S-Index (JSBML 1.1 API Specification)

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

S

SampledField - Class in org.sbml.jsbml.ext.spatial
SampledField() - Constructor for class org.sbml.jsbml.ext.spatial.SampledField
SampledField(SampledField) - Constructor for class org.sbml.jsbml.ext.spatial.SampledField
SampledField(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.SampledField
SampledField(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.SampledField
sampledField - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
SampledFieldGeometry - Class in org.sbml.jsbml.ext.spatial
SampledFieldGeometry() - Constructor for class org.sbml.jsbml.ext.spatial.SampledFieldGeometry
SampledFieldGeometry(SampledFieldGeometry) - Constructor for class org.sbml.jsbml.ext.spatial.SampledFieldGeometry
SampledFieldGeometry(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.SampledFieldGeometry
sampledFieldGeometry - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
sampledValue - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
SampledVolume - Class in org.sbml.jsbml.ext.spatial
SampledVolume() - Constructor for class org.sbml.jsbml.ext.spatial.SampledVolume
SampledVolume(SampledVolume) - Constructor for class org.sbml.jsbml.ext.spatial.SampledVolume
SampledVolume(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.SampledVolume
sampledVolume - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
samples - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
samplesLength - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
saturated - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
SAX2Parser - Interface in org.sbml.jsbml.util: An interface for XML SAX2 parsers.
SBase - Interface in org.sbml.jsbml: The interface to implement for each SBML element.
SBasePlugin - Interface in org.sbml.jsbml.ext: Defines the methods necessary for an SBase Plugin.
sBaseRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
SBaseRef - Class in org.sbml.jsbml.ext.comp: Contains the machinery for constructing references to specific components within enclosed models or even within external models located in other files.
SBaseRef() - Constructor for class org.sbml.jsbml.ext.comp.SBaseRef: Creates a SBaseRef instance.
SBaseRef(int, int) - Constructor for class org.sbml.jsbml.ext.comp.SBaseRef: Creates a SBaseRef instance with a level and version.
SBaseRef(SBaseRef) - Constructor for class org.sbml.jsbml.ext.comp.SBaseRef: Clone constructor
SBaseWithDerivedUnit - Interface in org.sbml.jsbml: This type represents an SBase object that is associated to a unit.
SBaseWithDimensionCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints: This checks if the given SBase is allowed to have a listOfDimensions.
SBaseWithDimensionCheck(Model, SBase) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.SBaseWithDimensionCheck: Creates a new SBaseWithDimensionCheck with a model and sbase.
SBaseWithUnit - Interface in org.sbml.jsbml: Defines a kind of SBase that is equipped with a defined unit.
SBMLCoreParser - Class in org.sbml.jsbml.xml.parsers: Parses the SBML core elements of an SBML file.
SBMLCoreParser() - Constructor for class org.sbml.jsbml.xml.parsers.SBMLCoreParser: Creates a SBMLCoreParser instance.
SBMLDocument - Class in org.sbml.jsbml: Represents the 'sbml' root node of a SBML file.
SBMLDocument() - Constructor for class org.sbml.jsbml.SBMLDocument: Creates a SBMLDocument instance.
SBMLDocument(int, int) - Constructor for class org.sbml.jsbml.SBMLDocument: Creates a SBMLDocument instance from a level and version.
SBMLDocument(SBMLDocument) - Constructor for class org.sbml.jsbml.SBMLDocument: Creates a new SBMLDocument instance from a given SBMLDocument.
SBMLDocumentAttributes - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
SBMLError - Exception in org.sbml.jsbml: Representation of errors, warnings and other diagnostics.
SBMLError() - Constructor for exception org.sbml.jsbml.SBMLError: Constructs a new SBMLError.
SBMLError(String) - Constructor for exception org.sbml.jsbml.SBMLError: Constructs a new SBMLError with the given message.
SBMLError.SEVERITY - Enum in org.sbml.jsbml
SBMLErrorConverter - Class in org.sbml.jsbml.xml.xstream.converter: Converts an SBMLError from the XML produced by the sbml.org online validator.
SBMLErrorConverter() - Constructor for class org.sbml.jsbml.xml.xstream.converter.SBMLErrorConverter
SBMLErrorLog - Class in org.sbml.jsbml: Log of errors and other events encountered during SBML processing.
SBMLErrorLog() - Constructor for class org.sbml.jsbml.SBMLErrorLog
SBMLException - Exception in org.sbml.jsbml: This class roughly corresponds to libSBML's SBMLError class.
SBMLException() - Constructor for exception org.sbml.jsbml.SBMLException: Creates a new SBMLException instance.
SBMLException(String) - Constructor for exception org.sbml.jsbml.SBMLException: Creates a new SBMLException instance.
SBMLException(String, Throwable) - Constructor for exception org.sbml.jsbml.SBMLException: Creates a new SBMLException instance.
SBMLException(Throwable) - Constructor for exception org.sbml.jsbml.SBMLException: Creates a new SBMLException instance.
SBMLException.Category - Enum in org.sbml.jsbml: Category of this exception.
SBMLException.Code - Enum in org.sbml.jsbml: Error codes.
SBMLException.Type - Enum in org.sbml.jsbml
SBMLInputConverter<T> - Interface in org.sbml.jsbml: This interface allows the implementing class to create a JSBML model based on some other data structure.
SBMLObjectForXML - Class in org.sbml.jsbml.xml.stax: An SBMLObjectForXML is an object to store the localName, prefix, namespace URI, attributes and text of a SBML component we want to write.
SBMLObjectForXML() - Constructor for class org.sbml.jsbml.xml.stax.SBMLObjectForXML
SBMLOutputConverter<T> - Interface in org.sbml.jsbml: This interface allows the implementing class to convert a JSBML model into another data structure.
SBMLRDFAnnotationParser - Class in org.sbml.jsbml.xml.parsers: Parses the RDF annotations as defined in the SBML specifications and put them into objects.
SBMLRDFAnnotationParser() - Constructor for class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
SBMLReader - Class in org.sbml.jsbml: Provides methods for reading SBML from files, text strings or streams.
SBMLReader() - Constructor for class org.sbml.jsbml.SBMLReader: Creates a new SBMLReader.
SBMLReader(SBMLReader) - Constructor for class org.sbml.jsbml.SBMLReader: Clone constructor.
SBMLReader - Class in org.sbml.jsbml.xml.stax: Provides all the methods to read a SBML file.
SBMLReader() - Constructor for class org.sbml.jsbml.xml.stax.SBMLReader
SBMLtools - Class in org.sbml.jsbml.util
SBMLtools() - Constructor for class org.sbml.jsbml.util.SBMLtools
SBMLTypeUndefinedException - Exception in org.sbml.jsbml: This error can be thrown whenever a data type is being initialized that is undefined for a certain SBML Level/Version combination.
SBMLTypeUndefinedException(Class<?>, int, int) - Constructor for exception org.sbml.jsbml.SBMLTypeUndefinedException
SBMLValidator - Class in org.sbml.jsbml.validator: Validates the SBML document given by filename.xml or located at the http:// URL.
SBMLValidator() - Constructor for class org.sbml.jsbml.validator.SBMLValidator
SBMLValidator.CHECK_CATEGORY - Enum in org.sbml.jsbml.validator: Enumerates the different possible check categories when performing the validation of an SBML document.
SBMLWriter - Class in org.sbml.jsbml: Provides methods for writing SBML to files, text strings or streams.
SBMLWriter() - Constructor for class org.sbml.jsbml.SBMLWriter: Creates a new SBMLWriter.
SBMLWriter(char, short) - Constructor for class org.sbml.jsbml.SBMLWriter: Creates a new SBMLWriter that uses the given character for indentation of the XML representation of SBML data structures (with the given number of such symbols).
SBMLWriter(SBMLWriter) - Constructor for class org.sbml.jsbml.SBMLWriter: Clone constructor.
SBMLWriter(String, String) - Constructor for class org.sbml.jsbml.SBMLWriter: Creates a new SBMLWriter for the program with the given name and version.
SBMLWriter(String, String, char, short) - Constructor for class org.sbml.jsbml.SBMLWriter: Creates a new SBMLWriter for the program with the given name and version that uses the given character for indentation of the XML representation of SBML data structures (with the given number of such symbols).
SBMLWriter - Class in org.sbml.jsbml.xml.stax: A SBMLWriter provides the methods to write a SBML file.
SBMLWriter() - Constructor for class org.sbml.jsbml.xml.stax.SBMLWriter: Creates a new SBMLWriter with default configuration for SBMLWriter.indentChar and SBMLWriter.indentCount.
SBMLWriter(char, short) - Constructor for class org.sbml.jsbml.xml.stax.SBMLWriter: Creates a new SBMLWriter with the given configuration for the SBMLWriter.indentChar and SBMLWriter.indentCount, i.e., the symbol to be used to indent elements in the XML representation of SBML data objects and the number of these symbols to be concatenated at the beginning of each new line for a new element.
SBO - Class in org.sbml.jsbml: Methods for interacting with Systems Biology Ontology (SBO) terms.
SBO() - Constructor for class org.sbml.jsbml.SBO
SBOFilter - Class in org.sbml.jsbml.util.filters: A Filter that accepts only instances of SBase whose SBO term field is set to a certain value of interest.
SBOFilter() - Constructor for class org.sbml.jsbml.util.filters.SBOFilter: Generates a new Filter for SBO terms but with an invalid SBO term as filter criterion.
SBOFilter(int...) - Constructor for class org.sbml.jsbml.util.filters.SBOFilter: Creates an SBO term filter with the given term as filter criterion.
sboNumberString(int) - Static method in class org.sbml.jsbml.SBO: Creates and returns a 7 digit SBO number for the given Term identifier (if this is a valid identifier).
sboTerm - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
scale - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
scaleX - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
scaleY - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
scaleZ - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
SCIENTIFIC_FORMAT - Static variable in class org.sbml.jsbml.util.StringTools
sec(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
sec(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
sec(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
sec(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
sec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
sec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
sec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
sec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
sec(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
sec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
sec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
sec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
sec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
sec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
sec(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the secant of a double value.
sech(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
sech(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
sech(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
sech(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
sech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
sech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
sech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
sech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
sech(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
sech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
sech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
sech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
sech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
sech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
sech(double) - Static method in class org.sbml.jsbml.util.Maths: This method computes the sech of n
section(String, boolean) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
section(String, boolean) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
selector(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
selector(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
selector(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
selector - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
selector(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
selector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
selector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
selector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
selector(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
selector(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
selector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
selector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
selector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
selector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
selector(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
serialVersionUID - Static variable in class org.sbml.jsbml.UnitDefinition: Generated serial version identifier.
set(int, T) - Method in class org.sbml.jsbml.ListOf
setAbout(String) - Method in class org.sbml.jsbml.Annotation: Sets the value of the about String of this object.
setAbsoluteCx(boolean) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of absoluteCx
setAbsoluteCx(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of absoluteCx
setAbsoluteCy(boolean) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of absoluteCy
setAbsoluteCy(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of absoluteCy
setAbsoluteCz(boolean) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of absoluteCz
setAbsoluteCz(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of absoluteCz
setAbsoluteFx(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of absoluteFx
setAbsoluteFy(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of absoluteFy
setAbsoluteFz(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of absoluteFz
setAbsoluteHeight(boolean) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of absoluteHeight
setAbsoluteHeight(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle: Set the value of absoluteHeight
setAbsoluteR(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of absoluteR
setAbsoluteRx(boolean) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of absoluteRx
setAbsoluteRx(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle: Set the value of absoluteRx
setAbsoluteRy(boolean) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of absoluteRy
setAbsoluteRy(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle: Set the value of absoluteRy
setAbsoluteWidth(boolean) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of absoluteWidth
setAbsoluteWidth(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle: Set the value of absoluteWidth
setAbsoluteX(boolean) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of absoluteX
setAbsoluteX(boolean) - Method in interface org.sbml.jsbml.ext.render.Point3D: Set the value of absoluteX
setAbsoluteX(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle
setAbsoluteX(boolean) - Method in class org.sbml.jsbml.ext.render.RenderPoint
setAbsoluteX(boolean) - Method in class org.sbml.jsbml.ext.render.Text
setAbsoluteX1(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of absoluteX1
setAbsoluteX2(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of absoluteX2
setAbsoluteY(boolean) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of absoluteY
setAbsoluteY(boolean) - Method in interface org.sbml.jsbml.ext.render.Point3D: Set the value of absoluteY
setAbsoluteY(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle
setAbsoluteY(boolean) - Method in class org.sbml.jsbml.ext.render.RenderPoint
setAbsoluteY(boolean) - Method in class org.sbml.jsbml.ext.render.Text
setAbsoluteY1(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of absoluteY1
setAbsoluteY2(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of absoluteY2
setAbsoluteZ(boolean) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of absoluteZ
setAbsoluteZ(boolean) - Method in interface org.sbml.jsbml.ext.render.Point3D: Set the value of absoluteZ
setAbsoluteZ(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle
setAbsoluteZ(boolean) - Method in class org.sbml.jsbml.ext.render.RenderPoint
setAbsoluteZ(boolean) - Method in class org.sbml.jsbml.ext.render.Text
setAbsoluteZ1(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of absoluteZ1
setAbsoluteZ2(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of absoluteZ2
setActiveObjective(Objective) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
setActiveObjective(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: The activeObjective refers to the id of an existing objective.
setActiveObjective(String) - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives: This attribute refers to an id of an existing Objective.
setAddGraphicalObjects(ListOf<GraphicalObject>) - Method in class org.sbml.jsbml.ext.layout.Layout: This element is optional.
setAndReplacement(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise: Sets the String that will be used to replace ' and ' (the mathML <and> element) in the boolean expressions.
setAnnotation(Annotation) - Method in class org.sbml.jsbml.AbstractSBase
setAnnotation(String) - Method in class org.sbml.jsbml.AbstractSBase
setAnnotation(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase
setAnnotation(Annotation) - Method in interface org.sbml.jsbml.SBase: Sets the value of the 'annotation' sub-element of this SBML object to a copy of annotation given as an Annotation instance.
