Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Enums
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors
• Deprecated Enum Constants

Deprecated Interfaces

Interface and Description
org.sbml.jsbml.ext.spatial.SpatialNamedSBase 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.

Deprecated Classes

Class and Description
org.sbml.jsbml.CompartmentType Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.ext.spatial.CoordinateReference Not present in spec 0.90, as be moved into DiffusionCoefficient.
org.sbml.jsbml.ext.fbc.FluxBound Only defined in FBC Version 1.
org.sbml.jsbml.ext.groups.ListOfMemberConstraint This class was removed from the specifications as of version 0.7 (2015-11-24) as no software wanted to implement support for it. It might be added back in a future version of the specifications if somebody want to implement it.
org.sbml.jsbml.util.ListOfWithName since JSBML 1.2 and the introduction of ListOf.setOtherListName(String), this class is not necessary any more.
org.sbml.jsbml.util.compilers.MathMLCompiler use MathMLXMLStreamCompiler instead.
org.sbml.jsbml.xml.parsers.MathMLParser this class should not be used anymore, replaced by MathMLStaxParser. But we keep it in case somebody want to use Document
org.sbml.jsbml.ext.groups.MemberConstraint This class was removed from the specifications as of version 0.7 (2015-11-24) as no software wanted to implement support for it. It might be added back in a future version of the specifications if somebody want to implement it.
org.sbml.jsbml.ext.spatial.PolygonObject
org.sbml.jsbml.ext.qual.QualitativeModel use QualModelPlugin instead.
org.sbml.jsbml.SpeciesType Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.StoichiometryMath Since SBML Level 3 Version 1 use AssignmentRule with instances of SpeciesReference as Variable instead.

Deprecated Enums

Enum and Description
org.sbml.jsbml.ext.fbc.FluxBound.Operation Only defined in FBC version 1.

Deprecated Fields

Field and Description
org.sbml.jsbml.ext.render.RenderConstants.absoluteCx Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteCy Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteCz Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteFx Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteFy Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteFz Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteHeight Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteR Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteRx Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteRy Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteWidth Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteX Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteX1 Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteX2 Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteY Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteY1 Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteY2 Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteZ Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteZ1 Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.render.RenderConstants.absoluteZ2 Made obsolete by the introduction of RelAbsVector
org.sbml.jsbml.ext.fbc.FBCConstants.geneProteinAssociation

