors() - Method in class org.sbml.jsbml.SBMLDocument

Returns the number of errors or warnings encountered during consistency checking.

getNumErrors() - Method in class org.sbml.jsbml.SBMLErrorLog

Returns the number of errors that have been logged.

getNumEventAssignments() - Method in class org.sbml.jsbml.Event

Returns the number of EventAssignments in this Event.

getNumEventAssignments() - Method in class org.sbml.jsbml.Model

Returns the number of EventAssignments of this Model.

getNumEvents() - Method in class org.sbml.jsbml.Model

Returns the number of Events of this Model.

getNumExternalModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the number of ExternalModelDefinition of this CompSBMLDocumentPlugin.

getNumFailsWithSeverity(SBMLError.SEVERITY) - Method in class org.sbml.jsbml.SBMLErrorLog

Returns the number of errors that have been logged with the given severity code.

getNumFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Deprecated.

Only defined in FBC version 1.

getNumFluxObjectives() - Method in class org.sbml.jsbml.ext.fbc.Objective

Deprecated.

use Objective.getFluxObjectiveCount()

getNumFunctionDefinitions() - Method in class org.sbml.jsbml.Model

Returns the number of FunctionDefinitions of this Model.

getNumGeneProducts() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Returns the number of GeneProducts in this FBCModelPlugin.

getNumGeometryDefinitions() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of GeometryDefinitions in this Geometry.

getNumGroups() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Returns the number of Groups of this GroupsModelPlugin.

getNumIndices() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the number of Indexs in this ArraysSBasePlugin.

getNumInitialAssignments() - Method in class org.sbml.jsbml.Model

Returns the number of InitialAssignments of this Model.

getNumInSpeciesTypeBonds() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the number of InSpeciesTypeBonds in this MultiSpeciesType.

getNumKineticLaws() - Method in class org.sbml.jsbml.Model

Returns the number of KineticLaws of this Model.

getNumLayouts() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

Returns the number of Layouts of this LayoutModelPlugin.

getNumListsOf() - Method in class org.sbml.jsbml.Model

Returns the number of ListOfs of this Model.

getNumLocalParameters() - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

use KineticLaw.getLocalParameterCount()

getNumLocalParameters() - Method in class org.sbml.jsbml.Model

Returns the number of parameters that are contained within kineticLaws in the reactions of this model.

getNumMathContainers() - Method in class org.sbml.jsbml.Model

Returns the number of elements that can contain math in the Model .

getNumMembers() - Method in class org.sbml.jsbml.ext.groups.Group

Returns the number of Members of this Group.

getNumModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the number of ModelDefinition of this CompSBMLDocumentPlugin.

getNumModifiedDates() - Method in class org.sbml.jsbml.History

Get the number of ModifiedDate objects in this History.

getNumModifiers() - Method in class org.sbml.jsbml.Reaction

getNumModifierSpeciesReferences() - Method in class org.sbml.jsbml.Model

Returns the number of ModifierSpeciesReferences in the Model.

getNumNamedSBases() - Method in class org.sbml.jsbml.Model

Returns the number of NamedSBases in the Model, so elements that can have a name.

getNumNamedSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.Model

Returns the number of NamedSBaseWithDerivedUnits in the Model, so elements that can have a name and a unit that can be derived.

getNumNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm

Returns the number of CVTerms in this CVTerm.

getNumObjective() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Return the number of Objectives in this FBCModelPlugin.

getNumObjects(ValidationContext, T) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.UniqueValidation

Returns the total number of objects which should be tested.

getNumOutwardBindingSites() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the number of OutwardBindingSites in this MultiSpeciesPlugin.

getNumParameters() - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

use KineticLaw.getLocalParameterCount()

getNumParameters() - Method in class org.sbml.jsbml.Model

Returns the number of Parameters of this Model.

getNumPlugins() - Method in class org.sbml.jsbml.AbstractSBase

getNumPlugins() - Method in class org.sbml.jsbml.ASTNode

Returns the number of ASTNodePlugins of this ASTNode.

getNumPlugins() - Method in interface org.sbml.jsbml.SBase

Returns the number of SBasePlugins of this SBase.

getNumPorts() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the number of Port of this CompModelPlugin.

getNumPossibleSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns the number of PossibleSpeciesFeatureValues in this SpeciesFeatureType.

getNumProducts() - Method in class org.sbml.jsbml.Reaction

getNumQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns the number of QualitativeSpecies of this QualModelPlugin.

getNumQuantities() - Method in class org.sbml.jsbml.Model

Returns the number of Quantitys of this Model.

getNumQuantitiesWithUnit() - Method in class org.sbml.jsbml.Model

Returns the number of QuantityWithUnits of this Model.

getNumReactants() - Method in class org.sbml.jsbml.Reaction

getNumReactionGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout

Returns the number of ReactionGlyphs of this Layout.

getNumReactions() - Method in class org.sbml.jsbml.Model

Returns the number of Reactions of this Model.

getNumReplacedElements() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns the number of ReplacedElement of this CompSBasePlugin.

getNumResources() - Method in class org.sbml.jsbml.CVTerm

Returns the number of resources for this CVTerm.

getNumRules() - Method in class org.sbml.jsbml.Model

Returns the number of Rules of this Model.

getNumSampledFields() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of SampledFields in this Geometry.

getNumSamples1() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of numSamples1

getNumSamples2() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of numSamples2

getNumSamples3() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of numSamples3

getNumSBases() - Method in class org.sbml.jsbml.Model

Returns the number of SBases of this Model.

getNumSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.Model

Returns the number of SBaseWithDerivedUnits of this Model.

getNumSemanticsAnnotations() - Method in class org.sbml.jsbml.ASTNode

Gets the number of semantic annotation elements inside this node.

getNumSpecies() - Method in class org.sbml.jsbml.Model

Returns the number of Species of this Model.

getNumSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the number of SpeciesFeatures in this MultiSpeciesPlugin.

getNumSpeciesFeatureTypes() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the number of SpeciesFeatureTypes in this MultiSpeciesType.

getNumSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the number of SpeciesFeatureValues in this SpeciesFeature.

getNumSpeciesGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout

Returns the number of SpeciesGlyphs of this Layout.

getNumSpeciesReferenceGlyphs() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

Deprecated.

use ReactionGlyph.getSpeciesReferenceGlyphCount()

getNumSpeciesReferences() - Method in class org.sbml.jsbml.Model

Returns the number of SpeciesReferences of this Model.

getNumSpeciesTypeComponentIndexes() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the number of SpeciesTypeComponentIndexs in this MultiSpeciesType.

getNumSpeciesTypeComponentMapInProducts() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Returns the number of SpeciesTypeComponentMapInProducts in this MultiSpeciesReferencePlugin.

getNumSpeciesTypeInstances() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the number of SpeciesTypeInstances in this MultiSpeciesType.

getNumSpeciesTypes() - Method in class org.sbml.jsbml.Model

Deprecated.

getNumSpeciesWithBoundaryCondition() - Method in class org.sbml.jsbml.Model

Returns the number of Species whose boundary condition is set to true.

getNumStoichiometryMath() - Method in class org.sbml.jsbml.Model

Deprecated.

since SBML L3V1.

getNumSubListOfSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the number of SubListOfSpeciesFeatures in this MultiSpeciesPlugin.

getNumSubmodels() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the number of Submodel of this CompModelPlugin.

getNumSymbols() - Method in class org.sbml.jsbml.Model

Returns the number of all instances of Symbol referenced within the model.

getNumTextGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout

Returns the number of TextGlyphs of this Layout.

getNumTransitions() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns the number of Transition of this QualModelPlugin.

getNumTriggers() - Method in class org.sbml.jsbml.Model

Returns the number of Trigger of this Model.

getNumUncertainties() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Returns the number of Uncertaintys in this DistribSBasePlugin.

getNumUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Returns the number of UncertParameters in this Uncertainty.

getNumUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the number of UncertParameters in this UncertParameter.

getNumUnitDefinitions() - Method in class org.sbml.jsbml.Model

Returns the number of UnitDefinitions of this Model.

getNumUnits() - Method in class org.sbml.jsbml.Model

Returns the number of Units of this Model.

getNumUnits() - Method in class org.sbml.jsbml.UnitDefinition

getNumVariables() - Method in class org.sbml.jsbml.Model

Returns the number of Variables of this Model.

getObject() - Method in class org.sbml.jsbml.ontology.Triple

Returns the object of this Triple.

getObjective(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Gets an element from the listOfObjectives at the given index.

getObjectiveCount() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Return the number of Objective in this FBCModelPlugin.

getObjectRole() - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

Returns the value of RenderGraphicalObjectPlugin.objectRole.

getOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the value of SpeciesFeature.occur.

getOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns the value of SpeciesFeatureType.occur.

getOffset() - Method in class org.sbml.jsbml.ext.render.GradientStop

getOffset() - Method in class org.sbml.jsbml.Unit

Deprecated.

getOmitXMLDeclaration() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getOmitXMLDeclaration() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser

Returns true if we need to omit the XML declaration.

getOntology() - Static method in class org.sbml.jsbml.ext.dyn.CBO

Grants access to the underlying Ontology form BioJava.

getOntology() - Static method in class org.sbml.jsbml.SBO

Grants access to the underlying Ontology form BioJava.

getOperation() - Method in class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

getOperationType() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

Returns the value of operationType

getOrder() - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph

Returns the value of order

getOrdinal() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

Returns the value of ordinal

getOrdinal() - Method in class org.sbml.jsbml.ext.spatial.CSGObject

Returns the value of ordinal

getOrdinal() - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

Returns the value of ordinal

getOrganisation() - Method in class org.sbml.jsbml.Creator

Returns the organisation from the Creator.

getOrganization() - Method in class org.sbml.jsbml.Creator

Returns the organisation from the Creator.

getOriginalModel() - Method in interface org.sbml.jsbml.SBMLInputConverter

getOriginOfText() - Method in class org.sbml.jsbml.ext.layout.TextGlyph

getOriginOfTextInstance() - Method in class org.sbml.jsbml.ext.layout.TextGlyph

getOrReplacement() - Method in class org.sbml.jsbml.util.compilers.ConfigurableLogicalFormulaCompiler

Gets the String that will be used to replace ' or ' (the mathML <or> element) in the boolean expressions.

getOrReplacement() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise

Gets the String that will be used to replace ' or ' (the mathML <or> element) in the boolean expressions.

getOtherAttribute(String) - Method in class org.sbml.jsbml.Creator

Deprecated.

those other attributes are not saved when writing the model

getOtherAttributes() - Method in class org.sbml.jsbml.Creator

Deprecated.

those other attributes are not saved when writing the model

getOtherListName() - Method in class org.sbml.jsbml.ListOf

Returns the XML element name used when the ListOf type is set to ListOf.Type.other.

getOutputCount() - Method in class org.sbml.jsbml.ext.qual.Transition

getOutputLevel() - Method in class org.sbml.jsbml.ext.qual.Output

Returns the outputLevel.

getOutside() - Method in class org.sbml.jsbml.Compartment

Returns the outside id of this compartment.

getOutsideInstance() - Method in class org.sbml.jsbml.Compartment

Returns the compartment instance which matches the outside id in Model.

getOutwardBindingSite(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Gets an element from the MultiSpeciesPlugin.listOfOutwardBindingSites at the given index.

getOutwardBindingSiteCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the number of OutwardBindingSites in this MultiSpeciesPlugin.

getPackage() - Method in exception org.sbml.jsbml.SBMLError

getPackageName() - Method in class org.sbml.jsbml.AbstractSBase

getPackageName() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getPackageName() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

Returns the package name of this plugin object.

getPackageName() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getPackageName() - Method in class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

getPackageName() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

getPackageName() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getPackageName() - Method in class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

getPackageName() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getPackageName() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getPackageName() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getPackageName() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getPackageName() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getPackageName() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getPackageName() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getPackageName() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getPackageName() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getPackageName() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin

getPackageName() - Method in interface org.sbml.jsbml.ext.SBasePlugin

Returns the package name of this plugin object.

getPackageName() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

getPackageName() - Method in interface org.sbml.jsbml.SBase

Returns the name of the SBML Level 3 package in which this element is defined, as defined in the sbml.org community wiki.