setAnnotation(XMLNode) - Method in interface org.sbml.jsbml.SBase
setAnnotation(String) - Method in interface org.sbml.jsbml.SBase
setAnnotation - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
setApplyToAll(boolean) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin: Sets the value of applyToAll
setAreaUnits(String) - Method in class org.sbml.jsbml.Model: Sets the areaUnitsID of this Model to 'areaUnitsID'
setAreaUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model
setAreaUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model: Sets the areaUnitsID of this Model to the id of the UnitDefinition 'areaUnits'.
setArrayData(String) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: Sets the value of arrayData
setArrayDataLength(int) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: Sets the value of arrayDataLength
setArrayDimension(int) - Method in class org.sbml.jsbml.ext.arrays.Dimension: Sets the value of arrayDimension
setArrayDimension(int) - Method in class org.sbml.jsbml.ext.arrays.Index: Sets the value of arrayDimension
setAssociatedSpecies(String) - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Sets the value of associatedSpecies
setAssociation(Association) - Method in class org.sbml.jsbml.ext.fbc.GeneProductAssociation: Sets the value of association
setAttributes(XMLAttributes) - Method in class org.sbml.jsbml.xml.XMLToken: Sets an XMLAttributes to this XMLToken.
setBackgroundColor(Color) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase: Set the value of backgroundColor
setBasePoint1(Point) - Method in class org.sbml.jsbml.ext.layout.CubicBezier: basePoint1 specifies represents the base point closer to the start point.
setBasePoint2(Point) - Method in class org.sbml.jsbml.ext.layout.CubicBezier
setBindingSite1(String) - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Sets the value of bindingSite1
setBindingSite2(String) - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond: Sets the value of bindingSite2
setBindingStatus(BindingStatus) - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite: Sets the value of bindingStatus
setBiologicalQualifierType(int) - Method in class org.sbml.jsbml.CVTerm: Sets the biological qualifier type, using the CVTerm.Qualifier.values() array.
setBiologicalQualifierType(CVTerm.Qualifier) - Method in class org.sbml.jsbml.CVTerm: Sets the biological qualifier type of this CVTerm.
setBoundaryCondition(boolean) - Method in class org.sbml.jsbml.Species: Sets the boundaryCondition Boolean.
setBoundaryDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition: Sets the value of boundaryDomainType
setBoundaryMaximum(Boundary) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent: Sets the value of boundaryMaximum
setBoundaryMinimum(Boundary) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent: Sets the value of boundaryMinimum
setBoundingBox(BoundingBox) - Method in class org.sbml.jsbml.ext.layout.GraphicalObject: This is the only required element (besides the SId) of the GraphicalObject.
setBoundingBox(BoundingBox) - Method in class org.sbml.jsbml.ext.render.LineEnding: Set the value of boundingBox
setCaseSensitive(boolean) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3: Sets the case sensitivity of the parser, for the mathml elements.
setCaseSensitive(boolean) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2: Sets the case sensitivity of the parser, for the mathml elements.
setCaseSensitive(boolean) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser: Sets the case sensitivity of the parser, for the mathml elements.
setCaseSensitive(boolean) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3: Sets the case sensitivity of the parser, for the mathml elements.
setCaseSensitive(boolean) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2: Sets the case sensitivity of the parser, for the mathml elements.
setCategory(String) - Method in exception org.sbml.jsbml.SBMLError: Sets the category of this SBMLError.
setCategory(SBMLException.Category) - Method in exception org.sbml.jsbml.SBMLException
setCategory(int) - Method in class org.sbml.jsbml.util.Detail
setCBOTerm(Term) - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin: Sets the value of CBO
setChangedBy(String) - Method in class org.sbml.jsbml.ext.req.ChangedMath: Sets the value of changedBy
setCharacter(char) - Method in class org.sbml.jsbml.ASTNode: Sets the value of this ASTNode to the given character.
setCharacter(char) - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode: Sets the value of this ASTArithmeticOperatorNode to the given character.
setCharacters(String) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
setCharacters(String) - Method in class org.sbml.jsbml.xml.XMLToken: Sets the characters in this XMLToken.
setCharge(int) - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Sets the value of charge.
setCharge(int) - Method in class org.sbml.jsbml.Species: Deprecated.
Only defined in SBML Level 1, Version 1 and 2, and Level 2 Version 1. Since Level 2 Version 2 it has been marked as a deprecated property, but has been completely removed in SBML Level 3.
setChemicalFormula(String) - Method in class org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin: Sets the value of chemicalFormula.
setChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode: Set the child of this node
setClassName(String) - Method in class org.sbml.jsbml.ASTNode: Sets the class name of the mathML element represented by this ASTNode.
setCode(int) - Method in exception org.sbml.jsbml.SBMLError: Sets the error code of this SBMLError.
setCode(SBMLException.Code) - Method in exception org.sbml.jsbml.SBMLException
setCoefficient(double) - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: The coefficient attribute takes the value of the coefficient that the FluxObjective takes in the context of the enclosing Objective class.
setColumn(int) - Method in exception org.sbml.jsbml.SBMLError
setCompartment(Compartment) - Method in interface org.sbml.jsbml.CompartmentalizedSBase: Sets the compartment identifiers of this CompartmentalizedSBase to the id of the Compartment 'compartment'.
setCompartment(String) - Method in interface org.sbml.jsbml.CompartmentalizedSBase: Sets the compartment attribute.
setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph
setCompartment(String) - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph
setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.multi.CompartmentReference
setCompartment(String) - Method in class org.sbml.jsbml.ext.multi.CompartmentReference
setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.multi.SpeciesType
setCompartment(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType
setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
setCompartment(String) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
setCompartment(Compartment) - Method in class org.sbml.jsbml.Reaction
setCompartment(String) - Method in class org.sbml.jsbml.Reaction: Sets the compartmentID of this Reaction to 'compartmentID'.
setCompartment(Compartment) - Method in class org.sbml.jsbml.Species
setCompartment(String) - Method in class org.sbml.jsbml.Species
setCompartmentMapping(CompartmentMapping) - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin: Sets the value of compartmentMapping
setCompartmentReference(String) - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin: Sets the value of compartmentReference
setCompartmentReference(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Sets the value of compartmentReference
setCompartmentType(CompartmentType) - Method in class org.sbml.jsbml.Compartment: Deprecated.
setCompartmentType(String) - Method in class org.sbml.jsbml.Compartment: Deprecated.
Only valid in Level 2.
setCompartmentType(String) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin: Sets the value of compartmentType
setComplementA(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Sets the value of complementA
setComplementB(String) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Sets the value of complementB
setComponent(String) - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite: Sets the value of component
setComponent(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: Sets the value of component
setComponent(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Sets the value of component
setComponents(Double...) - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent: Sets the value of components
setCompression(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of compression
setCompression(CompressionKind) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of compression
setCompression(CompressionKind) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of compression
setCompression(String) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: Sets the value of compression
setCompression(CompressionKind) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: Sets the value of compression
setConsistencyChecks(SBMLValidator.CHECK_CATEGORY, boolean) - Method in class org.sbml.jsbml.SBMLDocument: Controls the consistency checks that are performed when SBMLDocument.checkConsistency() is called.
setConstant(boolean) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies: Sets the constant attribute.
setConstant(boolean) - Method in class org.sbml.jsbml.SpeciesReference
setConstant(boolean) - Method in class org.sbml.jsbml.Symbol
setConstant(boolean) - Method in interface org.sbml.jsbml.Variable: Sets the constant boolean of this Variable.
setConversionFactor(String) - Method in class org.sbml.jsbml.ext.comp.ReplacedElement: Sets the value of the optional conversionFactor attribute.
setConversionFactor(Parameter) - Method in class org.sbml.jsbml.Model: Sets the conversionFactorID of this Model to the id of the Parameter 'conversionFactor'.
setConversionFactor(String) - Method in class org.sbml.jsbml.Model: Sets the conversionFactorID of this Model to 'conversionFactorID'.
setConversionFactor(Parameter) - Method in class org.sbml.jsbml.Species: Sets the conversionFactorID of this Species to the id of 'conversionFactor'.
setConversionFactor(String) - Method in class org.sbml.jsbml.Species: Sets the conversionFactorID of this Species to 'conversionFactorID'.
setCoord1(double) - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint: Sets the value of coord1
setCoord2(double) - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint: Sets the value of coord2
setCoord3(double) - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint: Sets the value of coord3
setCoordinate(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.AdvectionCoefficient: Sets the value of coordinate
setCoordinate(String) - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference: Deprecated.
setCoordinate(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference: Deprecated.
setCoordinateBoundary(String) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition: Sets the value of coordinateBoundary
setCoordinateReference1(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient: Sets the value of coordinateReference1
setCoordinateReference2(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient: Sets the value of coordinateReference2
setCoordinateSystem(GeometryKind) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Sets the value of coordinateSystem
setCreatedDate(Date) - Method in class org.sbml.jsbml.History: Sets the createdDate.
setCSGNode(CSGNode) - Method in class org.sbml.jsbml.ext.spatial.CSGObject: Sets the value of csgNode
setCSGNode(CSGNode) - Method in class org.sbml.jsbml.ext.spatial.CSGTransformation: Sets the value of csgNode
setCsgObjectRef(String) - Method in class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive: Sets the value of csgObjectRef
setCurve(Curve) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: This is an optional attribute of type Curve.
setCurve(Curve) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: The curve describes the center section of a ReactionGlyph.
setCurve(Curve) - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph: The curve is an optional element of type Curve.
setCurve(Curve) - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph: The curve is an optional element of type Curve.
setCx(double) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of cx
setCx(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of cx
setCy(Double) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of cy
setCy(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of cy
setCz(Double) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of cz
setCz(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of cz
setData(String) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of data
setData(XMLNode) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of data
setDataType(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of dataType
setDataType(DataKind) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of dataType
setDataType(DataKind) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of dataType
setDataType(String) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: Sets the value of dataType
setDataType(DataKind) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints: Sets the value of dataType
setDebugMode(boolean) - Static method in class org.sbml.jsbml.ListOf: Allows you to influence the behavior of the ListOf.toString() method.
setDebugStream(PrintStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager: Set debug output.
setDebugStream(PrintStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager: Set debug output.
setDebugStream(PrintStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager: Set debug output.
setDebugStream(PrintStream) - Method in class org.sbml.jsbml.math.parser.FormulaParserTokenManager: Set debug output.
setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager: Set debug output.
setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager: Set debug output.
setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager: Set debug output.
setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager: Set debug output.
setDebugStream(PrintStream) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager: Set debug output.
setDefaultTerm(boolean) - Method in class org.sbml.jsbml.ext.qual.FunctionTerm: Sets if this FunctionTerm is a defaultTerm.
setDefinitionURL(String) - Method in class org.sbml.jsbml.ASTNode
setDefinitionURL(String) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode: Set the definitionURL of the MathML element represented by this ASTCiFunctionNode
setDefinitionURL(String) - Method in class org.sbml.jsbml.math.ASTCiNumberNode: Set the definitionURL of the MathML element represented by this ASTCiNumberNode
setDelay(Delay) - Method in class org.sbml.jsbml.Event: Sets the delay of this Event to 'delay'.
setDeletion(String) - Method in class org.sbml.jsbml.ext.comp.ReplacedElement: Sets the value of the optional deletion attribute.
setDenominator(int) - Method in class org.sbml.jsbml.math.ASTCnRationalNode: Set the value of the denominator
setDenominator(int) - Method in class org.sbml.jsbml.SpeciesReference: Deprecated.
setDepth(double) - Method in class org.sbml.jsbml.ext.layout.Dimensions: Depth is an optional attribute and specifies the size along the positive z axis.
setDetail(Detail) - Method in exception org.sbml.jsbml.SBMLError
setDiffusionKind(DiffusionKind) - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient: Sets the value of diffusionKind
setDimensions(Dimensions) - Method in class org.sbml.jsbml.ext.layout.BoundingBox: The dimensions element is required and of type Dimensions.
setDimensions(Dimensions) - Method in class org.sbml.jsbml.ext.layout.Layout: The dimensions element of type Dimensions specifies the dimensions of this layout.
setDistinctAttribute(String) - Method in class org.sbml.jsbml.ext.groups.MemberConstraint: Deprecated.

Sets the value of distinctAttribute
setDomain1(String) - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains
setDomain2(String) - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains: Sets the value of domain2
setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume: Sets the value of domainType
setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping: Sets the value of domainType
setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.CSGObject: Sets the value of domainType
setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.Domain: Sets the value of domainType
setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of domain
setDomainType(String) - Method in class org.sbml.jsbml.ext.spatial.SampledVolume: Sets the value of domainType
setDrawFromDistribution(DrawFromDistribution) - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin: Sets the value of drawFromDistribution
setEmail(String) - Method in class org.sbml.jsbml.Creator: Sets the email if it follows the syntax rules of valid e-mail addresses according to http://en.wikipedia.org/wiki/E-mail_address.
setEnableRotationMapping(Boolean) - Method in class org.sbml.jsbml.ext.render.LineEnding: Set the value of enableRotationMapping
setEncoding(String) - Method in class org.sbml.jsbml.ASTNode: Sets the encoding of the mathML element represented by this ASTNode.
setEnd(Point) - Method in class org.sbml.jsbml.ext.layout.CurveSegment: Sets the End Point of this CurveSegment.
setEnd(Point) - Method in class org.sbml.jsbml.ext.layout.LineSegment
setEnd() - Method in class org.sbml.jsbml.xml.XMLToken: Declares this XML start element is also an end element.
setEndHead(String) - Method in class org.sbml.jsbml.ext.render.RenderCurve: Set the value of endHead
setEndHead(String) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of endHead
setEOF() - Method in class org.sbml.jsbml.xml.XMLToken: Declares this XMLToken is an end-of-file (input) marker.
setError(boolean) - Method in exception org.sbml.jsbml.SBMLException
setExcerpt(String) - Method in exception org.sbml.jsbml.SBMLError: Sets the excerpt of this SBMLError.
setExplicitlyConstant(boolean) - Method in class org.sbml.jsbml.LocalParameter: Deprecated.
