| src | |
| sbml | |
| annotation | |
| CVTerm.cpp | CVTerm I/O |
| CVTerm.h | Definition of a CVTerm class for adding annotations to a Model |
| Date.cpp | Date I/O |
| Date.h | Date I/O |
| ModelCreator.cpp | ModelCreator I/O |
| ModelCreator.h | ModelCreator I/O |
| ModelHistory.cpp | ModelHistory I/O |
| ModelHistory.h | ModelHistory I/O |
| RDFAnnotation.h | RDFAnnotation I/O |
| RDFAnnotationParser.cpp | RDFAnnotation I/O |
| RDFAnnotationParser.h | RDFAnnotation I/O |
| common | |
| common-documentation.h | Common text fragments used throughout libSBML's code documentation |
| common-sbmlerror-codes.h | |
| common.h | Common functions and macros for C and C++ |
| extern.h | Definitions of LIBSBML_EXTERN and related things |
| libsbml-config.h | Decides whether to #include Unix or Windows configuration variables |
| libsbml-version.cpp | Define libSBML version numbers for access from client software |
| libsbml-version.h | Define libSBML version numbers for access from client software |
| operationReturnValues.cpp | Enumeration of values returned by operations within libSBML |
| operationReturnValues.h | Enumeration of values returned by operations within libSBML |
| sbmlfwd.h | Forward declarations for all opaque C types |
| conversion | |
| ConversionOption.cpp | Implementation of ConversionOption, the class encapsulating conversion options |
| ConversionOption.h | Definition of ConversionOption, the class encapsulating conversion options |
| ConversionProperties.cpp | Implemenentation of ConversionProperties, the class encapsulating conversion configuration |
| ConversionProperties.h | Definition of ConversionProperties, the class encapsulating conversion configuration |
| ExpressionAnalyser.cpp | Implementation of ExpressionAnalyser |
| ExpressionAnalyser.h | Definition of ExpressionAnalyser, a class for analysing expressions |
| RegisterConverters.cpp | Registers all available converters |
| SBMLConverter.cpp | Implementation of SBMLConverter, the base class of package extensions |
| SBMLConverter.h | Definition of SBMLConverter, the base class for SBML conversion |
| SBMLConverterRegister.h | |
| SBMLConverterRegistry.cpp | Implementation of SBMLConverterRegistry, a registry of available converters |
| SBMLConverterRegistry.h | Definition of SBMLConverterRegistry, a registry of available converters |
| SBMLConverterTypes.h | Definition of SBMLConverterTypes |
| SBMLFunctionDefinitionConverter.cpp | Implementation of SBMLFunctionDefinitionConverter, a converter replacing function definitions |
| SBMLFunctionDefinitionConverter.h | Definition of SBMLFunctionDefinitionConverter, a converter replacing function definitions |
| SBMLIdConverter.cpp | Implementation of SBMLIdConverter, a converter renaming SIds |
| SBMLIdConverter.h | Definition of SBMLIdConverter, a converter renaming SIds |
| SBMLInferUnitsConverter.cpp | Implementation of SBMLInferUnitsConverter |
| SBMLInferUnitsConverter.h | Definition of SBMLInferUnitsConverter, infers units for parameters |
| SBMLInitialAssignmentConverter.cpp | Implementation of SBMLInitialAssignmentConverter, a converter inlining initial assignments |
| SBMLInitialAssignmentConverter.h | Definition of SBMLInitialAssignmentConverter, a converter inlining function definitions |
| SBMLLevel1Version1Converter.cpp | Implementation of SBMLLevel1Version1Converter |
| SBMLLevel1Version1Converter.h | Definition of SBMLLevel1Version1Converter |
| SBMLLevelVersionConverter.cpp | Implementation of SBMLLevelVersionConverter, the base class of package extensions |
| SBMLLevelVersionConverter.h | Definition of SBMLLevelVersionConverter, the base class for SBML conversion |
| SBMLLocalParameterConverter.cpp | Implementation of SBMLLocalParameterConverter, a converter replacing local parameters with global ones |
| SBMLLocalParameterConverter.h | Definition of SBMLLocalParameterConverter, a converter replacing local parameters with global ones |
| SBMLRateOfConverter.cpp | Implementation of SBMLRateOfConverter, a converter changing 'rateOf' into functionDefinition |
| SBMLRateOfConverter.h | Definition of SBMLRateOfConverter, a converter changing reactions into rate rules |
| SBMLRateRuleConverter.cpp | Implementation of SBMLRateRuleConverter, a converter from raterule to reaction |
| SBMLRateRuleConverter.h | Definition of SBMLRateRuleConverter, a converter from raterule to reaction |
| SBMLReactionConverter.cpp | Implementation of SBMLReactionConverter, a converter changing reactions into rate rules |
| SBMLReactionConverter.h | Definition of SBMLReactionConverter, a converter changing reactions into rate rules |
| SBMLRuleConverter.cpp | Implementation of SBMLRuleConverter, a converter sorting rules |
| SBMLRuleConverter.h | Definition of SBMLRuleConverter, a converter sorting rules |
| SBMLStripPackageConverter.cpp | Implementation of SBMLStripPackageConverter, the base class of package extensions |
| SBMLStripPackageConverter.h | Definition of SBMLStripPackageConverter, the base class for SBML conversion |
| SBMLUnitsConverter.cpp | Implementation of SBMLUnitsConverter, for converting units to SI |
| SBMLUnitsConverter.h | Definition of SBMLUnitsConverter, for converting units to SI |
| extension | |
| ASTBasePlugin.cpp | |
| ASTBasePlugin.h | |
| ISBMLExtensionNamespaces.cpp | |
| ISBMLExtensionNamespaces.h | |
| SBaseExtensionPoint.cpp | Implementation of SBaseExtensionPoint |
| SBaseExtensionPoint.h | Definition of SBaseExtensionPoint |
| SBasePlugin.cpp | Implementation of SBasePlugin, the base class of extension entities plugged in SBase derived classes in the SBML Core package |
| SBasePlugin.h | Definition of SBasePlugin, the base class of extension entities plugged in SBase derived classes in the SBML Core package |
| SBasePluginCreator.h | Template class for SBasePlugin-based classes |
| SBasePluginCreatorBase.cpp | Implementation of SBasePluginCreatorBase, the base class of SBasePlugin creator classes |
| SBasePluginCreatorBase.h | Definition of SBasePluginCreatorBase, the base class of SBasePlugin creator classes |
| SBMLDocumentPlugin.cpp | Implementation of SBMLDocumentPlugin, the derived class of SBasePlugin |
| SBMLDocumentPlugin.h | Definition of SBMLDocumentPlugin, the derived class of SBasePlugin |
| SBMLDocumentPluginNotRequired.cpp | Implementation of SBMLDocumentPluginNotRequired, the plugin class of layout package for the Model element |
| SBMLDocumentPluginNotRequired.h | Definition of SBMLDocumentPluginNotRequired, the plugin class of layout package for the SBMLDocument element, whose 'required' attribute must be 'false' |
| SBMLExtension.cpp | Implementation of SBMLExtension, the base class of package extensions |