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.CompParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.DistribParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.DynParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.FBCParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.GroupsParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.LayoutParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getPackageName() - Method in interface org.sbml.jsbml.xml.parsers.PackageParser

Returns the short name of this package.

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.QualParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.ReqParser

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getPackageName(String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager

Returns the name of the SBML package corresponding to the given namespace URI.

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.CompParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.DistribParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.DynParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.FBCParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.GroupsParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.LayoutParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getPackageNamespaces() - Method in interface org.sbml.jsbml.xml.parsers.PackageParser

Returns a List of all the valid namespaces for the package.

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.QualParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.ReqParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getPackageParser(String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager

Returns the PackageParser corresponding to the given name or namespace.

getPackageRequired(String) - Method in class org.sbml.jsbml.SBMLDocument

Returns the required attribute of the given package extension.

getPackageRequired(String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager

Returns the required attribute corresponding to the given name or namespace.

getPackageVersion() - Method in class org.sbml.jsbml.AbstractSBase

getPackageVersion() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin

getPackageVersion() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

getPackageVersion() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

Returns the package version of the package extension of this plugin object.

getPackageVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin

Returns the package version of the package extension of this plugin object.

getPackageVersion() - Method in interface org.sbml.jsbml.SBase

Returns the version of the SBML Level 3 package to which this element belongs.

getPackageVersion(String) - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Gets the package version to validate.

getParameter(int) - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

use KineticLaw.getLocalParameter(int)

getParameter(int) - Method in class org.sbml.jsbml.Model

Gets the n^th Parameter object in this Model.

getParameter(String) - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

use KineticLaw.getLocalParameter(String)

getParameter(String) - Method in class org.sbml.jsbml.Model

Returns the Parameter of the Model.listOfParameters which has 'id' as id

getParameterCount() - Method in class org.sbml.jsbml.Model

Returns the number of Parameters of this Model.

getParameterInstance() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

Returns the Parameter instance associated with ParameterType.variable.

getParamType() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin

getParent() - Method in class org.sbml.jsbml.AbstractSBase

This is equivalent to calling AbstractSBase.getParentSBMLObject(), but this method is needed for TreeNode.

getParent() - Method in class org.sbml.jsbml.AbstractTreeNode

getParent() - Method in class org.sbml.jsbml.ASTNode

getParent() - Method in class org.sbml.jsbml.CompartmentType

Deprecated.

getParent() - Method in class org.sbml.jsbml.Constraint

getParent() - Method in class org.sbml.jsbml.Delay

getParent() - Method in class org.sbml.jsbml.Event

getParent() - Method in class org.sbml.jsbml.EventAssignment

getParent() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getParent() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getParent() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

getParent() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

getParent() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getParent() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getParent() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getParent() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getParent() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getParent() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

getParent() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

getParent() - Method in class org.sbml.jsbml.FunctionDefinition

getParent() - Method in class org.sbml.jsbml.InitialAssignment

getParent() - Method in class org.sbml.jsbml.KineticLaw

getParent() - Method in class org.sbml.jsbml.LocalParameter

getParent() - Method in class org.sbml.jsbml.math.ASTUnknown

getParent() - Method in class org.sbml.jsbml.Priority

getParent() - Method in class org.sbml.jsbml.Reaction

getParent() - Method in class org.sbml.jsbml.Rule

getParent() - Method in class org.sbml.jsbml.SpeciesType

Deprecated.

getParent() - Method in class org.sbml.jsbml.StoichiometryMath

Deprecated.

getParent() - Method in class org.sbml.jsbml.Trigger

getParent() - Method in class org.sbml.jsbml.Unit

getParent() - Method in class org.sbml.jsbml.UnitDefinition

getParentReactionGlyph() - Method in class org.sbml.jsbml.ext.layout.Curve

getParents() - Method in class org.sbml.jsbml.validator.offline.constraints.helper.CycleDetectionTreeNode

getParentSBase(TreeNodeWithChangeSupport) - Static method in class org.sbml.jsbml.validator.offline.LoggingValidationContext

getParentSBMLObject() - Method in class org.sbml.jsbml.AbstractSBase

getParentSBMLObject() - Method in class org.sbml.jsbml.ASTNode

This method is convenient when holding an object nested inside other objects in an SBML model.

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

getParentSBMLObject() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

Returns the parent SBase object to which this plugin object is connected.

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getParentSBMLObject() - Method in interface org.sbml.jsbml.ext.SBasePlugin

Returns the parent SBase object to which this plugin object connected.

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.KineticLaw

This method is convenient when holding an object nested inside other objects in an SBML model.

getParentSBMLObject() - Method in class org.sbml.jsbml.LocalParameter

getParentSBMLObject() - Method in class org.sbml.jsbml.math.AbstractASTNode

getParentSBMLObject() - Method in interface org.sbml.jsbml.math.ASTNode2

Return the parentSBMLObject of this ASTNode2

getParentSBMLObject() - Method in class org.sbml.jsbml.math.ASTUnknown

getParentSBMLObject() - Method in interface org.sbml.jsbml.SBase

Returns the parent of this SBase.

getParentTerms() - Method in class org.sbml.jsbml.ontology.Term

Returns the parent Terms.

getPartialInhibitor() - Static method in class org.sbml.jsbml.SBO

getParticipant() - Static method in class org.sbml.jsbml.SBO

getParticipantRole() - Static method in class org.sbml.jsbml.SBO

The function of a physical or conceptual entity, that is its role, in the execution of an event or process.

getPattern() - Method in class org.sbml.jsbml.util.filters.CVTermFilter

getPersistent() - Method in class org.sbml.jsbml.Trigger

getPertubingAgent() - Static method in class org.sbml.jsbml.SBO

Perturbing agent.

getpH() - Static method in class org.sbml.jsbml.SBO

"A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution.

getPhenotype() - Static method in class org.sbml.jsbml.SBO

getPhysicalCompartment() - Static method in class org.sbml.jsbml.SBO

getPhysicalParticipant() - Static method in class org.sbml.jsbml.SBO

getPieceCount() - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode

Get the number of piece elements in this ASTPiecewiseFunctionNode

getPiecewiseMap() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise

Gets a Map of the piecewise expressions that have been transformed.

getPkgRequired(String) - Method in class org.sbml.jsbml.SBMLDocument

Deprecated.

use SBMLDocument.getPackageRequired(String)

getPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase

getPlugin(String) - Method in class org.sbml.jsbml.ASTNode

Returns an ASTNodePlugin for an SBML Level 3 package extension with the given package name or URI.

getPlugin(String) - Method in interface org.sbml.jsbml.SBase

Returns an SBasePlugin for an SBML Level 3 package extension with the given package name or URI.

getPMg() - Static method in class org.sbml.jsbml.SBO

An enumeration of the concentration of magnesium (Mg) in solution (pMg = -log10[Mg2+]).

getPointIndex() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Returns the value of ParametricObject.pointIndex.

getPointIndex() - Method in class org.sbml.jsbml.ext.spatial.PolygonObject

Deprecated.

Returns the value of pointIndex

getPointIndexLength() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Returns the value of pointIndexLength.

getPointOfContactToProduct() - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode

getPointOfContactToProduct() - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode

getPointOfContactToSubstrate() - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode

getPointOfContactToSubstrate() - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode

getPolygonType() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

Returns the value of polygonType

getPort(int) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the n-th Port object in this CompModelPlugin.

getPort(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns a Port element that has the given 'id' within this CompModelPlugin or null if no such element can be found.

getPortCount() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the number of Port objects in this CompModelPlugin.

getPortRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns the value of portRef

getPosition() - Method in class org.sbml.jsbml.ext.layout.BoundingBox

getPositiveInfinity() - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

getPositiveInfinity() - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

getPositiveInfinity() - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler

getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

getPositiveInfinity() - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

getPossibleEnzymes(String...) - Static method in class org.sbml.jsbml.SBO

Creates and returns a list of molecule types that are accepted as an enzyme for the given type names.

getPossibleSpeciesFeatureValue(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Gets an element from the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues at the given index.

getPossibleSpeciesFeatureValue(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Gets an element from the listOfPossibleSpeciesFeatureValues, with the given id.

getPossibleSpeciesFeatureValueCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns the number of PossibleSpeciesFeatureValues in this SpeciesFeatureType.

getPotentiator() - Static method in class org.sbml.jsbml.SBO

Substance that increases the probability of a chemical reaction without itself being consumed or transformed by the reaction.

getPredefinedUnit(String, int, int) - Static method in class org.sbml.jsbml.UnitDefinition

Returns the predefined unit with the given identifier for the specified level and version combination or null if either for the given combination of level and version there is no such predefined unit or the identifier is not one of those belonging to the group of predefined unit definitions.

getPredefinedUnitDefinition(String) - Method in class org.sbml.jsbml.Model

Returns a UnitDefinition representing one of the predefined units of SBML, returns null if the given unit kind is not a valid one for the SBML level and version of this Model.

getPredefinedUnitID() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit

Returns the predefined unit identifier for this data type with the current level/version combination.