Deprecated Methods

Method and Description
org.sbml.jsbml.Model.addCompartmentType(CompartmentType) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.ext.fbc.FBCModelPlugin.addFluxBound(FluxBound) Only defined in FBC version 1.
org.sbml.jsbml.SBMLDocument.addNamespace(String, String, String) use SBase.addDeclaredNamespace(String, String)
org.sbml.jsbml.KineticLaw.addParameter(LocalParameter) use KineticLaw.addLocalParameter(LocalParameter).
org.sbml.jsbml.KineticLaw.addParameter(Parameter) A KineticLaw can only contain instances of LocalParameters. Please use KineticLaw.addLocalParameter(LocalParameter) and create an instance of LocalParameter for your purposes.
org.sbml.jsbml.Model.addSpeciesType(SpeciesType) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.StoichiometryMath.clone()
org.sbml.jsbml.SpeciesType.clone()
org.sbml.jsbml.CompartmentType.clone()
org.sbml.jsbml.ext.fbc.FluxBound.clone()
org.sbml.jsbml.Event.containsUndeclaredUnits()
org.sbml.jsbml.ext.render.director.LayoutAlgorithm.createCompartmentGlyphPosition(CompartmentGlyph)
org.sbml.jsbml.Model.createCompartmentType() CompartmentTypes should no longer be used, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.createCompartmentType(String) CompartmentTypes should no longer be used, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.ext.render.RenderCurve.createElement() use#createRenderPoint()
org.sbml.jsbml.ext.fbc.FBCModelPlugin.createFluxBound() Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FBCModelPlugin.createFluxBound(String) Only defined in FBC version 1.
org.sbml.jsbml.Model.createSpeciesType() Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.createSpeciesType(String) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.SpeciesReference.createStoichiometryMath(ASTNode) since SBML Level 3 this should not be used anymore.
org.sbml.jsbml.ext.fbc.FluxBound.equals(Object)
org.sbml.jsbml.Annotation.getAnnotationBuilder()
org.sbml.jsbml.Species.getCharge()
org.sbml.jsbml.math.parser.SimpleCharStream.getColumn()
org.sbml.jsbml.text.parser.SimpleCharStream.getColumn()
org.sbml.jsbml.Compartment.getCompartmentType() Only defined in SBML Level 2 Versions 2 through 4.
org.sbml.jsbml.Model.getCompartmentType(int) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.getCompartmentType(String) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.getCompartmentTypeCount() using CompartmentType is not recommended, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Compartment.getCompartmentTypeInstance()
org.sbml.jsbml.SpeciesReference.getDenominator() Use for Level 1 only.
org.sbml.jsbml.Event.getDerivedUnitDefinition()
org.sbml.jsbml.Event.getDerivedUnits()
org.sbml.jsbml.Unit.getExponentAsDouble() use Unit.getExponent()
org.sbml.jsbml.Reaction.getFast()
org.sbml.jsbml.ext.fbc.FBCModelPlugin.getFluxBound(int) Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FBCModelPlugin.getFluxBoundCount() Only defined in FBC version 1.
org.sbml.jsbml.AbstractMathContainer.getFormula()
org.sbml.jsbml.MathContainer.getFormula() 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.
org.sbml.jsbml.ext.distrib.UncertParameter.getFormula()
org.sbml.jsbml.Model.getInitialAssignment(String) Since L3V2, every SBase can have an id. Use either Model.getInitialAssignmentById(String) or Model.getInitialAssignmentBySymbol(String)
org.sbml.jsbml.math.parser.SimpleCharStream.getLine()
org.sbml.jsbml.text.parser.SimpleCharStream.getLine()
org.sbml.jsbml.Model.getListOfCompartmentTypes() Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.ext.fbc.FBCModelPlugin.getListOfFluxBounds() Only defined in FBC version 1.
org.sbml.jsbml.KineticLaw.getListOfParameters() use KineticLaw.getListOfLocalParameters()
org.sbml.jsbml.Model.getListOfSpeciesTypes() Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.getModelHistory() use SBase.getHistory()
org.sbml.jsbml.math.ASTCiNumberNode.getName()
