- geneProduct - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
- GeneProduct - Class in org.sbml.jsbml.ext.fbc
-
Introduced to FBC in version 2.
- GeneProduct() - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct
-
- GeneProduct(GeneProduct) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct
-
- GeneProduct(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct
-
- GeneProduct(String) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct
-
- GeneProduct(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct
-
- GeneProduct(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProduct
-
- geneProductAssociation - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
- GeneProductAssociation - Class in org.sbml.jsbml.ext.fbc
-
Introduced to FBC in version 2.
- GeneProductAssociation() - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation
-
- GeneProductAssociation(GeneProductAssociation) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation
-
- GeneProductAssociation(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation
-
- GeneProductAssociation(String) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation
-
- GeneProductAssociation(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation
-
- GeneProductAssociation(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductAssociation
-
- geneProductIdentifier - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
- GeneProductRef - Class in org.sbml.jsbml.ext.fbc
-
Introduced to FBC in version 2.
- GeneProductRef() - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef
-
- GeneProductRef(GeneProductRef) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef
-
- GeneProductRef(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef
-
- GeneProductRef(String) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef
-
- GeneProductRef(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef
-
- GeneProductRef(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.GeneProductRef
-
- geneProductReference - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
- geneProteinAssociation - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
Deprecated.
- 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
-
- GeneralGlyph(GeneralGlyph) - Constructor for class org.sbml.jsbml.ext.layout.GeneralGlyph
-
- GeneralGlyph(String) - Constructor for class org.sbml.jsbml.ext.layout.GeneralGlyph
-
- GeneralGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.GeneralGlyph
-
- generalGlyph - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
-
- 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 - Class in org.sbml.jsbml.ext.spatial
-
- Geometry() - Constructor for class org.sbml.jsbml.ext.spatial.Geometry
-
- Geometry(Geometry) - Constructor for class org.sbml.jsbml.ext.spatial.Geometry
-
- Geometry(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.Geometry
-
- Geometry(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.Geometry
-
- geometry - 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(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 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- 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(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- geq(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Greater equal.
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- geq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- geq(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Greater equal.
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML
-
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- geq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- get(int) - Method in class org.sbml.jsbml.ListOf
-
Returns the element at the specified position in this list or null if the index is negative or too big.
- get(String) - Method in class org.sbml.jsbml.ListOf
-
Gets the list element which has the id 'id'.
- getAbout() - Method in class org.sbml.jsbml.Annotation
-
Returns the about String of this object.
- getActivator() - Static method in class org.sbml.jsbml.SBO
-
- 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
-
- getAdditionalGraphicalObject(int) - Method in class org.sbml.jsbml.ext.layout.Layout
-
- getAdditionalGraphicalObjectCount() - Method in class org.sbml.jsbml.ext.layout.Layout
-
- 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.DistribFunctionDefinitionPlugin
-
- getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin
-
- getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
- getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty
-
- 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.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.multi.SpeciesTypeComponentMapInProduct
-
- 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.LinearGradient
-
- getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.LineEnding
-
- 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.RenderCubicBezier
-
- 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.RenderPoint
-
- 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.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.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
-
- 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
-
- getArgument(int) - Method in class org.sbml.jsbml.FunctionDefinition
-
Get the nth argument to this function.
- getArgument(String) - Method in class org.sbml.jsbml.FunctionDefinition
-
- getArgumentCount() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getArrayData() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints
-
- 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
- getAssociatedSpecies() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct
-
- getAssociation() - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation
-
- getAssociation(int) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator
-
- getAssociation() - Static method in class org.sbml.jsbml.SBO
-
Interaction between several biochemical entities that results in the
formation of a non-covalent complex
- getAssociationCount() - Method in class org.sbml.jsbml.ext.fbc.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
.
- getBackgroundColor() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
-
- getBase() - Method in class org.sbml.jsbml.math.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
-
- 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
-
- getBindingSite2() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond
-
- getBindingStatus() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite
-
- getBiologicalQualifierFor(String) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier
-
- getBiologicalQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- getBody() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getBoundaryCondition() - Method in class org.sbml.jsbml.Species
-
- 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 class org.sbml.jsbml.ext.render.LineEnding
-
- getBundle(String) - Static method in class org.sbml.jsbml.util.ResourceManager
-
- getBundle(String, Locale) - Static method in class org.sbml.jsbml.util.ResourceManager
-
- getBvarCount() - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- getBytesFromResourceLocation(String) - Method in class org.sbml.jsbml.resources.Resource
-
Gets the byte data from a file at the given resource location.
- getCalculatedStoichiometry() - Method in class org.sbml.jsbml.SpeciesReference
-
This method computes the fraction of the stoichiometry and the
denominator.
- getCatalysis() - Static method in class org.sbml.jsbml.SBO
-
Modification of the velocity of a reaction by lowering the energy of the
transition state.
- getCatalyst() - Static method in class org.sbml.jsbml.SBO
-
Substance that accelerates the velocity of a chemical reaction without
itself being consumed or transformed.
- getCatalyticActivator() - Static method in class org.sbml.jsbml.SBO
-
- getCategory() - Method in exception org.sbml.jsbml.SBMLError
-
- getCategory() - Method in exception org.sbml.jsbml.SBMLException
-
- getCategory() - Method in class org.sbml.jsbml.util.Detail
-
- 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
-
- getCharge() - Method in class org.sbml.jsbml.Species
-
Deprecated.
- getChemicalFormula() - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin
-
- getChild(int) - Method in class org.sbml.jsbml.ASTNode
-
Gets a child of this node according to an index number.
- getChild() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
Get the child of this node
- getChild(int) - Method in class org.sbml.jsbml.xml.XMLNode
-
Returns the child
XMLNode
at index childIndex.
- getChildAt(int) - Method in class org.sbml.jsbml.AbstractMathContainer
-
- getChildAt(int) - Method in class org.sbml.jsbml.AbstractSBase
-
- getChildAt(int) - Method in class org.sbml.jsbml.Annotation
-
- getChildAt(int) - Method in class org.sbml.jsbml.ASTNode
-
- getChildAt(int) - Method in class org.sbml.jsbml.Constraint
-
- getChildAt(int) - Method in class org.sbml.jsbml.Creator
-
- getChildAt(int) - Method in class org.sbml.jsbml.CVTerm
-
- getChildAt(int) - Method in class org.sbml.jsbml.Event
-
- getChildAt(int) - Method in class org.sbml.jsbml.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.DistribFunctionDefinitionPlugin
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty
-
- 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.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.SpeciesFeature
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- 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.LinearGradient
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.render.LineEnding
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.render.Polygon
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.render.Rectangle
-
- getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
-
- 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.RenderPoint
-
- 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.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.DistribFunctionDefinitionPlugin
-
- getChildCount() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin
-
- getChildCount() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
- getChildCount() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty
-
- 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.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.SpeciesFeature
-
- getChildCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType
-
- getChildCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getChildCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- 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.LinearGradient
-
- getChildCount() - Method in class org.sbml.jsbml.ext.render.LineEnding
-
- 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.RenderCubicBezier
-
- 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.RenderPoint
-
- 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.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
-
- getCode() - Method in exception org.sbml.jsbml.SBMLException
-
- getCoefficient() - Method in class org.sbml.jsbml.ext.fbc.FluxObjective
-
Returns the value of coefficient
- 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.SpeciesType
-
- getCompartment() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
-
- getCompartment(int) - Method in class org.sbml.jsbml.Model
-
Gets the n
th Compartment
instance of the listOfCompartments.