getPredefinedUnitID() - Method in class org.sbml.jsbml.Compartment

getPredefinedUnitID() - Method in class org.sbml.jsbml.Event

getPredefinedUnitID() - Method in class org.sbml.jsbml.LocalParameter

getPredefinedUnitID() - Method in class org.sbml.jsbml.Parameter

getPredefinedUnitID() - Method in class org.sbml.jsbml.Species

getPredicate() - Method in class org.sbml.jsbml.ontology.Triple

Returns the predicate of this Triple.

getPrefix() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getPrefix() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

Returns the prefix of the package extension of this plugin object.

getPrefix() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getPrefix() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

getPrefix() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getPrefix() - Method in class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

getPrefix() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getPrefix() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getPrefix() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin

getPrefix() - Method in interface org.sbml.jsbml.ext.SBasePlugin

Returns the prefix of the package extension of this plugin object.

getPrefix() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

getPrefix() - Method in class org.sbml.jsbml.Unit

getPrefix() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML

getPrefix() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the namespace prefix of this XML element.

getPrefix() - Method in class org.sbml.jsbml.xml.XMLTriple

Returns the prefix portion of this XMLTriple.

getPrefix(int) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns the prefix of an attribute in this XMLAttributes set (by position).

getPrefix(int) - Method in class org.sbml.jsbml.xml.XMLNamespaces

Gets the prefix of an XML namespace declaration by its position.

getPrefix(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces

Gets the prefix of an XML namespace declaration by its URI.

getPrefixAsWord() - Method in class org.sbml.jsbml.Unit

getPrefixedName() - Method in class org.sbml.jsbml.xml.XMLTriple

Returns the prefixed name from this XMLTriple.

getPrefixedName(int) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns the prefixed name of an attribute in this XMLAttributes set (by position).

getPreviousParent() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent

Access the pointer to the previous parent node of the removed node, may be null.

getPrimitiveType() - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive

Returns the value of primitiveType

getPriority() - Method in class org.sbml.jsbml.Event

getProcess() - Static method in class org.sbml.jsbml.SBO

getProduct() - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

getProduct() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Return the product of the building process.

getProduct() - Static method in class org.sbml.jsbml.SBO

Substance that is produced in a reaction.

getProduct(int) - Method in class org.sbml.jsbml.Reaction

getProduct(String) - Method in class org.sbml.jsbml.Reaction

Searches the first SpeciesReference in the listOfProducts of this Reaction with the given identifier.

getProductComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns the value of SpeciesTypeComponentMapInProduct.productComponent.

getProductCount() - Method in class org.sbml.jsbml.Reaction

getProductForSpecies(String) - Method in class org.sbml.jsbml.Reaction

Returns the first SpeciesReference in the Reaction.listOfProducts of this Reaction whose 'species' attribute points to a Species with the given identifier.

getProduction() - Static method in class org.sbml.jsbml.SBO

Generation of a material or conceptual entity.

getProgramName() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getProgramName() - Method in class org.sbml.jsbml.SBMLWriter

getProgramVersion() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getProgramVersion() - Method in class org.sbml.jsbml.SBMLWriter

getProtein() - Static method in class org.sbml.jsbml.SBO

getQualifier() - Method in class org.sbml.jsbml.CVTerm

Returns the CVTerm.Qualifier for this CVTerm.

getQualifier() - Method in class org.sbml.jsbml.util.filters.CVTermFilter

getQualifierType() - Method in class org.sbml.jsbml.CVTerm

Returns the qualifier CVTerm.Type for this CVTerm.

getQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.Input

getQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.Output

Returns the qualitativeSpecies

getQualitativeSpecies(int) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Gets the ith QualitativeSpecies.

getQualitativeSpecies(String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Gets the QualitativeSpecies that has the given id.

getQualitativeSpeciesCount() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns the number of QualitativeSpecies objects in this QualModelPlugin.

getQualitativeSpeciesInstance() - Method in class org.sbml.jsbml.ext.qual.Input

getQualitativeSpeciesInstance() - Method in class org.sbml.jsbml.ext.qual.Output

getQuantitativeParameter() - Static method in class org.sbml.jsbml.SBO

getQuantityCount() - Method in class org.sbml.jsbml.Model

Returns the number of Quantitys of this Model.

getQuantityWithUnitCount() - Method in class org.sbml.jsbml.Model

Returns the number of QuantityWithUnits of this Model.

getR() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getRadicand() - Method in class org.sbml.jsbml.math.ASTRootNode

Return the radicand of this ASTRootNode

getRateLaw() - Static method in class org.sbml.jsbml.SBO

getRateOf(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

getRateOf(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

getRateOf(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

getRateOf(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

Returns the instantaneous rate of change, with respect to time, of an entity in the model.

getRateOf(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

getRateOf(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

getRateOf(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

getRateOf(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

getRateOf(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

getRateRuleByVariable(String) - Method in class org.sbml.jsbml.Model

Searches for the first instance of RateRule within this Model's Model.listOfRules, whose variable attribute is set to the value passed to this method.

getRatio() - Method in class org.sbml.jsbml.ext.render.Ellipse

getRatio() - Method in class org.sbml.jsbml.ext.render.Rectangle

getReactant() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns the value of SpeciesTypeComponentMapInProduct.reactant.

getReactant() - Static method in class org.sbml.jsbml.SBO

Substance consumed by a chemical reaction.

getReactant(int) - Method in class org.sbml.jsbml.Reaction

getReactant(String) - Method in class org.sbml.jsbml.Reaction

Searches the first SpeciesReference in the listOfReactants of this Reaction with the given identifier.

getReactantComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns the value of SpeciesTypeComponentMapInProduct.reactantComponent.

getReactantCount() - Method in class org.sbml.jsbml.Reaction

getReactantForSpecies(String) - Method in class org.sbml.jsbml.Reaction

Returns the first SpeciesReference in the Reaction.listOfReactants of this Reaction whose 'species' attribute points to a Species with the given identifier.

getReaction() - Method in class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

Only defined in FBC version 1.

getReaction() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective

Returns the value of reaction

getReaction() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

getReaction(int) - Method in class org.sbml.jsbml.Model

Gets the n-th Reaction object in this Model.

getReaction(String) - Method in class org.sbml.jsbml.Model

Returns the Reaction of the Model.listOfReactions which has 'id' as id.

getReactionCount() - Method in class org.sbml.jsbml.Model

Returns the number of Reactions of this Model.

getReactionGlyph() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

getReactionGlyph(int) - Method in class org.sbml.jsbml.ext.layout.Layout

getReactionGlyph(String) - Method in class org.sbml.jsbml.ext.layout.Layout

getReactionGlyphCount() - Method in class org.sbml.jsbml.ext.layout.Layout

Returns the number of ReactionGlyphs of this Layout.

getReactionInstance() - Method in class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

Only defined in FBC version 1.

getReactionInstance() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective

Returns the Reaction associated with this FluxObjective.

getReactionInstance() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

Note that the return type of this method is NamedSBase because it could be possible to link some element from other packages to this glyph.

getReadingParsers() - Method in class org.sbml.jsbml.xml.parsers.ParserManager

Gets a copy of the registered ReadingParsers map.

getReal() - Method in class org.sbml.jsbml.ASTNode

Gets the real-numbered value of this node.

getReal() - Method in class org.sbml.jsbml.math.ASTCnRealNode

Get the real value of this node.

getReceptor() - Static method in class org.sbml.jsbml.SBO

getReference() - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

Gets the reference.

getReferencedAttribute() - Method in class org.sbml.jsbml.ext.arrays.Index

Returns the value of referencedAttribute

getReferencedModel() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Resolves the external Model referenced by this and returns that model, under the assumption that the containing SBMLDocument a) exists and b) has a valid locationURI set (cf SBMLDocument.isSetLocationURI()).

getReferencedModel(URI) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Resolves the external Model referenced by this and returns that model, for a given path to the directory containing the SBML-file wherein this ExternalModelDefinition was made/the root directory for references by relative paths.

getReferencedNamedSBases() - Method in class org.sbml.jsbml.ASTNode

Returns a set of all the NamedSBase referenced on this node and all his descendant.

getReferenceInstance() - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

Gets the NamedSBase instance corresponding to the reference id.

getReferenceInstance() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode

Returns the variable (FunctionDefinition) of this ASTCiFunctionNode.

getReferenceInstance() - Method in class org.sbml.jsbml.math.ASTCiNumberNode

Returns the variable (CallableSBase) of this ASTCiNumberNode.

getReferenceRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getRefId() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode

Get refId attribute

getRefId() - Method in class org.sbml.jsbml.math.ASTCiNumberNode

Get refId attribute

getRelatedCompartments(Model, String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel

getRelatedReactions(Model, String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel

Returns an array of reaction id related to the reactsIds or speciesIds.

getRelatedSpecies(Model, String[], String[], String[]) - Static method in class org.sbml.jsbml.util.SubModel

getRelation() - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature

Returns the value of SubListOfSpeciesFeature.relation.

getRelativeValue() - Method in class org.sbml.jsbml.ext.render.RelAbsVector

getRenderFillColor(SpeciesGlyph) - Static method in class org.sbml.jsbml.ext.render.director.RenderProcessor

getRenderInformation() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

Deprecated.

This goes beyond/is besides the render-package's specification and will be removed in a future release. Use the methods RenderLayoutPlugin.getListOfLocalRenderInformation(), RenderLayoutPlugin.getLocalRenderInformation(int), and RenderListOfLayoutsPlugin.getListOfGlobalRenderInformation() respectively

getReplacedBy() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns the value of replacedBy

getReplacedElement(int) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns the n-th ReplacedElement object in this CompSBasePlugin.

getReplacedElement(String) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns a ReplacedElement element that has the given 'id' within this CompSBasePlugin or null if no such element can be found.

getReplacedElementCount() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns the number of ReplacedElement objects in this CompSBasePlugin.

getRepresentationType() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

Returns the value of MultiASTNodePlugin.representationType.

getResource(int) - Method in class org.sbml.jsbml.CVTerm

getResourceCount() - Method in class org.sbml.jsbml.CVTerm

Returns the number of resources for this CVTerm.

getResources() - Method in class org.sbml.jsbml.CVTerm

Returns the resources for this CVTerm.

getResourceURI(int) - Method in class org.sbml.jsbml.CVTerm

Returns the value of the nth resource for this CVTerm.

getResultLevel() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

Returns the resultLevel if it is set, otherwise throw a PropertyUndefinedError Exception.

getReverseTransformation() - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation

Returns the value of reverseTransformation

getReversible() - Method in class org.sbml.jsbml.Reaction

getRightChild() - Method in class org.sbml.jsbml.ASTNode

Returns the last child in the list of children of this node.

getRightChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode

Get the right child of this ASTBinaryFunctionNode

getRNA() - Static method in class org.sbml.jsbml.SBO

getRNASegment() - Static method in class org.sbml.jsbml.SBO

Fragment or region of an RNA macromolecule.

getRole() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph

getRole() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

getRoleList() - Method in class org.sbml.jsbml.ext.render.Style

getRoot() - Method in class org.sbml.jsbml.AbstractTreeNode

getRoot() - Method in class org.sbml.jsbml.math.ASTUnknown

getRoot() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

getRootConstraint() - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Returns the root constraint from this context.

getRootExponent() - Method in class org.sbml.jsbml.math.ASTRootNode

Return the root exponent of this ASTRootNode

getRotateAngleInRadians() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

Returns the value of rotateAngleInRadians

getRotateX() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

Returns the value of rotateAxisX

getRotateY() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

Returns the value of rotateAxisY

getRotateZ() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

Returns the value of rotateAxisZ

getRule(int) - Method in class org.sbml.jsbml.Model

Gets the n^th Rule of the listOfRules.

getRule(String) - Method in class org.sbml.jsbml.Model

Deprecated.

