A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

N

name - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

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

NamedSBase - Interface in org.sbml.jsbml

Base class for all the SBML components with an id and a name (optional or not) in SBML Level 3 Version 1 or lower.

NamedSBaseReferenceFilter - Class in org.sbml.jsbml.ext.layout

This is a special NameFilter that allows users to search for a AbstractReferenceGlyph that refers to a NamedSBase with the given identifier attribute.

NamedSBaseReferenceFilter() - Constructor for class org.sbml.jsbml.ext.layout.NamedSBaseReferenceFilter

Creates a new SpeciesReferenceFilter with undefined properties.

NamedSBaseReferenceFilter(NamedSBase) - Constructor for class org.sbml.jsbml.ext.layout.NamedSBaseReferenceFilter

Creates a new NamedSBaseReferenceFilter that only accepts instances of AbstractReferenceGlyph pointing to the id of the given NamedSBase.

NamedSBaseReferenceFilter(String) - Constructor for class org.sbml.jsbml.ext.layout.NamedSBaseReferenceFilter

NamedSBaseReferenceFilter(String, String) - Constructor for class org.sbml.jsbml.ext.layout.NamedSBaseReferenceFilter

NamedSBaseWithDerivedUnit - Interface in org.sbml.jsbml

All objects that implement this interface can be referenced in abstract syntax trees as implemented in ASTNode.

NameFilter - Class in org.sbml.jsbml.util.filters

This filter only accepts instances of SBase with the id or name as given in the constructor of this object.

NameFilter() - Constructor for class org.sbml.jsbml.util.filters.NameFilter

Creates a new NameFilter instance

NameFilter(String) - Constructor for class org.sbml.jsbml.util.filters.NameFilter

Creates a new NameFilter instance with the given id to search for.

NameFilter(String, String) - Constructor for class org.sbml.jsbml.util.filters.NameFilter

Creates a new NameFilter instance with the given id and/or name to search for.

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

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

namespaces - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

namespaces - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

namespaces - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

namespaces - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

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

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

namespaces - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

namespaces - Static variable in class org.sbml.jsbml.ext.req.ReqConstants

namespaces - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

namespaces_L2 - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

namespaces_L2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

namespaces_L3 - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

namespaces_L3 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

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

The namespace URI of this parser, this value can change between releases.

namespaceURI - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

The latest namespace URI of this parser, this value can change between releases.

namespaceURI - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

namespaceURI - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

The latest namespace URI of this parser, this value can change between releases.

namespaceURI - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

The latest namespace URI of this parser, this value can change between releases.

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

The namespace URI of this parser, this value can change between releases.

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

The latest namespace URI of this parser, this value can change between releases.

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

The latest namespace URI of this parser, this value can change between releases.

namespaceURI - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

The latest namespace URI of this parser, this value can change between releases.

namespaceURI - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

The latest namespace URI of this parser, this value can change between releases.

namespaceURI - Static variable in class org.sbml.jsbml.ext.req.ReqConstants

The latest namespace URI of this parser, this value can change between releases.

namespaceURI - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

The latest namespace URI of this parser, this value can change between releases.

namespaceURI_L2 - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

namespaceURI_L2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.req.ReqConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

namespaceURI_L3V1V2 - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 2.

namespaceURIrequired - Static variable in class org.sbml.jsbml.xml.parsers.SpatialParser

The name space of required elements.

nameToSId(String, SBMLDocument) - Static method in class org.sbml.jsbml.util.SBMLtools

Generates a valid SId from a given name.

NecessaryStimulation<T> - Interface in org.sbml.jsbml.ext.render.director

Interface for the SBGN specified necessary stimulation arc.

needsAction(SBase) - Method in class org.sbml.jsbml.util.converters.LevelVersionConverter

Test if a given instance of SBase requires an action during conversion.

needsAction(SBase) - Method in class org.sbml.jsbml.util.converters.ToL3Converter

needsAction(SBase) - Method in class org.sbml.jsbml.util.converters.ToL3V2Converter

NEGATIVE_ININITY - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler

NEGATIVE_ININITY - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler

neq(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode

Creates an ASTNode that performs a not equal comparison between two ASTNodes.

neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

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

Creates an ASTNode2 that performs a not equal comparison between two ASTNode2s.

neq(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

Not equal.