org.sbml.jsbml.Model.getNumCompartmentTypes()
org.sbml.jsbml.ext.fbc.FBCModelPlugin.getNumFluxBound() Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.Objective.getNumFluxObjectives() use Objective.getFluxObjectiveCount()
org.sbml.jsbml.KineticLaw.getNumLocalParameters() use KineticLaw.getLocalParameterCount()
org.sbml.jsbml.KineticLaw.getNumParameters() use KineticLaw.getLocalParameterCount()
org.sbml.jsbml.ext.layout.ReactionGlyph.getNumSpeciesReferenceGlyphs() use ReactionGlyph.getSpeciesReferenceGlyphCount()
org.sbml.jsbml.Model.getNumSpeciesTypes()
org.sbml.jsbml.Model.getNumStoichiometryMath() since SBML L3V1.
org.sbml.jsbml.Unit.getOffset()
org.sbml.jsbml.ext.fbc.FluxBound.getOperation()
org.sbml.jsbml.Creator.getOtherAttribute(String) those other attributes are not saved when writing the model
org.sbml.jsbml.Creator.getOtherAttributes() those other attributes are not saved when writing the model
org.sbml.jsbml.KineticLaw.getParameter(int) use KineticLaw.getLocalParameter(int)
org.sbml.jsbml.KineticLaw.getParameter(String) use KineticLaw.getLocalParameter(String)
org.sbml.jsbml.StoichiometryMath.getParent()
org.sbml.jsbml.SpeciesType.getParent()
org.sbml.jsbml.CompartmentType.getParent()
org.sbml.jsbml.SBMLDocument.getPkgRequired(String) use SBMLDocument.getPackageRequired(String)
org.sbml.jsbml.ext.fbc.FluxBound.getReaction() Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FluxBound.getReactionInstance() Only defined in FBC version 1.
org.sbml.jsbml.ext.render.AbstractRenderPlugin.getRenderInformation() This goes beyond/is besides the render-package's specification and will be removed in a future release. Use the methods RenderLayoutPlugin.getListOfLocalRenderInformation(), RenderLayoutPlugin.getLocalRenderInformation(int), and RenderListOfLayoutsPlugin.getListOfGlobalRenderInformation() respectively
org.sbml.jsbml.Model.getRule(String) Since L3V2 every SBase can have an id. Use either Model.getRuleById(String) or Model.getRuleByVariable(String).
org.sbml.jsbml.SBMLDocument.getSBMLDocumentNamespaces() use SBase.getDeclaredNamespaces()
org.sbml.jsbml.Compartment.getSpatialDimensionsAsDouble() use Compartment.getSpatialDimensions()
org.sbml.jsbml.ext.spatial.SpatialNamedSBase.getSpatialId() use SBase.getId()
org.sbml.jsbml.Species.getSpatialSizeUnits() Only valid for SBML Level 2 Versions 1 and 2.
org.sbml.jsbml.Species.getSpatialSizeUnitsInstance() Only valid for SBML Level 2 Versions 1 and 2.
org.sbml.jsbml.Species.getSpeciesType() Only valid for SBML Level 2 Versions 2, 3, and 4.
org.sbml.jsbml.Model.getSpeciesType(int) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.getSpeciesType(String) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.getSpeciesTypeCount() the use of SpeciesType is not recommended, because this data structure is only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Species.getSpeciesTypeInstance() Only valid for SBML Level 2 Versions 2, 3, and 4.
org.sbml.jsbml.SpeciesReference.getStoichiometryMath() since SBML Level 3 this should not be used anymore.
org.sbml.jsbml.Model.getStoichiometryMathCount() since SBML L3V1
org.sbml.jsbml.KineticLaw.getSubstanceUnits()
org.sbml.jsbml.KineticLaw.getSubstanceUnitsInstance()
org.sbml.jsbml.InitialAssignment.getSymbol() use InitialAssignment.getVariable()
org.sbml.jsbml.Event.getTimeUnits()
org.sbml.jsbml.KineticLaw.getTimeUnits()
org.sbml.jsbml.Event.getTimeUnitsID()
org.sbml.jsbml.Event.getTimeUnitsInstance()
org.sbml.jsbml.KineticLaw.getTimeUnitsInstance()
org.sbml.jsbml.Event.getUnits()
org.sbml.jsbml.KineticLaw.getUnits()
org.sbml.jsbml.ExplicitRule.getUnits() 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.
org.sbml.jsbml.Event.getUnitsInstance()
org.sbml.jsbml.KineticLaw.getUnitsInstance()
org.sbml.jsbml.ExplicitRule.getUnitsInstance() 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.