| SBMLExtension.h | Definition of SBMLExtension, the core component of SBML package extension |
| SBMLExtensionException.cpp | SBMLExtensionException class, the exception class for package extension |
| SBMLExtensionException.h | Class of exceptions thrown in some situations |
| SBMLExtensionNamespaces.cpp | Implementation of C-API for the SBMLExtensionNamespaces class |
| SBMLExtensionNamespaces.h | Class to store the SBML Level, Version and namespace of a package |
| SBMLExtensionRegister.h | Template class for registering extension packages |
| SBMLExtensionRegistry.cpp | Implementation of SBMLExtensionRegistry, the registry class in which extension packages are registered |
| SBMLExtensionRegistry.h | The registry class for tracking package extensions |
| math | |
| ASTNode.cpp | Abstract Syntax Tree (AST) for representing formula trees |
| ASTNode.h | Abstract Syntax Tree (AST) for representing formula trees |
| ASTNodeType.h | Enumeration for Abstract Syntax Tree (AST) |
| DefinitionURLRegistry.cpp | Implementation of DefinitionURLRegistry, a registry of available DefinitionURLs |
| DefinitionURLRegistry.h | Definition of DefinitionURLRegistry, a registry of available DefinitionURLs |
| FormulaFormatter.cpp | Formats an AST formula tree as an SBML formula string |
| FormulaFormatter.h | Formats an AST formula tree as an SBML formula string |
| FormulaParser.cpp | Parses an SBML formula string into an AST |
| FormulaParser.h | Parses an SBML formula string into an AST |
| FormulaTokenizer.cpp | Tokenizes an SBML formula string |
| FormulaTokenizer.h | Tokenizes an SBML formula string |
| L3FormulaFormatter.cpp | Formats an AST formula tree as an SBML L3 formula string |
| L3FormulaFormatter.h | Formats an L3 AST formula tree as an SBML formula string |
| L3Parser.cpp | |
| L3Parser.h | Definition of the level 3 infix-to-mathml parser C functions |
| L3ParserSettings.cpp | Definition of the level 3 infix-to-mathml parser settings |
| L3ParserSettings.h | Definition of the level 3 infix-to-mathml parser settings |
| MathML.cpp | Utilities for reading and writing MathML to/from text strings |
| MathML.h | Utilities for reading and writing MathML to/from text strings |
| packages | |
| comp | |
| common | |
| CompExtensionTypes.h | Include all SBML types of Comp extension in a single header file |
| compfwd.h | SBML Comp C structure declarations |
| extension | |
| CompExtension.cpp | Implementation of CompExtension, the core module of comp package |
| CompExtension.h | Definition of CompExtension, the core module of comp package |
| CompModelPlugin.cpp | Implementation of CompModelPlugin, the plugin class of comp package for the SBase element |
| CompModelPlugin.h | Definition of CompModelPlugin, the plugin class of comp package for the Model element |
| CompSBasePlugin.cpp | Implementation of CompSBasePlugin, the plugin class of comp package for the SBase element |
| CompSBasePlugin.h | Definition of CompSBasePlugin, the plugin class of comp package for the Model element |
| CompSBMLDocumentPlugin.cpp | Implementation of CompSBMLDocumentPlugin, the plugin class of comp package for the SBase element |
| CompSBMLDocumentPlugin.h | Definition of CompSBMLDocumentPlugin, the plugin class of comp package for the Model element |
| sbml | |
| CompBase.cpp | Implementation of CompBase, the base class of extension entities plugged in SBase derived classes in the SBML Core package |
| CompBase.h | Definition of CompBase, the base class of extension entities plugged in SBase derived classes in the SBML Core package |
| Deletion.cpp | Implementation of Deletion, the SBaseRef derived class of deletions package |
| Deletion.h | Definition of Deletion, the SBase derived class of deletions package |
| ExternalModelDefinition.cpp | Implementation of ExternalModelDefinition, the SBase-derived class of the comp package |
| ExternalModelDefinition.h | Definition of ExternalModelDefinition, the SBase derived class of the comp package |
| ListOfDeletions.cpp | Implementation of ListOfDeletions |
| ListOfDeletions.h | Definition of ListOfDeletions, the SBase derived class of deletions package |
| ListOfExternalModelDefinitions.cpp | Implementation of ListOfExternalModelDefinitions |
| ListOfExternalModelDefinitions.h | Definition of ListOfExternalModelDefinitions, the SBase derived class of the Hierarchial Model Defintions package |
| ListOfModelDefinitions.cpp | Implementation of ListOfModelDefinitions from the comp package |
| ListOfModelDefinitions.h | Definition of ListOfModelDefinitions, the SBase derived class of modelDefinitions package |
| ListOfPorts.cpp | Implementation of ListOfPorts |
| ListOfPorts.h | Definition of ListOfPorts, the SBase derived class of ports package |
| ListOfReplacedElements.cpp | Implementation of ListOfReplacedElements from the comp package |
| ListOfReplacedElements.h | Definition of ListOfReplacedElements, the SBase derived class of replacedElements package |
| ListOfSubmodels.cpp | Implementation of ListOfSubmodels |
| ListOfSubmodels.h | Definition of ListOfSubmodels, the SBase derived class of submodels package |
| ModelDefinition.cpp | Implementation of ModelDefinition, the SBase-derived class of the comp package |
| ModelDefinition.h | Definition of ModelDefinition, the SBase derived class of the comp package |
| Port.cpp | Implementation of Port, the SBase-derived class of the comp package |
| Port.h | Definition of Port, the SBase derived class of the comp package |
| ReplacedBy.cpp | Implementation of ReplacedBy, the SBaseRef derived class of the comp package |
| ReplacedBy.h | Definition of ReplacedBy, the Replacing-derived class of the comp package |
| ReplacedElement.cpp | Implementation of ReplacedElement, the SBaseRef derived class of replacedElements package |
| ReplacedElement.h | Definition of ReplacedElement, the SBase derived class of replacedElements package |
| Replacing.cpp | Implementation of Replacing, the SBaseRef derived class of Replacings package |
| Replacing.h | Definition of Replacing, the SBaseRef-derived class of the comp package |
| SBaseRef.cpp | Implementation of SBaseRef, the SBase-derived class of the comp package |
| SBaseRef.h | Definition of SBaseRef, the SBase derived class of the comp package |
| Submodel.cpp | Implementation of Submodel, the SBase-derived class of the comp package |
| Submodel.h | Definition of Submodel, the SBase derived class of the comp package |
| util | |
| CompFlatteningConverter.cpp | Implementation of a first flattening converter |
| CompFlatteningConverter.h | Definition of a first flattening converter |
| SBMLFileResolver.cpp | Implementation of SBMLFileResolver, the file system based resolver for SBML Documents |