- getCompartment(String) - Method in class org.sbml.jsbml.Model
-
Gets the
Compartment
of the listOfCompartments which has 'id' as
id.
- getCompartment() - Method in class org.sbml.jsbml.Reaction
-
Only available if Level >= 3.
- getCompartment() - Static method in class org.sbml.jsbml.SBO
-
Physical compartment.
- getCompartment() - Method in class org.sbml.jsbml.Species
-
- getCompartmentCount() - Method in class org.sbml.jsbml.Model
-
- 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
-
- getCompartmentInstance() - Method in interface org.sbml.jsbml.CompartmentalizedSBase
-
- 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.SpeciesType
-
- 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(int) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin
-
- getCompartmentReference(String) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin
-
Gets an element from the listOfCompartmentReferences, with the given id.
- getCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin
-
- getCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance
-
- getCompartmentReferenceCount() - Method in class org.sbml.jsbml.ext.multi.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
-
- 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.
- getCompetetiveInhibitor() - Static method in class org.sbml.jsbml.SBO
-
- 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
-
- getComponent() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite
-
- getComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- getComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex
-
- 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
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- getConstantAvogadro(String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getConstantAvogadro(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- getConstantE() - Method in 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 nth Constraint object in this Model.
- getConstraintCount() - Method in class org.sbml.jsbml.Model
-
- getConsumption() - Static method in class org.sbml.jsbml.SBO
-
Decrease in amount of a material or conceptual entity.
- getContinuousFramework() - Static method in class org.sbml.jsbml.SBO
-
- getConversionFactor() - Method in class org.sbml.jsbml.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
-
- 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
-
- 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.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
- 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
-
- getCreatorCount() - Method in class org.sbml.jsbml.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
- 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
-
- 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
-
- getCurveSegmentCount() - Method in class org.sbml.jsbml.ext.layout.Curve
-
- getCVTerm(int) - Method in class org.sbml.jsbml.AbstractSBase
-
- getCVTerm(int) - Method in class org.sbml.jsbml.Annotation
-
Returns the CVTerm at the ith position in the list of CVTerms.
- getCVTerm(int) - Method in interface org.sbml.jsbml.SBase
-
Returns the
CVTerm
instance at the position 'index' in the list of
CVTerm
s of this object.
- getCVTermCount() - Method in class org.sbml.jsbml.AbstractSBase
-
- getCVTermCount() - Method in class org.sbml.jsbml.Annotation
-
- getCVTermCount() - Method in interface org.sbml.jsbml.SBase
-
- getCVTerms() - Method in class org.sbml.jsbml.AbstractSBase
-
- getCVTerms() - Method in interface org.sbml.jsbml.SBase
-
Returns the list of
CVTerm
s of this object.
- 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.
- getDeclaredNamespaces() - Method in class org.sbml.jsbml.AbstractSBase
-
- getDeclaredNamespaces() - Method in class org.sbml.jsbml.Annotation
-
- getDeclaredNamespaces() - Method in interface org.sbml.jsbml.SBase
-
Returns all the namespaces declared on this object.
- getDefaultIndentChar() - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Returns the default symbol to be used to indent new elements in the XML
representation of SBML data structures.
- getDefaultIndentCount() - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Returns the default number of indent symbols to be concatenated at the
beginning of a new block in an XML representation of SBML data
structures.
- getDefaultLevel() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the default SBML Level of new SBMLDocument objects.
- getDefaultPossibleEnzymes() - Static method in class org.sbml.jsbml.SBO
-
Creates and returns a list of molecule types accepted as an enzyme by
default.
- getDefaultVersion() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the default Version of new SBMLDocument objects.
- getDefinition() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the definition of this
Term
, which is stored in the
corresponding OBO file under the key
def
.
- getDefinitionURIavogadro() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getDefinitionURIdelay() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getDefinitionURItime() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getDefinitionURL() - Method in class org.sbml.jsbml.ASTNode
-
Returns the definitionURL
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
Returns the definitionURL of the MathML element represented by this ASTCiFunctionNode
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getDefinitionURL() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- getDefinitionURL() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- getDelay() - Method in class org.sbml.jsbml.Event
-
- getDelayCount() - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
-
- 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.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
-
- 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.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
-
- 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
-
- getDiffusionKind() - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient
-
Returns the value of diffusionKind
- 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
-
- 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
-
This method 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
- getDistribInput(int) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
Gets an element from the listOfDistribInputs at the given index.
- getDistribInput(String) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
Gets an element from the listOfDistribInputs, with the given id.
- getDistribInputCount() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
- getDocument() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- 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
- 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
- getDomainTypeInstance() - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping
-
- getDrawFromDistribution() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin
-
Returns the value of drawFromDistribution
- 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.SBMLDocument
-
- getElementCount() - Method in class org.sbml.jsbml.ext.render.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.render.RenderGroup
-
- getElementName() - Method in class org.sbml.jsbml.ListOf
-
- getElementName() - Method in class org.sbml.jsbml.LocalParameter
-
- getElementName() - Method in interface org.sbml.jsbml.SBase
-
Returns the XML element name of this object.
- getElementName() - Method in class org.sbml.jsbml.SBMLDocument
-
- getElementName() - Method in class org.sbml.jsbml.Species
-
- getElementName() - Method in class org.sbml.jsbml.SpeciesReference
-
- getElementName() - Method in class org.sbml.jsbml.util.ListOfWithName
-
- getElementNameEquivalent() - Method in enum org.sbml.jsbml.CVTerm.Qualifier
-
Returns a name corresponding to this Qualifier Object.
- getElementNameEquivalent() - Method in enum org.sbml.jsbml.CVTerm.Type
-
Returns a name corresponding to this Type of qualifier Object.
- getElementNameEquivalentToQualifier(CVTerm.Qualifier) - Static method in class org.sbml.jsbml.Annotation
-
- getElementNamespace() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getElementNamespace() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
-
- 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
-
- 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
-
- 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.
- getEntity() - Static method in class org.sbml.jsbml.SBO
-
- getEnzymaticCatalysis() - Static method in class org.sbml.jsbml.SBO
-
- getError(int) - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the ith error or warning encountered during consistency checking.
- getError(long) - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the
nth
SBMLError
object in this log.
- getErrorCount() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the number of errors or warnings encountered during consistency checking.
- getErrorCount() - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the number of errors that have been logged.
- getErrorId() - Method in exception org.sbml.jsbml.xml.XMLException
-
- getErrorLog() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns a collection of all
SBMLError
s reflecting
problems in the overall data structure of this
SBMLDocument
.
- getErrorsBySeverity(SBMLError.SEVERITY) - Method in class org.sbml.jsbml.SBMLErrorLog
-
- getEssentialActivator() - Static method in class org.sbml.jsbml.SBO
-
- getEvent(int) - Method in class org.sbml.jsbml.Model
-
Gets the nth Event object in this Model.
- getEvent(String) - Method in class org.sbml.jsbml.Model
-
Gets the
Event
which as the given
id
as id.
- getEvent() - Static method in class org.sbml.jsbml.SBO
-
- getEventAssignment(int) - Method in class org.sbml.jsbml.Event
-
Gets an element from the listOfEventAssignments at the given index.
- getEventAssignment(String) - Method in class org.sbml.jsbml.Event
-
Gets an element from the listOfEventAssignments, with the given id.
