S-Index (JSBML 1.6.1-SNAPSHOT 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 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
SampledField - Class in org.sbml.jsbml.ext.spatial
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(SampledField) - Constructor for class org.sbml.jsbml.ext.spatial.SampledField
SampledFieldConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SampledField class.
SampledFieldConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SampledFieldConstraints
sampledFieldGeometry - 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: Creates a new SampledFieldGeometry instance.
SampledFieldGeometry(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.SampledFieldGeometry: Creates a new SampledFieldGeometry instance.
SampledFieldGeometry(SampledFieldGeometry) - Constructor for class org.sbml.jsbml.ext.spatial.SampledFieldGeometry: Creates a new SampledFieldGeometry instance cloned from the given sampledFieldGeometry.
SampledFieldGeometryConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SampledFieldGeometry class.
SampledFieldGeometryConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SampledFieldGeometryConstraints
sampledValue - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
sampledVolume - 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(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.SampledVolume
SampledVolume(SampledVolume) - Constructor for class org.sbml.jsbml.ext.spatial.SampledVolume
SampledVolumeConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SampledVolume class.
SampledVolumeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SampledVolumeConstraints
samples - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
sampleSize - org.sbml.jsbml.ext.distrib.UncertParameter.Type: The sample size is a direct count of the number of observations made or the number of samples measured.
samplesLength - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
SANS_SERIF - org.sbml.jsbml.ext.render.FontFamily
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.
SBaseConstraints - Class in org.sbml.jsbml.validator.offline.constraints
SBaseConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SBaseConstraints
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
SBaseRefConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SBaseRef class.
SBaseRefConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SBaseRefConstraints
SBaseWithDerivedUnit - Interface in org.sbml.jsbml: This type represents an SBase object that is associated to a unit.
SBaseWithDerivedUnitConstraints - Class in org.sbml.jsbml.validator.offline.constraints
SBaseWithDerivedUnitConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SBaseWithDerivedUnitConstraints
SBaseWithDimensionCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints: Checks that the given SBase does not have a listOfDimensions, otherwise reports an error.
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.
SBaseWithUnitConstraints - Class in org.sbml.jsbml.validator.offline.constraints
SBaseWithUnitConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SBaseWithUnitConstraints
SBGNArc<T> - Interface in org.sbml.jsbml.ext.render.director: interface for the different types of connecting arcs consumption reversible consumption production catalysis inhibition
SBGNNode<T> - Interface in org.sbml.jsbml.ext.render.director: interface for the different types of entity pool nodes unspecified entity simple chemical macromolecule source/sink
SBGNNodeWithCloneMarker<T> - Interface in org.sbml.jsbml.ext.render.director
SBGNProcessNode<T> - Interface in org.sbml.jsbml.ext.render.director: Interface for all SBGN specified process nodes.
SBML - org.sbml.jsbml.SBMLException.Category: General error not falling into another category below.
SBML_L1_COMPAT - org.sbml.jsbml.SBMLException.Category: Category of errors that can only occur during attempted translation from one Level/Version of SBML to another.
SBML_L2V1_COMPAT - org.sbml.jsbml.SBMLException.Category: Category of errors that can only occur during attempted translation from one Level/Version of SBML to another.
SBML_L2V2_COMPAT - org.sbml.jsbml.SBMLException.Category: Category of errors that can only occur during attempted translation from one Level/Version of SBML to another.
SBML_L2V3_COMPAT - org.sbml.jsbml.SBMLException.Category: Category of errors that can only occur during attempted translation from one Level/Version of SBML to another.
SBML_L2V4_COMPAT - org.sbml.jsbml.SBMLException.Category: Category of errors that can only occur during attempted translation from one Level/Version of SBML to another.
SBMLConverter - Interface in org.sbml.jsbml.util.converters
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
SBMLDocumentConstraints - Class in org.sbml.jsbml.validator.offline.constraints
SBMLDocumentConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SBMLDocumentConstraints
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
SBMLErrorCodes - Interface in org.sbml.jsbml.validator.offline.factory: Automatically generated file, using the python scripts extractErrors.py on the libSBML python library and createErrorCodeInterface.py on the generated json file.
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
SBMLErrorFactory - Class in org.sbml.jsbml.validator.offline.factory: Creates SBMLError populated with values coming from a json file.
SBMLErrorFactory() - Constructor for class org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory
SBMLErrorLog - Class in org.sbml.jsbml: Log of errors and other events encountered during SBML processing.
SBMLErrorLog() - Constructor for class org.sbml.jsbml.SBMLErrorLog
SBMLErrorMessage - Class in org.sbml.jsbml.validator.offline.i18n: Contains the messages for each SBMLError in the English language.
SBMLErrorMessage() - Constructor for class org.sbml.jsbml.validator.offline.i18n.SBMLErrorMessage
SBMLErrorPostMessage - Class in org.sbml.jsbml.validator.offline.i18n: Contains the post messages for each SBMLError in the English language.
SBMLErrorPostMessage() - Constructor for class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPostMessage
SBMLErrorPostMessage_fr - Class in org.sbml.jsbml.validator.offline.i18n.fr: Contains the post messages for each SBMLError in the French language.
SBMLErrorPostMessage_fr() - Constructor for class org.sbml.jsbml.validator.offline.i18n.fr.SBMLErrorPostMessage_fr
SBMLErrorPreMessage - Class in org.sbml.jsbml.validator.offline.i18n: Contains the pre messages for each SBMLError in the English language.
SBMLErrorPreMessage() - Constructor for class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPreMessage
SBMLErrorPreMessage_en_EN_L2V1 - Class in org.sbml.jsbml.validator.offline.i18n: Contains the pre messages for each SBMLError in the English language and for SBML level 2 version 1.
SBMLErrorPreMessage_en_EN_L2V1() - Constructor for class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPreMessage_en_EN_L2V1
SBMLErrorPreMessage_en_EN_L3V1 - Class in org.sbml.jsbml.validator.offline.i18n: Contains the pre messages for each SBMLError in the English language and for SBML level 2 version 1.
SBMLErrorPreMessage_en_EN_L3V1() - Constructor for class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPreMessage_en_EN_L3V1
SBMLErrorShortMessage - Class in org.sbml.jsbml.validator.offline.i18n: Contains the short messages for each SBMLError in the English language.
SBMLErrorShortMessage() - Constructor for class org.sbml.jsbml.validator.offline.i18n.SBMLErrorShortMessage
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.
SBMLNamespaceInAnnotation - org.sbml.jsbml.SBMLException.Code: Invalid use of SBML XML namespace in annotation
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 - Class in org.sbml.jsbml.xml.stax: Provides all the methods to read a SBML file.
SBMLReader() - Constructor for class org.sbml.jsbml.SBMLReader: Creates a new SBMLReader.
SBMLReader() - Constructor for class org.sbml.jsbml.xml.stax.SBMLReader
SBMLReader(SBMLReader) - Constructor for class org.sbml.jsbml.SBMLReader: Clone constructor.
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 - Class in org.sbml.jsbml.xml.stax: A SBMLWriter provides the methods to write a SBML file.
SBMLWriter() - Constructor for class org.sbml.jsbml.SBMLWriter: Creates a new SBMLWriter.
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.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(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.
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(SBMLWriter) - Constructor for class org.sbml.jsbml.SBMLWriter: Clone constructor.
SBO - Class in org.sbml.jsbml: Methods for interacting with Systems Biology Ontology (SBO) terms.
SBO() - Constructor for class org.sbml.jsbml.SBO
SBO_CONSISTENCY - org.sbml.jsbml.SBMLException.Category: Category of errors that can occur while validating SBO identifiers in a model.
SBO_CONSISTENCY - org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY: Consistency and validity of SBO identifiers (if any) used in the model.
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
SBOTermNotUniversalInL2v2 - org.sbml.jsbml.SBMLException.Code: The sboTerm attribute is invalid for this component in Level 2 Version 2
SBOTermNotValidAttributeBeforeL2V2 - org.sbml.jsbml.SBMLException.Code: The sboTerm attribute is invalid for this component before Level 2 Version 2
SBOTermNotValidAttributeBeforeL2V3 - org.sbml.jsbml.SBMLException.Code: sboTerm not available on this component before SBML Level 2 Version 3
SBOValidationConstraints - Class in org.sbml.jsbml.validator.offline.constraints.helper: Provides static methods for the different SBO checks.
SBOValidationConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.SBOValidationConstraints
scale - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
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(double) - Static method in class org.sbml.jsbml.util.Maths: Computes the secant of a double value.
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(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(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
sech(double) - Static method in class org.sbml.jsbml.util.Maths: Computes the sech of n
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(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(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
SECOND - org.sbml.jsbml.Unit.Kind: The second unit.
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 - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
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(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
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
SEMANTICS - org.sbml.jsbml.ASTNode.Type: MathML markup can be combined with other markup languages, and these mixing constructions are realized by the semantic annotation elements.
serialVersionUID - Static variable in class org.sbml.jsbml.UnitDefinition: Generated serial version identifier.
SERIF - org.sbml.jsbml.ext.render.FontFamily
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.
setAbsoluteValue(double) - Method in class org.sbml.jsbml.ext.render.RelAbsVector: Sets absolute part to new value and fires appropriate event
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: Sets the active objective.
setActiveObjective(Objective) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
setActiveObjective(Objective) - Method in class org.sbml.jsbml.ext.fbc.ListOfObjectives: Sets the value of ListOfObjectives.activeObjective to the id of the given Objective.
setAddGraphicalObjects(ListOf<GraphicalObject>) - Method in class org.sbml.jsbml.ext.layout.Layout: This element is optional.
setAddWhiskers(Boolean) - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector: Sets the value of addWhiskers
setAlgorithm(LayoutAlgorithm) - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector
setAndReplacement(String) - Method in class org.sbml.jsbml.util.compilers.ConfigurableLogicalFormulaCompiler: Sets the String that will be used to replace ' and ' (the mathML <and> element) in the boolean expressions.
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 - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
setAnnotation(String) - Method in class org.sbml.jsbml.AbstractSBase
setAnnotation(String) - Method in interface org.sbml.jsbml.SBase: Sets the non RDF part of the annotation.
setAnnotation(Annotation) - 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 class org.sbml.jsbml.AbstractSBase
setAnnotation(XMLNode) - Method in interface org.sbml.jsbml.SBase: Sets the non RDF part of the annotation.