| SBMLFileResolver.h | A file-based resolver for SBML Documents |
| SBMLResolver.cpp | Implementation of SBMLResolver, the base class of package extensions |
| SBMLResolver.h | Definition of SBMLResolver, the base class for resolving SBML documents |
| SBMLResolverRegistry.cpp | Implementation of SBMLResolverRegistry, a registry of available resolvers |
| SBMLResolverRegistry.h | Definition of SBMLResolverRegistry, a registry of available resolvers |
| SBMLUri.cpp | Implementation of SBMLUri, the utility class for handling uris |
| SBMLUri.h | Definition of SBMLUri, the utility class for handling URIs |
| validator | |
| CompConsistencyValidator.cpp | |
| CompConsistencyValidator.h | |
| CompIdentifierConsistencyValidator.cpp | |
| CompIdentifierConsistencyValidator.h | |
| CompSBMLError.h | Represents SBML errors and other diagnostics |
| CompSBMLErrorTable.h | Represents SBML errors and other diagnostics |
| CompUnitConsistencyValidator.cpp | |
| CompUnitConsistencyValidator.h | |
| CompValidator.cpp | |
| CompValidator.h | Base class for SBML CompValidators |
| distrib | |
| common | |
| DistribExtensionTypes.h | Definition of DistribExtensionTypes |
| distribfwd.h | Definition of distribfwd |
| extension | |
| DistribASTPlugin.cpp | Implementation of the DistribASTPlugin class |
| DistribASTPlugin.h | Definition of the DistribASTPlugin class |
| DistribExtension.cpp | Implementation of DistribExtension |
| DistribExtension.h | Definition of DistribExtension |
| DistribSBasePlugin.cpp | Implementation of the DistribSBasePlugin class |
| DistribSBasePlugin.h | Definition of the DistribSBasePlugin class |
| DistribSBMLDocumentPlugin.cpp | Implementation of the DistribSBMLDocumentPlugin class |
| DistribSBMLDocumentPlugin.h | Definition of the DistribSBMLDocumentPlugin class |
| sbml | |
| DistribBase.cpp | Implementation of the DistribBase class |
| DistribBase.h | Definition of the DistribBase class |
| ListOfUncertainties.cpp | Implementation of the ListOfUncertainties class |
| ListOfUncertainties.h | Definition of the ListOfUncertainties class |
| ListOfUncertParameters.cpp | Implementation of the ListOfUncertParameters class |
| ListOfUncertParameters.h | Definition of the ListOfUncertParameters class |
| Uncertainty.cpp | Implementation of the Uncertainty class |
| Uncertainty.h | Definition of the Uncertainty class |
| UncertParameter.cpp | Implementation of the UncertParameter class |
| UncertParameter.h | Definition of the UncertParameter class |
| UncertSpan.cpp | Implementation of the UncertSpan class |
| UncertSpan.h | Definition of the UncertSpan class |
| validator | |
| DistribConsistencyValidator.cpp | |
| DistribConsistencyValidator.h | |
| DistribIdentifierConsistencyValidator.cpp | |
| DistribIdentifierConsistencyValidator.h | |
| DistribMathMLConsistencyValidator.cpp | |
| DistribMathMLConsistencyValidator.h | |
| DistribSBMLError.h | Definition of the DistribSBMLError class |
| DistribSBMLErrorTable.h | Definition of the DistribSBMLErrorTable class |
| DistribUnitConsistencyValidator.cpp | |
| DistribUnitConsistencyValidator.h | |
| DistribValidator.cpp | Definition of DistribValidator |
| DistribValidator.h | Definition of DistribValidator |
| fbc | |
| common | |
| FbcExtensionTypes.h | Includes all SBML types of the fbc package extension in a single header file |
| fbcfwd.h | Implementation of the fbcfwd class |
| extension | |
| FbcExtension.cpp | Implementation of FbcExtension, the core module of fbc package |
| FbcExtension.h | Definition of FbcExtension, the core module of fbc package |
| FbcModelPlugin.cpp | Implementation of FbcModelPlugin, the plugin class of the fbc package for the Model element |
| FbcModelPlugin.h | Definition of FbcModelPlugin, the plugin class of fbc package for the Model element |
| FbcReactionPlugin.cpp | Implementation of the FbcReactionPlugin class |
| FbcReactionPlugin.h | Implementation of the FbcReactionPlugin class |
| FbcSBasePlugin.cpp | Implementation of the FbcSBasePlugin class |
| FbcSBasePlugin.h | Definition of the FbcSBasePlugin class |
| FbcSBMLDocumentPlugin.cpp | Implementation of the FbcSBMLDocumentPlugin class |
| FbcSBMLDocumentPlugin.h | Implementation of the FbcSBMLDocumentPlugin class |
| FbcSpeciesPlugin.cpp | Implementation of FbcSpeciesPlugin, the plugin class of the fbc package for the Species element |
| FbcSpeciesPlugin.h | Definition of FbcSpeciesPlugin, the plugin class of the fbc package for the Species element |
| sbml | |
| Association.cpp | Implementation of Association, the contents of a GeneAssociation |
| Association.h | Definition of Association, the contents of a GeneAssociation |
| FbcAnd.cpp | Implementation of the FbcAnd class |
| FbcAnd.h | Implementation of the FbcAnd class |
| FbcAssociation.cpp | Implementation of the FbcAssociation class |
| FbcAssociation.h | Implementation of the FbcAssociation class |
| FbcOr.cpp | Implementation of the FbcOr class |
| FbcOr.h | Implementation of the FbcOr class |
| FluxBound.cpp | Implementation of FluxBound, the SBase derived class of the fbc package |
| FluxBound.h | Definition of FluxBound, the SBase derived class of the fbc package |
| FluxObjective.cpp | Implementation of the FluxObjective class |
| FluxObjective.h | Definition of FluxObjective, the SBase derived class of the fbc package |
| GeneAssociation.cpp | Implementation of GeneAssociation, the SBase derived class of the fbc package |
| GeneAssociation.h | Definition of GeneAssociation, the SBase derived class of the fbc package |
| GeneProduct.cpp | Implementation of the GeneProduct class |
| GeneProduct.h | Implementation of the GeneProduct class |
| GeneProductAssociation.cpp | Implementation of the GeneProductAssociation class |
| GeneProductAssociation.h | Implementation of the GeneProductAssociation class |
| GeneProductRef.cpp | Implementation of the GeneProductRef class |
| GeneProductRef.h | Implementation of the GeneProductRef class |
| KeyValuePair.cpp | Implementation of the KeyValuePair class |
| KeyValuePair.h | Definition of the KeyValuePair class |
| ListOfKeyValuePairs.cpp | Implementation of the ListOfKeyValuePairs class |
| ListOfKeyValuePairs.h | Definition of the ListOfKeyValuePairs class |
| ListOfUserDefinedConstraintComponents.cpp | Implementation of the ListOfUserDefinedConstraintComponents class |
| ListOfUserDefinedConstraintComponents.h | Definition of the ListOfUserDefinedConstraintComponents class |
| ListOfUserDefinedConstraints.cpp | Implementation of the ListOfUserDefinedConstraints class |
| ListOfUserDefinedConstraints.h | Definition of the ListOfUserDefinedConstraints class |
| Objective.cpp | Implementation of the Objective class |
| Objective.h | Definition of Objective, the SBase derived class of the fbc package |