neq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

neq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

neq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

neq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler

neq(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

neq(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

Not equal.

neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML

neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler

neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

neq(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

newBundle(String, Locale, String, ClassLoader, boolean) - Method in class org.sbml.jsbml.util.XMLResourceBundleControl

newInstance(SBase, Class<T>) - Static method in class org.sbml.jsbml.ListOf

Initializes a new ListOf object for the given parent SBML object and with the given Class as the type of the list.

newLine() - Static method in class org.sbml.jsbml.util.StringTools

newToken(int, String) - Static method in class org.sbml.jsbml.math.parser.Token

Returns a new Token object, by default.

newToken(int) - Static method in class org.sbml.jsbml.math.parser.Token

newToken(int, String) - Static method in class org.sbml.jsbml.text.parser.Token

Returns a new Token object, by default.

newToken(int) - Static method in class org.sbml.jsbml.text.parser.Token

next - Variable in class org.sbml.jsbml.math.parser.Token

A reference to the next regular (non-special) token from the input stream.

next - Variable in class org.sbml.jsbml.text.parser.Token

A reference to the next regular (non-special) token from the input stream.

nextId(Model) - Static method in class org.sbml.jsbml.util.SBMLtools

Generate a valid SBML identifier using UUID.

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

Randomly creates a new String that can be used as a metaid, i.e., a String that is a valid metaid and that is not yet used by any other element within this SBMLDocument.

NO_WHISKERS - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector

nodeAdded(TreeNode) - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener

nodeAdded(TreeNode) - Method in interface org.sbml.jsbml.util.TreeNodeChangeListener

The TreeNode passed to this method has just been added to the a containing element.

nodeRemoved(TreeNodeRemovedEvent) - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener

nodeRemoved(TreeNodeRemovedEvent) - Method in interface org.sbml.jsbml.util.TreeNodeChangeListener

The TreeNodeRemovedEvent passed to this method provides information about the node that has been removed from a containing parent and does hence no longer belong to the SBMLDocument anymore.

NodeWriter - Interface in org.sbml.jsbml.util

A writer for XML DOM nodes.

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

normalize(GeneralPath) - Static method in class org.sbml.jsbml.ext.render.director.Geometry

not(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

not(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

not(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

not(ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory

Creates an ASTLogicalOperatorNode of type ASTNode.Type.LOGICAL_NOT and adds the given nodes as children.

not(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

not(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

not(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

not(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

not(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

NOT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants

RegularExpression Id.

NOT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants

RegularExpression Id.

NOT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

NOT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants

RegularExpression Id.

NOT - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants

RegularExpression Id.

NOT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants

RegularExpression Id.

NOT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants

RegularExpression Id.

NOT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

NOT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants

RegularExpression Id.

not(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

not(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

not(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

not(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

not(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

not(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

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

NotesToAnnotation - Class in org.sbml.jsbml.ext.fbc.converters

NotesToAnnotation transfers information from the Cobra style notes to the annotations.

NotesToAnnotation() - Constructor for class org.sbml.jsbml.ext.fbc.converters.NotesToAnnotation

NotImplementedException - Error in org.sbml.jsbml.util

This kind of Exception indicates currently missing functionality in JSBML.

NotImplementedException() - Constructor for error org.sbml.jsbml.util.NotImplementedException

NotImplementedException(String) - Constructor for error org.sbml.jsbml.util.NotImplementedException

NotImplementedException(Throwable) - Constructor for error org.sbml.jsbml.util.NotImplementedException

NotImplementedException(String, Throwable) - Constructor for error org.sbml.jsbml.util.NotImplementedException

NucleicAcidFeature<T> - Class in org.sbml.jsbml.ext.render.director

NucleicAcidFeature() - Constructor for class org.sbml.jsbml.ext.render.director.NucleicAcidFeature

NUMBER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants

RegularExpression Id.

NUMBER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants

RegularExpression Id.

NUMBER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

NUMBER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants

RegularExpression Id.

NUMBER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants

RegularExpression Id.

NUMBER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants

RegularExpression Id.

NUMBER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

NUMBER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants

RegularExpression Id.

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

numberOfClasses - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

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

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

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

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

numSamples1 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

numSamples2 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

numSamples3 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

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