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
setBoundingBox(BoundingBox) - Method in interface org.sbml.jsbml.ext.layout.IBoundingBox: Sets the BoundingBox.
setBoundingBox(BoundingBox) - Method in class org.sbml.jsbml.ext.render.LineEnding: Set the value of boundingBox
setBuilder(LayoutBuilder<P>) - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector
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(int) - Method in class org.sbml.jsbml.util.Detail
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
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.
setCloneMarker(boolean) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNNodeWithCloneMarker
setCloneMarker(boolean) - Method in interface org.sbml.jsbml.ext.render.director.SBGNNodeWithCloneMarker: Method to set the boolean clone marker value if the clone marker should be drawn.
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(String) - Method in interface org.sbml.jsbml.CompartmentalizedSBase: Sets the compartment attribute.
setCompartment(String) - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph
setCompartment(String) - Method in class org.sbml.jsbml.ext.multi.CompartmentReference
setCompartment(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType
setCompartment(String) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
setCompartment(String) - Method in class org.sbml.jsbml.Reaction: Sets the compartmentID of this Reaction to 'compartmentID'.
setCompartment(String) - Method in class org.sbml.jsbml.Species
setCompartment(Compartment) - Method in interface org.sbml.jsbml.CompartmentalizedSBase: Sets the compartment identifiers of this CompartmentalizedSBase to the id of the Compartment 'compartment'.
setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.layout.CompartmentGlyph
setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.multi.CompartmentReference
setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType
setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies
setCompartment(Compartment) - Method in class org.sbml.jsbml.Reaction
setCompartment(Compartment) - 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(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
setCompartmentType(CompartmentType) - Method in class org.sbml.jsbml.Compartment: Deprecated.
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
setComponent(String) - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature: Sets the value of component
setComponents(Double...) - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent: Sets the value of components
setComponentsLength(int) - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent: Sets the value of componentsLength
setCompression(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: 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.ParametricObject: Sets the value of compression
setCompression(CompressionKind) - Method in class org.sbml.jsbml.ext.spatial.SampledField: 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(String) - Method in class org.sbml.jsbml.Model: Sets the conversionFactorID of this Model to 'conversionFactorID'.
setConversionFactor(String) - Method in class org.sbml.jsbml.Species: Sets the conversionFactor of this Species to 'conversionFactorID'.
setConversionFactor(Parameter) - Method in class org.sbml.jsbml.Model: Sets the conversionFactorID of this Model to the id of the Parameter 'conversionFactor'.
setConversionFactor(Parameter) - Method in class org.sbml.jsbml.Species: Sets the conversionFactor of this Species to the id of 'conversionFactor'.
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(String) - Method in class org.sbml.jsbml.ext.render.RelAbsVector: Sets the relative and absolute value based on a String-encoding (like "1", "30%" or "50-20%"; as defined in the render-specification)
If the String does not represent a valid value, relative and absolute value are set to NaN
setCoordinate(String) - Method in class org.sbml.jsbml.ext.spatial.CoordinateReference: Deprecated.
setCoordinate(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.AdvectionCoefficient: Sets the value of coordinate
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: Sets the 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(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of cx
setCx(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of cx
setCy(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of cy
setCy(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of cy
setCz(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of cz
setCz(RelAbsVector) - 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(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.ParametricObject: Sets the value of dataType
setDataType(DataKind) - Method in class org.sbml.jsbml.ext.spatial.SampledField: 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 AbstractSBase.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.
setDefaultValue(String, String) - Method in class org.sbml.jsbml.ext.render.DefaultValues
setDefaultValues(DefaultValues) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation: Sets the value of defaultValues
setDefinitionURL(String) - Method in class org.sbml.jsbml.ASTNode
setDefinitionURL(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Sets the value of definitionURL
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
setDimensions(Dimensions) - Method in class org.sbml.jsbml.ext.layout.BoundingBox: Sets the 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
setElementName(String) - Method in class org.sbml.jsbml.ext.spatial.Boundary: Sets the value of the XML element name.
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: Sets 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() - Method in class org.sbml.jsbml.xml.XMLToken: Declares this XML start element is also an end element.
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
setEndHead(String) - Method in class org.sbml.jsbml.ext.render.RenderCurve: Sets 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(double) - Method in class org.sbml.jsbml.Unit: Sets the exponent of this Unit
setExponent(int) - Method in class org.sbml.jsbml.math.ASTCnExponentialNode: Set the exponent value of this node
setExponent(int) - Method in class org.sbml.jsbml.Unit: Deprecated.
use Unit.setExponent(double)
setExtendedASTNode(ASTNode) - Method in class org.sbml.jsbml.ext.AbstractASTNodePlugin: Sets the extended ASTNode.
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: Sets the value of the optional extentConversionFactor
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: Deprecated.
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(String) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle: Set the value of fontFamily
setFontFamily(String) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of fontFamily
setFontFamily(String) - Method in class org.sbml.jsbml.ext.render.Text
setFontFamily(FontFamily) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle: Set the value of fontFamily by using a FontFamily type.
setFontFamily(FontFamily) - Method in class org.sbml.jsbml.ext.render.Text
setFontSize(Short) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of fontSize
setFontSize(RelAbsVector) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle: Set the value of fontSize
setFontSize(RelAbsVector) - 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.Text
setFontStyleItalic(Boolean) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of fontStyleItalic
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.Text
setFontWeightBold(Boolean) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of fontWeightBold
setFormula(String) - Method in class org.sbml.jsbml.AbstractMathContainer: Deprecated.
setFormula(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: 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(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of fx
setFy(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RadialGradient: Set the value of fy
setFz(RelAbsVector) - 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(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.
setGraphicalObject(GraphicalObject) - Method in class org.sbml.jsbml.ext.layout.TextGlyph
setGroup(RenderGroup) - Method in class org.sbml.jsbml.ext.render.LineEnding: Sets 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(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of height
setHeight(RelAbsVector) - 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.AbstractSBase
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.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 interface org.sbml.jsbml.SBase: 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.IdFilter: Sets the id that will be searched for by the filter.
setId(String) - Method in class org.sbml.jsbml.util.filters.NameFilter: Sets the id to search for.
setId(String) - Method in class org.sbml.jsbml.util.filters.SIdFilter: Sets the id that will be searched for by the filter.
setIdenticalAttribute(String) - Method in class org.sbml.jsbml.ext.groups.MemberConstraint: Deprecated.

Sets the value of identicalAttribute
setIDList(List<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(SBase) - Method in class org.sbml.jsbml.ext.groups.Member: Sets the value of idRef, using the id defined in the given SBase
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
setIndentation(char, short) - Static method in class org.sbml.jsbml.TidySBMLWriter
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(int) - Method in class org.sbml.jsbml.xml.stax.SBMLWriter: Sets the indent for this SBMLWriter.
setIndentationCount(short) - Method in class org.sbml.jsbml.SBMLWriter: Influences the way how SBML data structures are represented in XML.
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
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 type
setInterpolationType(InterpolationKind) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of interpolation type
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
setIsSelfLogging(boolean) - Method in class org.sbml.jsbml.validator.offline.constraints.AbstractValidationFunction: Sets if this ValidationFunction is logging itself the SBMLError to the ValidationContext.
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
setLayout(Layout) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm
setLayout(Layout) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm
setLayoutIndex(int) - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector
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.text.parser.FormulaParserLL3: Sets the SBML Level.
setLevel(int) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setLevel(int) - Method in class org.sbml.jsbml.validator.offline.ValidationContext: Set the SBML level of the ValidationContext.
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) - Method in class org.sbml.jsbml.validator.offline.ValidationContext: Sets the level/version and clears the root constraint if one of these values differs from the current values.
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
setLineWidth(double) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNnode
setLineWidth(double) - Method in interface org.sbml.jsbml.ext.render.director.SBGNNode
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: Sets the Layout.listOfAdditionalGraphicalObjects.
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
setListOfCurveSegments(ListOf<CurveSegment>) - Method in interface org.sbml.jsbml.ext.layout.ICurve: The listOfCurveSegments element contains arbitrary number of curve segments that can be either of type LineSegment or of type CubicBezier.
setListOfCurveSegments(ListOf<CurveSegment>) - Method in class org.sbml.jsbml.ext.render.Polygon: Sets the given ListOf<CurveSegment>.
setListOfCurveSegments(ListOf<CurveSegment>) - Method in class org.sbml.jsbml.ext.render.RenderCurve: Sets the given ListOf<CurveSegment>.
setListOfDeletions(ListOf<Deletion>) - Method in class org.sbml.jsbml.ext.comp.Submodel: Sets the given ListOf<Deletion>.
setListOfDimensions(ListOf<Dimension>) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin: Sets the given ListOf<Dimension>.
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(ListOfGlobalRenderInformation) - 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.MultiSpeciesType: 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(ListOfLocalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin
setListOfLocalStyles(ListOf<LocalStyle>) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation
setListOfMembers(ListOfMembers) - 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(ListOfObjectives) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Sets the given ListOfObjectives.
setListOfObjectives(ListOf<Objective>) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin: Sets the given ListOf<Objective>.
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: Sets the GeneralGlyph.listOfReferenceGlyphs.
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'.
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.MultiSpeciesType: 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.
setListOfSpeciesReferenceGlyphs(ListOf<SpeciesReferenceGlyph>) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: Sets the list of SpeciesReferenceGlyphs.
setListOfSpeciesReferencesGlyph(ListOf<SpeciesReferenceGlyph>) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph: Deprecated.
use ReactionGlyph.setListOfSpeciesReferenceGlyphs(ListOf)
setListOfSpeciesTypeComponentIndexes(ListOf<SpeciesTypeComponentIndex>) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType: 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.MultiSpeciesType: Sets the given ListOf<SpeciesTypeInstance>.
setListOfSpeciesTypes(ListOf<MultiSpeciesType>) - 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.
setListOfSubListOfSpeciesFeatures(ListOf<SubListOfSpeciesFeature>) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin: Sets the given ListOf<SubListOfSpeciesFeature>.
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.
setListOfUncertainties(ListOf<Uncertainty>) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin: Sets the given ListOf<Uncertainty>.
setListOfUncertParameters(ListOf<UncertParameter>) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty: Sets the given ListOf<UncertParameter>.
setListOfUncertParameters(ListOf<UncertParameter>) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Sets the given ListOf<UncertParameter>.
