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O

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

Objective - Class in org.sbml.jsbml.ext.fbc

An integral component in a complete description of a steady-state model is the so-called 'objective function' which generally consists of a linear combination of model variables (fluxes) and a sense (direction).

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

Creates an Objective instance

Objective(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.Objective

Creates a Objective instance with a level and version.

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

Clone constructor

Objective(String) - Constructor for class org.sbml.jsbml.ext.fbc.Objective

Creates a Objective instance with an id.

Objective(String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.Objective

Creates a Objective instance with an id, level, and version.

Objective(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.fbc.Objective

Creates a Objective instance with an id, name, level, and version.

Objective.Type - Enum in org.sbml.jsbml.ext.fbc

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

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

of(L, V) - Static method in class org.sbml.jsbml.util.Pair

Static method to easily create a value pair of two given values.

of(L, V) - Static method in class org.sbml.jsbml.util.ValuePair

Static method to easily create a value pair of two given values.

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

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

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

OPEN_PAR - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

OPERATION_FAILED - Static variable in class org.sbml.jsbml.JSBML

OPERATION_SUCCESS - Static variable in class org.sbml.jsbml.JSBML

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

Option - Class in org.sbml.jsbml.util

Stores the options sent by the SBML online validator.

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

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

or(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

or(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

or(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

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

Introduced to FBC in version 2.

Or - Class in org.sbml.jsbml.ext.fbc

Introduced to FBC in version 2.

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

Or(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.Or

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

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

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

or(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

or(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

or(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

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

or(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

or(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler

or(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

OR - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

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

RegularExpression Id.

or(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML

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

or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler

or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

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

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

OrdinalMapping - Class in org.sbml.jsbml.ext.spatial

OrdinalMapping() - Constructor for class org.sbml.jsbml.ext.spatial.OrdinalMapping

OrdinalMapping(OrdinalMapping) - Constructor for class org.sbml.jsbml.ext.spatial.OrdinalMapping

OrdinalMapping(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.OrdinalMapping

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

This filter accepts an item if at least one of its filters accepts the given item.

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

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

org.sbml.jsbml - package org.sbml.jsbml

Pure Java™ implementation of the data structures to represent all SBML constructs.

org.sbml.jsbml.ext - package org.sbml.jsbml.ext

The base package for all SBML extensions.

org.sbml.jsbml.ext.arrays - package org.sbml.jsbml.ext.arrays

org.sbml.jsbml.ext.arrays.compiler - package org.sbml.jsbml.ext.arrays.compiler

org.sbml.jsbml.ext.arrays.flattening - package org.sbml.jsbml.ext.arrays.flattening

org.sbml.jsbml.ext.arrays.util - package org.sbml.jsbml.ext.arrays.util

org.sbml.jsbml.ext.arrays.validator - package org.sbml.jsbml.ext.arrays.validator

org.sbml.jsbml.ext.arrays.validator.constraints - package org.sbml.jsbml.ext.arrays.validator.constraints

org.sbml.jsbml.ext.comp - package org.sbml.jsbml.ext.comp

Provides classes for the Hierarchical Model Composition package.

org.sbml.jsbml.ext.distrib - package org.sbml.jsbml.ext.distrib

org.sbml.jsbml.ext.distrib.util - package org.sbml.jsbml.ext.distrib.util

org.sbml.jsbml.ext.dyn - package org.sbml.jsbml.ext.dyn

Provides classes for the Dynamic Structures package.

org.sbml.jsbml.ext.fbc - package org.sbml.jsbml.ext.fbc

Provides classes for the Flux Balance Constraints package (FBC).

org.sbml.jsbml.ext.groups - package org.sbml.jsbml.ext.groups

Provides classes for the Groups package.

org.sbml.jsbml.ext.layout - package org.sbml.jsbml.ext.layout

Provides classes for the Layout package.

org.sbml.jsbml.ext.multi - package org.sbml.jsbml.ext.multi

Provides classes for the Multi package.

org.sbml.jsbml.ext.qual - package org.sbml.jsbml.ext.qual

Provides classes for the Qualitative Models package.

