- Macromolecule<T> - Class in org.sbml.jsbml.ext.render.director
-
interface all the different graphical representations for macromolecule nodes
have to implement
- Macromolecule() - Constructor for class org.sbml.jsbml.ext.render.director.Macromolecule
-
- main(String[]) - Static method in class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder
-
- main(String[]) - Static method in class org.sbml.jsbml.ext.dyn.CBO
-
Test main class
- main(String[]) - Static method in class org.sbml.jsbml.ext.spatial.SpatialTest
-
- main(String[]) - Static method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
- main(String[]) - Static method in class org.sbml.jsbml.SBO
-
For testing purposes.
- main(String[]) - Static method in class org.sbml.jsbml.TidySBMLWriter
-
- main(String[]) - Static method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- main(String[]) - Static method in class org.sbml.jsbml.util.converters.ExpandFunctionDefinitionConverter
-
- main(String[]) - Static method in class org.sbml.jsbml.validator.SBMLValidator
-
- main(String[]) - Static method in class org.sbml.jsbml.xml.parsers.FBCParser
-
Tests this class
- main(String[]) - Static method in class org.sbml.jsbml.xml.parsers.ParserManager
-
For testing purposes.
- main(String[]) - Static method in class org.sbml.jsbml.xml.stax.SBMLReader
-
- main(String[]) - Static method in class org.sbml.jsbml.xml.stax.SBMLWriter
-
Tests this class
- mantissa - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- marshal(Object, HierarchicalStreamWriter, MarshallingContext) - Method in class org.sbml.jsbml.xml.xstream.converter.MessageConverter
-
- marshal(Object, HierarchicalStreamWriter, MarshallingContext) - Method in class org.sbml.jsbml.xml.xstream.converter.SBMLErrorConverter
-
- maskSpecialChars(String) - Static method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Masks all special characters used by LaTeX with a backslash including
hyphen symbols.
- maskSpecialChars(String) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Masks all special characters used by LaTeX with a backslash including
hyphen symbols.
- maskSpecialChars(String, boolean) - Static method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- maskSpecialChars(String, boolean) - Static method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- math - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
-
- math - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- math(Object) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Encloses the given formula in dollar symbols (inline math mode).
- math(Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Encloses the given formula in dollar symbols (inline math mode).
- MathContainer - Interface in org.sbml.jsbml
-
Base interface for all the SBML components which contain MathML nodes.
- MathContainerConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- MathContainerConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.MathContainerConstraints
-
- MATHML_CONSISTENCY - org.sbml.jsbml.SBMLException.Category
-
Category of errors that can occur while validating MathML formulas in
a model.
- MATHML_CONSISTENCY - org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY
-
Syntax of MathML constructs.
- mathMLClass - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- MathMLCompiler - Class in org.sbml.jsbml.util.compilers
-
- MathMLCompiler() - Constructor for class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- MathMLCompiler(ASTNode) - Constructor for class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- MathMLParser - Class in org.sbml.jsbml.xml.parsers
-
- MathMLParser() - Constructor for class org.sbml.jsbml.xml.parsers.MathMLParser
-
Deprecated.
- MathMLStaxParser - Class in org.sbml.jsbml.xml.parsers
-
A MathMLStaxParser is used to parse the MathML expressions injected into a SBML
file.
- MathMLStaxParser() - Constructor for class org.sbml.jsbml.xml.parsers.MathMLStaxParser
-
- MathMLXMLStreamCompiler - Class in org.sbml.jsbml.math.compiler
-
- MathMLXMLStreamCompiler - Class in org.sbml.jsbml.util.compilers
-
- MathMLXMLStreamCompiler() - Constructor for class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- MathMLXMLStreamCompiler(String) - Constructor for class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
- MathMLXMLStreamCompiler(XMLStreamWriter, String) - Constructor for class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler
-
Create a new MathMLXMLStreamCompiler.
- MathMLXMLStreamCompiler(XMLStreamWriter, String) - Constructor for class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler
-
Create a new MathMLXMLStreamCompiler.
- MathResultMustBeNumeric - org.sbml.jsbml.SBMLException.Code
-
Formula result is not a numerical value
- mathrm(char) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- mathrm(char) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- mathrm(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- mathrm(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- Maths - Class in org.sbml.jsbml.util
-
Provides several static methods for mathematical operations such
as faculty, logarithms and several trigonometric functions, which are not
part of standard Java, but necessary to evaluate the content of SBML files.
- mathtext(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- mathtext(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- mathtt(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Returns the LaTeX code to set the given String in type writer font within
a math environment.
- mathtt(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Returns the LaTeX code to set the given String in type writer font within
a math environment.
- max(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
-
- max(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
-
- max(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
-
- max(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Returns the maximum of the values.
- max(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- max(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- max(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- max(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- max(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- MAXIMIZE - org.sbml.jsbml.ext.fbc.Objective.Type
-
- maxLevel - Static variable in class org.sbml.jsbml.ext.qual.QualConstants
-
- maxOccur - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
-
- maxValue - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- mbox(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- mbox(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- md5 - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
-
- mean - org.sbml.jsbml.ext.distrib.UncertParameter.Type
-
The arithmetic mean (typically just the mean) is what is commonly called the average.
- mean - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
-
- median - org.sbml.jsbml.ext.distrib.UncertParameter.Type
-
The median is described as the numeric value separating the higher half of a sample (or population)
from the lower half.
- Member - Class in org.sbml.jsbml.ext.groups
-
- Member() - Constructor for class org.sbml.jsbml.ext.groups.Member
-
Creates a new
Member instance.
- Member(int, int) - Constructor for class org.sbml.jsbml.ext.groups.Member
-
Creates a new
Member instance.
- Member(Member) - Constructor for class org.sbml.jsbml.ext.groups.Member
-
Creates a new
Member instance.