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.
setLocationURI(String) - Method in class org.sbml.jsbml.SBMLDocument: Sets the locationURI of this SBMLDocument: Denotes, whence this Document is understood to have been read.
setLogBehavior(FormulaParserLL3.LOG_BEHAVIOR) - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3: Sets the parser behavior when encountering the 'log' operator with one argument.
setLowerFluxBound(String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Sets the value of lowerFluxBound
setLowerFluxBound(Parameter) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
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.ext.distrib.UncertParameter
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(String) - Method in class org.sbml.jsbml.util.Message
setMessage(Message) - Method in exception org.sbml.jsbml.SBMLError: Sets the message of this SBMLError.
setMessage(XMLNode) - Method in class org.sbml.jsbml.Constraint: Sets the message of this Constraint to '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'.
setMetaId(String) - Method in class org.sbml.jsbml.util.filters.MetaIdFilter: Sets the metaid that will be searched for by the filter.
setMetaidRef(String) - Method in class org.sbml.jsbml.ext.layout.GraphicalObject: Sets the value of metaidRef which uniquely references elements in the model.
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
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: Sets the value of the required modelRef
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.AbstractSBase
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.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 interface org.sbml.jsbml.SBase: Sets the name value with 'name'.
setName(String) - Method in class org.sbml.jsbml.util.filters.NameFilter: Sets the name to search for.
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: Sets the reference based on the id of the given NamedSBase.
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.AbstractASTNodePlugin: Sets the XML namespace to which this ASTNodePlugin 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(String) - Method in interface org.sbml.jsbml.SBase: Sets the notes with 'notes'.
setNotes(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase
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
setObjectRole(String) - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin: Sets the value of objectRole
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.Unit: Deprecated.
Only defined for SBML Level 2 Version 1.
setOffset(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.GradientStop: Set the value of offset
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
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.CobraToFbcV1Converter
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.CobraToFbcV2Converter
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV1ToCobraConverter
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV1ToFbcV2Converter
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV2ToCobraConverter
setOption(String, String) - Method in class org.sbml.jsbml.ext.fbc.converters.FbcV2ToFbcV1Converter
setOption(String, String) - Method in class org.sbml.jsbml.util.converters.ExpandFunctionDefinitionConverter
setOption(String, String) - Method in interface org.sbml.jsbml.util.converters.SBMLConverter: Sets options
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: Sets the oder.
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
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.
setOriginOfText(NamedSBase) - Method in class org.sbml.jsbml.ext.layout.TextGlyph
setOrReplacement(String) - Method in class org.sbml.jsbml.util.compilers.ConfigurableLogicalFormulaCompiler: Sets the String that will be used to replace ' or ' (the mathML <or> element) in the boolean expressions.
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
setOtherListName(String) - Method in class org.sbml.jsbml.ListOf: Sets the XML element name used when the ListOf type is set to ListOf.Type.other.
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(String) - Method in class org.sbml.jsbml.Compartment: Deprecated.
since Level 3 Version 1
setOutside(Compartment) - Method in class org.sbml.jsbml.Compartment: Deprecated.
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.AbstractASTNodePlugin
setPackageVersion(int) - Method in class org.sbml.jsbml.ext.AbstractSBasePlugin
setPackageVersion(int) - Method in interface org.sbml.jsbml.ext.ASTNodePlugin: Sets the package version.
setPackageVersion(int) - Method in interface org.sbml.jsbml.ext.SBasePlugin: Sets the package version.
setPackageVersion(int) - Method in interface org.sbml.jsbml.SBase: Sets the version of the SBML Level 3 package to which this element belongs.
setPackageVersion(String, int) - Method in class org.sbml.jsbml.validator.offline.ValidationContext: Sets the package version to validate
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(ASTNode, MathContainer) - Static method in class org.sbml.jsbml.ASTNode: Sets the Parent of the node and its children to the given value
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.ASTNode: Sets the Parent of the node to the given value
setParentSBMLObject(MathContainer) - Method in class org.sbml.jsbml.math.AbstractASTNode
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(Integer...) - Method in class org.sbml.jsbml.ext.spatial.PolygonObject: Deprecated.

Sets the value of pointIndex
setPointIndex(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of pointIndex
setPointIndexLength(int) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject: Sets the value of pointIndexLength
setPointOfContactToProduct(Point) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode
setPointOfContactToProduct(Point) - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode
setPointOfContactToSubstrate(Point) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode
setPointOfContactToSubstrate(Point) - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode
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: Sets the position.
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
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(RelAbsVector) - 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
setRatio(double) - Method in class org.sbml.jsbml.ext.render.Rectangle
setRatio(Double) - Method in class org.sbml.jsbml.ext.render.Ellipse: Sets the ratio-attribute to given value and fires appropriate change-events
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
setReaction(String) - 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.FluxObjective: Sets the reaction that this FluxObjective is associated with in the context of the enclosing Objective class.
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.
setReaction(Reaction) - 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: Sets the Reaction that this 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)
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: Sets the reference.
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(CallableSBase) - Method in class org.sbml.jsbml.math.ASTCiNumberNode: Set an instance of CallableSBase as the variable of this ASTCiNumberNode.
setReference(FunctionDefinition) - Method in class org.sbml.jsbml.math.ASTCiFunctionNode: Set an instance of FunctionDefinition as the variable of this ASTCiFunctionNode.
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
setRelation(Relation) - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature: Sets the value of relation
setRelativeValue(double) - Method in class org.sbml.jsbml.ext.render.RelAbsVector: Sets relative part to new value and fires appropriate event
setRenderInformation(GlobalRenderInformation) - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin: Deprecated.
This goes beyond/is besides the render-package's specification and will be removed in a future release. Use the LocalRenderInformation-related methods of RenderLayoutPlugin, and the GlobalRenderInformation-related methods of RenderListOfLayoutsPlugin instead. 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(List<String>) - Method in class org.sbml.jsbml.ext.render.Style: Set the value of roleList
setRootConstraint(AnyConstraint<Object>, Class<?>) - Method in class org.sbml.jsbml.validator.offline.ValidationContext: Sets the root constraints and the root constraint class type.
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
setRotateX(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Sets the value of rotateAxisX
setRotateY(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Sets the value of rotateAxisY
setRotateZ(double) - Method in class org.sbml.jsbml.ext.spatial.CSGRotation: Sets the value of rotateAxisZ
setRx(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of rx
setRx(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Rectangle: Set the value of Rectangle.rx
setRy(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Ellipse: Set the value of ry
setRy(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Rectangle: Set the value of Rectangle.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(int) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of samplesLength
setSamplesLength(String) - Method in class org.sbml.jsbml.ext.spatial.SampledField: Sets the value of samplesLength
setSBase(SBase) - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph: Sets the reference based on the id of the given SBase.
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(int) - Method in interface org.sbml.jsbml.SBase: Sets the value of the 'sboTerm' attribute.
setSBOTerm(String) - Method in class org.sbml.jsbml.AbstractSBase
setSBOTerm(String) - Method in interface org.sbml.jsbml.SBase: Sets the value of the 'sboTerm' attribute.
setSBOTerm(SBase, int) - Static method in class org.sbml.jsbml.util.SBMLtools
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(int) - Method in class org.sbml.jsbml.util.Detail
setSeverity(String) - Method in exception org.sbml.jsbml.SBMLError: Sets the severity of this SBMLError.
setShortMessage(String) - Method in exception org.sbml.jsbml.SBMLException
setShortMessage(Message) - Method in exception org.sbml.jsbml.SBMLError
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.
setSource(SBase) - Method in exception org.sbml.jsbml.SBMLError: Sets the source of this SBMLError.
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(int) - Method in class org.sbml.jsbml.ext.spatial.DomainType: Sets the value of spatialDimension
setSpatialDimensions(short) - Method in class org.sbml.jsbml.Compartment: Sets the spatialDimensions of this compartment to 'spatialDimensiosn'.
setSpatialId(String) - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
setSpatialId(String) - Method in interface org.sbml.jsbml.ext.spatial.SpatialNamedSBase: Deprecated.
use SBase.setId(String)
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.ParameterType: Sets the spatial reference
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(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(String) - Method in class org.sbml.jsbml.SimpleSpeciesReference: Sets the speciesID to 'spec'.
setSpecies(Species) - Method in class org.sbml.jsbml.ext.layout.SpeciesGlyph
setSpecies(Species) - Method in class org.sbml.jsbml.SimpleSpeciesReference: Sets the speciesID to the id of the Species 'species'.
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.
setSpeciesRef(String) - Method in class org.sbml.jsbml.ext.spatial.ParameterType: Sets the value of variable
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: Sets the value of variable
setSpeciesReference(SimpleSpeciesReference) - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph: See setSpeciesReference(String).
setSpeciesReferenceRole(SpeciesReferenceRole) - Method in class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
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(String) - Method in class org.sbml.jsbml.Species: Deprecated.
Only valid in SBML Level 2 from Version 2.
setSpeciesType(SpeciesType) - Method in class org.sbml.jsbml.Species: Deprecated.
This property is only valid for SBML Level 2 from Version 2.
setSpId(String) - Method in class org.sbml.jsbml.ext.spatial.ParameterType: Sets the spatial reference
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: Sets 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
setStrokeDashArray(List<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: Sets the value of the required submodelRef attribute.
setSubstanceUnits(String) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
Only defined for SBML Level 1 and Level 2 Version 1 and 2.
setSubstanceUnits(String) - Method in class org.sbml.jsbml.Model: Sets the Model.substanceUnitsID of this Model to 'substanceUnitsID'
setSubstanceUnits(String) - Method in class org.sbml.jsbml.Species: Sets the substanceUnitsID to 'unit'.
setSubstanceUnits(Unit) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setSubstanceUnits(Unit) - Method in class org.sbml.jsbml.Species: Sets the substanceUnits.
setSubstanceUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model
setSubstanceUnits(Unit.Kind) - Method in class org.sbml.jsbml.Species: Sets the substanceUnits.
setSubstanceUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model: Sets the substanceUnitsID of this Model to the id of '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.
setText(String) - Method in class org.sbml.jsbml.ext.render.Text: Set the value of the Text.text field (and fire appropriate property-change event)
setTextAnchor(HTextAnchor) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle: Set the value of textAnchor
setTextAnchor(HTextAnchor) - Method in class org.sbml.jsbml.ext.render.RenderGroup: Set the value of textAnchor
setTextAnchor(HTextAnchor) - 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: Sets the value of the optional timeConversionFactor
setTimeUnits(String) - Method in class org.sbml.jsbml.Event: Deprecated.