| UserDefinedConstraint.cpp | Implementation of the UserDefinedConstraint class |
| UserDefinedConstraint.h | Definition of the UserDefinedConstraint class |
| UserDefinedConstraintComponent.cpp | Implementation of the UserDefinedConstraintComponent class |
| UserDefinedConstraintComponent.h | Definition of the UserDefinedConstraintComponent class |
| util | |
| CobraToFbcConverter.cpp | Implementation of a cobra 2 fbc converter |
| CobraToFbcConverter.h | Definition of a cobra 2 fbc converter |
| FbcToCobraConverter.cpp | Implementation of a fbc 2 cobra converter |
| FbcToCobraConverter.h | Definition of a fbc 2 cobra converter |
| FbcV1ToV2Converter.cpp | Implementation of a fbc v1 to fbc v2 converter |
| FbcV1ToV2Converter.h | Definition of a fbc v1 to fbc v2 converter |
| FbcV2ToV1Converter.cpp | Implementation of a fbc v2 to fbc v1 converter |
| FbcV2ToV1Converter.h | Definition of a fbc v2 to fbc v1 converter |
| validator | |
| FbcConsistencyValidator.cpp | |
| FbcConsistencyValidator.h | |
| FbcIdentifierConsistencyValidator.cpp | |
| FbcIdentifierConsistencyValidator.h | |
| FbcSBMLError.h | Represents SBML errors and other diagnostics |
| FbcSBMLErrorTable.h | Represents SBML errors and other diagnostics |
| FbcValidator.cpp | Base class for SBML Validators |
| FbcValidator.h | Base class for SBML CompValidators |
| groups | |
| common | |
| GroupsExtensionTypes.h | Definition of GroupsExtensionTypes |
| groupsfwd.h | Definition of groupsfwd |
| extension | |
| GroupsExtension.cpp | Implementation of GroupsExtension |
| GroupsExtension.h | Definition of GroupsExtension |
| GroupsModelPlugin.cpp | Implementation of the GroupsModelPlugin class |
| GroupsModelPlugin.h | Definition of the GroupsModelPlugin class |
| GroupsSBMLDocumentPlugin.cpp | Implementation of the GroupsSBMLDocumentPlugin class |
| GroupsSBMLDocumentPlugin.h | Definition of the GroupsSBMLDocumentPlugin class |
| sbml | |
| Group.cpp | Implementation of the Group class |
| Group.h | Definition of the Group class |
| ListOfGroups.cpp | Implementation of the ListOfGroups class |
| ListOfGroups.h | Definition of the ListOfGroups class |
| ListOfMembers.cpp | Implementation of the ListOfMembers class |
| ListOfMembers.h | Definition of the ListOfMembers class |
| Member.cpp | Implementation of the Member class |
| Member.h | Definition of the Member class |
| validator | |
| GroupsConsistencyValidator.cpp | |
| GroupsConsistencyValidator.h | |
| GroupsIdentifierConsistencyValidator.cpp | |
| GroupsIdentifierConsistencyValidator.h | |
| GroupsSBMLError.h | Definition of the GroupsSBMLError class |
| GroupsSBMLErrorTable.h | Definition of the GroupsSBMLErrorTable class |
| GroupsValidator.cpp | Definition of GroupsValidator |
| GroupsValidator.h | Definition of GroupsValidator |
| layout | |
| common | |
| LayoutExtensionTypes.h | Include all SBML types of layout extension in a single header file |
| layoutfwd.h | C Structure declarations for SBML Layout |
| extension | |
| LayoutExtension.cpp | Implementation of LayoutExtension, the core module of layout package |
| LayoutExtension.h | Definition of LayoutExtension, the core module of layout package |
| LayoutModelPlugin.cpp | Implementation of LayoutModelPlugin, the plugin class of layout package for the Model element |
| LayoutModelPlugin.h | Definition of LayoutModelPlugin, the plugin class of layout package for Model element |
| LayoutSBMLDocumentPlugin.cpp | Implementation of the LayoutSBMLDocumentPlugin class |
| LayoutSBMLDocumentPlugin.h | Implementation of the LayoutSBMLDocumentPlugin class |
| LayoutSpeciesReferencePlugin.cpp | Implementation of LayoutSpeciesReferencePlugin, the plugin object of layout package (Level2) for the SpeciesReference and ModifierSpeciesReference elements |
| LayoutSpeciesReferencePlugin.h | Definition of LayoutSpeciesReferencePlugin, the plugin class of layout package (Level2) for the SpeciesReference and ModifierSpeciesReference elements |
| sbml | |
| BoundingBox.cpp | Implementation of BoundingBox for SBML Layout |
| BoundingBox.h | Definition of BoundingBox for SBML Layout |
| CompartmentGlyph.cpp | Implementation of CompartmentGlyph for SBML Layout |
| CompartmentGlyph.h | Definition of CompartmentGlyph for SBML Layout |
| CubicBezier.cpp | Implementation of CubicBezier for SBML Layout |
| CubicBezier.h | Definition of CubicBezier for SBML Layout |
| Curve.cpp | Implementation of Curve for SBML Layout |
| Curve.h | Definition of Curve for SBML Layout |
| Dimensions.cpp | Implementation of Dimensions for SBML Layout |
| Dimensions.h | Definition of Dimensions for SBML Layout |
| GeneralGlyph.cpp | Implementation of GeneralGlyph for SBML Layout |
| GeneralGlyph.h | Definition of GeneralGlyph for SBML Layout |
| GraphicalObject.cpp | Implementation of GraphicalObject for SBML Layout |
| GraphicalObject.h | Definition of GraphicalObject for SBML Layout |
| Layout.cpp | Implementation of Layout for SBML Layout |
| Layout.h | Definition of Layout for SBML Layout |
| LineSegment.cpp | Implementation of LineSegment for SBML Layout |
| LineSegment.h | Definition of LineSegment for SBML Layout |
| Point.cpp | Implementation of Point for SBML Layout |
| Point.h | Definition of Point for SBML Layout |
| ReactionGlyph.cpp | Implementation of ReactionGlyph for SBML Layout |
| ReactionGlyph.h | Definition of ReactionGlyph for SBML Layout |
| ReferenceGlyph.cpp | Implementation of ReferenceGlyph for SBML Layout |
| ReferenceGlyph.h | Definition of ReferenceGlyph for SBML Layout |
| SpeciesGlyph.cpp | Implementation of SpeciesGlyph for SBML Layout |
| SpeciesGlyph.h | Definition of SpeciesGlyph for SBML Layout |
| SpeciesReferenceGlyph.cpp | Implementation of SpeciesReferenceGlyph for SBML Layout |
| SpeciesReferenceGlyph.h | Definition of SpeciesReferenceGlyph for SBML Layout |
| SpeciesReferenceRole.h | Definition of SpeciesReferenceRole enum for SBML Layout |
| TextGlyph.cpp | Implementation of TextGlyph for SBML Layout |
| TextGlyph.h | Definition of TextGlyph for SBML Layout |
| util | |
| LayoutAnnotation.cpp | Layout annotation I/O |
| LayoutAnnotation.h | Layout annotation I/O |
| LayoutUtilities.cpp | Implementation of some methods used by many of the layout files |
| LayoutUtilities.h | Definition of LayoutUtilities for SBML Layout |
| validator | |
| LayoutConsistencyValidator.cpp | |
| LayoutConsistencyValidator.h | |
| LayoutIdentifierConsistencyValidator.cpp | |
| LayoutIdentifierConsistencyValidator.h | |
| LayoutSBMLError.h | Implementation of the LayoutSBMLError class |
| LayoutSBMLErrorTable.h | |
| LayoutValidator.cpp | Implementation of the LayoutValidator class |
| LayoutValidator.h | Implementation of the LayoutValidator class |