- memberConstraint - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants
-
- MemberConstraint - Class in org.sbml.jsbml.ext.groups
-
- MemberConstraint() - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint
-
Deprecated.
Creates an MemberConstraint instance
- MemberConstraint(int, int) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint
-
Deprecated.
Creates a MemberConstraint instance with a level and version.
- MemberConstraint(String) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint
-
Deprecated.
Creates a MemberConstraint instance with an id.
- MemberConstraint(String, int, int) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint
-
Deprecated.
Creates a MemberConstraint instance with an id, level, and version.
- MemberConstraint(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint
-
Deprecated.
Creates a MemberConstraint instance with an id, name, level, and version.
- MemberConstraint(MemberConstraint) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint
-
Deprecated.
Clone constructor
- membersShareType - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants
-
- merge(Unit, Unit) - Static method in class org.sbml.jsbml.Unit
-
Merges two
Unit objects with the same 'kind' attribute value into a
single
Unit.
- message - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- Message - Class in org.sbml.jsbml.util
-
- Message() - Constructor for class org.sbml.jsbml.util.Message
-
- MessageConverter - Class in org.sbml.jsbml.xml.xstream.converter
-
- MessageConverter(String) - Constructor for class org.sbml.jsbml.xml.xstream.converter.MessageConverter
-
- metaId - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- MetaIdFilter - Class in org.sbml.jsbml.util.filters
-
This filter only accepts instances of
SBase with the metaid as
given in the constructor of this object.
- MetaIdFilter() - Constructor for class org.sbml.jsbml.util.filters.MetaIdFilter
-
- MetaIdFilter(String) - Constructor for class org.sbml.jsbml.util.filters.MetaIdFilter
-
- MetaIdNotValidAttribute - org.sbml.jsbml.SBMLException.Code
-
Attribute metaid not supported in SBML Level 1
- metaidRef - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
-
- metaIdRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
-
- metaIdRef - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
-
- metaIdRef - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants
-
- metaIds() - Method in class org.sbml.jsbml.SBMLDocument
-
Provides access to all registered metaIds in this
SBMLDocument.
- METER - org.sbml.jsbml.Unit.Kind
-
- METRE - org.sbml.jsbml.Unit.Kind
-
The metre unit.
- MIDDLE - org.sbml.jsbml.ext.render.HTextAnchor
-
- MIDDLE - org.sbml.jsbml.ext.render.VTextAnchor
-
- midrule - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Produces a fancy line in tables.
- midrule - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Produces a fancy line in tables.
- min(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
-
- min(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
-
- min(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
-
- min(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Returns the minimum of the values.
- min(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- min(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- min(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- min(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- min(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
-
- MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
-
- MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
-
- MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
- MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants
-
- MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
-
- MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
-
- MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
-
- MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
-
- MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
-
- MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
- MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants
-
- MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
-
- MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
-
- MINIMIZE - org.sbml.jsbml.ext.fbc.Objective.Type
-
- minOccur - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
-
- minus(double) - Method in class org.sbml.jsbml.ASTNode
-
Subtracts the given number from this node.
- minus(int) - Method in class org.sbml.jsbml.ASTNode
-
Subtracts the given integer from this node.
- minus(int, String) - Method in class org.sbml.jsbml.ASTNode
-
- minus(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
-
- minus(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
-
- minus(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
-
- minus(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Subtraction.
- minus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- minus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- minus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- minus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- minus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- minus(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Subtraction.
- minus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- minus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- minus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- minus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- minus(ASTNode) - Method in class org.sbml.jsbml.ASTNode
-
Subtracts the given ASTNode from this node.
- minus(ASTNode2, double) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Subtracts the given number from an
ASTNode2
- minus(ASTNode2, int) - Static method in class org.sbml.jsbml.math.ASTFactory
-
Subtracts an integer number from
ASTNode2.
- minus(ASTNode2, int, String) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- minus(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- MINUS - org.sbml.jsbml.ASTNode.Type
-
- MINUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- MINUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- MINUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- MINUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- MINUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- MINUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- MINUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- MINUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- minValue - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- MissingAnnotationNamespace - org.sbml.jsbml.SBMLException.Code
-
Missing declaration of XML namespace for annotation
- MissingEventAssignment - org.sbml.jsbml.SBMLException.Code
-
Missing event assignment in event definition
- MissingModel - org.sbml.jsbml.SBMLException.Code
-
Missing model
- MissingOrInconsistentLevel - org.sbml.jsbml.SBMLException.Code
-
Missing or inconsistent value for level attribute
- MissingOrInconsistentVersion - org.sbml.jsbml.SBMLException.Code
-
Missing or inconsistent value for version attribute
- MissingSpeciesCompartment - org.sbml.jsbml.SBMLException.Code
-
Missing compartment value for species
- MissingTriggerInEvent - org.sbml.jsbml.SBMLException.Code
-
Missing trigger in event definition
- mixedGeometry - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- MixedGeometry - Class in org.sbml.jsbml.ext.spatial
-
- MixedGeometry() - Constructor for class org.sbml.jsbml.ext.spatial.MixedGeometry
-
- MixedGeometry(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.MixedGeometry
-
- MixedGeometry(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.MixedGeometry
-
- MixedGeometry(MixedGeometry) - Constructor for class org.sbml.jsbml.ext.spatial.MixedGeometry
-
- MixedGeometryConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- MixedGeometryConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.MixedGeometryConstraints
-
- MMOL_PER_G_DW - Static variable in class org.sbml.jsbml.util.ModelBuilder
-
Millimoles per gram of dry weight of a probe, used as extend units of
reactions.
- MMOL_PER_G_DW_PER_HR - Static variable in class org.sbml.jsbml.util.ModelBuilder
-
Extend units per time unit, millimoles per gram of dry weight.