This is only applicable for SBML Level 2, Versions 1 and 2.
setTimeUnits(String) - 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(Unit) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setTimeUnits(Unit.Kind) - Method in class org.sbml.jsbml.Model: Sets the Model.timeUnitsID of this Model to the given unit kind.
setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Event: Deprecated.
setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
Only defined for Level 1 and Level 2 Version 1.
setTimeUnits(UnitDefinition) - Method in class org.sbml.jsbml.Model: Sets the timeUnitsID of this Model to the id of the UnitDefinition 'timeUnits'.
setTimeUnitsID(String) - Method in class org.sbml.jsbml.Event: Deprecated.
setTransform(Double[]) - Method in class org.sbml.jsbml.ext.render.Transformation: 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(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(String) - Method in class org.sbml.jsbml.ext.spatial.BoundaryCondition
setType(String) - 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(String) - Method in class org.sbml.jsbml.math.ASTUnknown
setType(ASTNode.Type) - Method in class org.sbml.jsbml.ASTNode: Sets the type of this ASTNode to the given Type.
setType(ASTNode.Type) - Method in class org.sbml.jsbml.math.AbstractASTNode
setType(ASTNode.Type) - Method in interface org.sbml.jsbml.math.ASTNode2: Set the type of the MathML element represented by this ASTNode2
setType(ASTNode.Type) - Method in class org.sbml.jsbml.math.ASTUnknown
setType(ASTNode.Type) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
setType(ASTNode.Type) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setType(UncertParameter.Type) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Sets the value of type
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(CoordinateKind) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent: Sets the value of type
setType(DiffusionKind) - Method in class org.sbml.jsbml.ext.spatial.DiffusionCoefficient: Sets the value of diffusionKind
setTypeList(List<Style.Type>) - 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
setUnitRef(String) - Method in class org.sbml.jsbml.ext.comp.SBaseRef: Sets the value of the optional unitRef attribute
setUnits(String) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
setUnits(String) - Method in class org.sbml.jsbml.ASTNode: Sets the units attribute.
setUnits(String) - Method in class org.sbml.jsbml.Compartment: Sets the unitsID of this QuantityWithUnit.
setUnits(String) - Method in class org.sbml.jsbml.Event: 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(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Sets the value of units
setUnits(String) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent: Sets the value of unit
setUnits(String) - 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(String) - Method in interface org.sbml.jsbml.SBaseWithUnit: Sets the unitsID of this SBaseWithUnit.
setUnits(Unit) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
setUnits(Unit) - Method in class org.sbml.jsbml.Compartment: Sets the Unit of this Compartment.
setUnits(Unit) - Method in class org.sbml.jsbml.Event: Deprecated.
setUnits(Unit) - Method in class org.sbml.jsbml.ExplicitRule: Deprecated.
setUnits(Unit) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent
setUnits(Unit) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setUnits(Unit) - Method in interface org.sbml.jsbml.SBaseWithUnit: Sets the Unit of this SBaseWithUnit.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.ASTNode
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.Compartment: Sets the unit of this Compartment.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.Event: Deprecated.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.ExplicitRule: Deprecated.
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent
setUnits(Unit.Kind) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setUnits(Unit.Kind) - Method in interface org.sbml.jsbml.SBaseWithUnit: Sets the unit of this SBaseWithUnit.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.AbstractNamedSBaseWithUnit
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.ASTNode
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.Compartment: Set the unit attribute of this Compartment to the given unit definition.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.Event: 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(UnitDefinition) - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.KineticLaw: Deprecated.
setUnits(UnitDefinition) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
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
setUnknownQualifierName(String) - Method in class org.sbml.jsbml.CVTerm: Sets a name corresponding to the Qualifier of this CVTerm.
setUpperFluxBound(String) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin: Sets the value of upperFluxBound
setUpperFluxBound(Parameter) - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin
setUserObject(Object) - Method in class org.sbml.jsbml.util.TreeNodeAdapter
setUserTidy(Tidy) - Method in class org.sbml.jsbml.TidySBMLWriter: Sets the instance of Tidy that will be used to pretty print the SBML.
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
setValidateRecursively(boolean) - Method in class org.sbml.jsbml.validator.offline.ValidationContext: Sets the recursivity of the validation.
setValue(boolean) - Method in class org.sbml.jsbml.math.ASTBoolean: Set the value of this ASTBoolean
setValue(boolean) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
setValue(boolean) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
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) - Method in class org.sbml.jsbml.Compartment
setValue(double) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Sets the value of value
setValue(double) - Method in class org.sbml.jsbml.ext.fbc.FluxBound: Deprecated.
Only defined in FBC version 1.
setValue(double) - Method in class org.sbml.jsbml.ext.spatial.Boundary: Sets the value of value
setValue(double) - Method in class org.sbml.jsbml.math.ASTConstantNumber: Set the value of this ASTConstantNumber
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(double) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
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) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
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(long) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(short) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(Color) - Method in class org.sbml.jsbml.ext.render.ColorDefinition: Set the value of value
setValue(Boolean) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(Number) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setValue(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue: Sets the value of value
setValue(String) - 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(T) - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
setValue(V) - Method in class org.sbml.jsbml.util.Pair
setValueLower(double) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan: Sets the value of valueLower
setValueUpper(double) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan: Sets the value of valueUpper
setVar(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter: Sets the value of var
setVariable(String) - Method in interface org.sbml.jsbml.Assignment: Sets the variableID of this Assignment to the given value.
setVariable(String) - Method in class org.sbml.jsbml.EventAssignment
setVariable(String) - 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: Sets the value of variable
setVariable(String) - Method in class org.sbml.jsbml.InitialAssignment
setVariable(String) - Method in class org.sbml.jsbml.math.ASTCnNumberNode: Set the variable for this ASTNumber node
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(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(Variable) - Method in class org.sbml.jsbml.EventAssignment
setVariable(Variable) - Method in class org.sbml.jsbml.ExplicitRule
setVariable(Variable) - Method in class org.sbml.jsbml.InitialAssignment
setVarLower(String) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan: Sets the value of varLower
setVarUpper(String) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan: Sets the value of varUpper
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.text.parser.FormulaParserLL3: Sets the SBML Version.
setVersion(int) - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
setVersion(int) - Method in class org.sbml.jsbml.validator.offline.ValidationContext: Sets the version of the context and clears the root constraint.
setVersionMajor(int) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation
setVersionMajor(short) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation: Sets the value of versionMajor
setVersionMinor(int) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation
setVersionMinor(short) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation: Sets 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(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of width
setWidth(RelAbsVector) - 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(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of x
setX(RelAbsVector) - Method in interface org.sbml.jsbml.ext.render.Point3D: Set the value of x
setX(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Rectangle
setX(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RenderPoint
setX(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Text
setX1(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of x1
setX1(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of x1
setX2(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of x2
setX2(RelAbsVector) - 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(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of y
setY(RelAbsVector) - Method in interface org.sbml.jsbml.ext.render.Point3D: Set the value of y
setY(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Rectangle
setY(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RenderPoint
setY(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Text
setY1(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of y1
setY1(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of y1
setY2(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of y2
setY2(RelAbsVector) - 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(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Image: Set the value of z
setZ(RelAbsVector) - Method in interface org.sbml.jsbml.ext.render.Point3D: Set the value of z
setZ(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Rectangle
setZ(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RenderPoint
setZ(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.Text
setZ1(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of z1
setZ1(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of z1
setZ2(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.LinearGradient: Set the value of z2
setZ2(RelAbsVector) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier: Set the value of z2
shape - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
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
SIDEPRODUCT - org.sbml.jsbml.ext.layout.SpeciesReferenceRole
SIDESUBSTRATE - org.sbml.jsbml.ext.layout.SpeciesReferenceRole
SIdFilter - Class in org.sbml.jsbml.util.filters: This filter only accepts instances of SBase that implements UniqueSId, with the id as given in the constructor of this object.
SIdFilter() - Constructor for class org.sbml.jsbml.util.filters.SIdFilter: Creates a new instance of SIdFilter.
SIdFilter(String) - Constructor for class org.sbml.jsbml.util.filters.SIdFilter: Creates a new instance of SIdFilter.
SIEMENS - org.sbml.jsbml.Unit.Kind: The siemens unit.
SIEVERT - org.sbml.jsbml.Unit.Kind: The sievert unit.
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 - 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(InputStream) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader, int, int, int) - Constructor for class org.sbml.jsbml.math.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader, int, int, int) - Constructor for class org.sbml.jsbml.text.parser.SimpleCharStream: Constructor.
SimpleChemical<T> - Class in org.sbml.jsbml.ext.render.director: Abstract class that all the different graphical representations for simple chemical nodes have to extend.
SimpleChemical() - Constructor for class org.sbml.jsbml.ext.render.director.SimpleChemical
SimpleLayoutAlgorithm - Class in org.sbml.jsbml.ext.render.director: SimpleLayoutAlgorithm is a partial implementation of the LayoutAlgorithm interface which collects functions which are independent of the output format of the LayoutDirector.
SimpleLayoutAlgorithm() - Constructor for class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm
SimpleLayoutAlgorithm.RelativePosition - Enum in org.sbml.jsbml.ext.render.director: Enumeration types (enums) for relative positions.
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(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.
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.
SimpleSpeciesReferenceConstraints - Class in org.sbml.jsbml.validator.offline.constraints
SimpleSpeciesReferenceConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SimpleSpeciesReferenceConstraints
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() - Method in class org.sbml.jsbml.UnitDefinition: Simplifies the UnitDefinition so that any Unit objects occurring within the UnitDefinition.listOfUnits occurs only once.
simplify(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition: Returns a simplified version of the given UnitDefinition.
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(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
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
singleValueStatistic - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
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(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
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
size - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
size - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
size() - Method in class org.sbml.jsbml.ListOf
size() - Method in class org.sbml.jsbml.xml.XMLAttributes
skewness - org.sbml.jsbml.ext.distrib.UncertParameter.Type: The skewness of a random variable is a measure of how asymmetric the corresponding probability distribution is.
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
SourceSink<T> - Class in org.sbml.jsbml.ext.render.director: Abstract class that all the different graphical representations for the empty set sign have to implement
SourceSink() - Constructor for class org.sbml.jsbml.ext.render.director.SourceSink
spanStatistic - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
SPATIAL_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1210101: To conform to the Spatial Processes Package specification for SBML Level 3 Version 1, an SBML document must declare 'http://www.sbml.org/sbml/level3/version1/spatial/version1' as the XMLNamespace to use for elements of this package.
SPATIAL_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1210102: Wherever they appear in an SBML document, elements and attributes from the Spatial Processes Package must use the 'http://www.sbml.org/sbml/level3/version1/spatial/version1' namespace, declaring so either explicitly or implicitly.
SPATIAL_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1210301: (Extends validation rule #10301 in the SBML Level 3 Core specification.
SPATIAL_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1210302: The value of a 'spatial:id' must conform to the syntax of the <sbml> data type 'SId' Reference: L3V1 Spatial V1 Section
SPATIAL_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220101: In all SBML documents using the Spatial Processes Package, the <sbml> object must have the 'spatial:required' attribute.