- getEventAssignmentCount() - Method in class org.sbml.jsbml.Event
-
- getEventAssignmentCount() - Method in class org.sbml.jsbml.Model
-
- getEventCount() - Method in class org.sbml.jsbml.Model
-
- getExcerpt() - Method in exception org.sbml.jsbml.SBMLError
-
Returns a fragment of the original XML file that induced the error.
- getExponent() - Method in class org.sbml.jsbml.ASTNode
-
Gets the exponent value of this ASTNode.
- getExponent() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode
-
Get the exponent value of this node.
- getExponent() - Method in class org.sbml.jsbml.math.ASTPowerNode
-
- getExponent() - Method in class org.sbml.jsbml.Unit
-
- getExponentAsDouble() - Method in class org.sbml.jsbml.Unit
-
- getExtendedSBase() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getExtendedSBase() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the SBase object that is extended by this plug-in.
- 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 interface org.sbml.jsbml.SBase
-
Returns the
SBasePlugin
extension object which matches this package
name or URI.
- getExtensionCount() - Method in class org.sbml.jsbml.AbstractSBase
-
- getExtensionCount() - Method in interface org.sbml.jsbml.SBase
-
- getExtensionPackages() - Method in class org.sbml.jsbml.AbstractSBase
-
- getExtensionPackages() - Method in interface org.sbml.jsbml.SBase
-
- 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
-
- getExternalModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
-
- getExternalModelDefinitionCount() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
-
- getFamilyName() - Method in class org.sbml.jsbml.Creator
-
Returns the familyName from the
Creator
.
- getFast() - Method in class org.sbml.jsbml.Reaction
-
- getFieldCount() - Method in class org.sbml.jsbml.ext.arrays.compiler.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
-
The first element in this list.
- 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 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
-
- getFunctionDefinition(String) - Method in class org.sbml.jsbml.Model
-
- getFunctionDefinitionCount() - Method in class org.sbml.jsbml.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(int) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
-
- getGeneProduct(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
-
Gets an element from the listOfGeneProducts, with the given id.
- getGeneProduct() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef
-
- getGeneProductAssociation() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
-
- getGeneProductCount() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
-
- getGeneric() - Static method in class org.sbml.jsbml.SBO
-
- 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
- getGeometryInstance() - Method in class org.sbml.jsbml.ext.spatial.ParameterType
-
- 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
-
- getGroup(int) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin
-
- getGroup(String) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin
-
Gets the
Group
that has the given id.
- getGroup() - Method in class org.sbml.jsbml.ext.render.LineEnding
-
- getGroup() - Method in class org.sbml.jsbml.ext.render.Style
-
- getGroupCount() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin
-
- getHasOnlySubstanceUnits() - Method in class org.sbml.jsbml.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.AbstractNamedSBase
-
- getId() - Method in class org.sbml.jsbml.ASTNode
-
Returns the id of the mathML element represented by this ASTNode.
- getId() - Method in class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
-
- getId() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint
-
Deprecated.
- getId() - Method in class org.sbml.jsbml.ext.render.RenderGroup
-
- getId() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getId() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- getId() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Get the id of this node
- getId() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getId() - Method in interface org.sbml.jsbml.NamedSBase
-
- getId() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the SBO identifier of this
Term
, for instance:
SBO:0000031
.
- getId() - Method in class org.sbml.jsbml.util.filters.AssignmentVariableFilter
-
- getId() - Method in class org.sbml.jsbml.util.filters.NameFilter
-
- 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(NamedSBase) - 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
-
- 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
-
- getIndenting() - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getIndenting() - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- getIndex(TreeNode) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getIndex(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() - Method in class org.sbml.jsbml.ext.distrib.DistribInput
-
Returns the value of index
- getIndex(TreeNode) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getIndex(String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the index of an attribute with the given name.
- getIndex(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the index of an attribute with the given local name and namespace URI.
- getIndex(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the index of an attribute with the given
XMLTriple
.
- getIndex(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the index of an XML namespace declaration by URI.
- getIndexByPrefix(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the index of an XML namespace declaration by prefix.
- getIndexCount() - Method in class org.sbml.jsbml.ext.arrays.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
-
- getInitialAssignment(int) - Method in class org.sbml.jsbml.Model
-
- getInitialAssignment(String) - Method in class org.sbml.jsbml.Model
-
- getInitialAssignmentCount() - Method in class org.sbml.jsbml.Model
-
- getInitialConcentration() - Method in class org.sbml.jsbml.Species
-
- 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.SpeciesType
-
- getInSpeciesTypeBond(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
Gets an element from the listOfInSpeciesTypeBonds, with the given id.
- getInSpeciesTypeBondCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getInstance() - Static method in class org.sbml.jsbml.math.ASTUnknown
-
- getInstance() - Static method in class org.sbml.jsbml.resources.Resource
-
- getInstance() - Static method in class org.sbml.jsbml.util.JAXPFacade
-
Creates and returns a new JAXPFacade
.
- getInteger() - Method in class org.sbml.jsbml.ASTNode
-
Gets the value of this node as an integer.
- getInteger() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode
-
Get the integer value of this node.
- getInteraction() - Static method in class org.sbml.jsbml.SBO
-
- getInterpolation() - Method in class org.sbml.jsbml.ext.spatial.SampledField
-
Returns the value of interpolation
- getIon() - Static method in class org.sbml.jsbml.SBO
-
- getIonChannel() - Static method in class org.sbml.jsbml.SBO
-
- 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
-
- 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
-
- 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
-
- getL() - Method in class org.sbml.jsbml.util.ValuePair
-
- getLabel() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct
-
- 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(int) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin
-
- getLayoutCount() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin
-
- getLeftChild() - Method in class org.sbml.jsbml.ASTNode
-
Gets the left child of this node.
- getLeftChild() - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- getLength() - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the number of attributes in the set.
- getLength() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Returns the total number of URI-and-prefix pairs stored in this
particular
XMLNamespaces
instance.
- getLengthUnits() - Method in class org.sbml.jsbml.Model
-
Returns the length units ID of this
Model
.
- getLengthUnitsInstance() - Method in class org.sbml.jsbml.Model
-
- getLevel() - Method in class org.sbml.jsbml.AbstractSBase
-
- getLevel() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getLevel() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- getLevel() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
Returns the level of the SBML document that was the basis to create this
ASTNode2Value
.
- getLevel() - Method in interface org.sbml.jsbml.SBase
-
Returns the SBML Level of the overall SBML document.
- getLevel() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
Returns the level of the SBML document that was the basis to create this
ASTNodeValue
.
- getLevel() - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- getLevelAndVersion() - Method in class org.sbml.jsbml.AbstractSBase
-
- getLevelAndVersion() - Method in interface org.sbml.jsbml.SBase
-
Returns the Level and Version combination of this
SBase
.
- getLine() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Deprecated.
- getLine() - Method in exception org.sbml.jsbml.SBMLError
-
Returns the line where this
SBMLError
happened.
- getLine() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Deprecated.
- getLine() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the line at which this
XMLToken
occurred in the input document
or data stream.
- 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
-
- 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
-
- 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
-
- getListOfCreators() - Method in class org.sbml.jsbml.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
-
- 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.
- getListOfDistribInputs() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
Returns the listOfDistribInputs.
- 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
-
Get the listOfErrors after checking the model.
- getListOfErrors() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns a collection of all
SBMLError
s reflecting
problems in the overall data structure of this
SBMLDocument
.
- getListOfEventAssignments() - Method in class org.sbml.jsbml.Event
-
Returns the listOfEventAssignments.
- getListOfEvents() - Method in class org.sbml.jsbml.Model
-
Returns the listOfEvents of this
Model
.