org.sbml.jsbml.ext.fbc.FluxBound.getValue() Only defined in FBC version 1.
org.sbml.jsbml.Compartment.getVolume() The volume attribute is only defined in SBML Level 1. Please use Compartment.getSize().
org.sbml.jsbml.ext.fbc.FluxBound.hashCode()
org.sbml.jsbml.ext.fbc.FluxBound.initDefaults() Only defined in FBC version 1.
org.sbml.jsbml.UnitDefinition.isBuiltIn() use UnitDefinition.isPredefined()
org.sbml.jsbml.Unit.isBuiltIn(String, int) use Unit.isPredefined(String, int)
org.sbml.jsbml.UnitDefinition.isBuiltIn(UnitDefinition) use UnitDefinition.isPredefined()
org.sbml.jsbml.Unit.isCelsius() Unit.Kind.CELSIUS should no longer be used.
org.sbml.jsbml.xml.XMLTriple.isEmpty() libSBML internal
org.sbml.jsbml.Reaction.isFast()
org.sbml.jsbml.SpeciesType.isIdMandatory()
org.sbml.jsbml.CompartmentType.isIdMandatory()
org.sbml.jsbml.ext.fbc.FluxBound.isIdMandatory()
org.sbml.jsbml.SBMLDocument.isIgnoredPkg(String) use SBMLDocument.isIgnoredPackage(String)
org.sbml.jsbml.SBase.isPkgEnabled(String) use SBase.isPackageEnabled(String)
org.sbml.jsbml.AbstractSBase.isPkgEnabled(String)
org.sbml.jsbml.SBase.isPkgURIEnabled(String) use SBase.isPackageEnabled(String)
org.sbml.jsbml.AbstractSBase.isPkgURIEnabled(String)
org.sbml.jsbml.Compartment.isSetCompartmentTypeInstance()
org.sbml.jsbml.Model.isSetListOfCompartmentTypes() Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.ext.fbc.FBCModelPlugin.isSetListOfFluxBounds() Only defined in FBC version 1.
org.sbml.jsbml.KineticLaw.isSetListOfParameters() use KineticLaw.isSetListOfLocalParameters()
org.sbml.jsbml.ext.layout.ReactionGlyph.isSetListOfSpeciesReferencesGlyphs() use ReactionGlyph.isSetListOfSpeciesReferenceGlyphs()
org.sbml.jsbml.Model.isSetListOfSpeciesTypes() Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.isSetModelHistory() use SBase.isSetHistory()
org.sbml.jsbml.math.ASTCiNumberNode.isSetName()
org.sbml.jsbml.Unit.isSetOffset() the offset attribute should no longer be used.
org.sbml.jsbml.ext.fbc.FluxBound.isSetOperation() Only defined in FBC version 1.
org.sbml.jsbml.Annotation.isSetOtherAnnotationThanRDF() please use Annotation.isSetNonRDFannotation()
org.sbml.jsbml.Creator.isSetOtherAttributes() those other attributes are not saved when writing the model
org.sbml.jsbml.SBMLDocument.isSetPkgRequired(String) use SBMLDocument.isSetPackageRequired(String)
org.sbml.jsbml.ext.fbc.FluxBound.isSetReaction() Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FluxBound.isSetReactionInstance() Only defined in FBC version 1.
org.sbml.jsbml.ext.render.AbstractRenderPlugin.isSetRenderInformation() 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.
org.sbml.jsbml.ext.spatial.SpatialNamedSBase.isSetSpatialId() use SBase.isSetId()
org.sbml.jsbml.Species.isSetSpatialSizeUnits() Only valid for SBML Level 2 Versions 1 and 2.
org.sbml.jsbml.Species.isSetSpatialSizeUnitsInstance() Only valid for SBML Level 2 Versions 1 and 2.
org.sbml.jsbml.Species.isSetSpeciesType()
org.sbml.jsbml.Species.isSetSpeciesTypeInstance()
org.sbml.jsbml.SpeciesReference.isSetStoichiometryMath() since SBML L3V1
org.sbml.jsbml.KineticLaw.isSetSubstanceUnits()
org.sbml.jsbml.KineticLaw.isSetSubstanceUnitsInstance()
org.sbml.jsbml.Event.isSetTimeUnits()
org.sbml.jsbml.KineticLaw.isSetTimeUnits()
org.sbml.jsbml.Event.isSetTimeUnitsInstance()
org.sbml.jsbml.KineticLaw.isSetTimeUnitsInstance()
org.sbml.jsbml.CVTerm.isSetTypeQualifier() use CVTerm.isSetQualifier()
org.sbml.jsbml.Event.isSetUnits()
org.sbml.jsbml.KineticLaw.isSetUnits()
org.sbml.jsbml.ExplicitRule.isSetUnits() 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.
org.sbml.jsbml.Event.isSetUnitsInstance()
org.sbml.jsbml.KineticLaw.isSetUnitsInstance()
org.sbml.jsbml.ExplicitRule.isSetUnitsInstance() 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.
org.sbml.jsbml.ext.fbc.FluxBound.isSetValue() Only defined in FBC version 1.