Since SBML Level 3 it is no longer possible to explicitly set a LocalParameter to constant = true because LocalParameter instances always represent constant a Quantity.
setExponent(int) - Method in class org.sbml.jsbml.math.ASTCnExponentialNode: Set the exponent value of this node
setExponent(double) - Method in class org.sbml.jsbml.Unit: Sets the exponent of this Unit
setExponent(int) - Method in class org.sbml.jsbml.Unit: Deprecated.
use Unit.setExponent(double)
setExtendedSBase(SBase) - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin: Sets the extended SBase.
setExtentConversionFactor(String) - Method in class org.sbml.jsbml.ext.comp.Submodel: The optional extentConversionFactor attribute is provided to allow references and assumptions about the scale of a model's reaction extent to be converted to the scale of the containing model.
setExtentUnits(String) - Method in class org.sbml.jsbml.Model: Sets the extendUnitsID of this Model to 'extentUnitsID'.
setExtentUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model
setExtentUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model: Sets the extentUnitsID of this Model to the id of the UnitDefinition 'extentUnits'.
setFamilyName(String) - Method in class org.sbml.jsbml.Creator: Sets the family name
setFast(boolean) - Method in class org.sbml.jsbml.Reaction: Sets the fast Boolean of this Reaction.
setFatal(boolean) - Method in exception org.sbml.jsbml.SBMLException
setFile(File) - Method in class org.sbml.jsbml.SBMLErrorLog: Sets the file.
setFill(String) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D: Set the value of fill
setFillRule(GraphicalPrimitive2D.FillRule) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D: Set the value of fillRule
setFilterForReference(boolean) - Method in class org.sbml.jsbml.ext.layout.NamedSBaseReferenceFilter
setFilterForSpecies(boolean) - Method in class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
setFilters(Set<Filter>) - Method in class org.sbml.jsbml.util.filters.AndFilter
setFontFamily(FontFamily) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle: Set the value of fontFamily
setFontFamily(FontFamily) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of fontFamily
setFontFamily(FontFamily) - Method in class org.sbml.jsbml.ext.render.Text
setFontSize(short) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle: Set the value of fontSize
setFontSize(Short) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of fontSize
setFontSize(short) - Method in class org.sbml.jsbml.ext.render.Text
setFontStyleItalic(boolean) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle: Set the value of fontStyleItalic
setFontStyleItalic(Boolean) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of fontStyleItalic
setFontStyleItalic(boolean) - Method in class org.sbml.jsbml.ext.render.Text
setFontWeightBold(boolean) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle: Set the value of fontWeightBold
setFontWeightBold(Boolean) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of fontWeightBold
setFontWeightBold(boolean) - Method in class org.sbml.jsbml.ext.render.Text
setFormula(String) - Method in class org.sbml.jsbml.AbstractMathContainer: Deprecated.
setFormula(String) - Method in interface org.sbml.jsbml.MathContainer: Deprecated.
As this is part of SBML Level 1, it is strongly recommended not to work with the String representation of a formula, but to deal with a more flexible ASTNode. Please use ASTNode.parseFormula(String) to create an ASTNode object from your formula String.
setForwardTransformation(TransformationComponent) - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation: Sets the value of forwardTransformation
setFunctionType(FunctionKind) - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume: Sets the value of functionType
setFx(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of fx
setFy(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of fy
setFz(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of fz
setGeneProduct(String) - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef: Sets the value of geneProduct
setGeneProductAssociation(GeneProductAssociation) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Sets the value of FBCReactionPlugin.geneProductAssociation
setGeometry(Geometry) - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin: Sets the value of geometry
setGeometryDefinition(String) - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping: Sets the value of geometryDefinition
setGivenName(String) - Method in class org.sbml.jsbml.Creator: Sets the given name
setGlyph(String) - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph: It contains a reference to the id of a GraphicalObject (or derived) object that is to be connected to the GeneralGlyph.
setGraphicalObject(GraphicalObject) - Method in class org.sbml.jsbml.ext.layout.TextGlyph
setGraphicalObject(String) - Method in class org.sbml.jsbml.ext.layout.TextGlyph: The graphicalObject attribute contains the id of any GraphicalObject and specifies that the TextGlyph should be considered to be a label to that object.
setGroup(RenderGroup) - Method in class org.sbml.jsbml.ext.render.LineEnding: Set the value of group
setGroup(RenderGroup) - Method in class org.sbml.jsbml.ext.render.Style: Set the value of group
setHasOnlySubstanceUnits(boolean) - Method in class org.sbml.jsbml.Species: Sets hasOnlySubstanceUnits Boolean
setHeight(double) - Method in class org.sbml.jsbml.ext.layout.Dimensions: Height is a required attribute and specifies the size along the positive y axis.
setHeight(double) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of height
setHeight(double) - Method in class org.sbml.jsbml.ext.render.Rectangle: Set the value of height
setHistory(History) - Method in class org.sbml.jsbml.AbstractSBase
setHistory(History) - Method in class org.sbml.jsbml.Annotation: Changes the History instance to 'history'
setHistory(History) - Method in interface org.sbml.jsbml.SBase: Sets the history.
setHref(String) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of href
setId(String) - Method in class org.sbml.jsbml.AbstractNamedSBase
setId(String) - Method in class org.sbml.jsbml.ASTNode: Sets the id of the mathML element represented by this ASTNode.
setId(String) - Method in class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
setId(String) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.
setId(String) - Method in class org.sbml.jsbml.ext.render.RenderGroup
setId(String) - Method in class org.sbml.jsbml.FunctionDefinition
setId(String) - Method in class org.sbml.jsbml.math.AbstractASTNode
setId(String) - Method in interface org.sbml.jsbml.math.ASTNode2: Set the id of this node
setId(String) - Method in class org.sbml.jsbml.math.ASTUnknown
setId(String) - Method in interface org.sbml.jsbml.NamedSBase: sets the id value with 'id'
setId(String) - Method in class org.sbml.jsbml.UnitDefinition
setId(String) - Method in class org.sbml.jsbml.util.filters.AssignmentVariableFilter
setId(String) - Method in class org.sbml.jsbml.util.filters.NameFilter
setIdenticalAttribute(String) - Method in class org.sbml.jsbml.ext.groups.MemberConstraint: Deprecated.

Sets the value of identicalAttribute
setIDList(String[]) - Method in class org.sbml.jsbml.ext.render.LocalStyle: Set the value of idList
setIdRef(String) - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Sets the value of the optional idRef attribute.
setIdRef(String) - Method in class org.sbml.jsbml.ext.dyn.DynElement: Sets the value of idRef
setIdRef(String) - Method in class org.sbml.jsbml.ext.groups.Member: Sets the value of idRef
setIdRef(NamedSBase) - Method in class org.sbml.jsbml.ext.groups.Member: Sets the value of idRef, using the id defined in the given NamedSBase
setidToValue(Map<String, Double>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler: Sets the given map.
setIdToVector(Map<String, ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
setIndent(int) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser: Deprecated.
setIndent(int) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
setIndentationChar(char) - Method in class org.sbml.jsbml.SBMLWriter: Influences the way how SBML data structures are represented in XML.
setIndentationChar(char) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter: Sets other blank character(s) for indentation.
setIndentationCount(short) - Method in class org.sbml.jsbml.SBMLWriter: Influences the way how SBML data structures are represented in XML.
setIndentationCount(int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter: Sets the indent for this SBMLWriter.
setIndentationCount(short) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter: Sets the indent for this SBMLWriter.
setIndentifyingParent(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Sets the value of identifyingParent
setIndenting(boolean) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser: Deprecated.
setIndenting(boolean) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
setIndex(int) - Method in class org.sbml.jsbml.ext.distrib.DistribInput: Sets the value of index
setInfo(boolean) - Method in exception org.sbml.jsbml.SBMLException
setInitialAmount(double) - Method in class org.sbml.jsbml.Species: Sets the initialAmount of this Species.
setInitialConcentration(double) - Method in class org.sbml.jsbml.Species: Sets the initialConcentration of this Species.
setInitialLevel(int) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies: Sets the initialLevel attribute.
setInitialValue(boolean) - Method in class org.sbml.jsbml.Trigger: Can only be set if Level >= 3.
setInteger(int) - Method in class org.sbml.jsbml.math.ASTCnIntegerNode: Set the value of this node
setInternal(boolean) - Method in exception org.sbml.jsbml.SBMLException
setInterpolation(InterpolationKind) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of interpolation
setIsActive(boolean) - Method in class org.sbml.jsbml.ext.spatial.GeometryDefinition: Sets the value of isActive
setIsLocal(boolean) - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin: Sets the value of isLocal
setIsSetNumberType(boolean) - Method in class org.sbml.jsbml.ASTNode
setIsType(boolean) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin: Sets the value of isType
setKey(L) - Method in class org.sbml.jsbml.util.Pair
setKind(Group.Kind) - Method in class org.sbml.jsbml.ext.groups.Group
setKind(Unit.Kind) - Method in class org.sbml.jsbml.Unit: Sets the Unit.Kind of this Unit
setKineticLaw(KineticLaw) - Method in class org.sbml.jsbml.Reaction: Sets the kineticLaw of this Reaction.
setL(L) - Method in class org.sbml.jsbml.util.ValuePair
setLabel(String) - Method in class org.sbml.jsbml.ext.fbc.GeneProduct: Sets the value of GeneProduct.label
setLang(String) - Method in class org.sbml.jsbml.util.Message
setLeftChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode: Set the left child of this ASTBinaryFunctionNode
setLeftChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
setLengthUnits(String) - Method in class org.sbml.jsbml.Model: Sets the lengthUnitsID of this Model to 'lengthUnitsID'.
setLengthUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model
setLengthUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model: Sets the lengthUnitsID of this Model to the id of the UnitDefinition 'lengthUnits'.
setLevel(int) - Method in class org.sbml.jsbml.AbstractSBase
setLevel(int) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
setLevel(int) - Method in interface org.sbml.jsbml.SBase: Sets the level of this object with 'level'.
setLevel(int) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setLevelAndVersion(int, int) - Method in class org.sbml.jsbml.SBMLDocument: Sets the SBML Level and Version of this SBMLDocument instance, without attempting to convert the model.
setLevelAndVersion(int, int, boolean) - Method in class org.sbml.jsbml.SBMLDocument: Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.
setLevelAndVersion(T, int, int) - Static method in class org.sbml.jsbml.util.SBMLtools
setLine(int) - Method in exception org.sbml.jsbml.SBMLError
setListener(ProgressListener) - Method in interface org.sbml.jsbml.SBMLInputConverter
setListOf(List<T>) - Method in class org.sbml.jsbml.ListOf: Clears this ListOf if not empty and then adds all elements in the given List to this ListOf.
setListOfAdditionalGraphicalObjects(ListOf<GraphicalObject>) - Method in class org.sbml.jsbml.ext.layout.Layout: This element is optional.
setListOfAdjacentDomains(ListOf<AdjacentDomains>) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Sets the given ListOf<AdjacentDomain>.
setListOfAnalyticVolumes(ListOf<AnalyticVolume>) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry: Sets the given ListOf<AnalyticVolume>.
setListOfChangedMaths(ListOf<ChangedMath>) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin: Sets the given ListOf<ChangedMath>.
setListOfColorDefinitions(ListOf<ColorDefinition>) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
setListOfCompartmentGlyphs(ListOf<CompartmentGlyph>) - Method in class org.sbml.jsbml.ext.layout.Layout: This element is optional.
setListOfCompartmentReferences(ListOf<CompartmentReference>) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin: Sets the given ListOf<CompartmentReference>.
setListOfCompartments(ListOf<Compartment>) - Method in class org.sbml.jsbml.Model: Sets the listOfCompartments of this Model to 'listOfCompartments'.
setListOfCompartmentTypes(ListOf<CompartmentType>) - Method in class org.sbml.jsbml.Model: Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
setListOfConstraints(ListOf<Constraint>) - Method in class org.sbml.jsbml.Model: Sets the listOfConstraints of this Model to 'listOfConstraints'.
setListOfCoordinateComponents(ListOf<CoordinateComponent>) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Sets the given ListOf<CoordinateComponent>.
setListOfCSGNodes(ListOf<CSGNode>) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Sets the given ListOf<CSGNode>.
setListOfCSGObjects(ListOf<CSGObject>) - Method in class org.sbml.jsbml.ext.spatial.CSGeometry: Sets the given ListOf<CSGObject>.
setListOfCurveSegments(ListOf<CurveSegment>) - Method in class org.sbml.jsbml.ext.layout.Curve: The listOfCurveSegments element contains arbitrary number of cuve segments that can be either of type LineSegment or of type CubicBezier.
setListOfDeletions(ListOf<Deletion>) - Method in class org.sbml.jsbml.ext.comp.Submodel: This list specifies objects to be removed from the submodel when composing the overall model.
setListOfDimensions(ListOf<Dimension>) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Sets the given ListOf<Dimension>.
setListOfDistribInputs(ListOf<DistribInput>) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution: Sets the given ListOf<DistribInput>.
setListOfDomains(ListOf<Domain>) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Sets the given ListOf<Domain>.
setListOfDomainTypes(ListOf<DomainType>) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Sets the given ListOf<DomainType>.
setListOfDynElements(ListOf<DynElement>) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin: Sets the value of listOfDynElements
setListOfElements(ListOf<RenderPoint>) - Method in class org.sbml.jsbml.ext.render.Polygon: Set the value of listOfElements
setListOfElements(ListOf<RenderPoint>) - Method in class org.sbml.jsbml.ext.render.RenderCurve
setListOfElements(ListOf<Transformation2D>) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Sets the given ListOf<Transformation2D>.
setListOfEventAssignments(ListOf<EventAssignment>) - Method in class org.sbml.jsbml.Event: Sets the given ListOf<EventAssignment>.
setListOfEvents(ListOf<Event>) - Method in class org.sbml.jsbml.Model: Sets the listOfEvents of this Model to 'listOfEvents'.
setListOfExternalModelDefinitions(ListOf<ExternalModelDefinition>) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin: The listOfExternamModelDefinitions is an optional element of CompSBMLDocumentPlugin and defines external SBML document references within the ExternalModelDefinition object.
setListOfFluxBounds(ListOf<FluxBound>) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Deprecated.