SPATIAL_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220102: The value of attribute 'spatial:required' on the <sbml> object must be of data type 'boolean'.
SPATIAL_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220103: The value of attribute 'spatial:required' on the <sbml> object must be set to 'true'.
SPATIAL_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220201: A <model> object may contain one and only one instance of the <geometry> element.
SPATIAL_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220301: A <compartment> object may contain one and only one instance of the <compartmentMapping> element.
SPATIAL_20401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220401: A <species> object may have the optional attribute 'spatial:isSpatial'.
SPATIAL_20402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220402: The attribute 'spatial:isSpatial' on a <species> must have a value of data type 'boolean'.
SPATIAL_20501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220501: A <parameter> object may contain one and only one instance of each of the <spatialSymbolReference,> <advectionCoefficient,> <boundaryCondition> and <diffusionCoefficient> elements.
SPATIAL_20601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220601: A <reaction> object must have the required attribute 'spatial:isLocal'.
SPATIAL_20602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220602: The attribute 'spatial:isLocal' on a <reaction> must have a value of data type 'boolean'.
SPATIAL_20650 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_20701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220701: A <domainType> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_20702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220702: A <domainType> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_20703 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220703: A <domainType> object must have the required attributes 'spatial:id' and 'spatial:spatialDimensions', and may have the optional attribute 'spatial:name'.
SPATIAL_20704 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220704: The attribute 'spatial:spatialDimensions' on a <domainType> must have a value of data type 'integer'.
SPATIAL_20705 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220705: The attribute 'spatial:name' on a <domainType> must have a value of data type 'string'.
SPATIAL_20750 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_20751 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_20752 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_20801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220801: A <domain> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_20802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220802: A <domain> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_20803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220803: A <domain> object must have the required attributes 'spatial:id' and 'spatial:domainType', and may have the optional attribute 'spatial:name'.
SPATIAL_20804 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220804: A <domain> object may contain one and only one instance of the <listOfInteriorPoints> element.
SPATIAL_20805 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220805: The value of the attribute 'spatial:domainType' of a <domain> object must be the identifier of an existing <domainType> object defined in the enclosing <model> object.
SPATIAL_20806 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220806: The attribute 'spatial:name' on a <domain> must have a value of data type 'string'.
SPATIAL_20807 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220807: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfInteriorPoints> container object may only contain <interiorPoint> objects.
SPATIAL_20808 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220808: A <listOfInteriorPoints> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_20901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220901: An <interiorPoint> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_20902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220902: An <interiorPoint> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_20903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220903: An <interiorPoint> object must have the required attribute 'spatial:coordOne', and may have the optional attributes 'spatial:coordTwo' and 'spatial:coordThree'.
SPATIAL_20904 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220904: The attribute 'spatial:coordOne' on an <interiorPoint> must have a value of data type 'double'.
SPATIAL_20905 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220905: The attribute 'spatial:coordTwo' on an <interiorPoint> must have a value of data type 'double'.
SPATIAL_20906 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1220906: The attribute 'spatial:coordThree' on an <interiorPoint> must have a value of data type 'double'.
SPATIAL_21001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221001: A <boundary> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221002: A <boundary> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_21003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221003: A <boundary> object must have the required attributes 'spatial:id' and 'spatial:value', and may have the optional attribute 'spatial:name'.
SPATIAL_21004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221004: The attribute 'spatial:value' on a <boundary> must have a value of data type 'double'.
SPATIAL_21005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221005: The attribute 'spatial:name' on a <boundary> must have a value of data type 'string'.
SPATIAL_21101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221101: An <adjacentDomains> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221102: An <adjacentDomains> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_21103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221103: An <adjacentDomains> object must have the required attributes 'spatial:id', 'spatial:domainOne' and 'spatial:domainTwo', and may have the optional attribute 'spatial:name'.
SPATIAL_21104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221104: The value of the attribute 'spatial:domainOne' of an <adjacentDomains> object must be the identifier of an existing <domain> object defined in the enclosing <model> object.
SPATIAL_21105 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221105: The value of the attribute 'spatial:domainTwo' of an <adjacentDomains> object must be the identifier of an existing <domain> object defined in the enclosing <model> object.
SPATIAL_21106 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221106: The attribute 'spatial:name' on an <adjacentDomains> must have a value of data type 'string'.
SPATIAL_21201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221201: A <geometryDefinition> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221202: A <geometryDefinition> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_21203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221203: A <geometryDefinition> object must have the required attributes 'spatial:id' and 'spatial:isActive', and may have the optional attribute 'spatial:name'.
SPATIAL_21204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221204: The attribute 'spatial:isActive' on a <geometryDefinition> must have a value of data type 'boolean'.
SPATIAL_21205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221205: The attribute 'spatial:name' on a <geometryDefinition> must have a value of data type 'string'.
SPATIAL_21301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221301: A <compartmentMapping> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221302: A <compartmentMapping> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_21303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221303: A <compartmentMapping> object must have the required attributes 'spatial:id', 'spatial:domainType' and 'spatial:unitSize', and may have the optional attribute 'spatial:name'.
SPATIAL_21304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221304: The value of the attribute 'spatial:domainType' of a <compartmentMapping> object must be the identifier of an existing <domainType> object defined in the enclosing <model> object.
SPATIAL_21305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221305: The attribute 'spatial:unitSize' on a <compartmentMapping> must have a value of data type 'double'.
SPATIAL_21306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221306: The attribute 'spatial:name' on a <compartmentMapping> must have a value of data type 'string'.
SPATIAL_21401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221401: A <coordinateComponent> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221402: A <coordinateComponent> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_21403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221403: A <coordinateComponent> object must have the required attributes 'spatial:id' and 'spatial:type', and may have the optional attributes 'spatial:name' and 'spatial:unit'.
SPATIAL_21404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221404: A <coordinateComponent> object must contain one and only one instance of each of the Boundary and <boundary> elements.
SPATIAL_21405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221405: The value of the attribute 'spatial:type' of a <coordinateComponent> object must conform to the syntax of SBML data type 'CoordinateKind' and may only take on the allowed values of 'CoordinateKind' defined in SBML; that is, the value must be one of the following: 'cartesianX', 'cartesianY' or 'cartesianZ'.
SPATIAL_21406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221406: The attribute 'spatial:name' on a <coordinateComponent> must have a value of data type 'string'.
SPATIAL_21407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221407: The value of the attribute 'spatial:unit' on a <coordinateComponent> must have a taken from the following: the identifier of a <unitDefinition> object in the enclosing <model,> or one of the base units in SBML.
SPATIAL_21501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221501: A <sampledFieldGeometry> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21502 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221502: A <sampledFieldGeometry> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_21503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221503: A <sampledFieldGeometry> object must have the required attribute 'spatial:sampledField'.
SPATIAL_21504 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221504: A <sampledFieldGeometry> object may contain one and only one instance of the <listOfSampledVolumes> element.
SPATIAL_21505 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221505: The value of the attribute 'spatial:sampledField' of a <sampledFieldGeometry> object must be the identifier of an existing <sampledField> object defined in the enclosing <model> object.
SPATIAL_21506 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221506: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfSampledVolumes> container object may only contain <sampledVolume> objects.
SPATIAL_21507 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221507: A <listOfSampledVolumes> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221601: A <sampledField> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221602: A <sampledField> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_21603 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221603: A <sampledField> object must have the required attributes 'spatial:id', 'spatial:dataType', 'spatial:numSamplesOne', 'spatial:interpolationType', 'spatial:compression', 'spatial:samples' and 'spatial:samplesLength', and may have the optional attributes 'spatial:name', 'spatial:numSamplesTwo' and 'spatial:numSamplesThree'.
SPATIAL_21604 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221604: The value of the attribute 'spatial:dataType' of a <sampledField> object must conform to the syntax of SBML data type 'DataKind' and may only take on the allowed values of 'DataKind' defined in SBML; that is, the value must be one of the following: 'double', 'float', 'uint8', 'uint16' or 'uint32'.
SPATIAL_21605 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221605: The attribute 'spatial:numSamplesOne' on a <sampledField> must have a value of data type 'integer'.
SPATIAL_21606 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221606: The value of the attribute 'spatial:interpolationType' of a <sampledField> object must conform to the syntax of SBML data type 'InterpolationKind' and may only take on the allowed values of 'InterpolationKind' defined in SBML; that is, the value must be one of the following: 'nearestNeighbor' or 'linear'.
SPATIAL_21607 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221607: The value of the attribute 'spatial:compression' of a <sampledField> object must conform to the syntax of SBML data type 'CompressionKind' and may only take on the allowed values of 'CompressionKind' defined in SBML; that is, the value must be one of the following: 'uncompressed' or 'deflated'.
SPATIAL_21608 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221608: The value of the attribute 'spatial:samples' of a <sampledField> object must be an array of values of type 'int'.
SPATIAL_21609 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221609: The attribute 'spatial:samplesLength' on a <sampledField> must have a value of data type 'integer'.
SPATIAL_21610 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221610: The attribute 'spatial:name' on a <sampledField> must have a value of data type 'string'.
SPATIAL_21611 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221611: The attribute 'spatial:numSamplesTwo' on a <sampledField> must have a value of data type 'integer'.
SPATIAL_21612 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221612: The attribute 'spatial:numSamplesThree' on a <sampledField> must have a value of data type 'integer'.
SPATIAL_21650 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_21651 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_21652 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_21701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221701: A <sampledVolume> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221702: A <sampledVolume> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_21703 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221703: A <sampledVolume> object must have the required attributes 'spatial:id' and 'spatial:domainType', and may have the optional attributes 'spatial:name', 'spatial:sampledValue', 'spatial:minValue' and 'spatial:maxValue'.
SPATIAL_21704 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221704: The value of the attribute 'spatial:domainType' of a <sampledVolume> object must be the identifier of an existing <domainType> object defined in the enclosing <model> object.
SPATIAL_21705 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221705: The attribute 'spatial:name' on a <sampledVolume> must have a value of data type 'string'.
SPATIAL_21706 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221706: The attribute 'spatial:sampledValue' on a <sampledVolume> must have a value of data type 'double'.
SPATIAL_21707 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221707: The attribute 'spatial:minValue' on a <sampledVolume> must have a value of data type 'double'.
SPATIAL_21708 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221708: The attribute 'spatial:maxValue' on a <sampledVolume> must have a value of data type 'double'.
SPATIAL_21750 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_21751 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_21752 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_21753 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_21754 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_21801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221801: An <analyticGeometry> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221802: An <analyticGeometry> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_21803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221803: An <analyticGeometry> object may contain one and only one instance of the <listOfAnalyticVolumes> element.