- mmol_per_gDW_per_hr - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
-
- mode - org.sbml.jsbml.ext.distrib.UncertParameter.Type
-
The mode is the value that occurs the most frequently in a data set (or a probability distribution).
- model - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- Model - Class in org.sbml.jsbml
-
JSBML implementation of SBML's
Model construct.
- Model() - Constructor for class org.sbml.jsbml.Model
-
Creates a Model instance.
- Model(int, int) - Constructor for class org.sbml.jsbml.Model
-
Creates a Model instance.
- Model(String) - Constructor for class org.sbml.jsbml.Model
-
Creates a Model instance from an id.
- Model(String, int, int) - Constructor for class org.sbml.jsbml.Model
-
Creates a Model instance from an id, level and version.
- Model(Model) - Constructor for class org.sbml.jsbml.Model
-
Creates a Model instance from a Model.
- MODEL_ELEMENTS_ORDER - Static variable in class org.sbml.jsbml.validator.offline.constraints.ModelConstraints
-
- MODEL_QUALIFIER - org.sbml.jsbml.CVTerm.Type
-
If the MIRIAM qualifier is a model qualifier.
- ModelBuilder - Class in org.sbml.jsbml.util
-
This class provides a collection of convenient methods to create SBML models
and documents.
- ModelBuilder(int, int) - Constructor for class org.sbml.jsbml.util.ModelBuilder
-
- ModelBuilder(SBMLDocument) - Constructor for class org.sbml.jsbml.util.ModelBuilder
-
- ModelConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- ModelConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ModelConstraints
-
- ModelDefinition - Class in org.sbml.jsbml.ext.comp
-
Holder class for model definitions, which are
Models.
- ModelDefinition() - Constructor for class org.sbml.jsbml.ext.comp.ModelDefinition
-
- ModelDefinition(int, int) - Constructor for class org.sbml.jsbml.ext.comp.ModelDefinition
-
- ModelDefinition(String) - Constructor for class org.sbml.jsbml.ext.comp.ModelDefinition
-
- ModelDefinition(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.ModelDefinition
-
- ModelDefinition(Model) - Constructor for class org.sbml.jsbml.ext.comp.ModelDefinition
-
- MODELING_PRACTICE - org.sbml.jsbml.SBMLException.Category
-
Category of warnings about recommended good practices involving SBML
and computational modeling.
- MODELING_PRACTICE - org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY
-
Additional checks for recommended good modeling practice.
- ModelOverdeterminedException - Exception in org.sbml.jsbml.validator
-
This class represents an exception that is thrown when the model to be
simulated is overdetermined
- ModelOverdeterminedException() - Constructor for exception org.sbml.jsbml.validator.ModelOverdeterminedException
-
- ModelOverdeterminedException(String) - Constructor for exception org.sbml.jsbml.validator.ModelOverdeterminedException
-
- ModelOverdeterminedException(String, Throwable) - Constructor for exception org.sbml.jsbml.validator.ModelOverdeterminedException
-
- ModelOverdeterminedException(Throwable) - Constructor for exception org.sbml.jsbml.validator.ModelOverdeterminedException
-
- modelRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
-
- ModelSBOBranchChangedBeyondL2v2 - org.sbml.jsbml.SBMLException.Code
-
The allowable sboTerm values for model differ for this SBML
Level+Version
- ModelSBOBranchChangedBeyondL2v3 - org.sbml.jsbml.SBMLException.Code
-
The allowable sboTerm values for model differ for this SBML
Level+Version
- ModelSBOBranchChangedInL2v4 - org.sbml.jsbml.SBMLException.Code
-
The allowable sboTerm values for model differ for this SBML
Level+Version
- modifiedDate - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- MODIFIER - org.sbml.jsbml.ext.layout.SpeciesReferenceRole
-
- ModifierSpeciesReference - Class in org.sbml.jsbml
-
Represents the modifierSpeciesReference XML element of a SBML file.
- ModifierSpeciesReference() - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
-
- ModifierSpeciesReference(int, int) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
-
- ModifierSpeciesReference(String) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
-
- ModifierSpeciesReference(String, int, int) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
-
- ModifierSpeciesReference(ModifierSpeciesReference) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
-
- ModifierSpeciesReference(Species) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference
-
- Modulation<T> - Interface in org.sbml.jsbml.ext.render.director
-
Interface for the SBGN specified modulation arc.
- MODULO - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- MODULO - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- MODULO - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- MODULO - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- MODULO - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- MODULO - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- MOLE - org.sbml.jsbml.Unit.Kind
-
The mole unit.
- MONOSPACE - org.sbml.jsbml.ext.render.FontFamily
-
- MULTI_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010101:
To conform to Version 1 of the Multi package specification for SBML Level 3, an
SBML document must declare the use of the following XML Namespace:
'http://www.sbml.org/sbml/level3/version1/multi/version1' Reference: L3V1 Multi
V1.1 Section 3.1
- MULTI_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010102:
Wherever they appear in an SBML document, elements and attributes from the Multi
package must be declared either implicitly or explicitly to be in the XML
namespace 'http://www.sbml.org/sbml/level3/version1/comp/version1' Reference:
L3V1 Multi V1.1 Section 3.1
- MULTI_10201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010201:
A 'ci' element in a Math object may have the optional attributes
'multi:speciesReference' and 'multi:representationType'.
- MULTI_10202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010202:
The value of the 'multi:speciesReference' attribute on a given 'ci' element must
be the identifier of a SpeciesReference object within the same reaction.
- MULTI_10203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010203:
The value of the 'multi:representationType' attribute on a given 'ci' element
must conform to the syntax of the Multi data type 'RepresentationType'.
- MULTI_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010301:
(Extends validation rule #10301 in the SBML Level 3 Version 1 Core
specification.)
- MULTI_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010302:
The value of a multi:id attribute must always conform to the syntax of the SBML
data type SId.