Only defined in FBC version 1.
setListOfFluxObjectives(ListOf<FluxObjective>) - Method in class org.sbml.jsbml.ext.fbc.Objective: This list houses the actual fluxes to partake in this objective function, which are encoded by FluxObjective Sets the given ListOf<FluxObjective>.
setListOfFunctionDefinitions(ListOf<FunctionDefinition>) - Method in class org.sbml.jsbml.Model: Sets the listOfFunctionDefinitions of this Model to 'listOfFunctionDefinitions'.
setListOfFunctionTerms(ListOf<FunctionTerm>) - Method in class org.sbml.jsbml.ext.qual.Transition: The Transition element contains exactly one list of FunctionTerms.
setListOfGeneProducts(ListOf<GeneProduct>) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Sets the given ListOf<GeneProduct>.
setListOfGeometryDefinitions(ListOf<GeometryDefinition>) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Sets the given ListOf<GeometryDefinition>.
setListOfGeometryDefinitions(ListOf<GeometryDefinition>) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry: Sets the given ListOf<GeometryDefinition>.
setListOfGlobalRenderInformation(ListOf<GlobalRenderInformation>) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin
setListOfGradientDefinitions(ListOf<GradientBase>) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
setListOfGradientStops(ListOf<GradientStop>) - Method in class org.sbml.jsbml.ext.render.GradientBase
setListOfGroups(ListOf<Group>) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin
setListOfIndices(ListOf<Index>) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Sets the given ListOf<Index>.
setListOfInitialAssignments(ListOf<InitialAssignment>) - Method in class org.sbml.jsbml.Model: Sets the Model.listOfInitialAssignments of this Model to 'listOfInitialAssignments'.
setListOfInputs(ListOf<Input>) - Method in class org.sbml.jsbml.ext.qual.Transition: The Transition element contains at most one list of Inputs.
setListOfInSpeciesTypeBonds(ListOf<InSpeciesTypeBond>) - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Sets the given ListOf<InSpeciesTypeBond>.
setListOfInteriorPoints(ListOf<InteriorPoint>) - Method in class org.sbml.jsbml.ext.spatial.Domain: Sets the given ListOf<InteriorPoint>.
setListOfLayouts(ListOf<Layout>) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin: The listOfLayouts element must contain at least one Layout.
setListOfLineEndings(ListOf<LineEnding>) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
setListOfLocalParameters(ListOf<LocalParameter>) - Method in class org.sbml.jsbml.KineticLaw: Sets the listOfParameters of this KineticLaw to 'list'.
setListOfLocalRenderInformation(ListOf<LocalRenderInformation>) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin
setListOfLocalStyles(ListOf<LocalStyle>) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation
setListOfMembers(ListOf<Member>) - Method in class org.sbml.jsbml.ext.groups.Group: Sets the given ListOf<Member>.
setListOfModelDefinitions(ListOf<ModelDefinition>) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin: listOfModelDefinitions is an optional list of CompSBMLDocumentPlugin which specifies ModelDefinitions for the SBML document.
setListOfModifiers(ListOf<ModifierSpeciesReference>) - Method in class org.sbml.jsbml.Reaction: Sets the listOfModifiers of this Reaction.
setListOfNestedCVTerms(List<CVTerm>) - Method in class org.sbml.jsbml.CVTerm: Sets the given ListOf<CVTerm>.
setListOfObjectives(ListOf<Objective>) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Sets the given ListOf<Objective>.
setListOfObjectives(ListOfObjectives) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Sets the given ListOfObjectives.
setListOfOrdinalMappings(ListOf<OrdinalMapping>) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry: Sets the given ListOf<OrdinalMapping>.
setListOfOutputs(ListOf<Output>) - Method in class org.sbml.jsbml.ext.qual.Transition: The Transition element contains at most one list of Outputs.
setListOfOutwardBindingSites(ListOf<OutwardBindingSite>) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Sets the given ListOf<OutwardBindingSite>.
setListOfParameters(ListOf<Parameter>) - Method in class org.sbml.jsbml.Model: Sets the Model.listOfParameters of this Model to 'listOfParameters'.
setListOfParametricObjects(ListOf<ParametricObject>) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry: Sets the given ListOf<ParametricObject>.
setListOfPorts(ListOf<Port>) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin: Sets the optional ListOf<Port>.
setListOfPossibleSpeciesFeatureValues(ListOf<PossibleSpeciesFeatureValue>) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Sets the given ListOf<PossibleSpeciesFeatureValue>.
setListOfProducts(ListOf<SpeciesReference>) - Method in class org.sbml.jsbml.Reaction: Sets the Reaction.listOfProducts of this Reaction.
setListOfQualitativeSpecies(ListOf<QualitativeSpecies>) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: QualModelPlugin may contain at most one listOfQualitativeSpecies which must contain at least on QualitativeSpecies.
setListOfReactants(ListOf<SpeciesReference>) - Method in class org.sbml.jsbml.Reaction: Sets the listOfReactants of this Reaction.
setListOfReactionGlyphs(ListOf<ReactionGlyph>) - Method in class org.sbml.jsbml.ext.layout.Layout: This element is optional.
setListOfReactions(ListOf<Reaction>) - Method in class org.sbml.jsbml.Model: Sets the Model.listOfReactions of this Model to 'listOfReactions'.
setListOfReferenceGlyph(ListOf<ReferenceGlyph>) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: The listOfReferenceGlyphs is optional, since conceivable the GeneralGlyph could just contain a number of subglyphs.
setListOfReplacedElements(ListOf<ReplacedElement>) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin: Sets the listOfReplacedElements.
setListOfRules(ListOf<Rule>) - Method in class org.sbml.jsbml.Model: Sets the Model.listOfRules of this Model to 'listOfRules'.
setListOfSampledFields(ListOf<SampledField>) - Method in class org.sbml.jsbml.ext.spatial.Geometry: Sets the given ListOf<SampledField>.
setListOfSampledVolumes(ListOf<SampledVolume>) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry: Sets the given ListOf<SampledVolume>.
setListOfSpatialComponents(ListOf<SpatialComponent>) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin: Sets the value of listOfSpatialComponents
setListOfSpecies(ListOf<Species>) - Method in class org.sbml.jsbml.Model: Sets the listOfSpecies of this Model to 'listOfSpecies'.
setListOfSpeciesFeatureChanges(ListOf<SpeciesFeatureChange>) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Sets the given ListOf<SpeciesFeatureChange>.
setListOfSpeciesFeatures(ListOf<SpeciesFeature>) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Sets the given ListOf<SpeciesFeature>.
setListOfSpeciesFeatureTypes(ListOf<SpeciesFeatureType>) - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Sets the given ListOf<SpeciesFeatureType>.
setListOfSpeciesFeatureValues(ListOf<SpeciesFeatureValue>) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: Sets the given ListOf<SpeciesFeatureValue>.
setListOfSpeciesGlyphs(ListOf<SpeciesGlyph>) - Method in class org.sbml.jsbml.ext.layout.Layout: This element is optional.
setListOfSpeciesReferencesGlyph(ListOf<SpeciesReferenceGlyph>) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: Since the Species element can have several graphical representations in the layout there must be a way to specify which SpeciesGlyph should be connected to the ReactionGlyph.
setListOfSpeciesTypeComponentIndexes(ListOf<SpeciesTypeComponentIndex>) - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Sets the given ListOf<SpeciesTypeComponentIndex>.
setListOfSpeciesTypeComponentMapInProducts(ListOf<SpeciesTypeComponentMapInProduct>) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin: Sets the given ListOf<SpeciesTypeComponentMapInProduct>.
setListOfSpeciesTypeInstances(ListOf<SpeciesTypeInstance>) - Method in class org.sbml.jsbml.ext.multi.SpeciesType: Sets the given ListOf<SpeciesTypeInstance>.
setListOfSpeciesTypes(ListOf<SpeciesType>) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin: Sets the listOfSpeciesTypes.
setListOfSpeciesTypes(ListOf<SpeciesType>) - Method in class org.sbml.jsbml.Model: Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
setListOfStyles(ListOf<Style>) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation
setListOfSubGlyphs(ListOf<GraphicalObject>) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph: The listOfSubGlyphs is an optional list that can contain sub-glyphs of the GeneralGlyph.
setListOfSubmodels(ListOf<Submodel>) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin: Sets the optional ListOf<Submodel>.
setListOfTextGlyphs(ListOf<TextGlyph>) - Method in class org.sbml.jsbml.ext.layout.Layout: This element is optional.
setListOfTransitions(ListOf<Transition>) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin: QualModelPlugin can contain at most one listOfTransitions which must contain at least one Transition.
setListOfUnitDefinitions(ListOf<UnitDefinition>) - Method in class org.sbml.jsbml.Model: Sets the listOfUnitDefinitions of this Model to 'listOfUnitDefinitions'.
setListOfUnits(ListOf<Unit>) - Method in class org.sbml.jsbml.UnitDefinition: Sets the UnitDefinition.listOfUnits of this UnitDefinition.
setLogger(XMLLogger) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
setLowerFluxBound(Parameter) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
setLowerFluxBound(String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Sets the value of lowerFluxBound
setMantissa(double) - Method in class org.sbml.jsbml.math.ASTCnExponentialNode: Get the mantissa value of this node
setMath(ASTNode) - Method in class org.sbml.jsbml.AbstractMathContainer
setMath(ASTNode) - Method in class org.sbml.jsbml.FunctionDefinition
setMath(ASTNode) - Method in interface org.sbml.jsbml.MathContainer: Sets the math ASTNode of this MathContainer to the given value.
setMathMLClass(String) - Method in class org.sbml.jsbml.math.AbstractASTNode
setMathMLClass(String) - Method in interface org.sbml.jsbml.math.ASTNode2: Set the class of the MathML element represented by this ASTNode2
setMathMLClass(String) - Method in class org.sbml.jsbml.math.ASTUnknown
setMaxLevel(int) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies: Sets the maxLevel attribute.
setMaxValue(double) - Method in class org.sbml.jsbml.ext.spatial.SampledVolume: Sets the value of maxValue
setMd5(String) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition: Sets the value of the optional md5 attribute.
setMembersShareType(boolean) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.

Sets the value of membersShareType
setMessage(String) - Method in class org.sbml.jsbml.Constraint: Sets the message of this Constraint to 'message'.
setMessage(XMLNode) - Method in class org.sbml.jsbml.Constraint: Sets the message of this Constraint to 'message'.
setMessage(Message) - Method in exception org.sbml.jsbml.SBMLError: Sets the message of this SBMLError.
setMessage(String) - Method in class org.sbml.jsbml.util.Message
setMetaId(String) - Method in class org.sbml.jsbml.AbstractSBase
setMetaId(String) - Method in interface org.sbml.jsbml.SBase: Sets the metaid value with 'metaid'.
setMetaIdRef(String) - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Sets the value of the optional metaIdRef attribute.
setMetaIdRef(String) - Method in class org.sbml.jsbml.ext.dyn.DynElement: Sets the value of metaIdRef
setMetaIdRef(String) - Method in class org.sbml.jsbml.ext.groups.Member: Sets the value of metaIdRef
setMetaIdRef(SBase) - Method in class org.sbml.jsbml.ext.groups.Member: Sets the value of metaIdRef, using the metaid defined in the given SBase
setMetaidRef(String) - Method in class org.sbml.jsbml.ext.layout.GraphicalObject: Sets the value of metaidRef which uniquely references elements in the model.
setMinValue(double) - Method in class org.sbml.jsbml.ext.spatial.SampledVolume: Sets the value of minValue
setModel(Model) - Method in class org.sbml.jsbml.SBMLDocument: Sets the Model for this SBMLDocument to the given Model.
setModelHistory(History) - Method in class org.sbml.jsbml.Model: Deprecated.
use AbstractSBase.setHistory(History)
setModelQualifierType(int) - Method in class org.sbml.jsbml.CVTerm: Sets the model qualifier type of this CVTerm, using the CVTerm.Qualifier.values() array.
setModelQualifierType(CVTerm.Qualifier) - Method in class org.sbml.jsbml.CVTerm: Sets the model qualifier type of this CVTerm.
setModelRef(String) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition: Sets the value of the optional modelRef attribute.
setModelRef(String) - Method in class org.sbml.jsbml.ext.comp.Submodel: The whole purpose of a Submodel object is to instantiate a model definition, which is to say, either a Model object defined in the same enclosing SBML document, or a model defined in an external SBML document.
setModifiedDate(Date) - Method in class org.sbml.jsbml.History: Sets the modifiedDate.
setMultiplier(double) - Method in class org.sbml.jsbml.Unit: Sets the multiplier of this Unit
setName(String) - Method in class org.sbml.jsbml.AbstractNamedSBase
setName(String) - Method in class org.sbml.jsbml.ASTNode: Sets the value of this ASTNode to the given name.
setName(String) - Method in class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
setName(String) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.
setName(String) - Method in class org.sbml.jsbml.ext.render.RenderGroup
setName(String) - Method in class org.sbml.jsbml.FunctionDefinition
setName(String) - Method in class org.sbml.jsbml.math.ASTCiNumberNode: Deprecated.
setName(String) - Method in class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
setName(String) - Method in interface org.sbml.jsbml.math.ASTCSymbolBaseNode: Set the name of the MathML element represented by this ASTCSymbolBaseNode
setName(String) - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode
setName(String) - Method in class org.sbml.jsbml.math.ASTFunction: Set the name of the MathML element represented by this ASTFunction
setName(String) - Method in interface org.sbml.jsbml.NamedSBase: sets the name value with 'name'.
setName(String) - Method in class org.sbml.jsbml.util.filters.NameFilter
setName(String) - Method in class org.sbml.jsbml.util.Option
setName(String) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
setNamedSBase(NamedSBase) - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
setNamespace(String) - Method in class org.sbml.jsbml.AbstractSBase: Sets the XML namespace to which this SBase belong.
setNamespace(String) - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin: Sets the XML namespace to which this SBasePlugin belong.
setNamespace(String) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
setNamespaces(XMLNamespaces) - Method in class org.sbml.jsbml.xml.XMLToken: Sets an XMLnamespaces to this XML element.
setNode(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
setNonRDFAnnotation(String) - Method in class org.sbml.jsbml.Annotation: Sets the value of the non RDF annotations
setNonRDFAnnotation(XMLNode) - Method in class org.sbml.jsbml.Annotation: Sets the value of the non RDF annotations
setNotes(String) - Method in class org.sbml.jsbml.AbstractSBase
setNotes(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase
setNotes(String) - Method in interface org.sbml.jsbml.SBase: Sets the notes with 'notes'.
setNotes(XMLNode) - Method in interface org.sbml.jsbml.SBase: Sets the XMLNode containing the notes sub-element of this object.
setNotesKeyToUserObject(String) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
setNumber(T) - Method in class org.sbml.jsbml.math.ASTCnNumberNode: Set the numerical base of MathML element.
setNumerator(int) - Method in class org.sbml.jsbml.math.ASTCnRationalNode: Set the value of the numerator
setNumericValue(String) - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue: Sets the value of numericValue
setNumSamples1(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of numSamples1
setNumSamples2(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of numSamples2
setNumSamples3(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of numSamples3
setOccur(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: Sets the value of occur
setOccur(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Sets the value of occur
setOffset(double) - Method in class org.sbml.jsbml.ext.render.GradientStop: Set the value of offset
setOffset(double) - Method in class org.sbml.jsbml.Unit: Deprecated.