Since L3V2 every SBase can have an id. Use either Model.getRuleById(String) or Model.getRuleByVariable(String).

getRuleById(String) - Method in class org.sbml.jsbml.Model

Searches for the first instance of Rule within this Model's Model.listOfRules, whose id attribute is set to the value passed to this method.

getRuleByVariable(String) - Method in class org.sbml.jsbml.Model

Searches for the first instance of ExplicitRule within this Model's Model.listOfRules, whose variable attribute is set to the value passed to this method.

getRuleCount() - Method in class org.sbml.jsbml.Model

Returns the number of Rules of this Model.

getRx() - Method in class org.sbml.jsbml.ext.render.Ellipse

getRx() - Method in class org.sbml.jsbml.ext.render.Rectangle

getRy() - Method in class org.sbml.jsbml.ext.render.Ellipse

getRy() - Method in class org.sbml.jsbml.ext.render.Rectangle

getSampledField() - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

Returns the value of sampledField

getSampledField(int) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the Geometry.listOfSampledFields at the given index.

getSampledField(String) - Method in class org.sbml.jsbml.ext.spatial.Geometry

Gets an element from the listOfSampledFields, with the given id.

getSampledFieldCount() - Method in class org.sbml.jsbml.ext.spatial.Geometry

Returns the number of SampledFields in this Geometry.

getSampledValue() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

Returns the value of sampledValue

getSamples() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of SampledField.samples.

getSamplesLength() - Method in class org.sbml.jsbml.ext.spatial.SampledField

Returns the value of SampledField.samplesLength.

getSBaseById(String) - Method in class org.sbml.jsbml.Model

Returns an SBase element of the model that has the given 'id' as id or null if no element is found.

getSBaseCount() - Method in class org.sbml.jsbml.Model

Returns the number of SBases of this Model.

getSBaseInstance() - Method in class org.sbml.jsbml.ext.groups.Member

Gets the actual SBase instance referred by the idRef or metaIdRef, returns null if nothing is found.

getSBaseInstance() - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

Gets the SBase instance corresponding to the reference id.

getSBaseListType() - Method in class org.sbml.jsbml.ListOf

Returns the SBaseListType of this ListOf instance.

getSBaseRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns the value of sBaseRef

getSBaseWithDerivedUnitCount() - Method in class org.sbml.jsbml.Model

Returns the number of SBaseWithDerivedUnits of this Model.

getSBGNArc(int) - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

Creates the correct SBGNArc according to the given SBO term.

getSBGNArc(SpeciesReferenceRole) - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

Creates the correct SBGNArc according to the given SpeciesReferenceRole.

getSBGNNode(int) - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

Create the correct SBGNNode according to the given SBO term.

getSBGNReactionNode(int) - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

Create the correct process node according to the SBO term of the reaction.

getSBMLDocument() - Method in class org.sbml.jsbml.AbstractSBase

getSBMLDocument() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin

getSBMLDocument() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

getSBMLDocument() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

Returns the parent SBMLDocument of this plugin object.

getSBMLDocument() - Method in interface org.sbml.jsbml.ext.SBasePlugin

Returns the parent SBMLDocument of this plugin object.

getSBMLDocument() - Method in interface org.sbml.jsbml.SBase

Returns the parent SBMLDocument object.

getSBMLDocument() - Method in class org.sbml.jsbml.util.ModelBuilder

getSBMLDocumentAttributes() - Method in class org.sbml.jsbml.SBMLDocument

Returns the map of attribute names and values of this SBMLDocument.

getSBMLDocumentNamespaces() - Method in class org.sbml.jsbml.SBMLDocument

Deprecated.

use SBase.getDeclaredNamespaces()

getSBMLErrorMessageBundle() - Static method in class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory

Returns the SBMLErrorMessage bundle associated with the current Locale.

getSBMLErrorPostMessageBundle() - Static method in class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory

Returns the SBMLErrorPostMessage bundle associated with the current Locale.

getSBMLErrorPreMessageBundle() - Static method in class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory

Returns the SBMLErrorPreMessage bundle associated with the current Locale.

getSBMLErrorPreMessageBundle(Locale) - Static method in class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory

Returns the SBMLErrorPreMessage bundle associated with the given Locale.

getSBMLErrorShortMessageBundle() - Static method in class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory

Returns the SBMLErrorShortMessage bundle associated with the current Locale.

getSBMLNSAttribute() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getSBMLUnitsAttribute() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

getSBORoot() - Static method in class org.sbml.jsbml.SBO

Returns the root element of the SBO Ontology (SBO:0000000).

getSBOTerm() - Method in class org.sbml.jsbml.AbstractSBase

getSBOTerm() - Method in interface org.sbml.jsbml.SBase

Grants access to the Systems Biology Ontology (SBO) term associated with this SBase.

getSBOTermID() - Method in class org.sbml.jsbml.AbstractSBase

getSBOTermID() - Method in interface org.sbml.jsbml.SBase

Grants access to the Systems Biology Ontology (SBO) term associated with this SBase.

getScale() - Method in class org.sbml.jsbml.Unit

getScaleX() - Method in class org.sbml.jsbml.ext.spatial.CSGScale

Returns the value of scaleX

getScaleY() - Method in class org.sbml.jsbml.ext.spatial.CSGScale

Returns the value of scaleY

getScaleZ() - Method in class org.sbml.jsbml.ext.spatial.CSGScale

Returns the value of scaleZ

getSemanticsAnnotation(int) - Method in class org.sbml.jsbml.ASTNode

Gets the nth <semantics> annotation of this node.

getSeverity() - Method in exception org.sbml.jsbml.SBMLError

Returns the severity of the SBMLError

getSeverity() - Method in class org.sbml.jsbml.util.Detail

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter

Returns the shortLabel of the namespace parsed by this class.

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.CompParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.DistribParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.DynParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.FBCParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.GroupsParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.QualParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.ReqParser

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.SpatialParser

getShortMessage() - Method in exception org.sbml.jsbml.SBMLError

getShortMessage() - Method in exception org.sbml.jsbml.SBMLException

getSideProduct() - Static method in class org.sbml.jsbml.SBO

Returns the side product SBO term

getSideSubstrate() - Static method in class org.sbml.jsbml.SBO

Returns the side substrate SBO term

getSign() - Method in class org.sbml.jsbml.ext.qual.Input

getSimpleMolecule() - Static method in class org.sbml.jsbml.SBO

getSize() - Method in class org.sbml.jsbml.Compartment

Returns the size of this compartment.

getSize() - Method in class org.sbml.jsbml.ext.arrays.Dimension

Returns the value of size

getSize(Model, Dimension) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Gets the size of a Dimension object.

getSmallMolecule() - Static method in class org.sbml.jsbml.SBO

Simple, non-repetitive chemical entity.

getSource() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Returns the value of source or an empty String if it is not set.

getSource() - Method in class org.sbml.jsbml.ext.qual.QualConstants

getSource() - Method in exception org.sbml.jsbml.SBMLError

Returns the source for this SBMLError.

getSource() - Method in class org.sbml.jsbml.util.TreeNodeChangeEvent

getSource() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent

getSourceLV() - Method in class org.sbml.jsbml.util.converters.LevelVersionConverter

getSpatial() - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

getSpatialDimensions() - Method in class org.sbml.jsbml.Compartment

Returns the Compartment.spatialDimensions of this Compartment.

getSpatialDimensions() - Method in class org.sbml.jsbml.ext.spatial.DomainType

Returns the value of spatialDimension

getSpatialDimensionsAsDouble() - Method in class org.sbml.jsbml.Compartment

Deprecated.

use Compartment.getSpatialDimensions()

getSpatialId() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

getSpatialId() - Method in interface org.sbml.jsbml.ext.spatial.SpatialNamedSBase

Deprecated.

use SBase.getId()

getSpatialIndex() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

Returns the value of spatialIndex

getSpatialPoints() - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry

Returns the value of ParametricGeometry.spatialPoints.

getSpatialRef() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

Returns the spatial reference (id of any element defined in the Geometry of the model).

getSpatialSizeUnits() - Method in class org.sbml.jsbml.Species

Deprecated.

Only valid for SBML Level 2 Versions 1 and 2.

getSpatialSizeUnitsInstance() - Method in class org.sbml.jsbml.Species

Deprecated.

