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M

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.util.compilers.MathMLXMLStreamCompiler

main(String[]) - Static method in class org.sbml.jsbml.validator.SBMLValidator

main(String[]) - Static method in class org.sbml.jsbml.xml.parsers.DistribParser

Tests this class

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

Reads the file that is passed as argument and write it to the console, using the method SBMLWriter.write(SBMLDocument, java.io.OutputStream).

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, boolean) - Static method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

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.util.compilers.LaTeXCompiler

math - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

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).

math - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

MathContainer - Interface in org.sbml.jsbml

Base interface for all the SBML components which contain MathML nodes.

mathMLClass - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

MathMLCompiler - Class in org.sbml.jsbml.util.compilers

Deprecated.

use MathMLXMLStreamCompiler instead.

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

Deprecated.

this class should not be used anymore, replaced by MathMLStaxParser. But we keep it in case somebody want to use Document

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

Writes an ASTNode2 to mathML.

MathMLXMLStreamCompiler(XMLStreamWriter, String) - Constructor for class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler

Create a new MathMLXMLStreamCompiler.

MathMLXMLStreamCompiler - Class in org.sbml.jsbml.util.compilers

Writes an ASTNode the mathML.

MathMLXMLStreamCompiler(XMLStreamWriter, String) - Constructor for class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler

Create a new MathMLXMLStreamCompiler.

MathMLXMLStreamCompiler(String) - Constructor for class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler

MathMLXMLStreamCompiler() - Constructor for class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler

mathrm(char) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

mathrm(String) - 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.util.compilers.LaTeXCompiler

Maths - Class in org.sbml.jsbml.util

This class 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.

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

Member - Class in org.sbml.jsbml.ext.groups

Member() - Constructor for class org.sbml.jsbml.ext.groups.Member

Member(int, int) - Constructor for class org.sbml.jsbml.ext.groups.Member

Member(Member) - Constructor for class org.sbml.jsbml.ext.groups.Member

memberConstraint - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

MemberConstraint - Class in org.sbml.jsbml.ext.groups

Deprecated.

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.

MemberConstraint() - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint

Deprecated.

Creates an MemberConstraint instance

MemberConstraint(String) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint

Deprecated.

Creates a MemberConstraint instance with an id.

MemberConstraint(int, int) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint

Deprecated.

Creates a MemberConstraint instance with a level and version.

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 - Class in org.sbml.jsbml.util

Message() - Constructor for class org.sbml.jsbml.util.Message

message - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

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

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

metaidRef - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

metaIds() - Method in class org.sbml.jsbml.SBMLDocument

Provides access to all registered metaIds in this SBMLDocument.

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_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

minOccur - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

minus(ASTNode) - Method in class org.sbml.jsbml.ASTNode

Subtracts the given ASTNode from this node.

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(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Subtracts an ASTNode2 from another ASTNode2.

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

Subtracts an integer number from ASTNode2 and sets the units of ASTCnIntegerNode to the specified unitsID.

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 - 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.CobraFormulaParserConstants

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.

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

minValue - 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(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

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(Model) - Constructor for class org.sbml.jsbml.Model

Creates a Model instance from a Model.

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 - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

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

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(Model) - 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

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

modifiedDate - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

ModifierSpeciesReference - Class in org.sbml.jsbml

Represents the modifierSpeciesReference XML element of a SBML file.

ModifierSpeciesReference() - Constructor for class org.sbml.jsbml.ModifierSpeciesReference

Creates a ModifierSpeciesReference instance.

ModifierSpeciesReference(int, int) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference

Creates a ModifierSpeciesReference instance.

ModifierSpeciesReference(ModifierSpeciesReference) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference

Creates a ModifierSpeciesReference instance from a given ModifierSpeciesReference.

ModifierSpeciesReference(Species) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference

Creates a ModifierSpeciesReference instance from a given Species.

ModifierSpeciesReference(String) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference

Creates a ModifierSpeciesReference instance.

ModifierSpeciesReference(String, int, int) - Constructor for class org.sbml.jsbml.ModifierSpeciesReference

Creates a ModifierSpeciesReference instance.

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.

MultiASTNodePlugin - Class in org.sbml.jsbml.ext.multi

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

Creates a MultiCompartmentPlugin instance associated with the given Compartment.

MultiCompartmentPlugin(MultiCompartmentPlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Clone constructor

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 SpeciesTypes.

MultiModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.multi.MultiModelPlugin

MultiModelPlugin(MultiModelPlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiModelPlugin

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

multiplier - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

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

Multiplies an ASTNode2 with the given nodes, i.e., all given nodes will be children of this ASTArithmeticOperatorNode, whose type will be set to ASTNode.Type.TIMES.

multiplyWith(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Multiplies an ASTNode2 with another ASTNode2.

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(SimpleSpeciesReference) - Constructor for class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Creates a MultiSimpleSpeciesReferencePlugin instance with a SimpleSpeciesReference.

MultiSimpleSpeciesReferencePlugin(MultiSimpleSpeciesReferencePlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Clone constructor

MultiSpeciesPlugin - Class in org.sbml.jsbml.ext.multi

MultiSpeciesPlugin(Species) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

MultiSpeciesPlugin(MultiSpeciesPlugin) - 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(SpeciesReference) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Creates a MultiSpeciesReferencePlugin instance with a SpeciesReference.

MultiSpeciesReferencePlugin(MultiSpeciesReferencePlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Clone constructor

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