SPATIAL_21804 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221804: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfAnalyticVolumes> container object may only contain <analyticVolume> objects.
SPATIAL_21805 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221805: A <listOfAnalyticVolumes> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221901: An <analyticVolume> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_21902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221902: An <analyticVolume> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_21903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221903: An <analyticVolume> object must have the required attributes 'spatial:id', 'spatial:functionType' and 'spatial:domainType', and may have the optional attributes 'spatial:name' and 'spatial:ordinal'.
SPATIAL_21904 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221904: An <analyticVolume> object may contain one and only one instance of the ASTNode element.
SPATIAL_21905 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221905: The value of the attribute 'spatial:functionType' of an <analyticVolume> object must conform to the syntax of SBML data type 'FunctionKind' and may only take on the allowed values of 'FunctionKind' defined in SBML; that is, the value must be one of the following: 'layered'.
SPATIAL_21906 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221906: The value of the attribute 'spatial:domainType' of an <analyticVolume> object must be the identifier of an existing <domainType> object defined in the enclosing <model> object.
SPATIAL_21907 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221907: The attribute 'spatial:name' on an <analyticVolume> must have a value of data type 'string'.
SPATIAL_21908 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1221908: The attribute 'spatial:ordinal' on an <analyticVolume> must have a value of data type 'integer'.
SPATIAL_21950 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_22001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222001: A <parametricGeometry> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222002: A <parametricGeometry> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_22003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222003: A <parametricGeometry> object may contain one and only one instance of each of the SpatialPoints and <listOfParametricObjects> elements.
SPATIAL_22004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222004: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfParametricObjects> container object may only contain <parametricObject> objects.
SPATIAL_22005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222005: A <listOfParametricObjects> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222101: A <parametricObject> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222102: A <parametricObject> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_22103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222103: A <parametricObject> object must have the required attributes 'spatial:id', 'spatial:polygonType', 'spatial:domainType', 'spatial:pointIndex', 'spatial:pointIndexLength' and 'spatial:compression', and may have the optional attributes 'spatial:name' and 'spatial:dataType'.
SPATIAL_22104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222104: The value of the attribute 'spatial:polygonType' of a <parametricObject> object must conform to the syntax of SBML data type 'PolygonKind' and may only take on the allowed values of 'PolygonKind' defined in SBML; that is, the value must be one of the following: 'triangle' or 'quadrilateral'.
SPATIAL_22105 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222105: The value of the attribute 'spatial:domainType' of a <parametricObject> object must be the identifier of an existing <domainType> object defined in the enclosing <model> object.
SPATIAL_22106 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222106: The value of the attribute 'spatial:pointIndex' of a <parametricObject> object must be an array of values of type 'int'.
SPATIAL_22107 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222107: The attribute 'spatial:pointIndexLength' on a <parametricObject> must have a value of data type 'integer'.
SPATIAL_22108 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222108: The value of the attribute 'spatial:compression' of a <parametricObject> object must conform to the syntax of SBML data type 'CompressionKind' and may only take on the allowed values of 'CompressionKind' defined in SBML; that is, the value must be one of the following: 'uncompressed' or 'deflated'.
SPATIAL_22109 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222109: The attribute 'spatial:name' on a <parametricObject> must have a value of data type 'string'.
SPATIAL_22110 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222110: The value of the attribute 'spatial:dataType' of a <parametricObject> object must conform to the syntax of SBML data type 'DataKind' and may only take on the allowed values of 'DataKind' defined in SBML; that is, the value must be one of the following: 'double', 'float', 'uint8', 'uint16' or 'uint32'.
SPATIAL_22201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222201: A <cSGeometry> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222202: A <cSGeometry> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_22203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222203: A <cSGeometry> object may contain one and only one instance of the <listOfCSGObjects> element.
SPATIAL_22204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222204: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfCSGObjects> container object may only contain <cSGObject> objects.
SPATIAL_22205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222205: A <listOfCSGObjects> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222301: A <cSGObject> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222302: A <cSGObject> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_22303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222303: A <cSGObject> object must have the required attributes 'spatial:id' and 'spatial:domainType', and may have the optional attributes 'spatial:name' and 'spatial:ordinal'.
SPATIAL_22304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222304: A <cSGObject> object must contain one and only one instance of the CSGNode element.
SPATIAL_22305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222305: The value of the attribute 'spatial:domainType' of a <cSGObject> object must be the identifier of an existing <domainType> object defined in the enclosing <model> object.
SPATIAL_22306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222306: The attribute 'spatial:name' on a <cSGObject> must have a value of data type 'string'.
SPATIAL_22307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222307: The attribute 'spatial:ordinal' on a <cSGObject> must have a value of data type 'integer'.
SPATIAL_22350 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_22401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222401: A <cSGNode> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222402: A <cSGNode> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_22403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222403: A <cSGNode> object may have the optional attributes 'spatial:id' and 'spatial:name'.
SPATIAL_22404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222404: The attribute 'spatial:name' on a <cSGNode> must have a value of data type 'string'.
SPATIAL_22501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222501: A <cSGTransformation> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22502 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222502: A <cSGTransformation> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_22503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222503: A <cSGTransformation> object may contain one and only one instance of the CSGNode element.
SPATIAL_22601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222601: A <cSGTranslation> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222602: A <cSGTranslation> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_22603 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222603: A <cSGTranslation> object must have the required attribute 'spatial:translateX', and may have the optional attributes 'spatial:translateY' and 'spatial:translateZ'.
SPATIAL_22604 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222604: The attribute 'spatial:translateX' on a <cSGTranslation> must have a value of data type 'double'.
SPATIAL_22605 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222605: The attribute 'spatial:translateY' on a <cSGTranslation> must have a value of data type 'double'.
SPATIAL_22606 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222606: The attribute 'spatial:translateZ' on a <cSGTranslation> must have a value of data type 'double'.
SPATIAL_22701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222701: A <cSGRotation> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222702: A <cSGRotation> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_22703 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222703: A <cSGRotation> object must have the required attributes 'spatial:rotateX' and 'spatial:rotateAngleInRadians', and may have the optional attributes 'spatial:rotateY' and 'spatial:rotateZ'.
SPATIAL_22704 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222704: The attribute 'spatial:rotateX' on a <cSGRotation> must have a value of data type 'double'.
SPATIAL_22705 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222705: The attribute 'spatial:rotateAngleInRadians' on a <cSGRotation> must have a value of data type 'double'.
SPATIAL_22706 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222706: The attribute 'spatial:rotateY' on a <cSGRotation> must have a value of data type 'double'.
SPATIAL_22707 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222707: The attribute 'spatial:rotateZ' on a <cSGRotation> must have a value of data type 'double'.
SPATIAL_22801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222801: A <cSGScale> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222802: A <cSGScale> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_22803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222803: A <cSGScale> object must have the required attribute 'spatial:scaleX', and may have the optional attributes 'spatial:scaleY' and 'spatial:scaleZ'.
SPATIAL_22804 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222804: The attribute 'spatial:scaleX' on a <cSGScale> must have a value of data type 'double'.
SPATIAL_22805 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222805: The attribute 'spatial:scaleY' on a <cSGScale> must have a value of data type 'double'.
SPATIAL_22806 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222806: The attribute 'spatial:scaleZ' on a <cSGScale> must have a value of data type 'double'.
SPATIAL_22901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222901: A <cSGHomogeneousTransformation> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_22902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222902: A <cSGHomogeneousTransformation> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_22903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1222903: A <cSGHomogeneousTransformation> object must contain one and only one instance of the TransformationComponent element.
SPATIAL_23001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223001: A <transformationComponent> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223002: A <transformationComponent> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_23003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223003: A <transformationComponent> object must have the required attributes 'spatial:components' and 'spatial:componentsLength'.
SPATIAL_23004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223004: The value of the attribute 'spatial:components' of a <transformationComponent> object must be an array of values of type 'double'.
SPATIAL_23005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223005: The attribute 'spatial:componentsLength' on a <transformationComponent> must have a value of data type 'integer'.
SPATIAL_23101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223101: A <cSGPrimitive> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223102: A <cSGPrimitive> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_23103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223103: A <cSGPrimitive> object must have the required attribute 'spatial:primitiveType'.
SPATIAL_23104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223104: The value of the attribute 'spatial:primitiveType' of a <cSGPrimitive> object must conform to the syntax of SBML data type 'PrimitiveKind' and may only take on the allowed values of 'PrimitiveKind' defined in SBML; that is, the value must be one of the following: 'sphere', 'cube', 'cylinder', 'cone', 'circle' or 'square'.
SPATIAL_23201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223201: A <cSGSetOperator> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223202: A <cSGSetOperator> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_23203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223203: A <cSGSetOperator> object must have the required attribute 'spatial:operationType', and may have the optional attributes 'spatial:complementA' and 'spatial:complementB'.
SPATIAL_23204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223204: A <cSGSetOperator> object may contain one and only one instance of the <listOfCSGNodes> element.
SPATIAL_23205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223205: The value of the attribute 'spatial:operationType' of a <cSGSetOperator> object must conform to the syntax of SBML data type 'SetOperation' and may only take on the allowed values of 'SetOperation' defined in SBML; that is, the value must be one of the following: 'union', 'intersection' or 'difference'.
SPATIAL_23206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223206: The value of the attribute 'spatial:complementA' of a <cSGSetOperator> object must be the identifier of an existing <cSGNode> object defined in the enclosing <model> object.
SPATIAL_23207 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223207: The value of the attribute 'spatial:complementB' of a <cSGSetOperator> object must be the identifier of an existing <cSGNode> object defined in the enclosing <model> object.
SPATIAL_23208 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223208: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfCSGNodes> container object may only contain <cSGNode> objects.
SPATIAL_23209 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223209: A <listOfCSGNodes> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23250 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23251 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223301: A <spatialSymbolReference> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223302: A <spatialSymbolReference> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_23303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223303: A <spatialSymbolReference> object must have the required attribute 'spatial:spatialRef'.
SPATIAL_23304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223304: The value of the attribute 'spatial:spatialRef' of a <spatialSymbolReference> object must be the identifier of an existing <geometry> object defined in the enclosing <model> object.
SPATIAL_23401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223401: A <diffusionCoefficient> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223402: A <diffusionCoefficient> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_23403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223403: A <diffusionCoefficient> object must have the required attributes 'spatial:variable' and 'spatial:type', and may have the optional attributes 'spatial:coordinateReferenceOne' and 'spatial:coordinateReferenceTwo'.
SPATIAL_23404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223404: The value of the attribute 'spatial:variable' of a <diffusionCoefficient> object must be the identifier of an existing <species> object defined in the enclosing <model> object.