Only valid for SBML Level 2 Versions 1 and 2.

getSpecies() - Method in class org.sbml.jsbml.ext.layout.SpeciesGlyph

getSpecies() - Method in class org.sbml.jsbml.SimpleSpeciesReference

getSpecies(int) - Method in class org.sbml.jsbml.Model

Gets the n-th Species object in this Model.

getSpecies(String) - Method in class org.sbml.jsbml.Model

Gets the Species of the Model.listOfSpecies which has 'id' as id.

getSpeciesCount() - Method in class org.sbml.jsbml.Model

Returns the number of Species of this Model.

getSpeciesFeature(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Gets an element from the MultiSpeciesPlugin.listOfSpeciesFeatures at the given index.

getSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Gets an element from the listOfSpeciesFeatures, with the given id.

getSpeciesFeatureCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the number of SpeciesFeatures in this MultiSpeciesPlugin.

getSpeciesFeatureType() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the value of SpeciesFeature.speciesFeatureType.

getSpeciesFeatureType(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Gets an element from the MultiSpeciesType.listOfSpeciesFeatureTypes at the given index.

getSpeciesFeatureType(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Gets an element from the listOfSpeciesFeatureTypes, with the given id.

getSpeciesFeatureTypeCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the number of SpeciesFeatureTypes in this MultiSpeciesType.

getSpeciesFeatureValue(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Gets an element from the SpeciesFeature.listOfSpeciesFeatureValues at the given index.

getSpeciesFeatureValueCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the number of SpeciesFeatureValues in this SpeciesFeature.

getSpeciesGlyph() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

getSpeciesGlyph(int) - Method in class org.sbml.jsbml.ext.layout.Layout

getSpeciesGlyph(String) - Method in class org.sbml.jsbml.ext.layout.Layout

getSpeciesGlyphCount() - Method in class org.sbml.jsbml.ext.layout.Layout

Returns the number of SpeciesGlyphs of this Layout.

getSpeciesGlyphInstance() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

getSpeciesInstance() - Method in class org.sbml.jsbml.ext.layout.SpeciesGlyph

Note that the return type of this method is NamedSBase because it could be possible to link some element from other packages to this glyph.

getSpeciesInstance() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

Returns the Species instance associated with ParameterType.variable.

getSpeciesInstance() - Method in class org.sbml.jsbml.SimpleSpeciesReference

getSpeciesReference() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

getSpeciesReference() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

Returns the value of MultiASTNodePlugin.speciesReference.

getSpeciesReference() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

Returns the value of ParameterType.variable.

getSpeciesReferenceCount() - Method in class org.sbml.jsbml.Model

Returns the number of SpeciesReferences of this Model.

getSpeciesReferenceGlyph(int) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

getSpeciesReferenceGlyph(String) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

getSpeciesReferenceGlyphCount() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph

getSpeciesReferenceInstance() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

Note that the return type of this method is NamedSBase because it could be possible to link some element from other packages to this glyph.

getSpeciesReferenceRole() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph

getSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the value of MultiSpeciesPlugin.speciesType.

getSpeciesType() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Returns the value of SpeciesTypeInstance.speciesType.

getSpeciesType() - Method in class org.sbml.jsbml.Species

Deprecated.

Only valid for SBML Level 2 Versions 2, 3, and 4.

getSpeciesType(int) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Gets the ith MultiSpeciesType.

getSpeciesType(int) - Method in class org.sbml.jsbml.Model

Deprecated.

Only valid in SBML Level 2 for Versions 2 through 4.

getSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Gets the MultiSpeciesType that has the given id.

getSpeciesType(String) - Method in class org.sbml.jsbml.Model

Deprecated.

Only valid in SBML Level 2 for Versions 2 through 4.

getSpeciesTypeComponentIndex(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Gets an element from the MultiSpeciesType.listOfSpeciesTypeComponentIndexes at the given index.

getSpeciesTypeComponentIndex(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Gets an element from the listOfSpeciesTypeComponentIndexes, with the given id.

getSpeciesTypeComponentIndexCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the number of SpeciesTypeComponentIndexs in this MultiSpeciesType.

getSpeciesTypeComponentMapInProduct(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Gets an element from the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts at the given index.

getSpeciesTypeComponentMapInProductCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Returns the number of SpeciesTypeComponentMapInProducts in this MultiSpeciesReferencePlugin.

getSpeciesTypeCount() - Method in class org.sbml.jsbml.Model

Deprecated.

the use of SpeciesType is not recommended, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.

getSpeciesTypeInstance() - Method in class org.sbml.jsbml.Species

Deprecated.

Only valid for SBML Level 2 Versions 2, 3, and 4.

getSpeciesTypeInstance(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Gets an element from the MultiSpeciesType.listOfSpeciesTypeInstances at the given index.

getSpeciesTypeInstance(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Gets an element from the listOfSpeciesTypeInstances, with the given id.

getSpeciesTypeInstanceCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

Returns the number of SpeciesTypeInstances in this MultiSpeciesType.

getSpeciesWithBoundaryConditionCount() - Method in class org.sbml.jsbml.Model

Returns the number of Species whose boundary condition is set to true.

getSpecificActivator() - Static method in class org.sbml.jsbml.SBO

getSpId() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

Returns the spatial reference (id of any element defined in the Geometry of the model).

getSpreadMethod() - Method in class org.sbml.jsbml.ext.render.GradientBase

getStart() - Method in class org.sbml.jsbml.ext.layout.CurveSegment

Returns the Start Point of this CurveSegment.

getStart() - Method in class org.sbml.jsbml.ext.layout.LineSegment

getStartHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns the value of startHead

getStartHead() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getStateTransition() - Static method in class org.sbml.jsbml.SBO

getStatus() - Method in class org.sbml.jsbml.util.Option

getSteadyStateExpression() - Static method in class org.sbml.jsbml.SBO

getStimulation() - Static method in class org.sbml.jsbml.SBO

Positive modulation of the execution of a process.

getStimulator() - Static method in class org.sbml.jsbml.SBO

getStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference

getStoichiometryMath() - Method in class org.sbml.jsbml.SpeciesReference

Deprecated.

since SBML Level 3 this should not be used anymore.

getStoichiometryMathCount() - Method in class org.sbml.jsbml.Model

Deprecated.

since SBML L3V1

getStopColor() - Method in class org.sbml.jsbml.ext.render.GradientStop

getStreamFromResourceLocation(String) - Method in class org.sbml.jsbml.resources.Resource

Gets the byte data from a file at the given resource location.

getStrict() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin

Returns the value of FBCModelPlugin.strict.

getStroke() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

getStrokeDash(int) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

getStrokeDashArray() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

getStrokeWidth() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

getStyle() - Method in class org.sbml.jsbml.ASTNode

Returns the style of the mathML element represented by this ASTNode.

getStyle() - Method in class org.sbml.jsbml.math.AbstractASTNode

getStyle() - Method in interface org.sbml.jsbml.math.ASTNode2

Return the style of this node

getStyle() - Method in class org.sbml.jsbml.math.ASTUnknown

getSubject() - Method in class org.sbml.jsbml.ontology.Triple

Returns the subject of this Triple.

getSubListOfSpeciesFeature(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Gets an element from the MultiSpeciesPlugin.listOfSubListOfSpeciesFeatures at the given index.

getSubListOfSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Gets an element from the listOfSubListOfSpeciesFeatures, with the given id.

getSubListOfSpeciesFeatureCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the number of SubListOfSpeciesFeatures in this MultiSpeciesPlugin.

getSubmodel(int) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the n-th Submodel object in this CompModelPlugin.

getSubmodel(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns a Submodel element that has the given 'id' within this CompModelPlugin or null if no such element can be found.

getSubmodelCount() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the number of Submodel objects in this CompModelPlugin.

getSubmodelRef() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

Returns the value of submodelRef

getSubmodelRef() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Returns the value of submodelRef

getSubstanceUnits() - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

getSubstanceUnits() - Method in class org.sbml.jsbml.Model

Returns the substance units ID of this model.

getSubstanceUnits() - Method in class org.sbml.jsbml.Species

Returns the substanceUnits of this Species.

getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Model

Returns the UnitDefinition which has the Model.substanceUnitsID of this Model as id.

getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Species

Returns the substanceUnits of this Species as a UnitDefinition instance.

GetSuffix(int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream

Get the suffix.

GetSuffix(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream

Get the suffix.

getSymbol() - Method in class org.sbml.jsbml.InitialAssignment

Deprecated.

use InitialAssignment.getVariable()

getSymbol() - Method in enum org.sbml.jsbml.Unit.Kind

getSymbolCount() - Method in class org.sbml.jsbml.Model

Returns the number of all instances of Symbol referenced within the model.

getSynonyms() - Method in class org.sbml.jsbml.ontology.Term

Returns all Synonyms of this Term.

getTargetLV() - Method in class org.sbml.jsbml.util.converters.LevelVersionConverter

getTemplateReaction() - Static method in class org.sbml.jsbml.SBO

A composite biochemical process through which a gene sequence is fully converted into mature gene products.

getTemplateReactionRegulation() - Static method in class org.sbml.jsbml.SBO

A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone.

getTerm() - Method in class org.sbml.jsbml.ontology.Term

Grants access to the underlying BioJava org.biojava3.ontology.Term.

getTerm(int) - Static method in class org.sbml.jsbml.SBO

Gets the SBO term with the id 'sboTerm'.

getTerm(String) - Static method in class org.sbml.jsbml.ext.dyn.CBO

Gets the CBO term with the id 'cboTerm'.

getTerm(String) - Static method in class org.sbml.jsbml.SBO

Gets the SBO term with the id 'sboTerm'.

getTerms() - Static method in class org.sbml.jsbml.ext.dyn.CBO

Return the set of terms of the CBO.

getTerms() - Static method in class org.sbml.jsbml.SBO

Return the set of terms of the SBO Ontology.

getTerms() - Method in class org.sbml.jsbml.util.filters.SBOFilter

getText() - Method in class org.sbml.jsbml.ext.layout.TextGlyph

getText() - Method in class org.sbml.jsbml.ext.render.Text

getTextAnchor() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

getTextAnchor() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getTextAnchor() - Method in class org.sbml.jsbml.ext.render.Text

getTextGlyph(int) - Method in class org.sbml.jsbml.ext.layout.Layout

getTextGlyph(String) - Method in class org.sbml.jsbml.ext.layout.Layout

getTextGlyphCount() - Method in class org.sbml.jsbml.ext.layout.Layout

Returns the number of TextGlyphs of this Layout.

getThermodynamicTemperature() - Static method in class org.sbml.jsbml.SBO

Temperature is the physical property of a system which underlies the common notions of "hot" and "cold"; the material with the higher temperature is said to be hotter.

getThresholdLevel() - Method in class org.sbml.jsbml.ext.qual.Input

getTimeConversionFactor() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns the value of timeConversionFactor

getTimeUnits() - Method in class org.sbml.jsbml.Event

Deprecated.

getTimeUnits() - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

getTimeUnits() - Method in class org.sbml.jsbml.Model

Returns the time units ID of this Model.

getTimeUnitsID() - Method in class org.sbml.jsbml.Event

Deprecated.

getTimeUnitsInstance() - Method in class org.sbml.jsbml.Event

Deprecated.

getTimeUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

getTimeUnitsInstance() - Method in class org.sbml.jsbml.Model

Gets the UnitDefinition representing the time units of this Model.

getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParser

Get the specific Token.

getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2

Get the specific Token.

getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3

Get the specific Token.

getToken(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2

Get the specific Token.

getToken(int) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser

Get the specific Token.

getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParser

Get the specific Token.

getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2

Get the specific Token.

getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3

Get the specific Token.

getToken(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2

Get the specific Token.