org.sbml.jsbml.Compartment.isSetVolume() The volume attribute is only defined in SBML Level 1. Please use Compartment.isSetSize()
org.sbml.jsbml.AbstractNamedSBase.isValidId(String, int, int) use SyntaxChecker.isValidId(String, int, int)
org.sbml.jsbml.AbstractSBase.isValidMetaId(String) use SyntaxChecker.isValidMetaId(String)
org.sbml.jsbml.ext.fbc.FluxBound.readAttribute(String, String, String)
org.sbml.jsbml.Model.removeCompartmentType(int) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.removeCompartmentType(String) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.ext.fbc.FBCModelPlugin.removeFluxBound(FluxBound) Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FBCModelPlugin.removeFluxBound(int) Only defined in FBC version 1.
org.sbml.jsbml.KineticLaw.removeParameter(int) use KineticLaw.removeLocalParameter(int)
org.sbml.jsbml.KineticLaw.removeParameter(Parameter) use KineticLaw.removeLocalParameter(LocalParameter)
org.sbml.jsbml.KineticLaw.removeParameter(String) use KineticLaw.removeLocalParameter(String)
org.sbml.jsbml.Model.removeSpeciesType(int) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.removeSpeciesType(String) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Species.setCharge(int) 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.
org.sbml.jsbml.Compartment.setCompartmentType(CompartmentType)
org.sbml.jsbml.Compartment.setCompartmentType(String) Only valid in Level 2.
org.sbml.jsbml.SpeciesReference.setDenominator(int)
org.sbml.jsbml.LocalParameter.setExplicitlyConstant(boolean) 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.
org.sbml.jsbml.Unit.setExponent(int) use Unit.setExponent(double)
org.sbml.jsbml.Reaction.setFast(boolean)
org.sbml.jsbml.AbstractMathContainer.setFormula(String)
org.sbml.jsbml.MathContainer.setFormula(String) 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.
org.sbml.jsbml.ext.distrib.UncertParameter.setFormula(String)
org.sbml.jsbml.Model.setListOfCompartmentTypes(ListOf<CompartmentType>) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.ext.fbc.FBCModelPlugin.setListOfFluxBounds(ListOf<FluxBound>) Only defined in FBC version 1.
org.sbml.jsbml.ext.layout.ReactionGlyph.setListOfSpeciesReferencesGlyph(ListOf<SpeciesReferenceGlyph>) use ReactionGlyph.setListOfSpeciesReferenceGlyphs(ListOf)
org.sbml.jsbml.Model.setListOfSpeciesTypes(ListOf<SpeciesType>) Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.setModelHistory(History) use AbstractSBase.setHistory(History)
org.sbml.jsbml.math.ASTCiNumberNode.setName(String)
org.sbml.jsbml.Unit.setOffset(double) Only defined for SBML Level 2 Version 1.
org.sbml.jsbml.ext.fbc.FluxBound.setOperation(FluxBound.Operation) Only defined in FBC version 1.
org.sbml.jsbml.Creator.setOtherAttribute(String, String) those other attributes are not saved when writing the model
org.sbml.jsbml.Compartment.setOutside(Compartment)
org.sbml.jsbml.Compartment.setOutside(String) since Level 3 Version 1
org.sbml.jsbml.SBMLDocument.setPkgRequired(String, boolean) use SBMLDocument.setPackageRequired(String, boolean)
org.sbml.jsbml.ext.fbc.FluxBound.setReaction(Reaction) Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FluxBound.setReaction(String) Only defined in FBC version 1.
org.sbml.jsbml.ext.render.AbstractRenderPlugin.setRenderInformation(GlobalRenderInformation) 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
org.sbml.jsbml.ext.spatial.SpatialNamedSBase.setSpatialId(String) use SBase.setId(String)
org.sbml.jsbml.Species.setSpatialSizeUnits(String) This property is only valid for SBML Level 2 Versions 1 and 2.
org.sbml.jsbml.Species.setSpatialSizeUnits(UnitDefinition) Only valid for SBML Level 2 Versions 1 and 2.
org.sbml.jsbml.Species.setSpeciesType(SpeciesType) This property is only valid for SBML Level 2 from Version 2.
org.sbml.jsbml.Species.setSpeciesType(String) Only valid in SBML Level 2 from Version 2.
org.sbml.jsbml.SpeciesReference.setStoichiometryMath(StoichiometryMath)