- 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
-
- 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.SpeciesType
-
- 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
-
- 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
-
- getListOfNodes() - Method in class org.sbml.jsbml.ASTNode
-
Returns the list of children of the current ASTNode.
- getListOfNodes(Filter) - Method in class org.sbml.jsbml.ASTNode
-
Returns the list of children of the current ASTNode that satisfy the
given filter.
- getListOfNodes() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the list of children of the current ASTFunction.
- getListOfNodes(Filter) - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the list of children of the current ASTFunction that satisfy the
given filter.
- getListOfObjectives() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
-
- 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
-
- getListOfParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- getListOfParameters() - Method in class org.sbml.jsbml.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
-
- getListOfPredefinedUnitDefinitions() - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
.
- getListOfSpatialComponents() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin
-
Returns the value of listOfSpatialComponents
- getListOfSpecies() - Method in class org.sbml.jsbml.Model
-
- getListOfSpeciesFeatureChanges() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- getListOfSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- getListOfSpeciesFeatureTypes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getListOfSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- getListOfSpeciesGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout
-
- getListOfSpeciesReferenceGlyphs() - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph
-
- getListOfSpeciesTypeComponentIndexes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getListOfSpeciesTypeComponentMapInProducts() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin
-
- getListOfSpeciesTypeInstances() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- 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.
- 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
-
- 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
-
- getLogger() - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
-
- getLogger() - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
-
- getLogicalFramework() - Static method in class org.sbml.jsbml.SBO
-
- getLowerBound(Map<String, Double>) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath
-
This method is used to get the lower bound index from a collection of Dimension objects.
- getLowerFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
-
- 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
-
- 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 interface org.sbml.jsbml.MathContainer
-
- getMathContainerCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of elements that can contain math in the
Model
.
- getMathematicalExpression() - Static method in class org.sbml.jsbml.SBO
-
- getMathMLClass() - Method in class org.sbml.jsbml.math.AbstractASTNode
-
- getMathMLClass() - Method in interface org.sbml.jsbml.math.ASTNode2
-
Returns the class of the MathML element represented by
this
ASTNode2
- getMathMLClass() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getMathMLString() - Method in class org.sbml.jsbml.AbstractMathContainer
-
- getMathMLString() - Method in interface org.sbml.jsbml.MathContainer
-
- 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
-
- 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
-
- getMembersShareType() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint
-
Deprecated.
Returns the value of membersShareType
- getMessage() - Method in class org.sbml.jsbml.Constraint
-
- getMessage() - Method in error org.sbml.jsbml.math.parser.TokenMgrError
-
You can also modify the body of this method to customize your error messages.
- getMessage() - Method in exception org.sbml.jsbml.SBMLError
-
- getMessage() - Method in error org.sbml.jsbml.text.parser.TokenMgrError
-
You can also modify the body of this method to customize your error messages.
- getMessage() - Method in class org.sbml.jsbml.util.Message
-
- getMessageInstance() - Method in exception org.sbml.jsbml.SBMLError
-
- getMessageString() - Method in class org.sbml.jsbml.Constraint
-
- 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.
- 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
- getMetaidRef() - Method in class org.sbml.jsbml.ext.layout.GraphicalObject
-
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
-
- getModel() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
-
- 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
-
- getModel() - Method in class org.sbml.jsbml.util.ModelBuilder
-
- getModelDefinition(int) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
-
- getModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
-
- getModelDefinitionCount() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
-
- getModelHistory() - Method in class org.sbml.jsbml.Model
-
- getModellingFramework() - Static method in class org.sbml.jsbml.SBO
-
- getModelQualifierFor(String) - Static method in enum org.sbml.jsbml.CVTerm.Qualifier
-
- getModelQualifierType() - Method in class org.sbml.jsbml.CVTerm
-
- 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(int) - Method in class org.sbml.jsbml.Reaction
-
- getModifier(String) - Method in class org.sbml.jsbml.Reaction
-
- getModifier() - Static method in class org.sbml.jsbml.SBO
-
Substance that changes the velocity of a process without itself being
consumed or transformed by the reaction.
- getModifierCount() - Method in class org.sbml.jsbml.Reaction
-
- getModifierForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- getModifierSpeciesReferenceCount() - Method in class org.sbml.jsbml.Model
-
- getModifierSpeciesReferences() - Method in class org.sbml.jsbml.Model
-
- getModulation() - Static method in class org.sbml.jsbml.SBO
-
Modification of the execution of an event or a process.
- getMultiplier() - Method in class org.sbml.jsbml.Unit
-
- getName() - Method in class org.sbml.jsbml.AbstractNamedSBase
-
- getName() - Method in class org.sbml.jsbml.ASTNode
-
Gets the name of this node.
- getName() - Method in class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
-
- getName() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint
-
Deprecated.
- getName() - Method in class org.sbml.jsbml.ext.render.RenderGroup
-
- getName() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getName() - Method in class org.sbml.jsbml.math.ASTCiNumberNode
-
Deprecated.
- getName() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getName() - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode
-
- getName() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- getName() - Method in class org.sbml.jsbml.math.ASTFunction
-
Returns the name of the MathML element represented by
this
ASTFunction
- getName() - Method in interface org.sbml.jsbml.NamedSBase
-
- getName() - Method in class org.sbml.jsbml.ontology.Term
-
Returns the name of this
Term
, i.e., a very short characterization.
- getName() - Method in enum org.sbml.jsbml.Unit.Kind
-
Returns the name of this unit kind.
- getName() - Method in class org.sbml.jsbml.util.filters.NameFilter
-
- getName() - Method in class org.sbml.jsbml.util.Option
-
- getName() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- getName(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the local name of an attribute in this
XMLAttributes
set (by position).
- getName() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the (unqualified) name of this XML element.
- getName() - Method in class org.sbml.jsbml.xml.XMLTriple
-
- getNamedSBaseCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of
NamedSBase
s in the
Model
, so elements
that can have a name.
- getNamedSBaseInstance() - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
-
- getNamedSBaseWithDerivedUnitCount() - Method in class org.sbml.jsbml.Model
-
- getNameOrId(NamedSBase) - Static method in class org.sbml.jsbml.util.SBMLtools
-
- getNamespace() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNamespace() - Method in interface org.sbml.jsbml.SBase
-
Returns the namespace to which this
SBase
belong to.
- getNamespace() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
- getNamespaceFor(int, int, int) - Method in 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, 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.
- 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
-
- 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 class org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader
-
- 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
-
- getNamespaceURI() - Method in enum org.sbml.jsbml.CVTerm.Type
-
- 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
-
- 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
-
- getNamespaceURI(int, int, int) - Static method in class org.sbml.jsbml.ext.fbc.FBCConstants
-
- getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.groups.GroupsConstants
-
- 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
-
- getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.qual.QualConstants
-
- getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.render.RenderConstants
-
- 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(int, int) - Static method in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- 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(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
-
- getNestedCVTermCount() - Method in class org.sbml.jsbml.CVTerm
-
- 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
-
- getNonCompetetiveInhibitor() - Static method in class org.sbml.jsbml.SBO
-
- getNonCovalentComplex() - Static method in class org.sbml.jsbml.SBO
-
- getNonEssentialActivator() - Static method in class org.sbml.jsbml.SBO
-
- getNonRDFannotation() - Method in class org.sbml.jsbml.Annotation
-
Returns the
XMLNode
containing annotations other than
the official RDF annotation, as defined in the SBML specifications.