getTranscription() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'TRANSCRIPTION'

getTranscriptionalActivation() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'TRANSCRIPTIONAL_ACTIVATION'

getTranscriptionalInhibitor() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'TRANSCRIPTIONAL_INHIBITION'

getTransform() - Method in class org.sbml.jsbml.ext.render.Transformation

getTransform() - Method in class org.sbml.jsbml.ext.render.Transformation2D

getTransition(int) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Gets the ith Transition.

getTransition(String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Gets the Transition that has the given id.

getTransitionCount() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns the number of Transition objects in this QualModelPlugin.

getTransitionEffect() - Method in class org.sbml.jsbml.ext.qual.Input

getTransitionEffect() - Method in class org.sbml.jsbml.ext.qual.Output

Returns the transitionEffect

getTransitionOmitted() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'KNOWN_TRANSITION_OMITTED'

getTranslateX() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

Returns the value of translateX

getTranslateY() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

Returns the value of translateY

getTranslateZ() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

Returns the value of translateZ

getTranslation() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'TRANSLATION'

getTranslationalActivation() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'TRANSLATIONAL_ACTIVATION'

getTranslationalInhibitor() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'TRANSLATIONAL_INHIBITION'

getTransport() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'TRANSPORT'

getTransportWithBiochemicalReaction() - Static method in class org.sbml.jsbml.SBO

An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants.

getTreeNodeChangeListenerCount() - Method in class org.sbml.jsbml.AbstractTreeNode

getTreeNodeChangeListenerCount() - Method in class org.sbml.jsbml.math.ASTUnknown

getTreeNodeChangeListenerCount() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

getTrigger() - Method in class org.sbml.jsbml.Event

getTrigger() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'TRIGGER'

getTriggerCount() - Method in class org.sbml.jsbml.Model

Returns the number of Trigger of this Model.

getTriple() - Method in class org.sbml.jsbml.ontology.Triple

Grants access to the original BioJava Triple.

getTriples(Term, Term, Term) - Static method in class org.sbml.jsbml.ext.dyn.CBO

Returns a set of Triple which match the supplied subject, predicate and object.

getTriples(Term, Term, Term) - Static method in class org.sbml.jsbml.SBO

Returns a set of Triple which match the supplied subject, predicate and object.

getTruncated() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'TRUNCATED'

getType() - Method in class org.sbml.jsbml.ASTNode

Returns the type of this node.

getType() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the value of UncertParameter.type.

getType() - Method in class org.sbml.jsbml.ext.fbc.Objective

Returns the type.

getType() - Method in class org.sbml.jsbml.ext.layout.CurveSegment

getType() - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment

Returns the type.

getType() - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition

Returns the value of type

getType() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

Returns the value of type

getType() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient

Returns the value of diffusionKind

getType() - Method in class org.sbml.jsbml.math.AbstractASTNode

getType() - Method in interface org.sbml.jsbml.math.ASTNode2

Returns the type of this ASTNode2.

getType() - Method in class org.sbml.jsbml.math.ASTUnknown

getType() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

getType() - Method in exception org.sbml.jsbml.SBMLException

getType() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

getTypeFor(String) - Static method in enum org.sbml.jsbml.ASTNode.Type

Returns the ASTNode.Type corresponding to the given String.

getTypeList() - Method in class org.sbml.jsbml.ext.render.Style

getTypeOfNotes() - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader

getUncertainty(int) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Gets an element from the DistribSBasePlugin.listOfUncertainties at the given index.

getUncertainty(String) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Gets an element from the listOfUncertainties, with the given id.

getUncertaintyCount() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Returns the number of Uncertaintys in this DistribSBasePlugin.

getUncertParameter(int) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Gets an element from the Uncertainty.listOfUncertParameters at the given index.

getUncertParameter(int) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Gets an element from the UncertParameter.listOfUncertParameters at the given index.

getUncertParameter(String) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Gets an element from the listOfUncertParameters, with the given id.

getUncertParameter(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Gets an element from the listOfUncertParameters, with the given id.

getUncertParameterCount() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Returns the number of UncertParameters in this Uncertainty.

getUncertParameterCount() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the number of UncertParameters in this UncertParameter.

getUncompetitiveInhibitor() - Static method in class org.sbml.jsbml.SBO

An inhibitor which binds only to the complex formed between the enzyme and substrate (E-S complex).

getUnit(int) - Method in class org.sbml.jsbml.UnitDefinition

Returns a specific Unit instance belonging to this UnitDefinition.

getUnitCount() - Method in class org.sbml.jsbml.Model

Returns the number of Units of this Model.

getUnitCount() - Method in class org.sbml.jsbml.UnitDefinition

getUnitDefinition(int) - Method in class org.sbml.jsbml.Model

Gets the n^th UnitDefinition object in this Model .

getUnitDefinition(String) - Method in class org.sbml.jsbml.Model

Returns the UnitDefinition of the Model.listOfUnitDefinitions which has 'id' as id.

getUnitDefinitionById(String) - Method in class org.sbml.jsbml.Model

Returns a UnitDefinition element that has the given 'id' within this Model or null if no such element can be found.

getUnitDefinitionCount() - Method in class org.sbml.jsbml.Model

Returns the number of UnitDefinitions of this Model.

getUnitKindsDefinedIn(int, int) - Static method in enum org.sbml.jsbml.Unit.Kind

Returns a set of Unit.Kind objects for the given level/version combination of SBML.

getUnitOntologyIdentifier() - Method in enum org.sbml.jsbml.Unit.Kind

Creates a unit ontology identifier for this Unit.Kind if possible and returns it.

getUnitOntologyNumber() - Method in enum org.sbml.jsbml.Unit.Kind

Looks for the corresponding unit ontology resource for this Unit.Kind.

getUnitOntologyResource() - Method in enum org.sbml.jsbml.Unit.Kind

Creates a MIRIAM resource pointing to the entry in the unit ontology corresponding to this Unit.Kind.

getUnitRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns the value of unitRef

getUnits() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit

getUnits() - Method in class org.sbml.jsbml.ASTNode

Returns the units attribute.

getUnits() - Method in class org.sbml.jsbml.Compartment

getUnits() - Method in class org.sbml.jsbml.Event

Deprecated.

getUnits() - Method in class org.sbml.jsbml.ExplicitRule

Deprecated.

This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.

getUnits() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the value of UncertParameter.units.

getUnits() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

Returns the value of unit

getUnits() - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

getUnits() - Method in class org.sbml.jsbml.math.ASTCnNumberNode

Returns the units of the MathML element represented by this ASTCnNumberNode

getUnits() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

getUnits() - Method in interface org.sbml.jsbml.SBaseWithUnit

getUnits() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

getUnitsInstance() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit

getUnitsInstance() - Method in class org.sbml.jsbml.ASTNode

Creates or obtains a UnitDefinition corresponding to the unit that has been set for this ASTNode and returns a pointer to it.

getUnitsInstance() - Method in class org.sbml.jsbml.Compartment

getUnitsInstance() - Method in class org.sbml.jsbml.Event

Deprecated.

getUnitsInstance() - Method in class org.sbml.jsbml.ExplicitRule

Deprecated.

This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.

getUnitsInstance() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

getUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw

Deprecated.

getUnitsInstance() - Method in class org.sbml.jsbml.math.ASTCnNumberNode

Creates or obtains a UnitDefinition corresponding to the unit that has been set for this ASTCnNumberNode and returns a pointer to it.

getUnitsInstance() - Method in interface org.sbml.jsbml.SBaseWithUnit

getUnitSize() - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping

Returns the value of unitSize

getUnknownMolecule() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'UNKNOWN'

getUnknownQualifierName() - Method in class org.sbml.jsbml.CVTerm

Gets a name corresponding to the Qualifier of this CVTerm.

getUnknownTransition() - Static method in class org.sbml.jsbml.SBO

Returns the SBO id corresponding to the alias 'UNKNOWN_TRANSITION'

getUpperBound(Map<String, Double>) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Returns the upper bound index from a collection of Dimension objects.

getUpperFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

Returns the value of FBCReactionPlugin.upperFluxBound.

getUpperFluxBoundInstance() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

getURI() - Method in class org.sbml.jsbml.AbstractSBase

getURI() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getURI() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

Gets the URI to which this element belongs to.

getURI() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getURI() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

getURI() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getURI() - Method in class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

getURI() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getURI() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

getURI() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getURI() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getURI() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getURI() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getURI() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getURI() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getURI() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getURI() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin

getURI() - Method in interface org.sbml.jsbml.ext.SBasePlugin

Gets the URI to which this element belongs to.

getURI() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

getURI() - Method in interface org.sbml.jsbml.SBase

Returns the namespace to which this SBase belong to.

getURI() - Method in class org.sbml.jsbml.xml.XMLNamespaces

Gets the URI of an XML namespace declaration by the empty prefix.

getURI() - Method in class org.sbml.jsbml.xml.XMLToken

Returns the namespace URI of this XML element.

getURI() - Method in class org.sbml.jsbml.xml.XMLTriple

Returns the URI portion of this XMLTriple.

getURI(int) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns the namespace URI of an attribute in this XMLAttributes set (by position).

getURI(int) - Method in class org.sbml.jsbml.xml.XMLNamespaces

Gets the URI of an XML namespace declaration by its position.

getURI(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces

Gets the URI of an XML namespace declaration by its prefix.

getUserObject() - Method in class org.sbml.jsbml.util.TreeNodeAdapter

getUserObject(Object) - Method in class org.sbml.jsbml.AbstractTreeNode

getUserObject(Object) - Method in class org.sbml.jsbml.math.ASTUnknown

getUserObject(Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

getUserTidy() - Method in class org.sbml.jsbml.TidySBMLWriter

Returns the instance of Tidy that is used to pretty print the SBML.

getUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event

getV() - Method in class org.sbml.jsbml.util.ValuePair

getValidateRecursively() - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Returns true if the validation also validate every child of a TreeNode.

getValidationErrors() - Method in class org.sbml.jsbml.SBMLErrorLog

Returns the list of SBMLError

getValidationFunction() - Method in class org.sbml.jsbml.validator.offline.constraints.ValidationConstraint

Returns the ValidationFunction registered in this ValidationConstraint.

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AdjacentDomainsConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AdvectionCoefficientConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AlgebraicRuleConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AnalyticGeometryConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AnalyticVolumeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AndConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ArraysSBasePluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AssignmentConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AssignmentRuleConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BindingSiteSpeciesTypeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundaryConditionConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundaryConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundingBoxConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ColorDefinitionConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentGlyphConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentMappingConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentReferenceConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentTypeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompModelPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompSBasePluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompSBMLDocumentPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintConstraints

getValidationFunction(int, ValidationContext) - Method in interface org.sbml.jsbml.validator.offline.constraints.ConstraintDeclaration

Returns the ValidationFunction of the error code, if it's defined in this ConstraintDeclaration.