Only defined for SBML Level 2 Version 1.
setOmitXMLDeclaration(boolean) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser: Deprecated.
setOmitXMLDeclaration(boolean) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
setOperation(FluxBound.Operation) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
SetOperation - Enum in org.sbml.jsbml.ext.spatial: This enum type was created following the specifications defined in Spatial Package v0.90.
setOperationType(SetOperation) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator: Sets the value of operationType
setOptions(List<Option>) - Method in class org.sbml.jsbml.SBMLErrorLog: Sets the list of options.
setOrder(double) - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph: The order attribute is an optional attribute of type Double.
setOrdinal(int) - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume: Sets the value of ordinal
setOrdinal(int) - Method in class org.sbml.jsbml.ext.spatial.CSGObject: Sets the value of ordinal
setOrdinal(int) - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping: Sets the value of ordinal
setOrganisation(String) - Method in class org.sbml.jsbml.Creator: Sets the organisation
setOrganization(String) - Method in class org.sbml.jsbml.Creator: Sets the organisation Equal to Creator.setOrganisation(String).
setOriginOfText(NamedSBase) - Method in class org.sbml.jsbml.ext.layout.TextGlyph
setOriginOfText(String) - Method in class org.sbml.jsbml.ext.layout.TextGlyph: Additionally the optional attribute originOfText holds the id of an entity in the Model.
setOrReplacement(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise: Sets the String that will be used to replace ' or ' (the mathML <or> element) in the boolean expressions.
setOtherAttribute(String, String) - Method in class org.sbml.jsbml.Creator: Deprecated.
those other attributes are not saved when writing the model
setOutputLevel(int) - Method in class org.sbml.jsbml.ext.qual.Output: The outputLevel is a non-negative integer used along with the transitionEffect to specify the effect of the Transition on the corresponding QualitativeSpecies.
setOutside(Compartment) - Method in class org.sbml.jsbml.Compartment: Deprecated.
setOutside(String) - Method in class org.sbml.jsbml.Compartment: Deprecated.
since Level 3 Version 1
setPackage(String) - Method in exception org.sbml.jsbml.SBMLError
setPackageName(String) - Method in class org.sbml.jsbml.ListOf: Sets the name of the package to which this SBase belong.
setPackageRequired(String, boolean) - Method in class org.sbml.jsbml.SBMLDocument: Sets the required attribute value of the given package extension (does nothing in fact!).
setPackageVersion(int) - Method in class org.sbml.jsbml.AbstractSBase
setPackageVersion(int) - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
setPackageVersion(int) - Method in interface org.sbml.jsbml.ext.SBasePlugin
setPackageVersion(int) - Method in interface org.sbml.jsbml.SBase: Sets the version of the SBML Level 3 package to which this element belongs.
setParamType(ParameterType) - Method in class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin
setParent(TreeNode) - Method in class org.sbml.jsbml.AbstractTreeNode
setParent(TreeNode) - Method in class org.sbml.jsbml.math.AbstractASTNode
setParent(TreeNode) - Method in interface org.sbml.jsbml.math.ASTNode2
setParent(TreeNode) - Method in class org.sbml.jsbml.math.ASTUnknown
setParentSBMLObject(MathContainer) - Method in class org.sbml.jsbml.ASTNode: Sets the Parent of the node to the given value
setParentSBMLObject(MathContainer) - Method in class org.sbml.jsbml.math.AbstractASTNode
setParentSBMLObject(ASTNode2, MathContainer) - Static method in class org.sbml.jsbml.math.ASTFactory: Sets the Parent of the node and its children to the given value
setParentSBMLObject(MathContainer) - Method in class org.sbml.jsbml.math.ASTFunction
setParentSBMLObject(MathContainer) - Method in interface org.sbml.jsbml.math.ASTNode2: Sets the parentSBMLObject to container recursively
setParentSBMLObject(MathContainer) - Method in class org.sbml.jsbml.math.ASTUnknown
setPattern(String) - Method in class org.sbml.jsbml.util.filters.CVTermFilter
setPersistent(boolean) - Method in class org.sbml.jsbml.Trigger: Can only be set if Level >= 3.
setPkgRequired(String, boolean) - Method in class org.sbml.jsbml.SBMLDocument: Deprecated.
use SBMLDocument.setPackageRequired(String, boolean)
setPointIndex(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of pointIndex
setPointIndex(Integer...) - Method in class org.sbml.jsbml.ext.spatial.PolygonObject: Deprecated.

Sets the value of pointIndex
setPointIndexLength(int) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of pointIndexLength
setPolygonType(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of polygonType
setPolygonType(PolygonKind) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of polygonType
setPortRef(String) - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Sets the value of the optional portRef attribute.
setPosition(Point) - Method in class org.sbml.jsbml.ext.layout.BoundingBox: Position always specifies the upper left corner of the BoundingBox.
setPrefix(String) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
setPrefixNotationInLogicalOperations(boolean) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
setPrimitiveType(String) - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive: Sets the value of primitiveType
setPrimitiveType(PrimitiveKind) - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive: Sets the value of primitiveType
setPrintNameIfAvailable(boolean) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
setPrintNameIfAvailable(boolean) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
setPriority(Priority) - Method in class org.sbml.jsbml.Event
setProductComponent(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Sets the value of productComponent
setProductSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange: Sets the value of productSpeciesFeature
setProgramName(String) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase: Set the value of programmName
setProgramName(String) - Method in class org.sbml.jsbml.SBMLWriter: Sets the name of this program, i.e., the program that is about to write out the SBMLDocument.
setProgramVersion(String) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase: Set the value of programVersion
setProgramVersion(String) - Method in class org.sbml.jsbml.SBMLWriter: Sets the version of this program, i.e., the program that is about to write out the SBMLDocument.
setQualifier(CVTerm.Qualifier) - Method in class org.sbml.jsbml.CVTerm: Sets the CVTerm.Qualifier of this CVTerm, sets at the same time the CVTerm.Type to the proper value.
setQualifier(CVTerm.Qualifier) - Method in class org.sbml.jsbml.util.filters.CVTermFilter
setQualifierType(int) - Method in class org.sbml.jsbml.CVTerm: Sets the type of this CVTerm to the CVTerm.Type represented by 'qualifierType'.
setQualifierType(CVTerm.Type) - Method in class org.sbml.jsbml.CVTerm: Sets the type of this CVTerm to 'type', the value of the CVTerm.Qualifier is reset to CVTerm.Qualifier.BQB_UNKNOWN or CVTerm.Qualifier.BQM_UNKNOWN.
setQualitativeSpecies(String) - Method in class org.sbml.jsbml.ext.qual.Input: The required attribute qualitativeSpecies is used to identify the QualitativeSpecies that is the input of this Transition.
setQualitativeSpecies(String) - Method in class org.sbml.jsbml.ext.qual.Output: The required attribute qualitativeSpecies is used to identify the QualitativeSpecies that is the output of this Transition.
setR(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of r
setRadicand(ASTNode2) - Method in class org.sbml.jsbml.math.ASTRootNode: Set the radicand of this ASTRootNode
setReactant(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Sets the value of reactant
setReactantComponent(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Sets the value of reactantComponent
setReactantSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange: Sets the value of reactantSpeciesFeature
setReaction(Reaction) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
setReaction(String) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
setReaction(Reaction) - Method in class org.sbml.jsbml.ext.fbc.FluxObjective
setReaction(String) - Method in class org.sbml.jsbml.ext.fbc.FluxObjective: Sets the reaction that thie FluxObjective is associated with in the context of the enclosing Objective class.
setReaction(Reaction) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: See setReaction(String)
setReaction(String) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: The reaction attribute is used to specify the id of the corresponding Reaction in the Model.
setReal(double) - Method in class org.sbml.jsbml.math.ASTCnRealNode: Set the value of this node
setReference(String) - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
setReference(String) - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph: The reference is an optional attribute that is used to connect the ReferenceGlyph with an element of the containing Model.
setReference(FunctionDefinition) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode: Set an instance of FunctionDefinition as the variable of this ASTCiFunctionNode.
setReference(CallableSBase) - Method in class org.sbml.jsbml.math.ASTCiNumberNode: Set an instance of CallableSBase as the variable of this ASTCiNumberNode.
setReferencedAttribute(String) - Method in class org.sbml.jsbml.ext.arrays.Index: Sets the value of referencedAttribute
setReferenceRenderInformation(String) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase: Set the value of referenceRenderInformation
setRefId(String) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode: Set refId attribute
setRefId(String) - Method in class org.sbml.jsbml.math.ASTCiNumberNode: Set refId attribute
setRenderInformation(GlobalRenderInformation) - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin: Set the value of renderInformation
setReplacedBy(ReplacedBy) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin: Sets the value of the optional replacedBy element.
setRepresentationType(RepresentationType) - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin: Sets the value of representationType
setResultLevel(int) - Method in class org.sbml.jsbml.ext.qual.FunctionTerm: The result of a term is described by a resultLevel.
setReverseTransformation(TransformationComponent) - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation: Sets the value of reverseTransformation
setReversible(boolean) - Method in class org.sbml.jsbml.Reaction: Sets the reversible Boolean of this Reaction.
setRightChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode: Set the right child of this ASTBinaryFunctionNode
setRole(String) - Method in class org.sbml.jsbml.ext.layout.ReferenceGlyph: The role attribute is used to specify how the reference should be displayed.
setRole(SpeciesReferenceRole) - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph: The role attribute is of type SpeciesReferenceRole and is used to specify how the species reference should be displayed.
setRoleList(String[]) - Method in class org.sbml.jsbml.ext.render.Style: Set the value of roleList
setRootExponent(ASTNode2) - Method in class org.sbml.jsbml.math.ASTRootNode: Set the root exponent of this ASTRootNode
setRotateAngleInRadians(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Sets the value of rotateAngleInRadians
setRotateAxisX(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Sets the value of rotateAxisX
setRotateAxisY(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Sets the value of rotateAxisY
setRotateAxisZ(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Sets the value of rotateAxisZ
setRx(Double) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of rx
setRx(double) - Method in class org.sbml.jsbml.ext.render.Rectangle: Set the value of rx
setRy(Double) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of ry
setRy(double) - Method in class org.sbml.jsbml.ext.render.Rectangle: Set the value of ry
setSampledField(String) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry: Sets the value of sampledField
setSampledValue(double) - Method in class org.sbml.jsbml.ext.spatial.SampledVolume: Sets the value of sampledValue
setSamples(String) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of samples
setSamplesLength(String) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of samplesLength
setSamplesLength(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of samplesLength
setSBaseListType(Class<T>) - Method in class org.sbml.jsbml.ListOf: Sets the ListOf.Type of this ListOf instance to the ListOf.Type defined by the given Class.
setSBaseListType(ListOf.Type) - Method in class org.sbml.jsbml.ListOf: Sets the ListOf.Type of this ListOf instance to 'listType'.
setSBaseRef(SBaseRef) - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Sets the value of the optional sBaseRef element.
setSBMLDocumentAttributes(Map<String, String>) - Method in class org.sbml.jsbml.SBMLDocument: Sets the SBMLDocument.SBMLDocumentAttributes.
setSBOTerm(int) - Method in class org.sbml.jsbml.AbstractSBase
setSBOTerm(String) - Method in class org.sbml.jsbml.AbstractSBase
setSBOTerm(int) - Method in interface org.sbml.jsbml.SBase: Sets the value of the 'sboTerm' attribute.
setSBOTerm(String) - Method in interface org.sbml.jsbml.SBase: Sets the value of the 'sboTerm' attribute.
setScale(int) - Method in class org.sbml.jsbml.Unit: Sets the scale of this Unit
setScaleX(double) - Method in class org.sbml.jsbml.ext.spatial.CSGScale: Sets the value of scaleX
setScaleY(double) - Method in class org.sbml.jsbml.ext.spatial.CSGScale: Sets the value of scaleY
setScaleZ(double) - Method in class org.sbml.jsbml.ext.spatial.CSGScale: Sets the value of scaleZ
setSeverity(String) - Method in exception org.sbml.jsbml.SBMLError: Sets the severity of this SBMLError.
setSeverity(int) - Method in class org.sbml.jsbml.util.Detail
setShortMessage(Message) - Method in exception org.sbml.jsbml.SBMLError
setShortMessage(String) - Method in exception org.sbml.jsbml.SBMLException
setSign(Sign) - Method in class org.sbml.jsbml.ext.qual.Input: The sign of type Sign can be used as an indication as to whether the contribution of this Input is positive, negative, both (dual) or unknown.
setSize(double) - Method in class org.sbml.jsbml.Compartment: Sets the size of this compartment to 'size'.
setSize(String) - Method in class org.sbml.jsbml.ext.arrays.Dimension: Sets the value of size
setSource(String) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition: Sets the value of the required source attribute.
setSpatial(boolean) - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
setSpatialDimensions(double) - Method in class org.sbml.jsbml.Compartment: Sets the spatialDimensions of this compartment to 'i'.
setSpatialDimensions(int) - Method in class org.sbml.jsbml.Compartment
setSpatialDimensions(short) - Method in class org.sbml.jsbml.Compartment: Sets the spatialDimensions of this compartment to 'spatialDimensiosn'.
setSpatialDimensions(int) - Method in class org.sbml.jsbml.ext.spatial.DomainType: Sets the value of spatialDimension
setSpatialId(String) - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
setSpatialId(String) - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume
setSpatialId(String) - Method in interface org.sbml.jsbml.ext.spatial.SpatialNamedSBase: Sets the value of spatialId
setSpatialIndex(SpatialKind) - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent: Sets the value of spatialIndex
setSpatialPoints(SpatialPoints) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry: Sets the value of spatialPoints
setSpatialRef(String) - Method in class org.sbml.jsbml.ext.spatial.SpatialSymbolReference: Sets the value of spatialRef
setSpatialSizeUnits(String) - Method in class org.sbml.jsbml.Species: Deprecated.