SPATIAL_23405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223405: The value of the attribute 'spatial:type' of a <diffusionCoefficient> object must conform to the syntax of SBML data type 'DiffusionKind' and may only take on the allowed values of 'DiffusionKind' defined in SBML; that is, the value must be one of the following: 'isotropic', 'anisotropic' or 'tensor'.
SPATIAL_23406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223406: The value of the attribute 'spatial:coordinateReferenceOne' of a <diffusionCoefficient> object must conform to the syntax of SBML data type 'CoordinateKind' and may only take on the allowed values of 'CoordinateKind' defined in SBML; that is, the value must be one of the following: 'cartesianX', 'cartesianY' or 'cartesianZ'.
SPATIAL_23407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223407: The value of the attribute 'spatial:coordinateReferenceTwo' of a <diffusionCoefficient> object must conform to the syntax of SBML data type 'CoordinateKind' and may only take on the allowed values of 'CoordinateKind' defined in SBML; that is, the value must be one of the following: 'cartesianX', 'cartesianY' or 'cartesianZ'.
SPATIAL_23450 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23451 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23452 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223501: An <advectionCoefficient> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23502 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223502: An <advectionCoefficient> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_23503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223503: An <advectionCoefficient> object must have the required attributes 'spatial:variable' and 'spatial:coordinate'.
SPATIAL_23504 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223504: The value of the attribute 'spatial:variable' of an <advectionCoefficient> object must be the identifier of an existing <species> object defined in the enclosing <model> object.
SPATIAL_23505 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223505: The value of the attribute 'spatial:coordinate' of an <advectionCoefficient> object must conform to the syntax of SBML data type 'CoordinateKind' and may only take on the allowed values of 'CoordinateKind' defined in SBML; that is, the value must be one of the following: 'cartesianX', 'cartesianY' or 'cartesianZ'.
SPATIAL_23601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223601: A <boundaryCondition> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223602: A <boundaryCondition> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_23603 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223603: A <boundaryCondition> object must have the required attributes 'spatial:variable' and 'spatial:type', and may have the optional attributes 'spatial:coordinateBoundary' and 'spatial:boundaryDomainType'.
SPATIAL_23604 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223604: The value of the attribute 'spatial:variable' of a <boundaryCondition> object must be the identifier of an existing <species> object defined in the enclosing <model> object.
SPATIAL_23605 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223605: The value of the attribute 'spatial:type' of a <boundaryCondition> object must conform to the syntax of SBML data type 'BoundaryKind' and may only take on the allowed values of 'BoundaryKind' defined in SBML; that is, the value must be one of the following: 'Robin_valueCoefficient', 'Robin_inwardNormalGradientCoefficient', 'Robin_sum', 'Neumann' or 'Dirichlet'.
SPATIAL_23606 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223606: The value of the attribute 'spatial:coordinateBoundary' of a <boundaryCondition> object must be the identifier of an existing <boundary> object defined in the enclosing <model> object.
SPATIAL_23607 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223607: The value of the attribute 'spatial:boundaryDomainType' of a <boundaryCondition> object must be the identifier of an existing <domainType> object defined in the enclosing <model> object.
SPATIAL_23650 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223701: A <geometry> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223702: A <geometry> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_23703 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223703: A <geometry> object must have the required attribute 'spatial:coordinateSystem', and may have the optional attribute 'spatial:id'.
SPATIAL_23704 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223704: A <geometry> object may contain one and only one instance of each of the <listOfCoordinateComponents,> <listOfDomainTypes,> <listOfDomains,> <listOfAdjacentDomains,> <listOfGeometryDefinitions> and <listOfSampledFields> elements.
SPATIAL_23705 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223705: The value of the attribute 'spatial:coordinateSystem' of a <geometry> object must conform to the syntax of SBML data type 'GeometryKind' and may only take on the allowed values of 'GeometryKind' defined in SBML; that is, the value must be one of the following: 'cartesian'.
SPATIAL_23706 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223706: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfCoordinateComponents> container object may only contain <coordinateComponent> objects.
SPATIAL_23707 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223707: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfDomainTypes> container object may only contain <domainType> objects.
SPATIAL_23708 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223708: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfDomains> container object may only contain <domain> objects.
SPATIAL_23709 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223709: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfAdjacentDomains> container object may only contain <adjacentDomains> objects.
SPATIAL_23710 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223710: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfGeometryDefinitions> container object may only contain <geometryDefinition> objects.
SPATIAL_23711 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223711: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfSampledFields> container object may only contain <sampledField> objects.
SPATIAL_23712 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223712: A <listOfCoordinateComponents> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23713 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223713: A <listOfDomainTypes> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23714 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223714: A <listOfDomains> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23715 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223715: A <listOfAdjacentDomains> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23716 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223716: A <listOfGeometryDefinitions> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23717 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223717: A <listOfSampledFields> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23750 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23751 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23752 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23753 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23754 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223801: A <mixedGeometry> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223802: A <mixedGeometry> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_23803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223803: A <mixedGeometry> object may contain one and only one instance of each of the <listOfGeometryDefinitions> and <listOfOrdinalMappings> elements.
SPATIAL_23804 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223804: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfGeometryDefinitions> container object may only contain <geometryDefinition> objects.
SPATIAL_23805 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223805: Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfOrdinalMappings> container object may only contain <ordinalMapping> objects.
SPATIAL_23806 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223806: A <listOfGeometryDefinitions> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23807 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223807: A <listOfOrdinalMappings> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23850 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
SPATIAL_23901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223901: An <ordinalMapping> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_23902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223902: An <ordinalMapping> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_23903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223903: An <ordinalMapping> object must have the required attributes 'spatial:geometryDefinition' and 'spatial:ordinal'.
SPATIAL_23904 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223904: The value of the attribute 'spatial:geometryDefinition' of an <ordinalMapping> object must be the identifier of an existing <geometryDefinition> object defined in the enclosing <model> object.
SPATIAL_23905 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1223905: The attribute 'spatial:ordinal' on an <ordinalMapping> must have a value of data type 'integer'.
SPATIAL_24001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1224001: A <spatialPoints> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'.
SPATIAL_24002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1224002: A <spatialPoints> object may have the optional SBML Level 3 Core subobjects for notes and annotations.
SPATIAL_24003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1224003: A <spatialPoints> object must have the required attributes 'spatial:compression', 'spatial:arrayData' and 'spatial:arrayDataLength', and may have the optional attributes 'spatial:id', 'spatial:name' and 'spatial:dataType'.
SPATIAL_24004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1224004: The value of the attribute 'spatial:compression' of a <spatialPoints> object must conform to the syntax of SBML data type 'CompressionKind' and may only take on the allowed values of 'CompressionKind' defined in SBML; that is, the value must be one of the following: 'uncompressed' or 'deflated'.
SPATIAL_24005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1224005: The value of the attribute 'spatial:arrayData' of a <spatialPoints> object must be an array of values of type 'double'.
SPATIAL_24006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1224006: The attribute 'spatial:arrayDataLength' on a <spatialPoints> must have a value of data type 'integer'.
SPATIAL_24007 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1224007: The attribute 'spatial:name' on a <spatialPoints> must have a value of data type 'string'.
SPATIAL_24008 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes: Error code 1224008: The value of the attribute 'spatial:dataType' of a <spatialPoints> object must conform to the syntax of SBML data type 'DataKind' and may only take on the allowed values of 'DataKind' defined in SBML; that is, the value must be one of the following: 'double', 'float', 'uint8', 'uint16' or 'uint32'.
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
SpatialCompartmentPluginConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SpatialCompartmentPlugin class.
SpatialCompartmentPluginConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpatialCompartmentPluginConstraints
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(SpatialModelPlugin) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialModelPlugin
SpatialModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialModelPlugin
SpatialModelPluginConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SpatialModelPlugin class.
SpatialModelPluginConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpatialModelPluginConstraints
SpatialNamedSBase - Interface in org.sbml.jsbml.ext.spatial: Deprecated.
since id and name have been added to the spatial package classes, this interface is not needed any more and NamedSBase can be used instead.
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
SpatialParameterPluginConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SpatialParameterPlugin class.
SpatialParameterPluginConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpatialParameterPluginConstraints
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(String, 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
SpatialPointsConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SpatialPoints class.
SpatialPointsConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpatialPointsConstraints
SpatialReactionPlugin - Class in org.sbml.jsbml.ext.spatial
SpatialReactionPlugin() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin
SpatialReactionPlugin(SpatialReactionPlugin) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin
SpatialReactionPlugin(Reaction) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin
SpatialReactionPluginConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SpatialReactionPlugin class.
SpatialReactionPluginConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpatialReactionPluginConstraints
spatialRef - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
spatialSizeUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
SpatialSizeUnitsNotValidAttribute - org.sbml.jsbml.SBMLException.Code: Attribute spatialSizeUnits on species not supported in SBML Level 1
SpatialSizeUnitsRemoved - org.sbml.jsbml.SBMLException.Code: Attribute spatialSizeUnits not supported in this Level+Version of SBML
SpatialSpeciesPlugin - Class in org.sbml.jsbml.ext.spatial
SpatialSpeciesPlugin() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
SpatialSpeciesPlugin(SpatialSpeciesPlugin) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
SpatialSpeciesPlugin(Species) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin
SpatialSpeciesPluginConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SpatialSpeciesPlugin class.
SpatialSpeciesPluginConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpatialSpeciesPluginConstraints
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: Creates a new SpatialSymbolReference instance.
SpatialSymbolReference(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSymbolReference: Creates a new SpatialSymbolReference instance.
SpatialSymbolReference(SpatialSymbolReference) - Constructor for class org.sbml.jsbml.ext.spatial.SpatialSymbolReference: Creates a new SpatialSymbolReference instance.
SpatialSymbolReferenceConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SpatialSymbolReference class.
SpatialSymbolReferenceConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpatialSymbolReferenceConstraints
SpatialTest - Class in org.sbml.jsbml.ext.spatial
SpatialTest() - Constructor for class org.sbml.jsbml.ext.spatial.SpatialTest
SpatialUnitsInOneD - org.sbml.jsbml.SBMLException.Code: Invalid value of spatialSizeUnits for a one-dimensional compartment
SpatialUnitsInThreeD - org.sbml.jsbml.SBMLException.Code: Invalid value of spatialSizeUnits for a three-dimensional compartment
SpatialUnitsInTwoD - org.sbml.jsbml.SBMLException.Code: Invalid value of spatialSizeUnits for a two-dimensional compartment
SPECIAL_ROTATION_NEEDED - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector
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 - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
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(String) - Constructor for class org.sbml.jsbml.Species: Creates a new Species instance with the given id.