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CoordinateComponentConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGeometryConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGHomogeneousTransformationConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGObjectConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGPrimitiveConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGRotationConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGScaleConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGSetOperatorConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGTranslationConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CubicBezierConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CurveConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DefaultValuesConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DelayConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DeletionConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DiffusionCoefficientConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DimensionConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DimensionsConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DomainConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DomainTypeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EllipseConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EventAssignmentConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EventConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ExplicitRuleConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ExternalModelDefinitionConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FBCReactionPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionDefinitionConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionTermConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneralGlyphConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeometryConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeometryDefinitionConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GlobalRenderInformationConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GradientBaseConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GradientStopConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalObjectConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive1DConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive2DConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ImageConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.IndexConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InitialAssignmentConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InputConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InSpeciesTypeBondConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InteriorPointConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.KineticLawConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LayoutConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LayoutModelPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LinearGradientConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LineEndingConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LineSegmentConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalParameterConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalRenderInformationConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalStyleConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MathContainerConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MixedGeometryConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ModelConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiCompartmentPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiModelPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiSpeciesTypeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ObjectiveConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrdinalMappingConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OutputConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParameterConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParametricGeometryConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParametricObjectConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PointConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PolygonConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PortConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PossibleSpeciesFeatureValueConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PriorityConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualitativeSpeciesConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualModelPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RadialGradientConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RateRuleConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionGlyphConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RectangleConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReferenceGlyphConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderCubicBezierConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderCurveConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderGraphicalObjectPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderGroupConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderInformationBaseConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderLayoutPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderListOfLayoutsPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderPointConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReplacedByConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReplacedElementConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RuleConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledFieldConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledFieldGeometryConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledVolumeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseRefConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithDerivedUnitConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithUnitConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBMLDocumentConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SimpleSpeciesReferenceConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialCompartmentPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialModelPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialParameterPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialPointsConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialReactionPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialSpeciesPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialSymbolReferenceConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesFeatureTypeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesGlyphConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceGlyphConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeComponentIndexConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeInstanceConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.StyleConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SubmodelConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TextConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TextGlyphConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.Transformation2DConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransformationComponentConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransformationConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransitionConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TreeNodeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TriggerConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitDefinitionConstraints

getValue() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the value of UncertParameter.value.

getValue() - Method in class org.sbml.jsbml.ext.fbc.FluxBound

Deprecated.

Only defined in FBC version 1.

getValue() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

Returns the value of SpeciesFeatureValue.value.

getValue() - Method in class org.sbml.jsbml.ext.render.ColorDefinition

getValue() - Method in class org.sbml.jsbml.ext.spatial.Boundary

Returns the value of value

getValue() - Method in class org.sbml.jsbml.math.ASTBoolean

Get the value of this ASTBoolean

getValue() - Method in class org.sbml.jsbml.math.ASTConstantNumber

Get the value of this ASTConstantNumber

getValue() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode

getValue() - Method in class org.sbml.jsbml.math.ASTLogarithmNode

Return the value of this ASTLogarithmNode

getValue() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

getValue() - Method in class org.sbml.jsbml.math.parser.Token

An optional attribute value of the Token.

getValue() - Method in interface org.sbml.jsbml.Quantity

Returns the value of this Quantity.

getValue() - Method in class org.sbml.jsbml.QuantityWithUnit

getValue() - Method in class org.sbml.jsbml.SpeciesReference

getValue() - Method in class org.sbml.jsbml.text.parser.Token

An optional attribute value of the Token.

getValue() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

getValue() - Method in class org.sbml.jsbml.util.Pair

getValue(int) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns the value of an attribute in this XMLAttributes set (by position).

getValue(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Gets an element from the idToValue, with the given id.

getValue(String) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns an attribute's value by name.

getValue(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns a value of an attribute with the given local name and namespace URI.

getValue(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLAttributes

Returns a value of an attribute with the given XMLTriple.

getValueLower() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns the value of UncertSpan.valueLower.

getValueUpper() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns the value of UncertSpan.valueUpper.

getVar() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the value of UncertParameter.var.

getVariable() - Method in interface org.sbml.jsbml.Assignment

Returns the variableID of this Assignment.

getVariable() - Method in class org.sbml.jsbml.ASTNode

Returns the variable of this node.

getVariable() - Method in class org.sbml.jsbml.EventAssignment

getVariable() - Method in class org.sbml.jsbml.ExplicitRule

getVariable() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

Returns the value of variable

getVariable() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

Returns the value of ParameterType.variable.

getVariable() - Method in class org.sbml.jsbml.InitialAssignment

getVariable() - Method in class org.sbml.jsbml.math.ASTCnNumberNode

Get the variable for this ASTNumber node

getVariableCount() - Method in class org.sbml.jsbml.Model

Returns the number of Variables of this Model.

getVariableInstance() - Method in interface org.sbml.jsbml.Assignment

Returns the Variable instance which has the variableID of this Assignment as id.

getVariableInstance() - Method in class org.sbml.jsbml.EventAssignment

getVariableInstance() - Method in class org.sbml.jsbml.ExplicitRule

getVariableInstance() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

Returns the Species or Parameter instance associated with ParameterType.variable.

getVariableInstance() - Method in class org.sbml.jsbml.InitialAssignment

getVarLower() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns the value of UncertSpan.varLower.

getVarUpper() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns the value of UncertSpan.varUpper.

getVectorDimensionSizes(Model, ASTNode) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Returns a map containing a pair of array depth level and its size.

getVersion() - Method in class org.sbml.jsbml.AbstractSBase

getVersion() - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin

getVersion() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin

getVersion() - Method in interface org.sbml.jsbml.ext.ASTNodePlugin

Returns the SBML version of this plugin object.

getVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin

Returns the SBML version of this plugin object.

getVersion() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

getVersion() - Method in interface org.sbml.jsbml.SBase

Returns the Version within the SBML Level of the overall SBML document.

getVersion() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3

Returns the SBML Version.

getVersion() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

getVersion() - Method in class org.sbml.jsbml.validator.offline.ValidationContext

Returns the used version of SBML

getVersionMajor() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Returns the value of versionMajor

getVersionMinor() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Returns the value of versionMinor

getViableWithoutChange() - Method in class org.sbml.jsbml.ext.req.ChangedMath

Returns the value of viableWithoutChange

getVolume() - Method in class org.sbml.jsbml.Compartment

Deprecated.

The volume attribute is only defined in SBML Level 1. Please use Compartment.getSize().

getVolumeUnits() - Method in class org.sbml.jsbml.Model

Returns the volume units ID of this Model.

getVolumeUnitsInstance() - Method in class org.sbml.jsbml.Model

Returns the UnitDefinition instance which has the Model.volumeUnitsID of this Model as id.

getVTextAnchor() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

getVTextAnchor() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getVTextAnchor() - Method in class org.sbml.jsbml.ext.render.Text

getWarnings() - Method in interface org.sbml.jsbml.SBMLInputConverter

Creates an SBML error report and returns the list of errors.

getWidth() - Method in class org.sbml.jsbml.ext.layout.Dimensions

getWidth() - Method in class org.sbml.jsbml.ext.render.Image

getWidth() - Method in class org.sbml.jsbml.ext.render.Rectangle

getWordForNumber(long) - Static method in class org.sbml.jsbml.util.StringTools

Returns the number as an English word.

getWriteWarnings(T) - Method in interface org.sbml.jsbml.SBMLOutputConverter

getWritingParsers() - Method in class org.sbml.jsbml.xml.parsers.ParserManager

Gets a copy of the registered WritingParsers map.

getX() - Method in class org.sbml.jsbml.ext.layout.Point

Gets the x coordinate.

getX() - Method in class org.sbml.jsbml.ext.render.Image

getX() - Method in interface org.sbml.jsbml.ext.render.Point3D

getX() - Method in class org.sbml.jsbml.ext.render.Rectangle

getX() - Method in class org.sbml.jsbml.ext.render.RenderPoint

getX() - Method in class org.sbml.jsbml.ext.render.Text

getX1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getX1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

getX2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getX2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

getXMLnamespaceSBML() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

The additional MathML name space for units to numbers.

getXMLNode() - Method in class org.sbml.jsbml.Annotation

getXmlString() - Method in enum org.sbml.jsbml.ext.layout.CurveSegment.Type

Returns the xmlString

getXmlString() - Method in enum org.sbml.jsbml.ext.render.RenderCurveSegment.Type

Returns the String that will be written to XML.

getY() - Method in class org.sbml.jsbml.ext.layout.Point

Gets the y coordinate.

getY() - Method in class org.sbml.jsbml.ext.render.Image

getY() - Method in interface org.sbml.jsbml.ext.render.Point3D

getY() - Method in class org.sbml.jsbml.ext.render.Rectangle

getY() - Method in class org.sbml.jsbml.ext.render.RenderPoint

getY() - Method in class org.sbml.jsbml.ext.render.Text

getY1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getY1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

getY2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getY2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

getZ() - Method in class org.sbml.jsbml.ext.layout.Point

Gets the z coordinate.

getZ() - Method in class org.sbml.jsbml.ext.render.Image

getZ() - Method in interface org.sbml.jsbml.ext.render.Point3D

getZ() - Method in class org.sbml.jsbml.ext.render.Rectangle

getZ() - Method in class org.sbml.jsbml.ext.render.RenderPoint

getZ() - Method in class org.sbml.jsbml.ext.render.Text

getZ1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getZ1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

getZ2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

givenName - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

globalRenderInformation - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

GlobalRenderInformation - Class in org.sbml.jsbml.ext.render

GlobalRenderInformation() - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Creates an GlobalRenderInformation instance

GlobalRenderInformation(int, int) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Creates a GlobalRenderInformation instance with a level and version.

GlobalRenderInformation(String) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Creates a GlobalRenderInformation instance with an id.

GlobalRenderInformation(String, int, int) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Creates a GlobalRenderInformation instance with an id, level, and version.

GlobalRenderInformation(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Creates a GlobalRenderInformation instance with an id, name, level, and version.

GlobalRenderInformation(GlobalRenderInformation) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Clone constructor

GlobalRenderInformationConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the GlobalRenderInformation class.

GlobalRenderInformationConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GlobalRenderInformationConstraints

glyph - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

GlyphCreator - Class in org.sbml.jsbml.ext.render.director

This class creates a SBML layout for a model without layout information.