This property is only valid for SBML Level 2 Versions 1 and 2.
setSpatialSizeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Species: Deprecated.
Only valid for SBML Level 2 Versions 1 and 2.
setSpecies(Species) - Method in class org.sbml.jsbml.ext.layout.SpeciesGlyph
setSpecies(String) - Method in class org.sbml.jsbml.ext.layout.SpeciesGlyph: The species attribute allows modelers to link the SpeciesGlyph to the id of the corresponding Species object in the Model.
setSpecies(Species) - Method in class org.sbml.jsbml.SimpleSpeciesReference: Sets the speciesID to the id of the Species 'species'.
setSpecies(String) - Method in class org.sbml.jsbml.SimpleSpeciesReference: Sets the speciesID to 'spec'.
setSpeciesFeatureType(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature: Sets the value of speciesFeatureType
setSpeciesGlyph(String) - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph: The speciesGlyph attribute contains a reference to the id of a SpeciesGlyph object that is to be connected to the ReactionGlyph.
setSpeciesReference(SimpleSpeciesReference) - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph: See setSpeciesReference(String).
setSpeciesReference(String) - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph: The speciesReference is an optional attribute that allows modelers to connect the SpeciesReferenceGlyph with a particular SpeciesReference of the containing Model.
setSpeciesReference(String) - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin: Sets the value of speciesReference
setSpeciesReference(String) - Method in class org.sbml.jsbml.ext.spatial.ParameterType
setSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Sets the value of speciesType
setSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Sets the value of speciesType
setSpeciesType(SpeciesType) - Method in class org.sbml.jsbml.Species: Deprecated.
setSpeciesType(String) - Method in class org.sbml.jsbml.Species: Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
setSpeciesTypeComponentIndex(String) - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex: Sets the value of speciesTypeComponentIndex
setSpId(String) - Method in class org.sbml.jsbml.ext.spatial.ParameterType
setSpreadMethod(GradientBase.Spread) - Method in class org.sbml.jsbml.ext.render.GradientBase: Set the value of spreadMethod
setStart(Point) - Method in class org.sbml.jsbml.ext.layout.CurveSegment: Sets the Start Point of this CurveSegment.
setStart(Point) - Method in class org.sbml.jsbml.ext.layout.LineSegment
setStartHead(String) - Method in class org.sbml.jsbml.ext.render.RenderCurve: Set the value of startHead
setStartHead(String) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of startHead
setStatus(String) - Method in class org.sbml.jsbml.SBMLErrorLog: Sets the status.
setStatus(String) - Method in class org.sbml.jsbml.util.Option
setStoichiometry(double) - Method in class org.sbml.jsbml.SpeciesReference: Sets the stoichiometry of this SpeciesReference.
setStoichiometryMath(StoichiometryMath) - Method in class org.sbml.jsbml.SpeciesReference: Deprecated.
setStopColor(String) - Method in class org.sbml.jsbml.ext.render.GradientStop: Set the value of stopColor
setStrict(boolean) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Sets the value of strict
setStrictness(boolean) - Method in class org.sbml.jsbml.math.AbstractASTNode: Set the strictness of this node
setStrictness(boolean) - Method in interface org.sbml.jsbml.math.ASTNode2: Set the strictness of this node
setStrictness(boolean) - Method in class org.sbml.jsbml.math.ASTUnknown
setStroke(String) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D: Set the value of stroke
setStrokeDashArray(Short[]) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D: Set the value of strokeDashArray
setStrokeWidth(double) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D: Set the value of strokeWidth
setStyle(String) - Method in class org.sbml.jsbml.ASTNode: Sets the style of the mathML element represented by this ASTNode.
setStyle(String) - Method in class org.sbml.jsbml.math.AbstractASTNode
setStyle(String) - Method in interface org.sbml.jsbml.math.ASTNode2: Set the style of this node
setStyle(String) - Method in class org.sbml.jsbml.math.ASTUnknown
setSubmodelRef(String) - Method in class org.sbml.jsbml.ext.comp.ReplacedBy: Sets the value of the required submodelRef attribute.
setSubmodelRef(String) - Method in class org.sbml.jsbml.ext.comp.ReplacedElement: The required attribute submodelRef takes a value which must be the identifier of a Submodel object in the containing model.
setSubstanceUnits(String) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
Only defined for SBML Level 1 and Level 2 Version 1 and 2.
setSubstanceUnits(Unit) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setSubstanceUnits(String) - Method in class org.sbml.jsbml.Model: Sets the Model.substanceUnitsID of this Model to 'substanceUnitsID'
setSubstanceUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model: Sets the substanceUnitsID of this Model to the id of 'substanceUnits'.
setSubstanceUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model
setSubstanceUnits(String) - Method in class org.sbml.jsbml.Species: Sets the substanceUnitsID to 'unit'.
setSubstanceUnits(Unit) - Method in class org.sbml.jsbml.Species: Sets the substanceUnits.
setSubstanceUnits(Unit.Kind) - Method in class org.sbml.jsbml.Species: Sets the substanceUnits.
setSubstanceUnits(UnitDefinition) - Method in class org.sbml.jsbml.Species: Sets the substanceUnitsID to the id of 'units'.
setSymbol(String) - Method in class org.sbml.jsbml.InitialAssignment: Deprecated.
use InitialAssignment.setVariable(String).
setSystem(boolean) - Method in exception org.sbml.jsbml.SBMLException
setTerms(int...) - Method in class org.sbml.jsbml.util.filters.SBOFilter
setText(String) - Method in class org.sbml.jsbml.ext.layout.TextGlyph: The String text attribute facilitates adding of independent text, like a title or a comment to the diagram.
setTextAnchor(TextAnchor) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle: Set the value of textAnchor
setTextAnchor(TextAnchor) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of textAnchor
setTextAnchor(TextAnchor) - Method in class org.sbml.jsbml.ext.render.Text
setThisAsParentSBMLObject(SBase) - Method in class org.sbml.jsbml.AbstractSBase: Deprecated.
setThisAsParentSBMLObject(SBase) - Method in interface org.sbml.jsbml.SBase: Deprecated.
use SBase.registerChild(SBase)
setThresholdLevel(int) - Method in class org.sbml.jsbml.ext.qual.Input: The thresholdLevel is a non-negative integer that can be used to set the threshold level of the particular input.
setTimeConversionFactor(String) - Method in class org.sbml.jsbml.ext.comp.Submodel: The optional timeConversionFactor attribute is provided to allow references and assumptions about the scale of time in the Submodel to be converted to the scale of time in the containing model.
setTimeUnits(String) - Method in class org.sbml.jsbml.Event: Deprecated.
This is only applicable for SBML Level 2, Versions 1 and 2.
setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Event: Deprecated.
setTimeUnits(String) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
Only defined for Level 1 and Level 2 Version 1.
setTimeUnits(Unit) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
Only defined for Level 1 and Level 2 Version 1.
setTimeUnits(String) - Method in class org.sbml.jsbml.Model: Sets the timeUnits of this Model to 'timeUnistID'
setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model: Sets the timeUnitsID of this Model to the id of the UnitDefinition 'timeUnits'.
setTimeUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model: Sets the Model.timeUnitsID of this Model to the given unit kind.
setTimeUnitsID(String) - Method in class org.sbml.jsbml.Event: Deprecated.
setTransform(Double[]) - Method in class org.sbml.jsbml.ext.render.Transformation2D: Set the value of transform
setTransitionEffect(InputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Input: Each Input has a required attribute transitionEffect of type InputTransitionEffect which describes how the QualitativeSpecies referenced by the Input is affected by the Transition.
setTransitionEffect(OutputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Output: Each Output has a required attribute transitionEffect of type OutputTransitionEffect which describes how the QualitativeSpecies referenced by the Output is affected by the Transition.
setTranslateX(double) - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation: Sets the value of translateX
setTranslateY(double) - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation: Sets the value of translateY
setTranslateZ(double) - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation: Sets the value of translateZ
setTrigger(Trigger) - Method in class org.sbml.jsbml.Event: Sets the trigger of this Event to 'trigger'.
setTriple(XMLTriple) - Method in class org.sbml.jsbml.xml.XMLToken: Sets the XMLTripe (name, uri and prefix) of this XML element.
setType(String) - Method in class org.sbml.jsbml.ASTNode: Sets the type from a String.
setType(ASTNode.Type) - Method in class org.sbml.jsbml.ASTNode: Sets the type of this ASTNode to the given Type.
setType(String) - Method in class org.sbml.jsbml.ext.fbc.Objective: The required type attribute contains a Objective.Type which represents the sense of the optimality constraint and can take one of two values, minimize or maximize.
setType(Objective.Type) - Method in class org.sbml.jsbml.ext.fbc.Objective: Sets the value of type
setType(BoundaryConditionKind) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition: Sets the value of type
setType(String) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition
setType(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent: Sets the value of type
setType(String) - Method in class org.sbml.jsbml.math.AbstractASTNode
setType(ASTNode.Type) - Method in class org.sbml.jsbml.math.AbstractASTNode
setType(String) - Method in interface org.sbml.jsbml.math.ASTNode2: Sets the type from a String.
setType(ASTNode.Type) - Method in interface org.sbml.jsbml.math.ASTNode2: Set the type of the MathML element represented by this ASTNode2
setType(String) - Method in class org.sbml.jsbml.math.ASTUnknown
setType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTUnknown
setType(ASTNode.Type) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
setType(ASTNode.Type) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setTypeList(String[]) - Method in class org.sbml.jsbml.ext.render.Style: Set the value of typeList
setTypeOfNotes(String) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader: Sets the typeOfNote of this parser.
setUIFlag(boolean) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
setUIFlag(boolean) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setUncertainty(Uncertainty) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin: Sets the value of uncertainty
setUncertML(XMLNode) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution: Sets the value of uncertML
setUncertML(XMLNode) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty: Sets the value of uncertML
setUnitRef(String) - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Sets the value of the optional unitRef attribute This attribute is used to refer to the identifier of a UnitDefinition object.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
setUnits(String) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
setUnits(Unit) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
setUnits(String) - Method in class org.sbml.jsbml.ASTNode: Sets the units attribute.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.ASTNode
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.ASTNode
setUnits(String) - Method in class org.sbml.jsbml.Compartment: Sets the unitsID of this QuantityWithUnit.
setUnits(Unit) - Method in class org.sbml.jsbml.Compartment: Sets the Unit of this Compartment.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.Compartment: Sets the unit of this Compartment.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.Compartment: Set the unit attribute of this Compartment to the given unit definition.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.Event: Deprecated.
setUnits(String) - Method in class org.sbml.jsbml.Event: Deprecated.
setUnits(Unit) - Method in class org.sbml.jsbml.Event: Deprecated.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.Event: Deprecated.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.ExplicitRule: Deprecated.
setUnits(String) - Method in class org.sbml.jsbml.ExplicitRule: Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
setUnits(Unit) - Method in class org.sbml.jsbml.ExplicitRule: Deprecated.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.ExplicitRule: Deprecated.
This is a requirement for Level 1 Version 1 and Version 2, but can only be used in conjunction with Parameters. In this case this AssignmentRule represents the SBML element ParameterRule.
setUnits(String) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent: Sets the value of unit
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent
setUnits(Unit) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setUnits(String) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setUnits(Unit) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setUnits(String) - Method in class org.sbml.jsbml.math.ASTCnNumberNode: Set the units of the MathML element represented by this ASTCnNumberNode
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
setUnits(String) - Method in interface org.sbml.jsbml.SBaseWithUnit: Sets the unitsID of this SBaseWithUnit.
setUnits(Unit) - Method in interface org.sbml.jsbml.SBaseWithUnit: Sets the Unit of this SBaseWithUnit.
setUnits(Unit.Kind) - Method in interface org.sbml.jsbml.SBaseWithUnit: Sets the unit of this SBaseWithUnit.
setUnits(UnitDefinition) - Method in interface org.sbml.jsbml.SBaseWithUnit: Set the unit attribute of this SBaseWithUnit to the given unit definition.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setUnitSize(double) - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping: Sets the value of unitSize
setUpperFluxBound(Parameter) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
setUpperFluxBound(String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Sets the value of upperFluxBound
setUserObject(Object) - Method in class org.sbml.jsbml.util.TreeNodeAdapter
setUseValuesFromTriggerTime(boolean) - Method in class org.sbml.jsbml.Event: Sets the useValuesFromTriggerTime of this Event to 'useValuesFromTriggerTime'.
setV(V) - Method in class org.sbml.jsbml.util.ValuePair
setValue(double) - Method in class org.sbml.jsbml.ASTNode: Sets the value of this ASTNode to the given double number and sets the node type to REAL.
setValue(double, int) - Method in class org.sbml.jsbml.ASTNode: Sets the value of this ASTNode to the given real (double) in two parts: the mantissa and the exponent.
setValue(int) - Method in class org.sbml.jsbml.ASTNode: Sets the value of this ASTNode to the given (long) integer and sets the node type to INTEGER.
setValue(int, int) - Method in class org.sbml.jsbml.ASTNode: Sets the value of this ASTNode to the given rational in two parts: the numerator and denominator.
setValue(double) - Method in class org.sbml.jsbml.Compartment
setValue(double) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
setValue(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue: Sets the value of value
setValue(Color) - Method in class org.sbml.jsbml.ext.render.ColorDefinition: Set the value of value
setValue(double) - Method in class org.sbml.jsbml.ext.spatial.Boundary: Sets the value of value
setValue(boolean) - Method in class org.sbml.jsbml.math.ASTBoolean: Set the value of this ASTBoolean
setValue(double) - Method in class org.sbml.jsbml.math.ASTConstantNumber: Set the value of this ASTConstantNumber
setValue(boolean) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
setValue(T) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
setValue(double) - Method in interface org.sbml.jsbml.Quantity: Sets the value of this Quantity.
setValue(double) - Method in class org.sbml.jsbml.QuantityWithUnit
setValue(double) - Method in class org.sbml.jsbml.SpeciesReference
setValue(boolean) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(Boolean) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(double) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(int) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(long) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(CallableSBase) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(Node) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(Number) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(short) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(String) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(V) - Method in class org.sbml.jsbml.util.Pair
setVariable(String) - Method in interface org.sbml.jsbml.Assignment: Sets the variableID of this Assignment to the given value.
setVariable(Variable) - Method in interface org.sbml.jsbml.Assignment: Sets the variableID of this Assignment to the id of the Variable 'variable'.Listeners are notified about this change.
setVariable(CallableSBase) - Method in class org.sbml.jsbml.ASTNode: Allows you to directly set an instance of CallableSBase as the variable of this ASTNode.
setVariable(String) - Method in class org.sbml.jsbml.EventAssignment
setVariable(Variable) - Method in class org.sbml.jsbml.EventAssignment
setVariable(String) - Method in class org.sbml.jsbml.ExplicitRule
setVariable(Variable) - Method in class org.sbml.jsbml.ExplicitRule
setVariable(String) - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent: Sets the value of SpatialComponent.variable
setVariable(String) - Method in class org.sbml.jsbml.ext.spatial.ParameterType
setVariable(String) - Method in class org.sbml.jsbml.InitialAssignment
setVariable(Variable) - Method in class org.sbml.jsbml.InitialAssignment
setVariable(String) - Method in class org.sbml.jsbml.math.ASTCnNumberNode: Set the variable for this ASTNumber node
setVersion(int) - Method in class org.sbml.jsbml.AbstractSBase
setVersion(int) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
setVersion(int) - Method in interface org.sbml.jsbml.SBase: Sets the version of this object with 'version'.
setVersion(int) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setVersionMajor(short) - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin: Set the value of versionMajor
setVersionMinor(Short) - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin: Set the value of versionMinor
setViableWithoutChange(boolean) - Method in class org.sbml.jsbml.ext.req.ChangedMath: Sets the value of viableWithoutChange
setVolume(double) - Method in class org.sbml.jsbml.Compartment: Deprecated.