- getNonRDFannotationAsString() - Method in class org.sbml.jsbml.Annotation
-
Returns the String containing annotations other than RDF
annotation.
- getNotes() - Method in class org.sbml.jsbml.AbstractSBase
-
Returns an XMLNode
object that represent the notes of this element.
- getNotes() - Method in interface org.sbml.jsbml.SBase
-
Returns the XMLNode
containing the notes sub-element of
this object.
- getNotesString() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNotesString() - Method in interface org.sbml.jsbml.SBase
-
Returns the notes sub-element of this object as a
String
.
- getNumArguments() - Method in class org.sbml.jsbml.FunctionDefinition
-
- getNumAssociations() - Method in class org.sbml.jsbml.ext.fbc.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
-
- 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
-
- getNumCompartmentReferences() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin
-
- getNumCompartments() - Method in class org.sbml.jsbml.Model
-
- getNumCompartmentTypes() - Method in class org.sbml.jsbml.Model
-
Deprecated.
- getNumConstraints() - Method in class org.sbml.jsbml.Model
-
- getNumCreators() - Method in class org.sbml.jsbml.History
-
- getNumCVTerms() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNumCVTerms() - Method in class org.sbml.jsbml.Annotation
-
- getNumCVTerms() - Method in interface org.sbml.jsbml.SBase
-
- getNumDelays() - Method in class org.sbml.jsbml.Model
-
- getNumDimensions() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
-
- getNumDistribInputs() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
- getNumElements() - Method in class org.sbml.jsbml.ext.render.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
-
- getNumErrors() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the number of errors or warnings encountered during consistency checking.
- getNumErrors() - Method in class org.sbml.jsbml.SBMLErrorLog
-
Returns the number of errors that have been logged.
- getNumEventAssignments() - Method in class org.sbml.jsbml.Event
-
- getNumEventAssignments() - Method in class org.sbml.jsbml.Model
-
- getNumEvents() - Method in class org.sbml.jsbml.Model
-
- getNumExternalModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.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
-
- getNumFunctionDefinitions() - Method in class org.sbml.jsbml.Model
-
- getNumGeneProducts() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
-
- getNumGroups() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin
-
- getNumIndices() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
-
- getNumInitialAssignments() - Method in class org.sbml.jsbml.Model
-
- getNumInSpeciesTypeBonds() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getNumKineticLaws() - Method in class org.sbml.jsbml.Model
-
- getNumLayouts() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin
-
- getNumListsOf() - Method in class org.sbml.jsbml.Model
-
- getNumLocalParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- getNumLocalParameters() - Method in class org.sbml.jsbml.Model
-
Returns the number of parameters that are contained within kineticLaws in
the reactions of this model.
- getNumMathContainers() - Method in class org.sbml.jsbml.Model
-
Returns the number of elements that can contain math in the
Model
.
- getNumMembers() - Method in class org.sbml.jsbml.ext.groups.Group
-
- getNumModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.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
-
- getNumNamedSBases() - Method in class org.sbml.jsbml.Model
-
Returns the number of
NamedSBase
s in the
Model
, so elements
that can have a name.
- getNumNamedSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.Model
-
- getNumNestedCVTerms() - Method in class org.sbml.jsbml.CVTerm
-
- getNumObjective() - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
-
- getNumOutwardBindingSites() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- getNumParameters() - Method in class org.sbml.jsbml.KineticLaw
-
- getNumParameters() - Method in class org.sbml.jsbml.Model
-
- getNumPlugins() - Method in class org.sbml.jsbml.AbstractSBase
-
- getNumPlugins() - Method in interface org.sbml.jsbml.SBase
-
- getNumPorts() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin
-
- getNumPossibleSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType
-
- getNumProducts() - Method in class org.sbml.jsbml.Reaction
-
- getNumQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
-
- getNumQuantities() - Method in class org.sbml.jsbml.Model
-
- getNumQuantitiesWithUnit() - Method in class org.sbml.jsbml.Model
-
- getNumReactants() - Method in class org.sbml.jsbml.Reaction
-
- getNumReactionGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout
-
- getNumReactions() - Method in class org.sbml.jsbml.Model
-
- getNumReplacedElements() - Method in class org.sbml.jsbml.ext.comp.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
-
- 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
-
- getNumSBasesWithDerivedUnit() - Method in class org.sbml.jsbml.Model
-
- getNumSpecies() - Method in class org.sbml.jsbml.Model
-
- getNumSpeciesFeatureChanges() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- getNumSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- getNumSpeciesFeatureTypes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getNumSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- getNumSpeciesGlyphs() - Method in class org.sbml.jsbml.ext.layout.Layout
-
- getNumSpeciesReferences() - Method in class org.sbml.jsbml.Model
-
- getNumSpeciesTypeComponentIndexes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getNumSpeciesTypeComponentMapInProducts() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin
-
- getNumSpeciesTypeInstances() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- 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.
- getNumSubmodels() - Method in class org.sbml.jsbml.ext.comp.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
-
- getNumTransitions() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
-
- getNumTriggers() - Method in class org.sbml.jsbml.Model
-
- getNumUnitDefinitions() - Method in class org.sbml.jsbml.Model
-
- getNumUnits() - Method in class org.sbml.jsbml.Model
-
- getNumUnits() - Method in class org.sbml.jsbml.UnitDefinition
-
- getNumVariables() - Method in class org.sbml.jsbml.Model
-
- getObject() - Method in class org.sbml.jsbml.ontology.Triple
-
Returns the object of this
Triple
.
- 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
-
- getOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- getOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType
-
- 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
-
- 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.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
- 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
-
- getOutwardBindingSiteCount() - Method in class org.sbml.jsbml.ext.multi.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 class org.sbml.jsbml.ext.comp.CompSBasePlugin
-
- getPackageName() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin
-
- 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.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
-
- 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(String) - Method in class org.sbml.jsbml.xml.parsers.ParserManager
-
Returns the name of the SBML package corresponding to the given namespace URI.
- 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
-
- 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.AbstractSBasePlugin
-
- getPackageVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
Returns the package version of the package extension of this plugin object.
- getPackageVersion() - Method in interface org.sbml.jsbml.SBase
-
Returns the version of the SBML Level 3 package to which this element belongs.
- getParameter(int) - Method in class org.sbml.jsbml.KineticLaw
-
- getParameter(String) - Method in class org.sbml.jsbml.KineticLaw
-
- getParameter(int) - Method in class org.sbml.jsbml.Model
-
- getParameter(String) - Method in class org.sbml.jsbml.Model
-
- getParameterCount() - Method in class org.sbml.jsbml.Model
-
- getParamType() - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin
-
- getParent() - Method in class org.sbml.jsbml.AbstractSBase
-
- getParent() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getParent() - Method in class org.sbml.jsbml.ASTNode
-
- getParent() - Method in class org.sbml.jsbml.CompartmentType
-
Deprecated.
- getParent() - Method in class org.sbml.jsbml.Constraint
-
- getParent() - Method in class org.sbml.jsbml.Delay
-
- getParent() - Method in class org.sbml.jsbml.Event
-
- getParent() - Method in class org.sbml.jsbml.EventAssignment
-
- getParent() - Method in class org.sbml.jsbml.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
-
- getParentSBMLObject() - Method in class org.sbml.jsbml.AbstractSBase
-
- getParentSBMLObject() - Method in class org.sbml.jsbml.ASTNode
-
This method is convenient when holding an object nested inside other
objects in an SBML model.
- getParentSBMLObject() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getParentSBMLObject() - Method in 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.