GlyphCreator(Model) - Constructor for class org.sbml.jsbml.ext.render.director.GlyphCreator

glyphHasDimensions(GraphicalObject) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if a glyph has dimensions.

glyphHasPosition(GraphicalObject) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if a glyph has a position.

glyphIsLayouted(GraphicalObject) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if a glyph as complete layout information (i.e. if it as both dimensions and position).

GPRParser - Class in org.sbml.jsbml.ext.fbc.converters

Provides a method to converts gene association string as used in COBRA in SBML level 2 into GeneProductAssociation used in SBML level 3.

GPRParser() - Constructor for class org.sbml.jsbml.ext.fbc.converters.GPRParser

gradientBase - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

GradientBase - Class in org.sbml.jsbml.ext.render

GradientBase() - Constructor for class org.sbml.jsbml.ext.render.GradientBase

Creates an GradientBase instance

GradientBase(String, GradientStop) - Constructor for class org.sbml.jsbml.ext.render.GradientBase

Creates a GradientBase instance with an id.

GradientBase(String, GradientStop, int, int) - Constructor for class org.sbml.jsbml.ext.render.GradientBase

Creates a GradientBase instance with an id, name, level, and version.

GradientBase(GradientBase) - Constructor for class org.sbml.jsbml.ext.render.GradientBase

Clone constructor

GradientBase.Spread - Enum in org.sbml.jsbml.ext.render

The type GradientSpreadMethod is being used by GradientBase elements to decide how gradients propagate over the whole element they are applied to.

GradientBaseConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the GradientBase class.

GradientBaseConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GradientBaseConstraints

gradientStop - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

GradientStop - Class in org.sbml.jsbml.ext.render

GradientStop() - Constructor for class org.sbml.jsbml.ext.render.GradientStop

GradientStop(double, String) - Constructor for class org.sbml.jsbml.ext.render.GradientStop

Convenience-constructor: As by the specification, the offset ought to be purely relative-valued (i.e.e.g. 25d for 25%), the absolute part of the RelAbsVector is to be ignored anyways.

GradientStop(GradientStop) - Constructor for class org.sbml.jsbml.ext.render.GradientStop

Clone constructor

GradientStop(RelAbsVector, String) - Constructor for class org.sbml.jsbml.ext.render.GradientStop

Creates a GradientStop instance with an offset and a color.

GradientStop(RelAbsVector, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.GradientStop

Creates a GradientStop instance with an offset, color, level, and version.

GradientStopConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the GradientStop class.

GradientStopConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GradientStopConstraints

GRAM - org.sbml.jsbml.Unit.Kind

The gram unit.

graphicalObject - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

GraphicalObject - Class in org.sbml.jsbml.ext.layout

All the more specific layout elements (CompartmentGlyph, GeneralGlyph, SpeciesGlyph, ReactionGlyph, ReferenceGlyph, TextGlyph, and SpeciesReferenceGlyph) are derived from the class GraphicalObject.

GraphicalObject() - Constructor for class org.sbml.jsbml.ext.layout.GraphicalObject

GraphicalObject(int, int) - Constructor for class org.sbml.jsbml.ext.layout.GraphicalObject

GraphicalObject(String) - Constructor for class org.sbml.jsbml.ext.layout.GraphicalObject

GraphicalObject(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.GraphicalObject

GraphicalObject(GraphicalObject) - Constructor for class org.sbml.jsbml.ext.layout.GraphicalObject

GRAPHICALOBJECT - org.sbml.jsbml.ext.render.Style.Type

GraphicalObjectConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the GraphicalObject class.

GraphicalObjectConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GraphicalObjectConstraints

GraphicalPrimitive1D - Class in org.sbml.jsbml.ext.render

GraphicalPrimitive1D() - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Creates an GraphicalPrimitive1D instance

GraphicalPrimitive1D(int, int) - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Creates an GraphicalPrimitive1D instance

GraphicalPrimitive1D(GraphicalPrimitive1D) - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Clone constructor

GraphicalPrimitive1DConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the GraphicalPrimitive1D class.

GraphicalPrimitive1DConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive1DConstraints

GraphicalPrimitive2D - Class in org.sbml.jsbml.ext.render

GraphicalPrimitive2D() - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

Creates an GraphicalPrimitive2D instance

GraphicalPrimitive2D(int, int) - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

Creates an GraphicalPrimitive2D instance

GraphicalPrimitive2D(GraphicalPrimitive2D) - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

Clone constructor

GraphicalPrimitive2D.FillRule - Enum in org.sbml.jsbml.ext.render

The type FillRule enumeration describes how a surface created by connecting points on a Polygon are to be filled when rendered.

GraphicalPrimitive2DConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the GraphicalPrimitive2D class.

GraphicalPrimitive2DConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive2DConstraints

GRAY - org.sbml.jsbml.Unit.Kind

The gray unit.

GREATER - org.sbml.jsbml.ext.fbc.FluxBound.Operation

Deprecated.

greater

GREATER_EQUAL - org.sbml.jsbml.ext.fbc.FluxBound.Operation

Deprecated.

greaterEqual

group - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Group - Class in org.sbml.jsbml.ext.groups

Group() - Constructor for class org.sbml.jsbml.ext.groups.Group

Creates a new Group instance.

Group(int, int) - Constructor for class org.sbml.jsbml.ext.groups.Group

Creates a new Group instance.

Group(Group) - Constructor for class org.sbml.jsbml.ext.groups.Group

Creates a new Group instance from the given Group.

Group.Kind - Enum in org.sbml.jsbml.ext.groups

This is a collection of possible values for the kind attribute within a Group.

GROUPS_10100 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4010100:

GROUPS_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4010101: To conform to the Groups Package specification for SBML Level 3 Version 1, an SBML document must declare 'http://www.sbml.org/sbml/level3/version1/groups/version1' as the XMLNamespace to use for elements of this package.

GROUPS_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4010102: Wherever they appear in an SBML document, elements and attributes from the Groups Package must use the 'http://www.sbml.org/sbml/level3/version1/groups/version1' namespace, declaring so either explicitly or implicitly.

GROUPS_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4010301: (Extends validation rule #10301 in the SBML Level 3 Core specification.

GROUPS_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4010302: The value of a 'groups:id' must conform to the syntax of the <sbml> data type 'SId' Reference: L3V1 Groups V1 Section 3.3.1

GROUPS_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020101: In all SBML documents using the Groups Package, the <sbml> object must have the 'groups:required' attribute.

GROUPS_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020102: The value of attribute 'groups:required' on the <sbml> object must be of data type Boolean.

GROUPS_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020103: The value of attribute 'groups:required' on the <sbml> object must be set to 'false'.

GROUPS_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020201: A <model> object may contain one and only one instance of the <listOfGroups> element.

GROUPS_20202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020202: The <listOfGroups> subobject on a <model> object is optional, but if present, this container object must not be empty.

GROUPS_20203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020203: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfGroups> container object may only contain <group> objects.

GROUPS_20204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020204: A <listOfGroups> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

GROUPS_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020301: A <group> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

GROUPS_20302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020302: A <group> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

GROUPS_20303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020303: A <group> object must have the required attribute 'groups:kind', and may have the optional attributes 'groups:id' and 'groups:name'.

GROUPS_20304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020304: A <group> object may contain one and only one instance of the <listOfMembers> element.

GROUPS_20305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020305: The value of the attribute 'groups:kind' of a <group> object must conform to the syntax of SBML data type 'groupKind' and may only take on the allowed values of 'groupKind' defined in SBML; that is, the value must be one of the following: 'classification', 'partonomy' or 'collection'.

GROUPS_20306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020306: The attribute 'groups:name' on a <group> must have a value of data type 'string'.

GROUPS_20307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020307: The <listOfMembers> subobject on a <group> object is optional, but if present, this container object must not be empty.

GROUPS_20308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020308: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfMembers> container object may only contain <member> objects.

GROUPS_20309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020309: A <listOfMembers> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

GROUPS_20310 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020310: A <listOfMembers> object may have the optional attributes 'groups:id' and 'groups:name'.

GROUPS_20311 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020311: The attribute 'groups:name' on a <listOfMembers> must have a value of data type 'string'.

GROUPS_20312 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020312: If <listOfMembers> objects from different <group> objects contain <member> elements that reference the same SBase object, the 'sboTerm' attribute and any child <notes> or <annotation> elements set for those <listOfMembers> should be consistent, as they should all apply to the same referenced object.

GROUPS_20313 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020313: Member references may not be circular: no <member>'s 'idRef' or 'metaIdRef' may reference itself, its parent <listOfMembers>, nor its parent <group>.

GROUPS_20401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020401: A <member> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.

GROUPS_20402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020402: A <member> object may have the optional SBML Level 3 Core subobjects for notes and annotations.

GROUPS_20403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020403: A <member> object may have the optional attributes 'groups:id' and 'groups:name' and must have a value for one (and exactly one) of the attributes 'groups:idRef' and 'groups:metaIdRef'.

GROUPS_20404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020404: The attribute 'groups:name' on a <member> must have a value of data type 'string'.

GROUPS_20405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020405: The value of the attribute 'groups:idRef' of a <member> object must be the identifier of an existing object derived from the 'SBase' class and defined in the enclosing <model> object.

GROUPS_20406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020406: The value of the attribute 'groups:metaIdRef' of a <member> object must be the 'metaid' of an existing 'SBase' object defined in the enclosing <model> object.

GROUPS_20407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020407: The value of the attribute 'groups:idRef' of a <member> object must conform to the syntax of the SBML data type 'SId'.

GROUPS_20408 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes

Error code 4020408: The value of the attribute 'groups:metaIdRef' of a <member> object must conform to the syntax of the SBML data type 'ID'.

GroupsConstants - Class in org.sbml.jsbml.ext.groups

Contains some constants related to the groups package.

GroupsConstants() - Constructor for class org.sbml.jsbml.ext.groups.GroupsConstants

GroupsModelPlugin - Class in org.sbml.jsbml.ext.groups

GroupsModelPlugin(GroupsModelPlugin) - Constructor for class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Creates a new GroupsModelPlugin instance cloned from the given parameter.

GroupsModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Creates a new GroupsModelPlugin instance

GroupsParser - Class in org.sbml.jsbml.xml.parsers

This class is used to parse the groups extension package elements and attributes.

GroupsParser() - Constructor for class org.sbml.jsbml.xml.parsers.GroupsParser

gt(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode

Creates an ASTNode representing greater than for the two given left and right child.

gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

gt(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

Greater than.

gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML

gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler

gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

gt(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Creates an ASTRelationalOperatorNode representing greater than for the two given left and right child.

gt(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

Greater than.

gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler

gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

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