This method is only available for SBML Level 1. You should either use Compartment.setSize(double) or Compartment.setValue(double).
setVolumeUnits(String) - Method in class org.sbml.jsbml.Model: Sets the volumeUnitsID of this Model to 'volumeUnitsID'
setVolumeUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model
setVolumeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model: Sets the volumeUnitsID of this Model to the id of the UnitDefinition 'volumeUnits'.
setVTextAnchor(VTextAnchor) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle: Set the value of VTextAnchor
setVTextAnchor(VTextAnchor) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of vTextAnchor
setVTextAnchor(VTextAnchor) - Method in class org.sbml.jsbml.ext.render.Text
setWarning(boolean) - Method in exception org.sbml.jsbml.SBMLException
setWidth(double) - Method in class org.sbml.jsbml.ext.layout.Dimensions: Width is a required attribute and specifies the size along the positive x axis.
setWidth(double) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of width
setWidth(double) - Method in class org.sbml.jsbml.ext.render.Rectangle: Set the value of width
setX(double) - Method in class org.sbml.jsbml.ext.layout.Point: Sets the x coordinate.
setX(double) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of x
setX(double) - Method in interface org.sbml.jsbml.ext.render.Point3D: Set the value of x
setX(double) - Method in class org.sbml.jsbml.ext.render.Rectangle
setX(double) - Method in class org.sbml.jsbml.ext.render.RenderPoint
setX(double) - Method in class org.sbml.jsbml.ext.render.Text
setX1(double) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of x1
setX1(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of x1
setX2(double) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of x2
setX2(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of x2
setXML(boolean) - Method in exception org.sbml.jsbml.SBMLException
setXMLNode(XMLNode) - Method in class org.sbml.jsbml.Annotation
setY(double) - Method in class org.sbml.jsbml.ext.layout.Point: Sets the y coordinate.
setY(double) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of y
setY(double) - Method in interface org.sbml.jsbml.ext.render.Point3D: Set the value of y
setY(double) - Method in class org.sbml.jsbml.ext.render.Rectangle
setY(double) - Method in class org.sbml.jsbml.ext.render.RenderPoint
setY(double) - Method in class org.sbml.jsbml.ext.render.Text
setY1(double) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of y1
setY1(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of y1
setY2(double) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of y2
setY2(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of y2
setZ(double) - Method in class org.sbml.jsbml.ext.layout.Point: Sets the z coordinate.
setZ(double) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of z
setZ(double) - Method in interface org.sbml.jsbml.ext.render.Point3D: Set the value of z
setZ(double) - Method in class org.sbml.jsbml.ext.render.Rectangle
setZ(double) - Method in class org.sbml.jsbml.ext.render.RenderPoint
setZ(double) - Method in class org.sbml.jsbml.ext.render.Text
setZ1(double) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of z1
setZ1(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of z1
setZ2(double) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of z2
setZ2(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of z2
shortLabel - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
shortLabel - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
shortLabel - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
shortLabel - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
shortLabel - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
shortLabel - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants
shortLabel - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
shortLabel - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
shortLabel - Static variable in class org.sbml.jsbml.ext.qual.QualConstants: The short name/label of the package
shortLabel - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
shortLabel - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
shortLabel - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
sign - Static variable in class org.sbml.jsbml.ext.qual.QualConstants
Sign - Enum in org.sbml.jsbml.ext.qual: The sign is an enumeration of values used to indicate direction of an Input within the system.
SimpleCharStream - Class in org.sbml.jsbml.math.parser: An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
SimpleCharStream(Reader, int, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream - Class in org.sbml.jsbml.text.parser: An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
SimpleCharStream(Reader, int, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleSpeciesReference - Class in org.sbml.jsbml: The base class of SpeciesReference and ModifierSpeciesReference.
SimpleSpeciesReference() - Constructor for class org.sbml.jsbml.SimpleSpeciesReference: Creates a SimpleSpeciesReference instance.
SimpleSpeciesReference(int, int) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference: Creates a SimpleSpeciesReference instance.
SimpleSpeciesReference(SimpleSpeciesReference) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference: Creates a SimpleSpeciesReference instance from a given SimpleSpeciesReference.
SimpleSpeciesReference(Species) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference: Creates a SimpleSpeciesReference instance from a given Species.
SimpleSpeciesReference(String) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference: Creates a SimpleSpeciesReference instance.
SimpleSpeciesReference(String, int, int) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference: Creates a SimpleSpeciesReference instance.
SimpleSpeciesReference(String, String, int, int) - Constructor for class org.sbml.jsbml.SimpleSpeciesReference: Creates a SimpleSpeciesReference instance.
SimpleTreeNodeChangeListener - Class in org.sbml.jsbml.util: This very simple implementation of an TreeNodeChangeListener writes all the events to the standard out stream.
SimpleTreeNodeChangeListener() - Constructor for class org.sbml.jsbml.util.SimpleTreeNodeChangeListener: Creates an TreeNodeChangeListener that writes all events to the standard output.
simplify(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
simplify() - Method in class org.sbml.jsbml.UnitDefinition: Simplifies the UnitDefinition so that any Unit objects occurring within the UnitDefinition.listOfUnits occurs only once.
sin(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
sin(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
sin(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
sin(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
sin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
sin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
sin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
sin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
sin(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
sin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
sinh(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
sinh(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
sinh(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
sinh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
sinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
sinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
sinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
sinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
sinh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
sinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
sinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
sinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
sinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
sinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
size - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
size() - Method in class org.sbml.jsbml.ListOf
size - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
size() - Method in class org.sbml.jsbml.xml.XMLAttributes
SLPITTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants: RegularExpression Id.
SLPITTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants: RegularExpression Id.
SLPITTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants: RegularExpression Id.
SLPITTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants: RegularExpression Id.
SLPITTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants: RegularExpression Id.
SLPITTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants: RegularExpression Id.
source - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
SpatialCompartmentPlugin - Class in org.sbml.jsbml.ext.spatial
SpatialCompartmentPlugin() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin
SpatialCompartmentPlugin(Compartment) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin
SpatialCompartmentPlugin(SpatialCompartmentPlugin) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin
spatialComponent - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
SpatialComponent - Class in org.sbml.jsbml.ext.dyn
SpatialComponent() - Constructor for class org.sbml.jsbml.ext.dyn.SpatialComponent: Empty constructor
SpatialComponent(int, int) - Constructor for class org.sbml.jsbml.ext.dyn.SpatialComponent: Constructor
SpatialComponent(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.dyn.SpatialComponent: Constructor
SpatialComponent(SpatialComponent) - Constructor for class org.sbml.jsbml.ext.dyn.SpatialComponent: Constructor
SpatialConstants - Class in org.sbml.jsbml.ext.spatial: Contains some constants related to the spatial package.
SpatialConstants() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialConstants
spatialDimensions - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
spatialDimensions - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
spatialId - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
spatialIndex - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
SpatialKind - Enum in org.sbml.jsbml.ext.dyn: This is a collection of possible values for the spatialIndex attribute within a SpatialComponent.
SpatialModelPlugin - Class in org.sbml.jsbml.ext.spatial
SpatialModelPlugin() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialModelPlugin
SpatialModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialModelPlugin
SpatialModelPlugin(SpatialModelPlugin) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialModelPlugin
SpatialNamedSBase - Interface in org.sbml.jsbml.ext.spatial
SpatialParameterPlugin - Class in org.sbml.jsbml.ext.spatial
SpatialParameterPlugin() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin
SpatialParameterPlugin(SpatialParameterPlugin) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin
SpatialParameterPlugin(Parameter) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialParameterPlugin
SpatialParser - Class in org.sbml.jsbml.xml.parsers
SpatialParser() - Constructor for class org.sbml.jsbml.xml.parsers.SpatialParser
spatialPoints - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
SpatialPoints - Class in org.sbml.jsbml.ext.spatial
SpatialPoints() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialPoints: Creates an SpatialPoints instance
SpatialPoints(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialPoints: Creates a SpatialPoints instance with a level and version.
SpatialPoints(SpatialPoints) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialPoints: Clone constructor
SpatialReactionPlugin - Class in org.sbml.jsbml.ext.spatial
SpatialReactionPlugin() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin
SpatialReactionPlugin(Reaction) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin
SpatialReactionPlugin(SpatialReactionPlugin) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin
spatialRef - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
spatialSizeUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
SpatialSpeciesPlugin - Class in org.sbml.jsbml.ext.spatial
SpatialSpeciesPlugin() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
SpatialSpeciesPlugin(Species) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
SpatialSpeciesPlugin(SpatialSpeciesPlugin) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
spatialSymbolReference - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
SpatialSymbolReference - Class in org.sbml.jsbml.ext.spatial
SpatialSymbolReference() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSymbolReference
SpatialSymbolReference(SpatialSymbolReference) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSymbolReference
SpatialSymbolReference(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSymbolReference
SpatialTest - Class in org.sbml.jsbml.ext.spatial
SpatialTest() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialTest
specialToken - Variable in class org.sbml.jsbml.math.parser.Token: This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
specialToken - Variable in class org.sbml.jsbml.text.parser.Token: This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
species - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
Species - Class in org.sbml.jsbml: Represents the species XML element of a SBML file.
Species() - Constructor for class org.sbml.jsbml.Species: Creates a Species instance.
Species(int, int) - Constructor for class org.sbml.jsbml.Species: Creates a Species instance from a level and version.
Species(Species) - Constructor for class org.sbml.jsbml.Species: Creates a Species instance from a Species.
Species(String) - Constructor for class org.sbml.jsbml.Species
Species(String, int, int) - Constructor for class org.sbml.jsbml.Species: Creates a Species instance from a level and verison.
Species(String, String, int, int) - Constructor for class org.sbml.jsbml.Species
species - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
SpeciesFeature - Class in org.sbml.jsbml.ext.multi
SpeciesFeature() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature: Creates an SpeciesFeature instance
SpeciesFeature(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature: Creates a SpeciesFeature instance with an id.
SpeciesFeature(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature: Creates a SpeciesFeature instance with a level and version.
SpeciesFeature(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature: Creates a SpeciesFeature instance with an id, level, and version.
SpeciesFeature(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature: Creates a SpeciesFeature instance with an id, name, level, and version.
SpeciesFeature(SpeciesFeature) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature: Clone constructor
SpeciesFeatureChange - Class in org.sbml.jsbml.ext.multi
SpeciesFeatureChange() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange: Creates an SpeciesFeatureChange instance
SpeciesFeatureChange(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange: Creates a SpeciesFeatureChange instance with an id.
SpeciesFeatureChange(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange: Creates a SpeciesFeatureChange instance with a level and version.
SpeciesFeatureChange(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange: Creates a SpeciesFeatureChange instance with an id, level, and version.
SpeciesFeatureChange(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange: Creates a SpeciesFeatureChange instance with an id, name, level, and version.
SpeciesFeatureChange(SpeciesFeatureChange) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange: Clone constructor
speciesFeatureType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
SpeciesFeatureType - Class in org.sbml.jsbml.ext.multi: A species type (SpeciesType) can carry any number of features (SpeciesFeatureType), which are characteristic properties specific for this type of species (Species).
SpeciesFeatureType() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Creates an SpeciesFeatureType instance
SpeciesFeatureType(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Creates a SpeciesFeatureType instance with an id.
SpeciesFeatureType(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Creates a SpeciesFeatureType instance with a level and version.
SpeciesFeatureType(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Creates a SpeciesFeatureType instance with an id, level, and version.
SpeciesFeatureType(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Creates a SpeciesFeatureType instance with an id, name, level, and version.
SpeciesFeatureType(SpeciesFeatureType) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Clone constructor
SpeciesFeatureValue - Class in org.sbml.jsbml.ext.multi
SpeciesFeatureValue() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureValue: Creates an SpeciesFeatureValue instance
SpeciesFeatureValue(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureValue: Creates a SpeciesFeatureValue instance with a level and version.
SpeciesFeatureValue(SpeciesFeatureValue) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureValue: Clone constructor
speciesGlyph - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
SpeciesGlyph - Class in org.sbml.jsbml.ext.layout: The SpeciesGlyph class has an optional species attribute, in addition to to the attributes from GraphicalObject.