org.sbml.jsbml.ext.render - package org.sbml.jsbml.ext.render

Provides classes for the render package, see the specification at sbml.org.

org.sbml.jsbml.ext.req - package org.sbml.jsbml.ext.req

org.sbml.jsbml.ext.spatial - package org.sbml.jsbml.ext.spatial

Provides classes for the Spatial Geometries and Processes package.

org.sbml.jsbml.math - package org.sbml.jsbml.math

org.sbml.jsbml.math.compiler - package org.sbml.jsbml.math.compiler

org.sbml.jsbml.math.compiler.resources - package org.sbml.jsbml.math.compiler.resources

org.sbml.jsbml.math.parser - package org.sbml.jsbml.math.parser

Provides classes to parse formula Strings and to convert these into abstract syntax tree data structures.

org.sbml.jsbml.ontology - package org.sbml.jsbml.ontology

org.sbml.jsbml.resources - package org.sbml.jsbml.resources

Contains classes to deal with and to manage non-Java resources, such as configuration files.

org.sbml.jsbml.text.parser - package org.sbml.jsbml.text.parser

Provides classes to parse formula Strings and to convert these into abstract syntax tree data structures.

org.sbml.jsbml.util - package org.sbml.jsbml.util

A collection of handy utilities when working with JSBML classes, such as classes for String manipulation or mathematical operations.

org.sbml.jsbml.util.compilers - package org.sbml.jsbml.util.compilers

The classes in this package can be used to evaluate the information represented by abstract syntax trees (ASTNode objects).

org.sbml.jsbml.util.filters - package org.sbml.jsbml.util.filters

Filters are useful to decide whether or not to accept a certain item.

org.sbml.jsbml.validator - package org.sbml.jsbml.validator

This package provides methods to validate the content of SBML models, whether given in a file or as a data structure.

org.sbml.jsbml.xml - package org.sbml.jsbml.xml

This package provides classes and methods to deal with SBML in form of XML elements, i.e., here you can find parsers and writers for SBML and also elements to define XML nodes to be used for notes or annotations.

org.sbml.jsbml.xml.parsers - package org.sbml.jsbml.xml.parsers

Contains classes that implement ReadingParser and/or WritingParser to read or write some specific parts of an SBML file.

org.sbml.jsbml.xml.stax - package org.sbml.jsbml.xml.stax

Contains classes that use the Streaming API for XML (StAX) to read or write an SBML file.

org.sbml.jsbml.xml.xstream.converter - package org.sbml.jsbml.xml.xstream.converter

Contains classes that uses the XStream to read or write XML.

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

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

Output - Class in org.sbml.jsbml.ext.qual

Each Output refers to a QualitativeSpecies that participates in (is affected by) the corresponding Transition.

Output() - Constructor for class org.sbml.jsbml.ext.qual.Output

Output(String) - Constructor for class org.sbml.jsbml.ext.qual.Output

Output(QualitativeSpecies, OutputTransitionEffect) - Constructor for class org.sbml.jsbml.ext.qual.Output

Output(String, QualitativeSpecies, OutputTransitionEffect) - Constructor for class org.sbml.jsbml.ext.qual.Output

Output(int, int) - Constructor for class org.sbml.jsbml.ext.qual.Output

Output(String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Output

Output(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Output

Output(Output) - Constructor for class org.sbml.jsbml.ext.qual.Output

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

OutputTransitionEffect - Enum in org.sbml.jsbml.ext.qual

The transitionOutputEffect is an enumeration of values used to indicate the effect of an Output Transition within the system.

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

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

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

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

Creates an OutwardBindingSite instance

OutwardBindingSite(int, int) - Constructor for class org.sbml.jsbml.ext.multi.OutwardBindingSite

Creates a OutwardBindingSite instance with a level and version.

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

Clone constructor

OverdeterminationValidator - Class in org.sbml.jsbml.validator

This class creates a bipartite graph and a matching for the given model using the algorithm by Hopcroft and Karp (1973).

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

Creates a new OverdeterminationValidator for the given model

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