Species(String, int, int) - Constructor for class org.sbml.jsbml.Species: Creates a Species instance from a level and version.
Species(String, String, int, int) - Constructor for class org.sbml.jsbml.Species: Creates a new Species instance with the given id.
Species(Species) - Constructor for class org.sbml.jsbml.Species: Creates a Species instance from a Species.
SPECIES_RELATIVE_DOCKING_POINT - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector: Constant for use as the key for relative docking points for a species, also see LayoutDirector.PN_RELATIVE_DOCKING_POINT.
SpeciesCompartmentRequiredInL1 - org.sbml.jsbml.SBMLException.Code: In SBML Level 1, a value for compartment is mandatory in species definitions
SpeciesConstraints - Class in org.sbml.jsbml.validator.offline.constraints
SpeciesConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesConstraints
SpeciesFeature - Class in org.sbml.jsbml.ext.multi: Defines the state of a component in a species by selecting values from the listOfPossibleSpeciesFeatureValues of the referenced SpeciesFeatureType.
SpeciesFeature() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature: Creates an SpeciesFeature instance
SpeciesFeature(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature: Creates a SpeciesFeature instance with a level and version.
SpeciesFeature(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature: Creates a SpeciesFeature instance with an id.
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
speciesFeatureType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
SpeciesFeatureType - Class in org.sbml.jsbml.ext.multi: A species type (MultiSpeciesType) 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(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Creates a SpeciesFeatureType instance with a level and version.
SpeciesFeatureType(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType: Creates a SpeciesFeatureType instance with an id.
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
SpeciesFeatureTypeConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Constraints declaration for the MultiCompartmentPlugin class.
SpeciesFeatureTypeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesFeatureTypeConstraints
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(String) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesGlyph
SpeciesGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesGlyph
SpeciesGlyph(SpeciesGlyph) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesGlyph
SPECIESGLYPH - org.sbml.jsbml.ext.render.Style.Type
SpeciesGlyphConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SpeciesGlyph class.
SpeciesGlyphConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesGlyphConstraints
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(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.
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.
SpeciesReferenceConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SpeciesReference class.
SpeciesReferenceConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceConstraints
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(String) - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
SpeciesReferenceFilter(String, String) - Constructor for class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
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.
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(String) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
SpeciesReferenceGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
SpeciesReferenceGlyph(SpeciesReferenceGlyph) - Constructor for class org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph
SPECIESREFERENCEGLYPH - org.sbml.jsbml.ext.render.Style.Type
SpeciesReferenceGlyphConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the SpeciesReferenceGlyph class.
SpeciesReferenceGlyphConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceGlyphConstraints
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 - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
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(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(SpeciesType) - Constructor for class org.sbml.jsbml.SpeciesType: Deprecated.
speciesTypeComponentIndex - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
SpeciesTypeComponentIndex - Class in org.sbml.jsbml.ext.multi: Provides a way to identify or index a component within a MultiSpeciesType.
SpeciesTypeComponentIndex() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Creates an SpeciesTypeComponentIndex instance
SpeciesTypeComponentIndex(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Creates a SpeciesTypeComponentIndex instance with a level and version.
SpeciesTypeComponentIndex(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex: Creates a SpeciesTypeComponentIndex instance with an id.
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
SpeciesTypeComponentIndexConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Constraints declaration for the MultiCompartmentPlugin class.
SpeciesTypeComponentIndexConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeComponentIndexConstraints
SpeciesTypeComponentMapInProduct - Class in org.sbml.jsbml.ext.multi: A speciesTypeComponentMapInProduct defines the mapping between a component in a reactant and a component in a product.
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
SpeciesTypeConstraints - Class in org.sbml.jsbml.validator.offline.constraints
SpeciesTypeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeConstraints
SpeciesTypeInstance - Class in org.sbml.jsbml.ext.multi: Provides a way to construct MultiSpeciesTypes and Species with multiple components.
SpeciesTypeInstance() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Creates an SpeciesTypeInstance instance
SpeciesTypeInstance(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Creates a SpeciesTypeInstance instance with a level and version.
SpeciesTypeInstance(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance: Creates a SpeciesTypeInstance instance with an id.
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
SpeciesTypeInstanceConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Constraints declaration for the MultiCompartmentPlugin class.
SpeciesTypeInstanceConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeInstanceConstraints
SpeciesTypeNotValidAttribute - org.sbml.jsbml.SBMLException.Code: Attribute speciesType on species not supported in SBML Level 1
SpeciesTypeNotValidComponent - org.sbml.jsbml.SBMLException.Code: Species types not supported in SBML Level 1
speciesTypeRestriction - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
speciesTypeState - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
sphere - org.sbml.jsbml.ext.spatial.PrimitiveKind: sphere
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() - Method in class org.sbml.jsbml.ASTNode: Applies the square root function on this syntax tree and returns the resulting tree.
sqrt(Object) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
sqrt(Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
sqrt(ASTNode) - Static method in class org.sbml.jsbml.ASTNode: Creates a root ASTNode.
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(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler: Square root.
sqrt(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
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
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(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
square - org.sbml.jsbml.ext.spatial.PrimitiveKind: square
standardDeviation - org.sbml.jsbml.ext.distrib.UncertParameter.Type: The standard deviation of a distribution or population is the square root of its variance.
standardError - org.sbml.jsbml.ext.distrib.UncertParameter.Type: The standard error is the standard deviation of estimates of a population value.
start - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
START - org.sbml.jsbml.ext.render.HTextAnchor
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.
stddev - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
STERADIAN - org.sbml.jsbml.Unit.Kind: The steradian unit.
Stimulation<T> - Interface in org.sbml.jsbml.ext.render.director: Interface for the SBGN specified stimulation arc.
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.
StoichiometryMathNotValidComponent - org.sbml.jsbml.SBMLException.Code: lt;stoichiometryMath> not supported in SBML Level 1
stop - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
stopColor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
storeElementsOrder(String, Object) - Static method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter: Stores a list of elements as they are given.
strict - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in Version 2 Release 4.
StrictSBORequiredInL2v2 - org.sbml.jsbml.SBMLException.Code: SBML Level 2 Version 2 requires strict sbo consistency
StrictSBORequiredInL2v3 - org.sbml.jsbml.SBMLException.Code: SBML Level 2 Version 3 requires strict sbo consistency
StrictUnitsRequiredInL1 - org.sbml.jsbml.SBMLException.Code: SBML Level 1 requires strict unit consistency
StrictUnitsRequiredInL2v1 - org.sbml.jsbml.SBMLException.Code: SBML Level 2 Version 1 requires strict unit consistency
StrictUnitsRequiredInL2v2 - org.sbml.jsbml.SBMLException.Code: SBML Level 2 Version 2 requires strict unit consistency
StrictUnitsRequiredInL2v3 - org.sbml.jsbml.SBMLException.Code: SBML Level 2 Version 3 requires strict unit consistency
string() - Method in class org.sbml.jsbml.math.parser.FormulaParser
string() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
string() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
string() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
string() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
string() - Method in class org.sbml.jsbml.text.parser.FormulaParser
string() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
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.math.parser.FormulaParserASTNode2Constants: RegularExpression Id.
STRING - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants: RegularExpression Id.
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 - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants: RegularExpression Id.
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 - 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 - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
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(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(RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.Style: Creates a Style instance with a group
Style(Style) - Constructor for class org.sbml.jsbml.ext.render.Style: Clone constructor
Style.Type - Enum in org.sbml.jsbml.ext.render: The type StyleType is used by LocalStyle and GlobalStyle elements, in order to apply a particular style to a GraphicalObject.
StyleConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the Style class.
Note: Since global styles are not explicitly implemented in JSBML, this class combines the constraints placed on both Style and GlobalStyle (which is not a problem, since GlobalStyle does not add any meaningfully new constraints)
StyleConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.StyleConstraints
subList(int, int) - Method in class org.sbml.jsbml.ListOf
SubListOfSpeciesFeature - Class in org.sbml.jsbml.ext.multi: Allows to regroup a set of SpeciesFeature that have a specific Relation between them.
SubListOfSpeciesFeature() - Constructor for class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature: Creates an SubListOfSpeciesFeature instance
SubListOfSpeciesFeature(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature: Creates a SubListOfSpeciesFeature instance with a level and version.
SubListOfSpeciesFeature(String) - Constructor for class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature: Creates a SubListOfSpeciesFeature instance with an id.
SubListOfSpeciesFeature(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature: Creates a SubListOfSpeciesFeature instance with an id, level, and version.
SubListOfSpeciesFeature(SubListOfSpeciesFeature) - Constructor for class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature: Clone constructor
subListOfSpeciesFeatures - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
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(int, int) - Constructor for class org.sbml.jsbml.ext.comp.Submodel: Creates a Submodel instance with a level and version.
Submodel(String) - Constructor for class org.sbml.jsbml.ext.comp.Submodel: Creates a Submodel instance with an id.
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
SubmodelConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the Submodel class.
SubmodelConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SubmodelConstraints
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(int, int) - Static method in class org.sbml.jsbml.UnitDefinition: Returns the predefined unit for substance.
SUBSTANCE - Static variable in class org.sbml.jsbml.UnitDefinition: Identifier of the (for the SBML Levels 1 and 2) predefined UnitDefinition substance.
substanceUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
SUBSTRATE - org.sbml.jsbml.ext.layout.SpeciesReferenceRole
subsubsection(String, boolean) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
subsubsection(String, boolean) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
SubsUnitsAllowedInKL - org.sbml.jsbml.SBMLException.Code: Disallowed value for attribute substanceUnits
SubsUnitsNoLongerValid - org.sbml.jsbml.SBMLException.Code: substanceUnits not supported in this Level+Version of SBML
sum - org.sbml.jsbml.ext.multi.RepresentationType
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.
sum(ASTNode...) - Static method in class org.sbml.jsbml.ASTNode: Creates a new ASTNode of type Plus with the given nodes as children.
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(MathContainer, CallableSBase...) - Static method in class org.sbml.jsbml.ASTNode: Sum of several NamedSBase objects.
SUM - org.sbml.jsbml.ASTNode.Type
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 - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
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(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(QuantityWithUnit) - Constructor for class org.sbml.jsbml.Symbol: Creates a Symbol instance.
Symbol(Symbol) - Constructor for class org.sbml.jsbml.Symbol: Creates a Symbol instance from a given Symbol.
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.
SYSTEM - org.sbml.jsbml.SBMLException.Category: These are operating system errors - like 'out of memory' and would have numbers in the range 00001 - 00005.
SYSTEM - org.sbml.jsbml.SBMLException.Type

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