SpeciesGlyph() - Constructor for class org.sbml.jsbml.ext.layout.SpeciesGlyph
SpeciesGlyph(int, int) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesGlyph
SpeciesGlyph(SpeciesGlyph) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesGlyph
SpeciesGlyph(String) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesGlyph
SpeciesGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesGlyph
speciesReference - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
speciesReference - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
SpeciesReference - Class in org.sbml.jsbml: Represents the speciesReference XML element of a SBML file.
SpeciesReference() - Constructor for class org.sbml.jsbml.SpeciesReference: Creates a SpeciesReference instance.
SpeciesReference(int, int) - Constructor for class org.sbml.jsbml.SpeciesReference: Creates a SpeciesReference instance.
SpeciesReference(Species) - Constructor for class org.sbml.jsbml.SpeciesReference: Creates a SpeciesReference instance from a Species.
SpeciesReference(SpeciesReference) - Constructor for class org.sbml.jsbml.SpeciesReference: Creates a SpeciesReference instance from a given SpeciesReference.
SpeciesReference(String) - Constructor for class org.sbml.jsbml.SpeciesReference: Creates a SpeciesReference instance.
SpeciesReference(String, int, int) - Constructor for class org.sbml.jsbml.SpeciesReference: Creates a SpeciesReference instance.
SpeciesReference(String, String, int, int) - Constructor for class org.sbml.jsbml.SpeciesReference: Creates a SpeciesReference instance.
SpeciesReferenceFilter - Class in org.sbml.jsbml.util.filters: This is a special NameFilter that allows users to search for a SimpleSpeciesReference that refers to a Species with the given identifier attribute.
SpeciesReferenceFilter() - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter: Creates a new SpeciesReferenceFilter with undefined properties.
SpeciesReferenceFilter(Species) - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter: Creates a new SpeciesReferenceFilter that only accepts instances of SpeciesReference pointing to the id of the given Species.
SpeciesReferenceFilter(String) - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
SpeciesReferenceFilter(String, String) - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
speciesReferenceGlyph - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
SpeciesReferenceGlyph - Class in org.sbml.jsbml.ext.layout: The SpeciesReferenceGlyph class describes the graphical connection between a SpeciesGlyph and a ReactionGlyph (which would be an arrow or some curve in most cases).
SpeciesReferenceGlyph() - Constructor for class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
SpeciesReferenceGlyph(int, int) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
SpeciesReferenceGlyph(SpeciesReferenceGlyph) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
SpeciesReferenceGlyph(String) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
SpeciesReferenceGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
SpeciesReferenceRole - Enum in org.sbml.jsbml.ext.layout: Enumeration that defines the different SpeciesReferenceRoles that are encoded by the Layout package.
speciesType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
SpeciesType - Class in org.sbml.jsbml.ext.multi: The element SpeciesType, which is part of SBML Level 2 Version 4 specification, is not part of SBML Level 3 Version 1 Core any more.
SpeciesType() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType: Creates an SpeciesType instance
SpeciesType(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType: Creates a SpeciesType instance with a level and version.
SpeciesType(SpeciesType) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType: Clone constructor
SpeciesType(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType: Creates a SpeciesType instance with an id.
SpeciesType(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType: Creates a SpeciesType instance with an id, level, and version.
SpeciesType(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType: Creates a SpeciesType instance with an id, name, level, and version.
SpeciesType - Class in org.sbml.jsbml: Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
SpeciesType() - Constructor for class org.sbml.jsbml.SpeciesType: Deprecated.
SpeciesType(int, int) - Constructor for class org.sbml.jsbml.SpeciesType: Deprecated.
SpeciesType(SpeciesType) - Constructor for class org.sbml.jsbml.SpeciesType: Deprecated.
SpeciesType(String) - Constructor for class org.sbml.jsbml.SpeciesType: Deprecated.
SpeciesType(String, int, int) - Constructor for class org.sbml.jsbml.SpeciesType: Deprecated.
SpeciesType(String, String, int, int) - Constructor for class org.sbml.jsbml.SpeciesType: Deprecated.
speciesType - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
speciesTypeComponentIndex - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
SpeciesTypeComponentIndex - Class in org.sbml.jsbml.ext.multi
SpeciesTypeComponentIndex() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Creates an SpeciesTypeComponentIndex instance
SpeciesTypeComponentIndex(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Creates a SpeciesTypeComponentIndex instance with an id.
SpeciesTypeComponentIndex(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Creates a SpeciesTypeComponentIndex instance with a level and version.
SpeciesTypeComponentIndex(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Creates a SpeciesTypeComponentIndex instance with an id, level, and version.
SpeciesTypeComponentIndex(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Creates a SpeciesTypeComponentIndex instance with an id, name, level, and version.
SpeciesTypeComponentIndex(SpeciesTypeComponentIndex) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Clone constructor
SpeciesTypeComponentMapInProduct - Class in org.sbml.jsbml.ext.multi
SpeciesTypeComponentMapInProduct() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Creates an SpeciesTypeComponentMapInProduct instance
SpeciesTypeComponentMapInProduct(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Creates a SpeciesTypeComponentMapInProduct instance with a level and version.
SpeciesTypeComponentMapInProduct(SpeciesTypeComponentMapInProduct) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct: Clone constructor
SpeciesTypeInstance - Class in org.sbml.jsbml.ext.multi
SpeciesTypeInstance() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Creates an SpeciesTypeInstance instance
SpeciesTypeInstance(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Creates a SpeciesTypeInstance instance with an id.
SpeciesTypeInstance(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Creates a SpeciesTypeInstance instance with a level and version.
SpeciesTypeInstance(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Creates a SpeciesTypeInstance instance with an id, level, and version.
SpeciesTypeInstance(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Creates a SpeciesTypeInstance instance with an id, name, level, and version.
SpeciesTypeInstance(SpeciesTypeInstance) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Clone constructor
speciesTypeRestriction - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
speciesTypeState - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
SPLITTER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants: RegularExpression Id.
SPLITTER - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants: RegularExpression Id.
SPLITTER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants: RegularExpression Id.
spreadMethod - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
sqrt(ASTNode) - Static method in class org.sbml.jsbml.ASTNode: Creates a root ASTNode.
sqrt() - Method in class org.sbml.jsbml.ASTNode: Applies the square root function on this syntax tree and returns the resulting tree.
sqrt(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
sqrt(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
sqrt(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
sqrt(ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory: Creates a square root of type ASTRootNode with the specified radicand of type ASTNode2.
sqrt(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler: Square root.
sqrt(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
sqrt(Object) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
sqrt(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
sqrt(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
sqrt(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
sqrt(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
sqrt(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler: Square root.
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
sqrt(Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
start - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
startHead - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
stateFeature - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
stateFeatureInstance - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
stateFeatureValue - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
StaticallyComputableCompiler - Class in org.sbml.jsbml.ext.arrays.compiler: This compiler is used to check if an ASTNode object contains only constant values or Dimension ids.
StaticallyComputableCompiler(Model) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler: Constructs a new StaticallyComputableCompiler object
staticFlag - Static variable in class org.sbml.jsbml.math.parser.SimpleCharStream: Whether parser is static.
staticFlag - Static variable in class org.sbml.jsbml.text.parser.SimpleCharStream: Whether parser is static.
stoichiometry - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
StoichiometryMath - Class in org.sbml.jsbml: Deprecated.
Since SBML Level 3 Version 1 use AssignmentRule with instances of SpeciesReference as Variable instead.
StoichiometryMath() - Constructor for class org.sbml.jsbml.StoichiometryMath: Deprecated.
StoichiometryMath(int, int) - Constructor for class org.sbml.jsbml.StoichiometryMath: Deprecated.
StoichiometryMath(StoichiometryMath) - Constructor for class org.sbml.jsbml.StoichiometryMath: Deprecated.
stopColor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
strict - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in Version 2 Release 4.
string() - Method in class org.sbml.jsbml.math.parser.FormulaParser
string() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
STRING - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants: RegularExpression Id.
STRING - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants: RegularExpression Id.
string() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
string() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
STRING - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants: RegularExpression Id.
STRING - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants: RegularExpression Id.
string() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
STRING - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants: RegularExpression Id.
string() - Method in class org.sbml.jsbml.text.parser.FormulaParser
string() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
STRING - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants: RegularExpression Id.
STRING - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants: RegularExpression Id.
string() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
string() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
STRING - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants: RegularExpression Id.
STRING - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants: RegularExpression Id.
stringToInt(String) - Static method in class org.sbml.jsbml.SBO: Returns the string as a correctly formatted SBO integer portion.
StringTools - Class in org.sbml.jsbml.util: This class provides a collection of convenient methods for manipulating Strings.
StringTools() - Constructor for class org.sbml.jsbml.util.StringTools
stringToTimestamp(String) - Method in class org.sbml.jsbml.xml.stax.DateProcessor: Convert timezone of datetime string to GMT.
stringToType - Static variable in class org.sbml.jsbml.math.parser.FormulaParser
stringToType - Static variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
stringToType - Static variable in class org.sbml.jsbml.math.parser.FormulaParserLL3
stringToType - Static variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
stringToType - Static variable in class org.sbml.jsbml.text.parser.CobraFormulaParser
stringToType - Static variable in class org.sbml.jsbml.text.parser.FormulaParser
stringToType - Static variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
stringToType - Static variable in class org.sbml.jsbml.text.parser.FormulaParserLL3
stringToType - Static variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
stroke - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
strokeDashArray - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
strokeWidth - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
style - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
Style - Class in org.sbml.jsbml.ext.render
Style() - Constructor for class org.sbml.jsbml.ext.render.Style: Creates a Style instance with a group
Style(RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.Style: Creates a Style instance with a group
Style(int, int, RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.Style: Creates a Style instance with a level and version.
Style(String, int, int, RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.Style: Creates a Style instance with an id, name, level, and version.
Style(Style) - Constructor for class org.sbml.jsbml.ext.render.Style: Clone constructor
style - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
subList(int, int) - Method in class org.sbml.jsbml.ListOf
Submodel - Class in org.sbml.jsbml.ext.comp: Submodels are instantiations of models contained within other models.
Submodel() - Constructor for class org.sbml.jsbml.ext.comp.Submodel: Creates an Submodel instance
Submodel(String) - Constructor for class org.sbml.jsbml.ext.comp.Submodel: Creates a Submodel instance with an id.
Submodel(int, int) - Constructor for class org.sbml.jsbml.ext.comp.Submodel: Creates a Submodel instance with a level and version.
Submodel(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Submodel: Creates a Submodel instance with an id, level, and version.
Submodel(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Submodel: Creates a Submodel instance with an id, name, level, and version.
Submodel(Submodel) - Constructor for class org.sbml.jsbml.ext.comp.Submodel: Clone constructor
SubModel - Class in org.sbml.jsbml.util: Generates a sub-Model containing the elements passed as argument and all the necessary dependencies.
SubModel() - Constructor for class org.sbml.jsbml.util.SubModel
submodelRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
subsection(String, boolean) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
subsection(String, boolean) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
SUBSTANCE - Static variable in class org.sbml.jsbml.UnitDefinition: Identifier of the (for the SBML Levels 1 and 2) predefined UnitDefinition substance.
substance(int, int) - Static method in class org.sbml.jsbml.UnitDefinition: Predefined unit for substance.
substanceUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
subsubsection(String, boolean) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
subsubsection(String, boolean) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
sum(ASTNode...) - Static method in class org.sbml.jsbml.ASTNode: Creates a new ASTNode of type Plus with the given nodes as children.
sum(MathContainer, CallableSBase...) - Static method in class org.sbml.jsbml.ASTNode: Sum of several NamedSBase objects.
sum(ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory: Creates an ASTArithmeticOperatorNode of type ASTNode.Type.SUM and adds the given nodes as children.
sum(Object...) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler: Returns the sum of the given elements as StringBuffer.
sum(Object...) - Static method in class org.sbml.jsbml.math.compiler.HTMLFormula: Returns the sum of the given elements as StringBuffer.
sum(Object...) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler: Returns the sum of the given elements as StringBuffer.
sum(Object...) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula: Returns the sum of the given elements as StringBuffer.
swapChildren(ASTNode) - Method in class org.sbml.jsbml.ASTNode: Swaps the children of this ASTNode with the children of that ASTNode.
swapChildren(ASTFunction) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode: Swaps the children of this ASTFunction with the children of that ASTFunction.
swapChildren(ASTFunction) - Method in class org.sbml.jsbml.math.ASTFunction: Swaps the children of this ASTFunction with the children of that ASTFunction.
swapChildren(ASTFunction) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
SwitchTo(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager: Switch to specified lex state.
SwitchTo(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager: Switch to specified lex state.
SwitchTo(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager: Switch to specified lex state.
SwitchTo(int) - Method in class org.sbml.jsbml.math.parser.FormulaParserTokenManager: Switch to specified lex state.
SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager: Switch to specified lex state.
SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager: Switch to specified lex state.
SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager: Switch to specified lex state.
SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager: Switch to specified lex state.
SwitchTo(int) - Method in class org.sbml.jsbml.text.parser.FormulaParserTokenManager: Switch to specified lex state.
Symbol - Class in org.sbml.jsbml: The base class for Compartment, Species, Parameter.
Symbol() - Constructor for class org.sbml.jsbml.Symbol: Creates a Symbol instance.
Symbol(int, int) - Constructor for class org.sbml.jsbml.Symbol: Creates a Symbol instance from a level and version.
Symbol(QuantityWithUnit) - Constructor for class org.sbml.jsbml.Symbol: Creates a Symbol instance.
Symbol(String) - Constructor for class org.sbml.jsbml.Symbol: Creates a Symbol instance.
Symbol(String, int, int) - Constructor for class org.sbml.jsbml.Symbol: Creates a Symbol instance from an id, level and version.
Symbol(String, String, int, int) - Constructor for class org.sbml.jsbml.Symbol: Creates a Symbol instance from an id, name, level and version.
Symbol(Symbol) - Constructor for class org.sbml.jsbml.Symbol: Creates a Symbol instance from a given Symbol.
symbol - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
symbolTime(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
symbolTime(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
symbolTime(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
symbolTime(String) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler: The simulation time.
symbolTime(String) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
symbolTime(String) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
symbolTime(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
symbolTime(String) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
symbolTime(String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler: The simulation time.
symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler: Deprecated.
symbolTime(String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
SyntaxChecker - Class in org.sbml.jsbml.validator: A collection of methods for checking the validity of SBML identifiers.

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