| multi | |
| common | |
| MultiExtensionTypes.h | : Implementation of the MultiExtensionTypes class |
| multifwd.h | : Implementation of the multifwd class |
| extension | |
| MultiASTPlugin.cpp | Implementation of MultiASTPlugin, the plugin class of multi package for the AST element |
| MultiASTPlugin.h | Definition of MultiASTPlugin, the plugin class of multi package for the AST element |
| MultiCompartmentPlugin.cpp | : Implementation of the MultiCompartmentPlugin class |
| MultiCompartmentPlugin.h | : Implementation of the MultiCompartmentPlugin class |
| MultiExtension.cpp | : Implementation of the MultiExtension class |
| MultiExtension.h | : Implementation of the MultiExtension class |
| MultiListOfReactionsPlugin.cpp | : Implementation of the MultiListOfReactionsPlugin class |
| MultiListOfReactionsPlugin.h | : Implementation of the MultiListOfReactionsPlugin class |
| MultiModelPlugin.cpp | : Implementation of the MultiModelPlugin class |
| MultiModelPlugin.h | : Implementation of the MultiModelPlugin class |
| MultiSBMLDocumentPlugin.cpp | : Implementation of the MultiSBMLDocumentPlugin class |
| MultiSBMLDocumentPlugin.h | : Implementation of the MultiSBMLDocumentPlugin class |
| MultiSimpleSpeciesReferencePlugin.cpp | : Implementation of the MultiSimpleSpeciesReferencePlugin class |
| MultiSimpleSpeciesReferencePlugin.h | : Implementation of the MultiSimpleSpeciesReferencePlugin class |
| MultiSpeciesPlugin.cpp | : Implementation of the MultiSpeciesPlugin class |
| MultiSpeciesPlugin.h | : Implementation of the MultiSpeciesPlugin class |
| MultiSpeciesReferencePlugin.cpp | : Implementation of the MultiSpeciesReferencePlugin class |
| MultiSpeciesReferencePlugin.h | : Implementation of the MultiSpeciesReferencePlugin class |
| sbml | |
| BindingSiteSpeciesType.cpp | : Implementation of the BindingSiteSpeciesType class |
| BindingSiteSpeciesType.h | : Implementation of the BindingSiteSpeciesType class |
| CompartmentReference.cpp | : Implementation of the CompartmentReference class |
| CompartmentReference.h | : Implementation of the CompartmentReference class |
| InSpeciesTypeBond.cpp | : Implementation of the InSpeciesTypeBond class |
| InSpeciesTypeBond.h | : Implementation of the InSpeciesTypeBond class |
| IntraSpeciesReaction.cpp | : Implementation of the IntraSpeciesReaction class |
| IntraSpeciesReaction.h | : Implementation of the IntraSpeciesReaction class |
| MultiSpeciesType.cpp | : Implementation of the MultiSpeciesType class |
| MultiSpeciesType.h | : Implementation of the MultiSpeciesType class |
| OutwardBindingSite.cpp | : Implementation of the OutwardBindingSite class |
| OutwardBindingSite.h | : Implementation of the OutwardBindingSite class |
| PossibleSpeciesFeatureValue.cpp | : Implementation of the PossibleSpeciesFeatureValue class |
| PossibleSpeciesFeatureValue.h | : Implementation of the PossibleSpeciesFeatureValue class |
| SpeciesFeature.cpp | : Implementation of the SpeciesFeature class |
| SpeciesFeature.h | : Implementation of the SpeciesFeature class |
| SpeciesFeatureType.cpp | : Implementation of the SpeciesFeatureType class |
| SpeciesFeatureType.h | : Implementation of the SpeciesFeatureType class |
| SpeciesFeatureValue.cpp | : Implementation of the SpeciesFeatureValue class |
| SpeciesFeatureValue.h | : Implementation of the SpeciesFeatureValue class |
| SpeciesTypeComponentIndex.cpp | : Implementation of the SpeciesTypeComponentIndex class |
| SpeciesTypeComponentIndex.h | : Implementation of the SpeciesTypeComponentIndex class |
| SpeciesTypeComponentMapInProduct.cpp | : Implementation of the SpeciesTypeComponentMapInProduct class |
| SpeciesTypeComponentMapInProduct.h | : Implementation of the SpeciesTypeComponentMapInProduct class |
| SpeciesTypeInstance.cpp | : Implementation of the SpeciesTypeInstance class |
| SpeciesTypeInstance.h | : Implementation of the SpeciesTypeInstance class |
| SubListOfSpeciesFeatures.cpp | : Implementation of the SubListOfSpeciesFeatures class |
| SubListOfSpeciesFeatures.h | : Implementation of the SubListOfSpeciesFeatures class |
| validator | |
| MultiConsistencyValidator.cpp | |
| MultiConsistencyValidator.h | |
| MultiIdentifierConsistencyValidator.cpp | |
| MultiIdentifierConsistencyValidator.h | |
| MultiMathMLConsistencyValidator.cpp | |
| MultiMathMLConsistencyValidator.h | |
| MultiSBMLError.h | : Implementation of the MultiSBMLError class |
| MultiSBMLErrorTable.h | : Implementation of the MultiSBMLErrorTable class |
| MultiValidator.cpp | : Implementation of the MultiValidator class |
| MultiValidator.h | : Implementation of the MultiValidator class |
| qual | |
| common | |
| QualExtensionTypes.h | Include all SBML types of qual extension in a single header file |
| qualfwd.h | SBML Qual C structure declarations |
| extension | |
| QualExtension.cpp | Implementation of QualExtension, the core module of qual package |
| QualExtension.h | Definition of QualExtension, the core module of qual package |
| QualModelPlugin.cpp | Implementation of QualModelPlugin, the plugin class of qual package for the Model element |
| QualModelPlugin.h | Definition of QualModelPlugin, the plugin class of qual package for the Model element |
| QualSBMLDocumentPlugin.cpp | Implementation of QualSBMLDocumentPlugin, the plugin class of qual package for the SBase element |
| QualSBMLDocumentPlugin.h | Implementation of the QualSBMLDocumentPlugin class |
| sbml | |
| DefaultTerm.cpp | Implementation of the DefaultTerm class |
| DefaultTerm.h | Implementation of the DefaultTerm class |
| FunctionTerm.cpp | Implementation of the FunctionTerm class |
| FunctionTerm.h | Implementation of the FunctionTerm class |
| Input.cpp | Implementation of the Input class |
| Input.h | Implementation of the Input class |
| Output.cpp | Implementation of the Output class |
| Output.h | Implementation of the Output class |
| QualitativeSpecies.cpp | Implementation of the QualitativeSpecies class |
| QualitativeSpecies.h | Implementation of the QualitativeSpecies class |
| Transition.cpp | Implementation of the Transition class |
| Transition.h | Implementation of the Transition class |
| validator | |
| QualConsistencyValidator.cpp | |
| QualConsistencyValidator.h | |
| QualIdentifierConsistencyValidator.cpp | |
| QualIdentifierConsistencyValidator.h | |
| QualMathConsistencyValidator.cpp | |
| QualMathConsistencyValidator.h | |
| QualSBMLError.h | Represents SBML errors and other diagnostics |
| QualSBMLErrorTable.h | Represents SBML errors and other diagnostics |
| QualValidator.cpp | Base class for SBML Validators |
| QualValidator.h | Implementation of the QualValidator class |
| render | |
| common | |