org.sbml.jsbml.KineticLaw.setSubstanceUnits(String) Only defined for SBML Level 1 and Level 2 Version 1 and 2.
org.sbml.jsbml.KineticLaw.setSubstanceUnits(Unit)
org.sbml.jsbml.InitialAssignment.setSymbol(String) use InitialAssignment.setVariable(String).
org.sbml.jsbml.SBase.setThisAsParentSBMLObject(SBase) use SBase.registerChild(SBase)
org.sbml.jsbml.AbstractSBase.setThisAsParentSBMLObject(SBase)
org.sbml.jsbml.Event.setTimeUnits(String) This is only applicable for SBML Level 2, Versions 1 and 2.
org.sbml.jsbml.KineticLaw.setTimeUnits(String) Only defined for Level 1 and Level 2 Version 1.
org.sbml.jsbml.KineticLaw.setTimeUnits(Unit)
org.sbml.jsbml.Event.setTimeUnits(UnitDefinition)
org.sbml.jsbml.KineticLaw.setTimeUnits(UnitDefinition) Only defined for Level 1 and Level 2 Version 1.
org.sbml.jsbml.Event.setTimeUnitsID(String)
org.sbml.jsbml.Event.setUnits(String)
org.sbml.jsbml.KineticLaw.setUnits(String)
org.sbml.jsbml.ExplicitRule.setUnits(String) 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.
org.sbml.jsbml.Event.setUnits(Unit.Kind)
org.sbml.jsbml.KineticLaw.setUnits(Unit.Kind)
org.sbml.jsbml.ExplicitRule.setUnits(Unit.Kind)
org.sbml.jsbml.Event.setUnits(Unit)
org.sbml.jsbml.KineticLaw.setUnits(Unit)
org.sbml.jsbml.ExplicitRule.setUnits(Unit)
org.sbml.jsbml.Event.setUnits(UnitDefinition)
org.sbml.jsbml.KineticLaw.setUnits(UnitDefinition)
org.sbml.jsbml.ExplicitRule.setUnits(UnitDefinition) 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.
org.sbml.jsbml.ext.fbc.FluxBound.setValue(double) Only defined in FBC version 1.
org.sbml.jsbml.Compartment.setVolume(double) This method is only available for SBML Level 1. You should either use Compartment.setSize(double) or Compartment.setValue(double).
org.sbml.jsbml.Species.unsetCharge() 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.
org.sbml.jsbml.Reaction.unsetFast()
org.sbml.jsbml.AbstractMathContainer.unsetFormula()
org.sbml.jsbml.MathContainer.unsetFormula() use MathContainer.unsetMath()
org.sbml.jsbml.ext.distrib.UncertParameter.unsetFormula()
org.sbml.jsbml.Model.unsetListOfCompartmentTypes() Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.ext.fbc.FBCModelPlugin.unsetListOfFluxBounds() Only defined in FBC version 1.
org.sbml.jsbml.KineticLaw.unsetListOfParameters() use KineticLaw.unsetListOfLocalParameters()
org.sbml.jsbml.ext.layout.ReactionGlyph.unsetListOfSpeciesReferencesGlyph() use ReactionGlyph.unsetListOfSpeciesReferenceGlyphs()
org.sbml.jsbml.Model.unsetListOfSpeciesTypes() Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.unsetModelHistory() use AbstractSBase.unsetHistory().
org.sbml.jsbml.Unit.unsetOffset() the offset attribute should no longer be used.
org.sbml.jsbml.ext.fbc.FluxBound.unsetOperation() Only defined in FBC version 1.
org.sbml.jsbml.Compartment.unsetOutside() since Level 3 Version 1
org.sbml.jsbml.ext.fbc.FluxBound.unsetReaction() Only defined in FBC version 1.
org.sbml.jsbml.ext.render.AbstractRenderPlugin.unsetRenderInformation() 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. Unsets the variable renderInformation
org.sbml.jsbml.ext.spatial.SpatialNamedSBase.unsetSpatialId() use SBase.unsetId()
org.sbml.jsbml.Species.unsetSpatialSizeUnits() Only valid for SBML Level 2 Versions 1 and 2.
org.sbml.jsbml.SpeciesReference.unsetStoichiometryMath()
org.sbml.jsbml.KineticLaw.unsetSubstanceUnits()
org.sbml.jsbml.KineticLaw.unsetTimeUnits()
org.sbml.jsbml.KineticLaw.unsetUnits()
org.sbml.jsbml.ExplicitRule.unsetUnits() 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 ExplicitRule represents the SBML element ParameterRule.
org.sbml.jsbml.ext.fbc.FluxBound.unsetValue() Only defined in FBC version 1.
org.sbml.jsbml.Compartment.unsetVolume() The volume attribute is only defined in SBML Level 1. Please use Compartment.unsetSize()
org.sbml.jsbml.ext.fbc.FluxBound.writeXMLAttributes()