- MULTI_10303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010303:
The value of a 'multi:name' attribute must always conform to the syntax of type
string.
- MULTI_10304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010304:
The value of a multi:id attribute on SpeciesTypeInstance objects must be unique
across the set of all multi:id attribute values of all the SpeciesTypeInstance
objects under the direct parent SpeciesType object in which it is located.
- MULTI_10305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010305:
The value of a multi:id attribute on SpeciesTypeComponentIndex objects must be
unique across the set of all multi:id attribute values of all the
SpeciesTypeComponentIndex objects under the direct parent SpeciesType object in
which it is located.
- MULTI_10306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010306:
The value of a multi:id attribute on InSpeciesTypeBond objects must be unique
across the set of all multi:id attribute values of all the InSpeciesTypeBond
objects under the direct parent SpeciesType object in which it is it is located.
- MULTI_10307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010307:
The value of a multi:id attribute on SpeciesFeatureType objects must be unique
across the set of all multi:id attribute values of all the SpeciesFeature
objects under the direct parent SpeciesType object in which it is located.
- MULTI_10308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010308:
The value of a multi:id attribute on SubListOfSpeciesFeatures objects must be
unique across the set ofall id and multi:id attribute values of all objects in
the Species object in which it is located.
- MULTI_10309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010309:
The value of a multi:id attribute on SpeciesFeature objects must be unique
across the set ofall id and multi:id attribute values of all objects in the
Species object in which it is located.
- MULTI_10310 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010310:
The value of a multi:id attribute on CompartmentReference objects must be unique
across the set of all id and multi:id attribute values of all objects in the
Compartment object in which it is located.
- MULTI_10311 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010311:
The value of a multi:compartment attribute on SpeciesType objects must conform
to the syntax of the SBML data type SIdRef.
- MULTI_10312 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010312:
The value of a multi:numericValue attribute on PossibleSpeciesFeatureValue
objects must conform to the syntax of the SBML data type SIdRef.
- MULTI_10313 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010313:
The value of a multi:speciesType attribute on SpeciesTypeInstance objects must
conform to the syntax of the SBML data type SIdRef.
- MULTI_10314 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010314:
The value of a multi:compartmentReference attribute on SpeciesTypeInstance
objects must conform to the syntax of the SBML data type SIdRef.
- MULTI_10315 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010315:
The value of a multi:component attribute on SpeciesTypeComponentIndex objects
must conform to the syntax of the SBML data type SIdRef.
- MULTI_10316 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010316:
The value of a multi:identifyingParent attribute on SpeciesTypeComponentIndex
objects must conform to the syntax of the SBML data type SIdRef.
- MULTI_10317 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010317:
The value of a multi:bindingSite1 attribute on InSpeciesTypeBond objects must
conform to the syntax of the SBML data type SIdRef.
- MULTI_10318 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010318:
The value of a multi:bindingSite2 attribute on InSpeciesTypeBond objects must
conform to the syntax of the SBML data type SIdRef.
- MULTI_10319 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010319:
The value of a multi:speciesType attribute on extended Species objects must
conform to the syntax of the SBML data type SIdRef.
- MULTI_10320 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010320:
The value of a multi:component attribute on OutwardBindingSite objects must
conform to the syntax of the SBML data type SIdRef.
- MULTI_10321 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010321:
The value of a multi:speciesFeatureType attribute on SpeciesFeature objects must
conform to the syntax of the SBML data type SIdRef.
- MULTI_10322 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010322:
The value of a multi:component attribute on SpeciesFeature objects must conform
to the syntax of the SBML data type SIdRef.
- MULTI_10323 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010323:
The value of a multi:value attribute on SpeciesFeatureValue objects must conform
to the syntax of the SBML data type SIdRef.
- MULTI_10324 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010324:
The value of a multi:compartmentReference attribute on extended
SimpleSpeciesReference objects must conform to the syntax of the SBML data type
SIdRef.
- MULTI_10325 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010325:
The value of a multi:reactant attribute on SpeciesTypeComponentMapInProduct
objects must conform to the syntax of the SBML data type SIdRef.
- MULTI_10326 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010326:
The value of a multi:reactantComponent attribute on
SpeciesTypeComponentMapInProduct objects must conform to the syntax of the SBML
data type SIdRef.
- MULTI_10327 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010327:
The value of a multi:productComponent attribute on
SpeciesTypeComponentMapInProduct objects must conform to the syntax of the SBML
data type SIdRef.
- MULTI_10328 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010328:
The value of a multi:compartmentType attribute on extended Compartment objects
must conform to the syntax of the SBML data type SIdRef.
- MULTI_10329 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7010329:
The value of a multi:compartment attribute on CompartmentReference objects must
conform to the syntax of the SBML data type SIdRef.
- MULTI_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020101:
In all SBML documents using the Multi package, the SBML object must include a
value for the 'multi:required' attribute.
- MULTI_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020102:
The value of attribute 'multi:required' on the SBML object must be of the data
type Boolean.
- MULTI_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020103:
The value of attribute 'multi:required' on the SBML object must be set to
'true'.
- MULTI_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020201:
There may be at most one instance of ListOfSpeciesTypes within an extended Model
object that uses the SBML Level 3 Multi package.
- MULTI_20202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020202:
A ListOfSpeciesTypes object within an ExModel object is optional, but if
present, must not be empty.
- MULTI_20203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020203:
A ListOfSpeciesTypes object may have the optional SBML core attributes 'metaid'
and 'sboTerm'.
- MULTI_20204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020204:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfSpeciesTypes container object may only contain SpeciesType
objects.
- MULTI_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020301:
An extended Compartment object must have the required attribute 'multi:isType',
and may also have the optional attribute 'multi:compartmentType'.
- MULTI_20302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020302:
The value of a 'multi:isType' attribute on an extended Compartment object must
always confirm to the syntax of the SBML data type 'boolean'.