| RenderExtensionTypes.h | Definition of RenderExtensionTypes |
| renderfwd.h | Definition of renderfwd |
| extension | |
| RenderExtension.cpp | Implementation of RenderExtension, the core module of the render package |
| RenderExtension.h | Definition of RenderExtension, the core module of the render package |
| RenderGraphicalObjectPlugin.cpp | Implementation of RenderGraphicalObjectPlugin, the plugin class of the render package for the GraphicalObject element |
| RenderGraphicalObjectPlugin.h | Definition of RenderGraphicalObjectPlugin, the plugin class of the render package for the GraphicalObject element |
| RenderLayoutPlugin.cpp | Implementation of RenderLayoutPlugin, the plugin class of the fbc package for the Model element |
| RenderLayoutPlugin.h | Definition of RenderLayoutPlugin, the plugin class of fbc package for the Model element |
| RenderListOfLayoutsPlugin.cpp | Implementation of RenderListOfLayoutsPlugin, the plugin class of the fbc package for the Model element |
| RenderListOfLayoutsPlugin.h | Definition of RenderListOfLayoutsPlugin, the plugin class of fbc package for the Model element |
| RenderSBMLDocumentPlugin.cpp | Implementation of the RenderSBMLDocumentPlugin class |
| RenderSBMLDocumentPlugin.h | Definition of the RenderSBMLDocumentPlugin class |
| sbml | |
| ColorDefinition.cpp | Implementation of the ColorDefinition class |
| ColorDefinition.h | Definition of the ColorDefinition class |
| DefaultValues.cpp | Implementation of the DefaultValues class |
| DefaultValues.h | Definition of the DefaultValues class |
| Ellipse.cpp | Implementation of the Ellipse class |
| Ellipse.h | Definition of the Ellipse class |
| GlobalRenderInformation.cpp | Class for the storage of global render information |
| GlobalRenderInformation.h | Definition of the GlobalRenderInformation class |
| GlobalStyle.cpp | Implementation of the GlobalStyle class |
| GlobalStyle.h | Definition of the GlobalStyle class |
| GradientBase.cpp | Abstract base class for gradient objects |
| GradientBase.h | Abstract base class for gradient definitions |
| GradientStop.cpp | Class representing a stop in a gradient definition |
| GradientStop.h | Class for representing a stop in a gradient definition |
| GraphicalPrimitive1D.cpp | Abstract base class for graphical 1D objects |
| GraphicalPrimitive1D.h | Definition of the GraphicalPrimitive1D class |
| GraphicalPrimitive2D.cpp | Implementation of the GraphicalPrimitive2D class |
| GraphicalPrimitive2D.h | Definition of the GraphicalPrimitive2D class |
| Image.cpp | Implementation of the Image class |
| Image.h | Definition of the Image class |
| LinearGradient.cpp | Implementation of the LinearGradient class |
| LinearGradient.h | Definition of the LinearGradient class |
| LineEnding.cpp | Class representing line endings,e.g |
| LineEnding.h | Class representing line endings, e.g |
| ListOfColorDefinitions.cpp | Implementation of the ListOfColorDefinitions class |
| ListOfColorDefinitions.h | Definition of the ListOfColorDefinitions class |
| ListOfCurveElements.cpp | Storage class for curve elements |
| ListOfCurveElements.h | Definition of the ListOfCurveElements class |
| ListOfDrawables.cpp | Implementation of the ListOfDrawables class |
| ListOfDrawables.h | Definition of the ListOfDrawables class |
| ListOfGlobalRenderInformation.cpp | Implementation of the ListOfGlobalRenderInformation class |
| ListOfGlobalRenderInformation.h | Definition of the ListOfGlobalRenderInformation class |
| ListOfGlobalStyles.cpp | Implementation of the ListOfGlobalStyles class |
| ListOfGlobalStyles.h | Definition of the ListOfGlobalStyles class |
| ListOfGradientDefinitions.cpp | Implementation of the ListOfGradientDefinitions class |
| ListOfGradientDefinitions.h | Definition of the ListOfGradientDefinitions class |
| ListOfGradientStops.cpp | Implementation of the ListOfGradientStops class |
| ListOfGradientStops.h | Definition of the ListOfGradientStops class |
| ListOfLineEndings.cpp | Implementation of the ListOfLineEndings class |
| ListOfLineEndings.h | Definition of the ListOfLineEndings class |
| ListOfLocalRenderInformation.cpp | Implementation of the ListOfLocalRenderInformation class |
| ListOfLocalRenderInformation.h | Definition of the ListOfLocalRenderInformation class |
| ListOfLocalStyles.cpp | Implementation of the ListOfLocalStyles class |
| ListOfLocalStyles.h | Definition of the ListOfLocalStyles class |
| LocalRenderInformation.cpp | Implementation of the LocalRenderInformation class |
| LocalRenderInformation.h | Definition of the LocalRenderInformation class |
| LocalStyle.cpp | Class for representing a local style |
| LocalStyle.h | Definition of the LocalStyle class |
| Polygon.cpp | Implementation of the Polygon class |
| Polygon.h | Class representing a polygon |
| RadialGradient.cpp | Implementation of the RadialGradient class |
| RadialGradient.h | Definition of the RadialGradient class |
| Rectangle.cpp | Implementation of the Rectangle class |
| Rectangle.h | Definition of the Rectangle class |
| RelAbsVector.cpp | Class for representing coordinates that can have a relative and an absolute part |
| RelAbsVector.h | Definition of the RelAbsVector class |
| RenderCubicBezier.cpp | Implementation of the RenderCubicBezier class |
| RenderCubicBezier.h | Definition of the RenderCubicBezier class |
| RenderCurve.cpp | Implementation of the RenderCurve class |
| RenderCurve.h | Definition of the RenderCurve class |
| RenderGroup.cpp | Implementation of the RenderGroup class |
| RenderGroup.h | Definition of the RenderGroup class |
| RenderInformationBase.cpp | Implementation of the RenderInformationBase class |
| RenderInformationBase.h | Definition of the RenderInformationBase class |
| RenderPoint.cpp | Implementation of the RenderPoint class |
| RenderPoint.h | Definition of the RenderPoint class |
| Style.cpp | Implementation of the Style class |
| Style.h | Definition of the Style class |
| Text.cpp | Implementation of the Text class |
| Text.h | Definition of the Text class |
| Transformation.cpp | Class representing a 3D affine transformation |
| Transformation.h | Abstract class for representing 3D affine transformations |
| Transformation2D.cpp | Class representing a 2D affine transformation |
| Transformation2D.h | Abstract base class for representing 2D affine transformations |
| util | |
| RenderLayoutConverter.cpp | Simple converter to convert Layout + Render from l2 to L3 and vice versa |
| RenderLayoutConverter.h | Simple converter to convert Layout + Render from l2 to L3 and vice versa |
| RenderUtilities.cpp | Implementation of RenderUtilities, a class of utility functions for the render package |
| RenderUtilities.h | Definition of RenderUtilities, a class of utility functions for the render package |