Deprecated Constructors

Constructor and Description
org.sbml.jsbml.CompartmentType()
org.sbml.jsbml.CompartmentType(CompartmentType)
org.sbml.jsbml.CompartmentType(int, int)
org.sbml.jsbml.CompartmentType(String)
org.sbml.jsbml.CompartmentType(String, int, int)
org.sbml.jsbml.CompartmentType(String, String, int, int)
org.sbml.jsbml.ext.fbc.FluxBound() Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FluxBound(FluxBound) Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FluxBound(int, int) Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FluxBound(String) Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FluxBound(String, int, int) Only defined in FBC version 1.
org.sbml.jsbml.ext.fbc.FluxBound(String, String, int, int) Only defined in FBC version 1.
org.sbml.jsbml.ext.qual.QualitativeModel(Model) use QualModelPlugin instead.
org.sbml.jsbml.ext.qual.QualitativeModel(QualModelPlugin) use QualModelPlugin instead.
org.sbml.jsbml.SpeciesType()
org.sbml.jsbml.SpeciesType(int, int)
org.sbml.jsbml.SpeciesType(SpeciesType)
org.sbml.jsbml.SpeciesType(String)
org.sbml.jsbml.SpeciesType(String, int, int)
org.sbml.jsbml.SpeciesType(String, String, int, int)
org.sbml.jsbml.StoichiometryMath()
org.sbml.jsbml.StoichiometryMath(int, int)
org.sbml.jsbml.StoichiometryMath(StoichiometryMath)

Deprecated Enum Constants

Enum Constant and Description
org.sbml.jsbml.Unit.Kind.CELSIUS use Unit.Kind.KELVIN instead (1 Celsius = 1 K + 271.15)
org.sbml.jsbml.Unit.Kind.LITER use Unit.Kind.LITRE instead.
org.sbml.jsbml.Unit.Kind.METER use Unit.Kind.METRE instead.