O-Index (JSBML 1.6.1-SNAPSHOT API Specification)

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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(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(Objective) - Constructor for class org.sbml.jsbml.ext.fbc.Objective: Clone constructor
OBJECTIVE_COEFFICIENT - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
Objective.Type - Enum in org.sbml.jsbml.ext.fbc
ObjectiveConstraints - Class in org.sbml.jsbml.validator.offline.constraints
ObjectiveConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ObjectiveConstraints
objectRole - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
ObseleteSBOTerm - org.sbml.jsbml.SBMLException.Code: Obsolete sboTerm value
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
OffsetNoLongerValid - org.sbml.jsbml.SBMLException.Code: offset not supported in this Level+Version of SBML
OffsetNotValidAttribute - org.sbml.jsbml.SBMLException.Code: Attribute offset on units only available in SBML Level 2 Version 1
OHM - org.sbml.jsbml.Unit.Kind: The ohm unit.
OmittedProcessNode<T> - Interface in org.sbml.jsbml.ext.render.director
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
OpsNeedCorrectNumberOfArgs - org.sbml.jsbml.SBMLException.Code: Incorrect number of arguments to operator
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 - org.sbml.jsbml.ext.multi.Relation
or - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants: Introduced to FBC in version 2.
or - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
or - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
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(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
or(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.ConfigurableLogicalFormulaCompiler
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(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
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(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(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 - Class in org.sbml.jsbml.ext.fbc: This class represents a set of two or more associations that are related in an order independent ‘and’ relationship.
Or() - Constructor for class org.sbml.jsbml.ext.fbc.Or: Creates a new Or instance.
Or(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.Or: Creates a new Or instance.
Or(Or) - Constructor for class org.sbml.jsbml.ext.fbc.Or: Creates a new Or instance.
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.
OrConstraints - Class in org.sbml.jsbml.validator.offline.constraints
OrConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.OrConstraints
order - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
ordinal - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
ordinalMapping - 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(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.OrdinalMapping
OrdinalMapping(OrdinalMapping) - Constructor for class org.sbml.jsbml.ext.spatial.OrdinalMapping
OrdinalMappingConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the OrdinalMapping class.
OrdinalMappingConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.OrdinalMappingConstraints
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.comp.util - package org.sbml.jsbml.ext.comp.util
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.fbc.converters - package org.sbml.jsbml.ext.fbc.converters
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.multi.util - package org.sbml.jsbml.ext.multi.util
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.render.director - package org.sbml.jsbml.ext.render.director: This package contains interfaces and classes to create an implementation to create a graphical representation of the Layout of a SBML document.
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.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.converters - package org.sbml.jsbml.util.converters
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.validator.offline - package org.sbml.jsbml.validator.offline: Provides classes to validate any kind of object offline.
org.sbml.jsbml.validator.offline.constraints - package org.sbml.jsbml.validator.offline.constraints: Any validation constraints related to the multi package.
org.sbml.jsbml.validator.offline.constraints.helper - package org.sbml.jsbml.validator.offline.constraints.helper
org.sbml.jsbml.validator.offline.factory - package org.sbml.jsbml.validator.offline.factory
org.sbml.jsbml.validator.offline.i18n - package org.sbml.jsbml.validator.offline.i18n: Contains the messages and short messages for the SBML errors in different languages.
org.sbml.jsbml.validator.offline.i18n.fr - package org.sbml.jsbml.validator.offline.i18n.fr: Contains the messages and short messages for the SBML errors in french.
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
other - org.sbml.jsbml.ListOf.Type: For instance, it is not possible to decide between reactants and products because both elements are of the same type.
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: Creates a new Output instance.
Output(int, int) - Constructor for class org.sbml.jsbml.ext.qual.Output: Creates a new Output instance.
Output(String) - Constructor for class org.sbml.jsbml.ext.qual.Output: Creates a new Output instance.
Output(String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Output: Creates a new Output instance.
Output(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Output: Creates a new Output instance.
Output(String, QualitativeSpecies, OutputTransitionEffect) - Constructor for class org.sbml.jsbml.ext.qual.Output: Creates a new Output instance.
Output(Output) - Constructor for class org.sbml.jsbml.ext.qual.Output: Creates a new Output instance.
Output(QualitativeSpecies, OutputTransitionEffect) - Constructor for class org.sbml.jsbml.ext.qual.Output: Creates a new Output instance.
OutputConstraints - Class in org.sbml.jsbml.validator.offline.constraints: Defines validation rules (as ValidationFunction instances) for the Output class.
OutputConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.OutputConstraints
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: A binding site not involved in any InSpeciesTypeBond object in the MultiSpeciesType referenced by a Species is an outwardBindingSite.
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
OVERDETERMINED_MODEL - org.sbml.jsbml.SBMLException.Category: Error in the system of equations in the model: the system is overdetermined, therefore violating a tenet of proper SBML.
OVERDETERMINED_MODEL - org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY: Static analysis of whether the system of equations implied by a model is mathematically overdetermined.
OverdeterminedSystem - org.sbml.jsbml.SBMLException.Code: Model is overdetermined

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