- getPhenotype() - Static method in class org.sbml.jsbml.SBO
-
- getPhysicalCompartment() - Static method in class org.sbml.jsbml.SBO
-
- getPhysicalParticipant() - Static method in class org.sbml.jsbml.SBO
-
- getPieceCount() - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- getPiecewiseMap() - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
-
Gets a
Map
of the piecewise expressions that have been
transformed.
- getPkgRequired(String) - Method in class org.sbml.jsbml.SBMLDocument
-
- getPlugin(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- getPlugin(String) - Method in interface org.sbml.jsbml.SBase
-
Returns an
SBasePlugin
for an SBML Level 3 package extension
with the given package name or URI.
- getPointIndex() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject
-
- 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.
- 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
-
- 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
-
- 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
-
- 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
-
- getPredefinedUnit(String, int, int) - Static method in class org.sbml.jsbml.UnitDefinition
-
This method returns the predefined unit with the given identifier for the
specified level and version combination or null if either for the given
combination of level and version there is no such predefined unit or the
identifier is not one of those belonging to the group of predefined unit
definitions.
- getPredefinedUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
Returns a
UnitDefinition
representing one of the predefined units of SBML,
returns
null
if the given unit kind is not a valid one for the SBML level
and version of this
Model
.
- getPredefinedUnitID() - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
Returns the predefined unit identifier for this data type with the
current level/version combination.
- getPredefinedUnitID() - Method in class org.sbml.jsbml.Compartment
-
- getPredefinedUnitID() - Method in class org.sbml.jsbml.Event
-
- getPredefinedUnitID() - Method in class org.sbml.jsbml.LocalParameter
-
- getPredefinedUnitID() - Method in class org.sbml.jsbml.Parameter
-
- getPredefinedUnitID() - Method in class org.sbml.jsbml.Species
-
- getPredicate() - Method in class org.sbml.jsbml.ontology.Triple
-
Returns the predicate of this
Triple
.
- getPrefix() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
-
- getPrefix() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin
-
- getPrefix() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin
-
- 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.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(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the prefix of an attribute in this
XMLAttributes
set (by position).
- getPrefix(int) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the prefix of an XML namespace declaration by its position.
- getPrefix(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the prefix of an XML namespace declaration by its URI.
- getPrefix() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the namespace prefix of this XML element.
- getPrefix() - Method in class org.sbml.jsbml.xml.XMLTriple
-
Returns the
prefix portion of this
XMLTriple
.
- getPrefixAsWord() - Method in class org.sbml.jsbml.Unit
-
- getPrefixedName(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the prefixed name of an attribute in this
XMLAttributes
set (by position).
- getPrefixedName() - Method in class org.sbml.jsbml.xml.XMLTriple
-
Returns the prefixed name from this
XMLTriple
.
- getPreviousParent() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent
-
Access the pointer to the previous parent node of the removed node, may be
null
.
- 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(int) - Method in class org.sbml.jsbml.Reaction
-
- getProduct(String) - Method in class org.sbml.jsbml.Reaction
-
- getProduct() - Static method in class org.sbml.jsbml.SBO
-
Substance that is produced in a reaction.
- getProductComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- getProductCount() - Method in class org.sbml.jsbml.Reaction
-
- getProductForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- getProduction() - Static method in class org.sbml.jsbml.SBO
-
Generation of a material or conceptual entity.
- getProductSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange
-
- 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
-
- getQualifier() - Method in class org.sbml.jsbml.util.filters.CVTermFilter
-
- getQualifierType() - Method in class org.sbml.jsbml.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
-
- getQualitativeSpecies(String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
-
- getQualitativeSpeciesCount() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
-
- getQuantitativeParameter() - Static method in class org.sbml.jsbml.SBO
-
- getQuantityCount() - Method in class org.sbml.jsbml.Model
-
- getQuantityWithUnitCount() - Method in class org.sbml.jsbml.Model
-
- getR() - Method in class org.sbml.jsbml.ext.render.RadialGradient
-
- getRadicand() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- getRateLaw() - Static method in class org.sbml.jsbml.SBO
-
- getReactant() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- getReactant(int) - Method in class org.sbml.jsbml.Reaction
-
- getReactant(String) - Method in class org.sbml.jsbml.Reaction
-
- getReactant() - Static method in class org.sbml.jsbml.SBO
-
Substance consumed by a chemical reaction.
- getReactantComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- getReactantCount() - Method in class org.sbml.jsbml.Reaction
-
- getReactantForSpecies(String) - Method in class org.sbml.jsbml.Reaction
-
- getReactantSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange
-
- 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
-
- getReactionCount() - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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.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
-
- 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
-
- getReferencedAttribute() - Method in class org.sbml.jsbml.ext.arrays.Index
-
Returns the value of referencedAttribute
- 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
-
- getReferenceInstance() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode
-
- getReferenceInstance() - Method in class org.sbml.jsbml.math.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
-
- getRenderInformation() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin
-
- 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
-
- getReplacedElement(String) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin
-
- getReplacedElementCount() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin
-
- getRepresentationType() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin
-
- 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
-
- 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
-
- getRNA() - Static method in class org.sbml.jsbml.SBO
-
- getRole() - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph
-
- 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
-
- getRootExponent() - Method in class org.sbml.jsbml.math.ASTRootNode
-
- getRotateAngleInRadians() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation
-
Returns the value of rotateAngleInRadians
- getRotateAxisX() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation
-
Returns the value of rotateAxisX
- getRotateAxisY() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation
-
Returns the value of rotateAxisY
- getRotateAxisZ() - 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
-
- getRuleCount() - Method in class org.sbml.jsbml.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
- 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
-
- getSamplesLength() - Method in class org.sbml.jsbml.ext.spatial.SampledField
-
- getSBaseCount() - Method in class org.sbml.jsbml.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.
- getSBaseListType() - Method in class org.sbml.jsbml.ListOf
-
- getSBaseRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef
-
Returns the value of sBaseRef
- getSBaseWithDerivedUnitCount() - Method in class org.sbml.jsbml.Model
-
- getSBMLDocument() - Method in class org.sbml.jsbml.AbstractSBase
-
- getSBMLDocument() - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- getSBMLDocument() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- getSBMLDocument() - Method in interface org.sbml.jsbml.SBase
-
- getSBMLDocument() - Method in class org.sbml.jsbml.util.ModelBuilder
-
- getSBMLDocumentAttributes() - Method in class org.sbml.jsbml.SBMLDocument
-
Returns the map of attribute names and values of this SBMLDocument.
- getSBMLDocumentNamespaces() - Method in class org.sbml.jsbml.SBMLDocument
-
- getSBMLNSAttribute() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getSBMLUnitsAttribute() - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- getSBORoot() - Static method in class org.sbml.jsbml.SBO
-
Returns the root element of the SBO Ontology (SBO:0000000).
- getSBOTerm() - Method in class org.sbml.jsbml.AbstractSBase
-
- getSBOTerm() - Method in interface org.sbml.jsbml.SBase
-
Grants access to the Systems Biology Ontology (SBO) term associated with
this
SBase
.
- getSBOTermID() - Method in class org.sbml.jsbml.AbstractSBase
-
- getSBOTermID() - Method in interface org.sbml.jsbml.SBase
-
Grants access to the Systems Biology Ontology (SBO) term associated with
this
SBase
.
- getScale() - Method in class org.sbml.jsbml.Unit
-
- 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
- getSeverity() - Method in exception org.sbml.jsbml.SBMLError
-
- getSeverity() - Method in class org.sbml.jsbml.util.Detail
-
- getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
Returns the shortLabel of the namespace parsed by this class.