- MULTI_20303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020303:
Extended Compartment: 'isType' attribute is required.
- MULTI_20304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020304:
The value of the 'multi:isType' attribute of the Compartment object referenced
by a CompartmentReference object must be the same as that of the 'multi:isType'
attribute of the parent Compartment object of the ListOfCompartmentReferences
object which contains the CompartmentReference object.
- MULTI_20305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020305:
The 'multi:compartmentType' attribute on a Compartment object must not be
defined if the value of the 'multi:isType' is 'true'.
- MULTI_20306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020306:
There may be at most one ListOfCompartmentReferences container object within a
Compartment object.
- MULTI_20307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020307:
A ListOfCompartmentReferences object within a Compartment object is optional,
but if present, must not be empty.
- MULTI_20308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020308:
A ListOfCompartmentReferences object may have the optional SBML core attributes
'metaid' and 'sboTerm'.
- MULTI_20309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020309:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfCompartmentReferences container object may only contain
CompartmentReference objects.
- MULTI_20401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020401:
A SpeciesType object may have the optional SBML Level~3 Core attributes 'metaid'
and 'sboTerm'.
- MULTI_20402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020402:
A SpeciesType object may have the optional SBML Level~3 Core subobjects for
'notes' and 'annotation'.
- MULTI_20403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020403:
A SpeciesType object must have the required attribute 'multi:id', and may have
the optional attributes 'multi:name' and 'multi:compartment'.
- MULTI_20404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020404:
The value of the 'multi:compartment' attribute, if set on a given SpeciesType
object, must be the value of an 'id' attribute on an existing Compartment object
in the 'SId' namespace of the parent Model object.
- MULTI_20405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020405:
The various 'ListOf' subobjects within a SpeciesType object are optional, but if
present, these container objects must not be empty.
- MULTI_20406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020406:
There may be at most one ListOfSpeciesFeatureTypes container object within a
SpeciesType object.
- MULTI_20407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020407:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfSpeciesFeatureTypes container object may only contain
SpeciesFeatureType objects.
- MULTI_20408 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020408:
A ListOfSpeciesFeatureTypes object may have the optional SBML core attributes
'metaid' and 'sboTerm'.
- MULTI_20409 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020409:
There may be at most one ListOfSpeciesTypeInstances container object within a
SpeciesType object.
- MULTI_20410 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020410:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfSpeciesTypeInstances container object may only contain
SpeciesTypeInstance objects.
- MULTI_20411 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020411:
A ListOfSpeciesTypeInstances object may have the optional SBML core attributes
'metaid' and 'sboTerm'.
- MULTI_20412 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020412:
There may be at most one ListOfSpeciesTypeComponentIndexes container object
within a SpeciesType object.
- MULTI_20413 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020413:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfSpeciesTypeComponentIndexes container object may only contain
SpeciesTypeComponentIndex objects.
- MULTI_20414 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020414:
A ListOfSpeciesTypeComponentIndexes object may have the optional SBML core
attributes 'metaid' and 'sboTerm'.
- MULTI_20415 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020415:
There may be at most one ListOfInSpeciesTypeBonds container object within a
SpeciesType object.
- MULTI_20416 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020416:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfInSpeciesTypeBonds container object may only contain
InSpeciesTypeBond objects.
- MULTI_20417 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020417:
A ListOfInSpeciesTypeBonds object may have the optional SBML core attributes
'metaid' and 'sboTerm'.
- MULTI_20501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020501:
A BindingSiteSpeciesType object is not permitted to have any
ListOfSpeciesTypeInstances subobject.
- MULTI_20601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020601:
A SpeciesFeatureType object may have the optional SBML Level~3 Core attributes
'metaid' and 'sboTerm'.
- MULTI_20602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020602:
A SpeciesFeatureType object may have the optional SBML Level~3 Core subobjects
for 'notes' and 'annotation'.
- MULTI_20603 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020603:
A SpeciesFeatureType object must have the required attributes 'multi:id' and
'multi:occur', and may have the optional attribute 'multi:name'.
- MULTI_20604 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020604:
The value of the 'multi:occur' attribute on a given SpeciesFeatureType object
must conform to the syntax of the SBML data type 'positiveInteger'.
- MULTI_20605 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020605:
One ListOfPossibleSpeciesFeatureValues subobject in a SpeciesFeatureType object
is required.
- MULTI_20606 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020606:
A ListOfPossibleSpeciesFeatureValues object may have the optional SBML core
attributes 'metaid' and 'sboTerm'.
- MULTI_20607 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020607:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfPossibleSpeciesFeatureValues container object may only contain
PossibleSpeciesFeatureValue objects.
- MULTI_20608 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020608:
A ListOfPossibleSpeciesFeatureValues object must not be empty.
- MULTI_20701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020701:
A PossibleSpeciesFeatureValue object may have the optional SBML Level~3 Core
attributes 'metaid' and 'sboTerm'.
- MULTI_20702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020702:
A PossibleSpeciesFeatureValue object may have the optional SBML Level~3 Core
subobjects for 'notes' and 'annotation'.
- MULTI_20703 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020703:
A PossibleSpeciesFeatureValue object must have the required attribute
'multi:id', and may have the optional attributes 'multi:name' and
'multi:numericValue'.
- MULTI_20704 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020704:
The value of the 'multi:numericValue' attribute on a given
PossibleSpeciesFeatureValue object must be the identifier of a Parameter object
defined in the same Model object.
- MULTI_20801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020801:
A SpeciesTypeInstance object may have the optional SBML Level~3 Core attributes
'metaid' and 'sboTerm'.
- MULTI_20802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020802:
A SpeciesTypeInstance object may have the optional SBML Level~3 Core subobjects
for 'notes' and 'annotation'.
