Deprecated API

Contents

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

Deprecated Classes

Class and Description
org.sbml.jsbml.CompartmentType Only valid in SBML Level 2 for Versions 2 through 4.
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.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 Fields

Field and Description
org.sbml.jsbml.Species.charge
org.sbml.jsbml.Compartment.compartmentTypeID
org.sbml.jsbml.Reaction.fast
org.sbml.jsbml.Model.listOfCompartmentTypes only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Model.listOfSpeciesTypes only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.Unit.offset the offset attribute should no longer be used.
org.sbml.jsbml.Compartment.outsideID
org.sbml.jsbml.Species.spatialSizeUnitsID Only valid for SBML Level 2 Versions 1 and 2.
org.sbml.jsbml.Species.speciesTypeID
org.sbml.jsbml.SpeciesReference.stoichiometryMath
org.sbml.jsbml.KineticLaw.substanceUnitsID
org.sbml.jsbml.KineticLaw.timeUnitsID
org.sbml.jsbml.ExplicitRule.unitsID 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.KineticLaw.unitsID

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.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.SpeciesType.clone()
org.sbml.jsbml.StoichiometryMath.clone()
org.sbml.jsbml.CompartmentType.clone()
org.sbml.jsbml.Event.containsUndeclaredUnits()
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.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.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.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.AbstractMathContainer.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.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.KineticLaw.getNumLocalParameters() use KineticLaw.getLocalParameterCount()
org.sbml.jsbml.KineticLaw.getNumParameters() use KineticLaw.getLocalParameterCount()
org.sbml.jsbml.Model.getNumSpeciesTypes()
org.sbml.jsbml.Model.getNumStoichiometryMath() since SBML L3V1.
org.sbml.jsbml.Unit.getOffset()
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.SpeciesType.getParent()
org.sbml.jsbml.StoichiometryMath.getParent()
org.sbml.jsbml.CompartmentType.getParent()
org.sbml.jsbml.SBMLDocument.getPkgRequired(String) use SBMLDocument.getPackageRequired(String)
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.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.KineticLaw.getTimeUnits()
org.sbml.jsbml.Event.getTimeUnits()
org.sbml.jsbml.Event.getTimeUnitsID()
org.sbml.jsbml.KineticLaw.getTimeUnitsInstance()
org.sbml.jsbml.Event.getTimeUnitsInstance()
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.KineticLaw.getUnits()
org.sbml.jsbml.Event.getUnits()
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.KineticLaw.getUnitsInstance()
org.sbml.jsbml.Event.getUnitsInstance()
org.sbml.jsbml.Compartment.getVolume() The volume attribute is only defined in SBML Level 1. Please use Compartment.getSize().
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.SBMLDocument.isIgnoredPkg(String) use SBMLDocument.isIgnoredPackage(String)
org.sbml.jsbml.AbstractSBase.isPkgEnabled(String)
org.sbml.jsbml.SBase.isPkgEnabled(String) use SBase.isPackageEnabled(String)
org.sbml.jsbml.AbstractSBase.isPkgURIEnabled(String)
org.sbml.jsbml.SBase.isPkgURIEnabled(String) use SBase.isPackageEnabled(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.KineticLaw.isSetListOfParameters() use KineticLaw.isSetListOfLocalParameters()
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.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.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.KineticLaw.isSetTimeUnits()
org.sbml.jsbml.Event.isSetTimeUnits()
org.sbml.jsbml.KineticLaw.isSetTimeUnitsInstance()
org.sbml.jsbml.Event.isSetTimeUnitsInstance()
org.sbml.jsbml.CVTerm.isSetTypeQualifier() use CVTerm.isSetQualifier()
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.KineticLaw.isSetUnits()
org.sbml.jsbml.Event.isSetUnits()
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.KineticLaw.isSetUnitsInstance()
org.sbml.jsbml.Event.isSetUnitsInstance()
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.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.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.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.AbstractMathContainer.setFormula(String)
org.sbml.jsbml.Model.setListOfCompartmentTypes(ListOf<CompartmentType>) Only valid in SBML Level 2 for Versions 2 through 4.
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.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.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)
org.sbml.jsbml.Species.setSpeciesType(String) Only valid in SBML Level 2 for Versions 2 through 4.
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.AbstractSBase.setThisAsParentSBMLObject(SBase)
org.sbml.jsbml.SBase.setThisAsParentSBMLObject(SBase) use SBase.registerChild(SBase)
org.sbml.jsbml.KineticLaw.setTimeUnits(String) Only defined for Level 1 and Level 2 Version 1.
org.sbml.jsbml.Event.setTimeUnits(String) This is only applicable for SBML Level 2, Versions 1 and 2.
org.sbml.jsbml.KineticLaw.setTimeUnits(Unit)
org.sbml.jsbml.KineticLaw.setTimeUnits(UnitDefinition) Only defined for Level 1 and Level 2 Version 1.
org.sbml.jsbml.Event.setTimeUnits(UnitDefinition)
org.sbml.jsbml.Event.setTimeUnitsID(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.KineticLaw.setUnits(String)
org.sbml.jsbml.Event.setUnits(String)
org.sbml.jsbml.ExplicitRule.setUnits(Unit.Kind)
org.sbml.jsbml.KineticLaw.setUnits(Unit.Kind)
org.sbml.jsbml.Event.setUnits(Unit.Kind)
org.sbml.jsbml.ExplicitRule.setUnits(Unit)
org.sbml.jsbml.KineticLaw.setUnits(Unit)
org.sbml.jsbml.Event.setUnits(Unit)
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.KineticLaw.setUnits(UnitDefinition)
org.sbml.jsbml.Event.setUnits(UnitDefinition)
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()
org.sbml.jsbml.Reaction.unsetFast()
org.sbml.jsbml.MathContainer.unsetFormula() use MathContainer.unsetMath()
org.sbml.jsbml.AbstractMathContainer.unsetFormula()
org.sbml.jsbml.Model.unsetListOfCompartmentTypes() Only valid in SBML Level 2 for Versions 2 through 4.
org.sbml.jsbml.KineticLaw.unsetListOfParameters() use KineticLaw.unsetListOfLocalParameters()
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.Compartment.unsetOutside() since Level 3 Version 1
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.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.KineticLaw.unsetUnits()
org.sbml.jsbml.Compartment.unsetVolume() The volume attribute is only defined in SBML Level 1. Please use Compartment.unsetSize()

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.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.