- 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.
- 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 class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- getSource() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent
-
- getSpatial() - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
-
- getSpatialDimensions() - Method in class org.sbml.jsbml.Compartment
-
- getSpatialDimensions() - Method in class org.sbml.jsbml.ext.spatial.DomainType
-
Returns the value of spatialDimension
- getSpatialDimensionsAsDouble() - Method in class org.sbml.jsbml.Compartment
-
- getSpatialId() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
-
- getSpatialId() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume
-
- getSpatialId() - Method in interface org.sbml.jsbml.ext.spatial.SpatialNamedSBase
-
Returns the value of spatialId
- 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
-
- getSpatialRef() - Method in class org.sbml.jsbml.ext.spatial.SpatialSymbolReference
-
- 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(int) - Method in class org.sbml.jsbml.Model
-
Gets the n-th
Species
object in this Model.
- getSpecies(String) - Method in class org.sbml.jsbml.Model
-
- getSpecies() - Method in class org.sbml.jsbml.SimpleSpeciesReference
-
- getSpeciesCount() - Method in class org.sbml.jsbml.Model
-
- getSpeciesFeature(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- getSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
Gets an element from the listOfSpeciesFeatures, with the given id.
- getSpeciesFeatureChange(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- getSpeciesFeatureChange(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
Gets an element from the listOfSpeciesFeatureChanges, with the given id.
- getSpeciesFeatureChangeCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct
-
- getSpeciesFeatureCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- getSpeciesFeatureType() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- getSpeciesFeatureType(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getSpeciesFeatureType(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
Gets an element from the listOfSpeciesFeatureTypes, with the given id.
- getSpeciesFeatureTypeCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getSpeciesFeatureValue(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- getSpeciesFeatureValueCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- getSpeciesGlyph(int) - Method in class org.sbml.jsbml.ext.layout.Layout
-
- getSpeciesGlyph(String) - Method in class org.sbml.jsbml.ext.layout.Layout
-
- getSpeciesGlyph() - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
-
- getSpeciesGlyphCount() - Method in class org.sbml.jsbml.ext.layout.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
-
- 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
-
- getSpeciesReference() - Method in class org.sbml.jsbml.ext.spatial.ParameterType
-
- getSpeciesReferenceCount() - Method in class org.sbml.jsbml.Model
-
- getSpeciesReferenceGlyph(int) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph
-
- getSpeciesReferenceGlyph(String) - 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(int) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin
-
- getSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin
-
- getSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- getSpeciesType() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance
-
- 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.Model
-
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
- getSpeciesType() - Method in class org.sbml.jsbml.Species
-
Deprecated.
Only valid for SBML Level 2 Versions 2, 3, and 4.
- getSpeciesTypeComponentIndex() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex
-
- getSpeciesTypeComponentIndex(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getSpeciesTypeComponentIndex(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
Gets an element from the listOfSpeciesTypeComponentIndexes, with the given id.
- getSpeciesTypeComponentIndexCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getSpeciesTypeComponentMapInProduct(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin
-
- getSpeciesTypeComponentMapInProductCount() - Method in class org.sbml.jsbml.ext.multi.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(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- getSpeciesTypeInstance(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
Gets an element from the listOfSpeciesTypeInstances, with the given id.
- getSpeciesTypeInstance() - Method in class org.sbml.jsbml.Species
-
Deprecated.
Only valid for SBML Level 2 Versions 2, 3, and 4.
- getSpeciesTypeInstanceCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesType
-
- 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
-
- getSpreadMethod() - Method in class org.sbml.jsbml.ext.render.GradientBase
-
- getStart() - Method in class org.sbml.jsbml.ext.layout.CurveSegment
-
- getStart() - Method in class org.sbml.jsbml.ext.layout.LineSegment
-
- getStartHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve
-
- 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
-
- getStroke() - 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
.
- getSubmodel(int) - Method in class org.sbml.jsbml.ext.comp.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
-
- 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
-
- getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.KineticLaw
-
Deprecated.
- getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Model
-
- getSubstanceUnitsInstance() - Method in class org.sbml.jsbml.Species
-
- GetSuffix(int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Get the suffix.
- GetSuffix(int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Get the suffix.
- getSymbol() - Method in class org.sbml.jsbml.InitialAssignment
-
- getSymbol() - Method in enum org.sbml.jsbml.Unit.Kind
-
- getSymbolCount() - Method in class org.sbml.jsbml.Model
-
Returns the number of all instances of
Symbol
referenced within the
model.
- getSynonyms() - Method in class org.sbml.jsbml.ontology.Term
-
Returns all
Synonym
s of this
Term
.
- getTerm(String) - Static method in class org.sbml.jsbml.ext.dyn.CBO
-
Gets the CBO term with the id 'cboTerm'.
- getTerm() - Method in class org.sbml.jsbml.ontology.Term
-
Grants access to the underlying BioJava
Term
.
- getTerm(int) - Static method in class org.sbml.jsbml.SBO
-
Gets the SBO term with the id 'sboTerm'.
- getTerm(String) - Static method in class org.sbml.jsbml.SBO
-
Gets the SBO term with the id 'sboTerm'.
- getTerms() - Static method in class org.sbml.jsbml.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
-
- 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
-
- 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
-
- 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.Transformation2D
-
- getTransition(int) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
-
- getTransition(String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
-
- getTransitionCount() - Method in class org.sbml.jsbml.ext.qual.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'
- getTreeNodeChangeListenerCount() - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getTreeNodeChangeListenerCount() - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getTreeNodeChangeListenerCount() - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- getTrigger() - Method in class org.sbml.jsbml.Event
-
- getTrigger() - Static method in class org.sbml.jsbml.SBO
-
Returns the SBO id corresponding to the alias 'TRIGGER'
- getTriggerCount() - Method in class org.sbml.jsbml.Model
-
- getTriple() - Method in class org.sbml.jsbml.ontology.Triple
-
Grants access to the original BioJava
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.fbc.Objective
-
Returns the type.
- getType() - Method in class org.sbml.jsbml.ext.layout.CurveSegment
-
- 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.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
-
- getTypeList() - Method in class org.sbml.jsbml.ext.render.Style
-
- getTypeOfNotes() - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- getUncertainty() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin
-
- getUncertML() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution
-
Returns the value of uncertML
- getUncertML() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty
-
- getUnit(int) - Method in class org.sbml.jsbml.UnitDefinition
-
Returns a specific Unit instance belonging to this UnitDefinition.
- getUnitCount() - Method in class org.sbml.jsbml.Model
-
- getUnitCount() - Method in class org.sbml.jsbml.UnitDefinition
-
- getUnitDefinition(int) - Method in class org.sbml.jsbml.Model
-
- getUnitDefinition(String) - Method in class org.sbml.jsbml.Model
-
- getUnitDefinitionCount() - Method in class org.sbml.jsbml.Model
-
- getUnitKindsDefinedIn(int, int) - Static method in enum org.sbml.jsbml.Unit.Kind
-
Returns a set of
Unit.Kind
objects for the given level/version
combination of SBML.
- getUnitOntologyIdentifier() - Method in enum org.sbml.jsbml.Unit.Kind
-
Creates a unit ontology identifier for this
Unit.Kind
if possible
and returns it.
- getUnitOntologyNumber() - Method in enum org.sbml.jsbml.Unit.Kind
-
Looks for the corresponding unit ontology resource for this
Unit.Kind
.