- MULTI_20803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020803:
A SpeciesTypeInstance object must have the required attributes 'multi:id',
'multi:speciesType' and 'multi:occur', and may have the optional attributes
'multi:name' and 'mulit:compartmentReference'.
- MULTI_20805 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020805:
The value of the 'multi:speciesType' attribute on a given SpeciesTypeInstance
object must be the identifier of a SpeciesType object defined in the same Model
object.
- MULTI_20806 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020806:
The value of the 'multi:compartmentReference' attribute, if present on a given
SpeciesTypeInstance object, must be the identifier of a CompartmentReference
object defined in the same Model object.
- MULTI_20901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020901:
A SpeciesTypeComponentIndex object may have the optional SBML Level~3 Core
attributes 'metaid' and 'sboTerm'.
- MULTI_20902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020902:
A SpeciesTypeComponentIndex object may have the optional SBML Level~3 Core
subobjects for 'notes' and 'annotation'.
- MULTI_20903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020903:
A SpeciesTypeComponentIndex object must have the required attributes 'multi:id'
and 'multi:compartment' , and may have the optional attribute
'mulit:identifyingParent'.
- MULTI_20904 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020904:
The value of the 'mulit:component' attribute on a given
SpeciesTypeComponentIndex object must be the identifier of a SpeciesTypeInstance
object, or a SpeciesTypeComponentIndex object under the SpeciesType object that
this SpeciesTypeComponentIndex object belongs to, or the SpeciesType object
itself.
- MULTI_20907 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7020907:
The value of the 'multi:identifyingParent' attribute on a given
SpeciesTypeComponentIndex object must be the identifier of a component object
under the SpeciesType object that this SpeciesTypeComponentIndex object belongs
to.
- MULTI_21101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021101:
An InSpeciesTypeBond object may have the optional SBML Level~3 Core attributes
'metaid' and 'sboTerm'.
- MULTI_21102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021102:
An InSpeciesTypeBond object may have the optional SBML Level~3 Core subobjects
for 'notes' and 'annotation'.
- MULTI_21103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021103:
An InSpeciesTypeBond object must have the required attributes,
'multi:bindingSite1' and 'multi:BindingSite2', and may have the optional
attributes, 'multi:id' and 'multi:name'.
- MULTI_21104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021104:
The value of the 'multi:bindingSite1' attribute on a given InSpeciesTypeBond
object must be the identifier of a SpeciesTypeInstance object or
SpeciesTypeComponentIndex which ultimately reference a object of
BindingSiteSpeciesType.
- MULTI_21105 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021105:
The value of the 'multi:bindingSite2' attribute on a given InSpeciesTypeBond
object must be the identifier of a SpeciesTypeInstance object or
SpeciesTypeComponentIndex which ultimately reference a object of
BindingSiteSpeciesType.
- MULTI_21106 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021106:
The 'multi:bindingSite1' and 'multi:bindingSite2' attributes must not reference
the same BindingSiteSpeciesType object.
- MULTI_21201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021201:
A Species object may have the optional attribute, 'multi:speciesType'.
- MULTI_21202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021202:
The value of a 'multi:speciesTypeAtt' attribute, if present on a Species object,
must be the identifier of a SpeciesType object.
- MULTI_21203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021203:
Two 'ListOf' subobjects with a Species object are optional, but if present,
these container object must not be empty.
- MULTI_21204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021204:
A ListOfOutwardBindingSites object may have the optional SBML core attributes
'metaid' and 'sboTerm'.
- MULTI_21205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021205:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfOutwardBindingSites container object may only contain
OutwardBindingSite objects.
- MULTI_21206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021206:
A ListOfSpeciesFeatures object may have the optional SBML core attributes
'metaid' and 'sboTerm'.
- MULTI_21207 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021207:
A SubListOfSpeciesFeatures object may have the optional attributes multi:id,
multi:relation and multi:component.
- MULTI_21208 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021208:
The value of the 'multi:relation' attribute, if presented on a
SubListOfSpeciesFeatures object, must conform to the syntax of the Multi data
type 'Relation'.
- MULTI_21209 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021209:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfSpeciesFeatures container object may only contain
SpeciesFeature and/or SubListOfSpeciesFeatures objects.
- MULTI_21210 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021210:
A SubListOfSpeciesFeatures object may have the optional SBML core attributes
'metaid' and 'sboTerm'.
- MULTI_21211 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021211:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a SubListOfSpeciesFeatures container object may only contain
SpeciesFeature objects.
- MULTI_21212 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021212:
The value of the 'multi:component' attribute on a given SubListOfSpeciesFeatures
object must be the identifier of an object of SpeciesTypeInstance,
SpeciesTypeComponentIndex or SpeciesType which contains the SpeciesFeature
objects in this subListOfSpeciesFeatures.
- MULTI_21213 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021213:
A species must have its 'speciesType' attribute defined when it has a
'listOfOutwardBindingSites.'
- MULTI_21214 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021214:
A species must have its 'speciesType' attribute defined when it has a
'listOfSpeciesFeatures.'
- MULTI_21215 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021215:
The 'relation' attribute of a subListOfSpeciesFeatures can only have the value
'and' if any speciesFeature involved references a speciesFeatureType with occur
> 1 Reference: L3V1 Multi V1.1 Section 3.17.2
- MULTI_21216 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021216:
A SubListOfSpeciesFeatures object must have at least two speciesFeatures.
- MULTI_21301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021301:
An OutwardBindingSite object may have the optional SBML Level~3 Core attributes
'metaid' and 'sboTerm.
- MULTI_21302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021302:
An OutwardBindingSite object may have the optional SBML Level~3 Core subobjects
for 'notes' and 'annotation.
- MULTI_21303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021303:
An OutwardBindingSite object must have the required attributes,
'multi:bindingStatus' and 'mulit:component'.
- MULTI_21304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021304:
The value of the 'multi:bindingStatus' attribute on a given OutwardBindingSite
object must confirm to the syntax of the Multi data type 'BindingStatus'.