| validator | |
| RenderConsistencyValidator.cpp | |
| RenderConsistencyValidator.h | |
| RenderIdentifierConsistencyValidator.cpp | |
| RenderIdentifierConsistencyValidator.h | |
| RenderSBMLError.h | Definition of the RenderSBMLError class |
| RenderSBMLErrorTable.h | Definition of the RenderSBMLErrorTable class |
| RenderValidator.cpp | Definition of RenderValidator |
| RenderValidator.h | Definition of RenderValidator |
| spatial | |
| common | |
| CompressionUtil.cpp | Functions useful for various compression algorithms |
| CompressionUtil.h | Functions useful for various compression algorithms |
| SpatialExtensionTypes.h | Definition of SpatialExtensionTypes |
| spatialfwd.h | Definition of spatialfwd |
| extension | |
| SpatialCompartmentPlugin.cpp | Implementation of the SpatialCompartmentPlugin class |
| SpatialCompartmentPlugin.h | Definition of the SpatialCompartmentPlugin class |
| SpatialExtension.cpp | Implementation of SpatialExtension |
| SpatialExtension.h | Definition of SpatialExtension |
| SpatialModelPlugin.cpp | Implementation of the SpatialModelPlugin class |
| SpatialModelPlugin.h | Definition of the SpatialModelPlugin class |
| SpatialParameterPlugin.cpp | Implementation of the SpatialParameterPlugin class |
| SpatialParameterPlugin.h | Definition of the SpatialParameterPlugin class |
| SpatialReactionPlugin.cpp | Implementation of the SpatialReactionPlugin class |
| SpatialReactionPlugin.h | Definition of the SpatialReactionPlugin class |
| SpatialSBMLDocumentPlugin.cpp | Implementation of the SpatialSBMLDocumentPlugin class |
| SpatialSBMLDocumentPlugin.h | Definition of the SpatialSBMLDocumentPlugin class |
| SpatialSpeciesPlugin.cpp | Implementation of the SpatialSpeciesPlugin class |
| SpatialSpeciesPlugin.h | Definition of the SpatialSpeciesPlugin class |
| sbml | |
| AdjacentDomains.cpp | Implementation of the AdjacentDomains class |
| AdjacentDomains.h | Definition of the AdjacentDomains class |
| AdvectionCoefficient.cpp | Implementation of the AdvectionCoefficient class |
| AdvectionCoefficient.h | Definition of the AdvectionCoefficient class |
| AnalyticGeometry.cpp | Implementation of the AnalyticGeometry class |
| AnalyticGeometry.h | Definition of the AnalyticGeometry class |
| AnalyticVolume.cpp | Implementation of the AnalyticVolume class |
| AnalyticVolume.h | Definition of the AnalyticVolume class |
| Boundary.cpp | Implementation of the Boundary class |
| Boundary.h | Definition of the Boundary class |
| BoundaryCondition.cpp | Implementation of the BoundaryCondition class |
| BoundaryCondition.h | Definition of the BoundaryCondition class |
| CompartmentMapping.cpp | Implementation of the CompartmentMapping class |
| CompartmentMapping.h | Definition of the CompartmentMapping class |
| CoordinateComponent.cpp | Implementation of the CoordinateComponent class |
| CoordinateComponent.h | Definition of the CoordinateComponent class |
| CSGeometry.cpp | Implementation of the CSGeometry class |
| CSGeometry.h | Definition of the CSGeometry class |
| CSGHomogeneousTransformation.cpp | Implementation of the CSGHomogeneousTransformation class |
| CSGHomogeneousTransformation.h | Definition of the CSGHomogeneousTransformation class |
| CSGNode.cpp | Implementation of the CSGNode class |
| CSGNode.h | Definition of the CSGNode class |
| CSGObject.cpp | Implementation of the CSGObject class |
| CSGObject.h | Definition of the CSGObject class |
| CSGPrimitive.cpp | Implementation of the CSGPrimitive class |
| CSGPrimitive.h | Definition of the CSGPrimitive class |
| CSGRotation.cpp | Implementation of the CSGRotation class |
| CSGRotation.h | Definition of the CSGRotation class |
| CSGScale.cpp | Implementation of the CSGScale class |
| CSGScale.h | Definition of the CSGScale class |
| CSGSetOperator.cpp | Implementation of the CSGSetOperator class |
| CSGSetOperator.h | Definition of the CSGSetOperator class |
| CSGTransformation.cpp | Implementation of the CSGTransformation class |
| CSGTransformation.h | Definition of the CSGTransformation class |
| CSGTranslation.cpp | Implementation of the CSGTranslation class |
| CSGTranslation.h | Definition of the CSGTranslation class |
| DiffusionCoefficient.cpp | Implementation of the DiffusionCoefficient class |
| DiffusionCoefficient.h | Definition of the DiffusionCoefficient class |
| Domain.cpp | Implementation of the Domain class |
| Domain.h | Definition of the Domain class |
| DomainType.cpp | Implementation of the DomainType class |
| DomainType.h | Definition of the DomainType class |
| Geometry.cpp | Implementation of the Geometry class |
| Geometry.h | Definition of the Geometry class |
| GeometryDefinition.cpp | Implementation of the GeometryDefinition class |
| GeometryDefinition.h | Definition of the GeometryDefinition class |
| InteriorPoint.cpp | Implementation of the InteriorPoint class |
| InteriorPoint.h | Definition of the InteriorPoint class |
| ListOfAdjacentDomains.cpp | Implementation of the ListOfAdjacentDomains class |
| ListOfAdjacentDomains.h | Definition of the ListOfAdjacentDomains class |
| ListOfAnalyticVolumes.cpp | Implementation of the ListOfAnalyticVolumes class |
| ListOfAnalyticVolumes.h | Definition of the ListOfAnalyticVolumes class |
| ListOfCoordinateComponents.cpp | Implementation of the ListOfCoordinateComponents class |
| ListOfCoordinateComponents.h | Definition of the ListOfCoordinateComponents class |
| ListOfCSGNodes.cpp | Implementation of the ListOfCSGNodes class |
| ListOfCSGNodes.h | Definition of the ListOfCSGNodes class |
| ListOfCSGObjects.cpp | Implementation of the ListOfCSGObjects class |
| ListOfCSGObjects.h | Definition of the ListOfCSGObjects class |
| ListOfDomains.cpp | Implementation of the ListOfDomains class |
| ListOfDomains.h | Definition of the ListOfDomains class |
| ListOfDomainTypes.cpp | Implementation of the ListOfDomainTypes class |
| ListOfDomainTypes.h | Definition of the ListOfDomainTypes class |
| ListOfGeometryDefinitions.cpp | Implementation of the ListOfGeometryDefinitions class |
| ListOfGeometryDefinitions.h | Definition of the ListOfGeometryDefinitions class |
| ListOfInteriorPoints.cpp | Implementation of the ListOfInteriorPoints class |
| ListOfInteriorPoints.h | Definition of the ListOfInteriorPoints class |
| ListOfOrdinalMappings.cpp | Implementation of the ListOfOrdinalMappings class |
| ListOfOrdinalMappings.h | Definition of the ListOfOrdinalMappings class |
| ListOfParametricObjects.cpp | Implementation of the ListOfParametricObjects class |
| ListOfParametricObjects.h | Definition of the ListOfParametricObjects class |
| ListOfSampledFields.cpp | Implementation of the ListOfSampledFields class |