- getUnitOntologyResource() - Method in enum org.sbml.jsbml.Unit.Kind
-
Creates a MIRIAM resource pointing to the entry in the unit ontology
corresponding to this
Unit.Kind
.
- 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 Parameter
s.
In this case this AssignmentRule
represents the SBML
element ParameterRule.
- 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 Parameter
s.
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
-
- 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'
- 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
-
This method is used to get the upper bound index from a collection of Dimension objects.
- getUpperFluxBound() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
-
- 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 class org.sbml.jsbml.ext.comp.CompSBasePlugin
-
- getURI() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin
-
- 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.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(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the namespace URI of an attribute in this
XMLAttributes
set (by position).
- getURI(int) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the URI of an XML namespace declaration by its position.
- getURI(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the URI of an XML namespace declaration by its prefix.
- getURI() - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Gets the URI of an XML namespace declaration by the empty prefix.
- getURI() - Method in class org.sbml.jsbml.xml.XMLToken
-
Returns the namespace URI of this XML element.
- getURI() - Method in class org.sbml.jsbml.xml.XMLTriple
-
- getUserObject(Object) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- getUserObject(Object) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- getUserObject() - Method in class org.sbml.jsbml.util.TreeNodeAdapter
-
- getUserObject(Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- getUseValuesFromTriggerTime() - Method in class org.sbml.jsbml.Event
-
- getV() - Method in class org.sbml.jsbml.util.ValuePair
-
- getValidationErrors() - Method in class org.sbml.jsbml.SBMLErrorLog
-
- getValue(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
-
Gets an element from the idToValue, with the given id.
- 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
-
- 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
-
- getValue() - Method in class org.sbml.jsbml.math.ASTConstantNumber
-
- getValue() - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- getValue() - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- getValue() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- getValue() - Method in class org.sbml.jsbml.math.parser.Token
-
An optional attribute value of the Token.
- getValue() - Method in interface org.sbml.jsbml.Quantity
-
- getValue() - Method in class org.sbml.jsbml.QuantityWithUnit
-
- getValue() - Method in class org.sbml.jsbml.SpeciesReference
-
- getValue() - Method in class org.sbml.jsbml.text.parser.Token
-
An optional attribute value of the Token.
- getValue() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- getValue() - Method in class org.sbml.jsbml.util.Pair
-
- getValue(int) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns the value of an attribute in this
XMLAttributes
set (by position).
- getValue(String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns an attribute's value by name.
- getValue(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns a value of an attribute with the given local name and namespace URI.
- getValue(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Returns a value of an attribute with the given
XMLTriple
.
- getVariable() - Method in interface org.sbml.jsbml.Assignment
-
- getVariable() - Method in class org.sbml.jsbml.ASTNode
-
Returns the variable of this node.
- getVariable() - Method in class org.sbml.jsbml.EventAssignment
-
- getVariable() - Method in class org.sbml.jsbml.ExplicitRule
-
- getVariable() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent
-
Returns the value of variable
- getVariable() - Method in class org.sbml.jsbml.ext.spatial.ParameterType
-
- getVariable() - Method in class org.sbml.jsbml.InitialAssignment
-
- getVariable() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
- getVariableCount() - Method in class org.sbml.jsbml.Model
-
- getVariableInstance() - Method in interface org.sbml.jsbml.Assignment
-
- getVariableInstance() - Method in class org.sbml.jsbml.EventAssignment
-
- getVariableInstance() - Method in class org.sbml.jsbml.ExplicitRule
-
- getVariableInstance() - Method in class org.sbml.jsbml.ext.spatial.ParameterType
-
- getVariableInstance() - Method in class org.sbml.jsbml.InitialAssignment
-
- getVectorDimensionSizes(Model, ASTNode) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath
-
This is used to obtain 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.AbstractSBasePlugin
-
- getVersion() - Method in interface org.sbml.jsbml.ext.SBasePlugin
-
- getVersion() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- getVersion() - Method in interface org.sbml.jsbml.SBase
-
Returns the Version within the SBML Level of the overall SBML document.
- getVersion() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- getVersionMajor() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin
-
- getVersionMinor() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin
-
- getViableWithoutChange() - Method in class org.sbml.jsbml.ext.req.ChangedMath
-
Returns the value of viableWithoutChange
- getVolume() - Method in class org.sbml.jsbml.Compartment
-
- getVolumeUnits() - Method in class org.sbml.jsbml.Model
-
Returns the volume units ID of this
Model
.
- getVolumeUnitsInstance() - Method in class org.sbml.jsbml.Model
-
- 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
-
- 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
- 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
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- getZ2() - Method in class org.sbml.jsbml.ext.render.LinearGradient
-
- getZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier
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- givenName - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
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- GlobalRenderInformation - Class in org.sbml.jsbml.ext.render
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- GlobalRenderInformation() - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation
-
Creates an GlobalRenderInformation instance
- GlobalRenderInformation(GlobalRenderInformation) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation
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Clone constructor
- 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
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- GlobalRenderInformation(String, int, int) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation
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- GlobalRenderInformation(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation
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- globalRenderInformation - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
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- glyph - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
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- GradientBase - Class in org.sbml.jsbml.ext.render
-
- GradientBase() - Constructor for class org.sbml.jsbml.ext.render.GradientBase
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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
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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 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- GradientStop - Class in org.sbml.jsbml.ext.render
-
- GradientStop(Double, String) - Constructor for class org.sbml.jsbml.ext.render.GradientStop
-
Creates a GradientStop instance with an offset and a color.
- GradientStop(Double, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.GradientStop
-
Creates a GradientStop instance with an offset, color, level, and version.
- GradientStop(GradientStop) - Constructor for class org.sbml.jsbml.ext.render.GradientStop
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Clone constructor
- GradientStop() - Constructor for class org.sbml.jsbml.ext.render.GradientStop
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- gradientStop - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
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- GraphicalObject - Class in org.sbml.jsbml.ext.layout
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- GraphicalObject() - Constructor for class org.sbml.jsbml.ext.layout.GraphicalObject
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- GraphicalObject(GraphicalObject) - Constructor for class org.sbml.jsbml.ext.layout.GraphicalObject
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- GraphicalObject(int, int) - Constructor for class org.sbml.jsbml.ext.layout.GraphicalObject
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- GraphicalObject(String) - Constructor for class org.sbml.jsbml.ext.layout.GraphicalObject
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- GraphicalObject(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.GraphicalObject
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- graphicalObject - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
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- 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
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Clone constructor
- GraphicalPrimitive2D - Class in org.sbml.jsbml.ext.render
-
- GraphicalPrimitive2D() - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive2D
-
- GraphicalPrimitive2D(int, int) - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive2D
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- GraphicalPrimitive2D(GraphicalPrimitive2D) - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive2D
-
Clone constructor
- GraphicalPrimitive2D.FillRule - Enum in org.sbml.jsbml.ext.render
-
- Group - Class in org.sbml.jsbml.ext.groups
-
- Group() - Constructor for class org.sbml.jsbml.ext.groups.Group
-
- Group(Group) - Constructor for class org.sbml.jsbml.ext.groups.Group
-
- Group(int, int) - Constructor for class org.sbml.jsbml.ext.groups.Group
-
- group - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- Group.Kind - Enum in org.sbml.jsbml.ext.groups
-
This is a collection of possible values for the
kind
attribute within
a
Group
.
- 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
-
- GroupsModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.groups.GroupsModelPlugin
-
- 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(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- gt(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Greater than.
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- gt(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- gt(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Greater than.
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML
-
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- gt(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-