- MULTI_21305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021305:
The value of the 'multi:component' attribute on a given OutwardBindingSite
object must be the identifier of an object of SpeciesTypeInstance,
SpeciesTypeComponentIndex or SpeciesType which ultimately reference an object of
BindingSiteSpeciesType.
- MULTI_21306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021306:
An outwardBindingSite can not be a binding site referenced by any
inSpeciesTypeBond in the species.
- MULTI_21401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021401:
A SpeciesFeature object may have the optional SBML Level~3 Core attributes
'metaid' and 'sboTerm'.
- MULTI_21402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021402:
A SpeciesFeature object may have the optional SBML Level~3 Core subobjects for
'notes' and 'annotation'.
- MULTI_21403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021403:
A SpeciesFeature object must have the required attributes,
'multi:speciesFeatureType' and 'mulit:occur', and may have the optional
attribute, 'multi:id' and 'multi:component'.
- MULTI_21404 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021404:
The value of the 'multi:speciesFeatureType' attribute on a given SpeciesFeature
object must be the identifier of a SpeciesFeatureType object which is in the
SpeciesType object referenced by the Species object containing this
SpeciesFeature object.
- MULTI_21405 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021405:
The value of the 'mulit:occur' attribute on a given SpeciesFeature object must
conform to the syntax of the SBML data type 'positiveInteger'.
- MULTI_21406 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021406:
The value of the 'multi:component' attribute on a given SpeciesFeature object
must be the identifier of an object of SpeciesTypeInstance,
SpeciesTypeComponentIndex or SpeciesType which contains this SpeciesFeature
object.
- MULTI_21407 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021407:
One ListOfSpeciesFeatureValues subobject within a SpeciesFeature object is
required.
- MULTI_21408 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021408:
A ListOfSpeciesFeatureValues object must not be empty.
- MULTI_21409 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021409:
A ListOfSpeciesFeatureValues object may have the optional SBML core attributes
'metaid' and 'sboTerm'.
- MULTI_21410 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021410:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfSpeciesFeatureValues container object may only contain
SpeciesFeatureValue objects.
- MULTI_21501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021501:
A SpeciesFeatureValue object may have the optional SBML Level~3 Core attributes
'metaid' and 'sboTerm'.
- MULTI_21502 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021502:
A SpeciesFeatureValue object may have the optional SBML Level~3 Core subobjects
for 'notes' and 'annotation'.
- MULTI_21503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021503:
A SpeciesFeatureValue object must have the required attribute 'multi:value'.
- MULTI_21504 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021504:
The value of the 'multi:value' attribute on a given SpeciesFeatureValue object
must be the identifier of a PossibleSpeciesFeatureValue object defined in the
SpeciesFeatureType object referenced by the SpeciesFeature object containing
this SpeciesFeatureValue object.
- MULTI_21601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021601:
An IntraSpeciesReaction object may have the optional SBML Level~3 Core
attributes 'metaid' and 'sboTerm'.
- MULTI_21602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021602:
An IntraSpeciesReaction object may have the optional SBML Level~3 Core
subobjects for 'notes' and 'annotation'.
- MULTI_21701 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021701:
An extended SimpleSpeciesReference object may have the optional attribute,
'multi:compartmentReference'.
- MULTI_21702 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021702:
An extended SimpleSpeciesReference object may have the optional attribute,
'multi:compartmentReference'.
- MULTI_21801 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021801:
A ListOfSpeciesTypeComponentMapsInProduct object within an extended
SpeciesReference object is optional, but if present, must not be empty.
- MULTI_21802 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021802:
A ListOfSpeciesTypeComponentMapsInProduct object may have the optional SBML core
attributes 'metaid' and 'sboTerm'.
- MULTI_21803 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021803:
Apart from the general 'notes' and 'annotation' subobjects permitted on all SBML
objects, a ListOfSpeciesTypeComponentMapsInProduct container object may only
contain SpeciesTypeComponentMapInProduct objects.
- MULTI_21901 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021901:
A SpeciesTypeComponentMapInProduct object may have the optional SBML Level~3
Core attributes 'metaid' and 'sboTerm'.
- MULTI_21902 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021902:
A SpeciesTypeComponentMapInProduct object may have the optional SBML Level~3
Core subobjects for 'notes' and 'annotation'.
- MULTI_21903 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021903:
A SpeciesTypeComponentMapInProduct object must have the required attributes
'multi:reactant', 'multi:reactantComponent', and 'multi:productComponent'.
- MULTI_21904 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021904:
The value of the 'multi:reactant' attribute on a given
SpeciesTypeComponentMapInProduct object must be the identifier of a reactant
SpeciesReference object within a reaction.
- MULTI_21905 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021905:
The value of the 'multi:reactantComponent' attribute on a given
SpeciesTypeComponentMapInProduct object must be the identifier of an object of
SpeciesTypeInstance, SpeciesTypeComponentIndex or SpeciesType.
- MULTI_21906 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7021906:
The value of the 'multi:productComponent' attribute on a given
SpeciesTypeComponentMapInProduct object must be the identifier of an object of
SpeciesTypeInstance, SpeciesTypeComponentIndex or SpeciesType.
- MULTI_22001 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7022001:
A CompartmentReference object may have the optional SBML Level~3 Core attributes
'metaid' and 'sboTerm'.
- MULTI_22002 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7022002:
A CompartmentReference object may have the optional SBML Level~3 Core subobjects
for 'notes' and 'annotation'.
- MULTI_22003 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7022003:
A CompartmentReference object must have the required attribute
'multi:compartment', and may have the optional attributes 'multi:id' and
'multi:name'.
- MULTI_22004 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7022004:
The value of the 'multi:compartment' attribute must be the value of an 'id'
attribute on an existing Compartment object in the 'SId' namespace of the parent
model.
- MULTI_22005 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7022005:
If some or all compartmentReferences within a ListOfCompartmentReferences object
reference the same compartment, those compartmentReferences are required to have
its 'multi:id' attribute defined to distinguish different compartmentReferences.
- MULTI_22006 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 7022006:
A <compartmentReference> cannot reference a <compartment> that directly or
indirectly contains teh <compartmentReference>.
- MultiASTNodePlugin - Class in org.sbml.jsbml.ext.multi
-
- MultiASTNodePlugin() - Constructor for class org.sbml.jsbml.ext.multi.MultiASTNodePlugin
-
- MultiASTNodePlugin(ASTNode) - Constructor for class org.sbml.jsbml.ext.multi.MultiASTNodePlugin
-
- MultiASTNodePlugin(MultiASTNodePlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiASTNodePlugin
-
- MultiCompartmentPlugin - Class in org.sbml.jsbml.ext.multi
-
- MultiCompartmentPlugin() - Constructor for class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin
-
Creates an MultiCompartmentPlugin instance.
- MultiCompartmentPlugin(Compartment) - Constructor for class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin
-
- MultiCompartmentPlugin(MultiCompartmentPlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin
-
Clone constructor.
- MultiCompartmentPluginConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- MultiCompartmentPluginConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.MultiCompartmentPluginConstraints
-
- MultiConstants - Class in org.sbml.jsbml.ext.multi
-
Contains some constants related to the multi package.
- MultiConstants() - Constructor for class org.sbml.jsbml.ext.multi.MultiConstants
-
- MultiModelPlugin - Class in org.sbml.jsbml.ext.multi
-
In order to encode the structures needed to define and use multistate and multi-component
complexes, the element model is extended to be linked to a list of
MultiSpeciesTypes.
- MultiModelPlugin(MultiModelPlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiModelPlugin
-
- MultiModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.multi.MultiModelPlugin
-
- MultiModelPluginConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- MultiModelPluginConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.MultiModelPluginConstraints
-
- MultiParser - Class in org.sbml.jsbml.xml.parsers
-
A MultiParser is used to parse the multi extension package elements and
attributes.
- MultiParser() - Constructor for class org.sbml.jsbml.xml.parsers.MultiParser
-
- MultipleAssignmentOrRateRules - org.sbml.jsbml.SBMLException.Code
-
Multiple rules for the same variable
- MultipleEventAssignmentsForId - org.sbml.jsbml.SBMLException.Code
-
Multiple event assignments for the same variable
- MultipleInitAssignments - org.sbml.jsbml.SBMLException.Code
-
Multiple initial assignments for the same symbol value
- multiplier - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- MultiplierNotValidAttribute - org.sbml.jsbml.SBMLException.Code
-
Attribute multiplier on units not supported in SBML Level 1
- multiplyWith(ASTNode) - Method in class org.sbml.jsbml.ASTNode
-
Multiplies this
ASTNode with the given node
- multiplyWith(ASTNode...) - Method in class org.sbml.jsbml.ASTNode
-
Multiplies this
ASTNode with the given nodes, i.e., all given nodes
will be children of this node, whose type will be set to
ASTNode.Type.TIMES.
- multiplyWith(CallableSBase) - Method in class org.sbml.jsbml.ASTNode
-
Multiplies this
ASTNode with the given SBML element.
- multiplyWith(ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- multiplyWith(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- multiplyWith(UnitDefinition) - Method in class org.sbml.jsbml.UnitDefinition
-
Multiplies this unit with the given unit definition, i.e., adds a clone
of each unit object in the list of units of the given definition to the
list of this unit.
- MultiSimpleSpeciesReferencePlugin - Class in org.sbml.jsbml.ext.multi
-
- MultiSimpleSpeciesReferencePlugin() - Constructor for class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin
-
Creates an MultiSimpleSpeciesReferencePlugin instance
- MultiSimpleSpeciesReferencePlugin(MultiSimpleSpeciesReferencePlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin
-
Clone constructor
- MultiSimpleSpeciesReferencePlugin(SimpleSpeciesReference) - Constructor for class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin
-
- MultiSpeciesPlugin - Class in org.sbml.jsbml.ext.multi
-
A species in the Multi package is extended from a pool to a
template or pattern which multiple pools may map to.
- MultiSpeciesPlugin(MultiSpeciesPlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- MultiSpeciesPlugin(Species) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- MultiSpeciesReferencePlugin - Class in org.sbml.jsbml.ext.multi
-
- MultiSpeciesReferencePlugin() - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin
-
Creates an MultiSpeciesReferencePlugin instance
- MultiSpeciesReferencePlugin(MultiSpeciesReferencePlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin
-
Clone constructor
- MultiSpeciesReferencePlugin(SpeciesReference) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin
-
- MultiSpeciesType - Class in org.sbml.jsbml.ext.multi
-
The element MultiSpeciesType, which is part of SBML Level 2 Version 4 specification, is not part
of SBML Level 3 Version 1 Core any more.
- MultiSpeciesType() - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesType
-
Creates an MultiSpeciesType instance
- MultiSpeciesType(int, int) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesType
-
Creates a MultiSpeciesType instance with a level and version.
- MultiSpeciesType(String) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesType
-
Creates a MultiSpeciesType instance with an id.
- MultiSpeciesType(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesType
-
Creates a MultiSpeciesType instance with an id, level, and version.
- MultiSpeciesType(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesType
-
Creates a MultiSpeciesType instance with an id, name, level, and version.
- MultiSpeciesType(MultiSpeciesType) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesType
-
- MultiSpeciesTypeConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- MultiSpeciesTypeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.MultiSpeciesTypeConstraints
-
- MultSpeciesSameTypeInCompartment - org.sbml.jsbml.SBMLException.Code
-
Cannot have multiple species of the same type in the same compartment