| ListOfSampledFields.h | Definition of the ListOfSampledFields class |
| ListOfSampledVolumes.cpp | Implementation of the ListOfSampledVolumes class |
| ListOfSampledVolumes.h | Definition of the ListOfSampledVolumes class |
| MixedGeometry.cpp | Implementation of the MixedGeometry class |
| MixedGeometry.h | Definition of the MixedGeometry class |
| OrdinalMapping.cpp | Implementation of the OrdinalMapping class |
| OrdinalMapping.h | Definition of the OrdinalMapping class |
| ParametricGeometry.cpp | Implementation of the ParametricGeometry class |
| ParametricGeometry.h | Definition of the ParametricGeometry class |
| ParametricObject.cpp | Implementation of the ParametricObject class |
| ParametricObject.h | Definition of the ParametricObject class |
| SampledField.cpp | Implementation of the SampledField class |
| SampledField.h | Definition of the SampledField class |
| SampledFieldGeometry.cpp | Implementation of the SampledFieldGeometry class |
| SampledFieldGeometry.h | Definition of the SampledFieldGeometry class |
| SampledVolume.cpp | Implementation of the SampledVolume class |
| SampledVolume.h | Definition of the SampledVolume class |
| SpatialPoints.cpp | Implementation of the SpatialPoints class |
| SpatialPoints.h | Definition of the SpatialPoints class |
| SpatialSymbolReference.cpp | Implementation of the SpatialSymbolReference class |
| SpatialSymbolReference.h | Definition of the SpatialSymbolReference class |
| TransformationComponent.cpp | Implementation of the TransformationComponent class |
| TransformationComponent.h | Definition of the TransformationComponent class |
| validator | |
| SpatialCompartmentMappingUnitSizesCheck.cpp | |
| SpatialCompartmentMappingUnitSizesCheck.h | |
| SpatialConsistencyValidator.cpp | |
| SpatialConsistencyValidator.h | |
| SpatialIdentifierConsistencyValidator.cpp | |
| SpatialIdentifierConsistencyValidator.h | |
| SpatialOrdinalMappingGeometryDefinitionCheck.cpp | |
| SpatialOrdinalMappingGeometryDefinitionCheck.h | |
| SpatialSampledVolumeRangeOverlapCheck.cpp | |
| SpatialSampledVolumeRangeOverlapCheck.h | |
| SpatialSampledVolumeValueNotInRangeCheck.cpp | |
| SpatialSampledVolumeValueNotInRangeCheck.h | |
| SpatialSBMLError.h | Definition of the SpatialSBMLError class |
| SpatialSBMLErrorTable.h | Definition of the SpatialSBMLErrorTable class |
| SpatialSpatialSymbolReferenceUniqueRefCheck.cpp | |
| SpatialSpatialSymbolReferenceUniqueRefCheck.h | |
| SpatialUniqueAdvectionCoefficientsCheck.cpp | |
| SpatialUniqueAdvectionCoefficientsCheck.h | |
| SpatialUniqueAnalyticVolumeOrdinalsCheck.cpp | |
| SpatialUniqueAnalyticVolumeOrdinalsCheck.h | |
| SpatialUniqueBoundaryConditionsCheck.cpp | |
| SpatialUniqueBoundaryConditionsCheck.h | |
| SpatialUniqueCSGObjectOrdinalsCheck.cpp | |
| SpatialUniqueCSGObjectOrdinalsCheck.h | |
| SpatialUniqueDiffusionCoefficientsCheck.cpp | |
| SpatialUniqueDiffusionCoefficientsCheck.h | |
| SpatialUniqueOrdinalMappingOrdinalsCheck.cpp | |
| SpatialUniqueOrdinalMappingOrdinalsCheck.h | |
| SpatialUniqueSampledVolumeValueCheck.cpp | |
| SpatialUniqueSampledVolumeValueCheck.h | |
| SpatialValidator.cpp | Definition of SpatialValidator |
| SpatialValidator.h | Definition of SpatialValidator |
| util | |
| CallbackRegistry.cpp | |
| CallbackRegistry.h | |
| ElementFilter.cpp | |
| ElementFilter.h | Base class of element filters |
| IdentifierTransformer.cpp | |
| IdentifierTransformer.h | |
| IdFilter.cpp | |
| IdFilter.h | |
| IdList.cpp | |
| IdList.h | |
| List.cpp | Simple, generic list class |
| List.h | Simple, generic list utility class |
| MathFilter.cpp | |
| MathFilter.h | |
| memory.c | |
| memory.h | |
| MetaIdFilter.cpp | |
| MetaIdFilter.h | |
| PrefixTransformer.cpp | |
| PrefixTransformer.h | |
| Stack.c | |
| Stack.h | |
| StringBuffer.c | |
| StringBuffer.h | |
| util.cpp | Utility functions |
| util.h | Utility functions |
| validator | |
| ConsistencyValidator.cpp | |
| ConsistencyValidator.h | |
| ConstraintMacros.h | Defines the validator constraint "language" |
| IdentifierConsistencyValidator.cpp | |
| IdentifierConsistencyValidator.h | |
| InternalConsistencyValidator.cpp | |
| InternalConsistencyValidator.h | |
| L1CompatibilityValidator.cpp | |
| L1CompatibilityValidator.h | |
| L2v1CompatibilityValidator.cpp | |
| L2v1CompatibilityValidator.h | |
| L2v2CompatibilityValidator.cpp | |
| L2v2CompatibilityValidator.h | |
| L2v3CompatibilityValidator.cpp | |
| L2v3CompatibilityValidator.h | |
| L2v4CompatibilityValidator.cpp | |
| L2v4CompatibilityValidator.h | |
| L3v1CompatibilityValidator.cpp | |
| L3v1CompatibilityValidator.h | |
| L3v2CompatibilityValidator.cpp | |
| L3v2CompatibilityValidator.h | |
| MathMLConsistencyValidator.cpp | |
| MathMLConsistencyValidator.h | |
| ModelingPracticeValidator.cpp | |
| ModelingPracticeValidator.h | |
| OverdeterminedValidator.cpp | |
| OverdeterminedValidator.h | |
| SBMLExternalValidator.cpp | |
| SBMLExternalValidator.h | |
| SBMLInternalValidator.cpp | Implementation of SBMLInternalValidator, the validator for all internal validation performed by libSBML |
| SBMLInternalValidator.h | Definition of SBMLInternalValidator, the validator for all internal validation performed by libSBML |
| SBMLValidator.cpp | Implementation of SBMLValidator, the base class for user callable SBML validators |
| SBMLValidator.h | Definition of SBMLValidator, the base class for user callable SBML validators |
| SBOConsistencyValidator.cpp | |
| SBOConsistencyValidator.h | |
| StrictUnitConsistencyValidator.cpp | |
| StrictUnitConsistencyValidator.h | |
| UnitConsistencyValidator.cpp | |
| UnitConsistencyValidator.h | |
| Validator.cpp | Base class for SBML Validators |
| Validator.h | Base class for SBML Validators |
| VConstraint.cpp | Base class for all SBML Validator Constraints |
| VConstraint.h | Base class for all SBML Validator Constraints |
| xml | |
| ExpatAttributes.cpp | |
| ExpatAttributes.h | |
| ExpatHandler.cpp | |
| ExpatHandler.h | |
| ExpatParser.cpp | |
| ExpatParser.h | |
| LibXMLAttributes.cpp | |
| LibXMLAttributes.h | |
| LibXMLHandler.cpp | |
| LibXMLHandler.h | |
| LibXMLNamespaces.cpp | Extracts XML namespace declarations from LibXML prefix/URI pairs |
| LibXMLNamespaces.h | Extracts XML namespace declarations from LibXML prefix/URI pairs |
| LibXMLParser.cpp | |
| LibXMLParser.h | |
| LibXMLTranscode.cpp | |
| LibXMLTranscode.h | |
| XercesAttributes.cpp | |
| XercesAttributes.h | |
| XercesHandler.cpp | |
| XercesHandler.h | |
| XercesNamespaces.cpp | |
| XercesNamespaces.h | |
| XercesParser.cpp | |
| XercesParser.h | |
| XercesTranscode.cpp | |
| XercesTranscode.h | |
| XMLAttributes.cpp | XMLAttributes are a list of name/value pairs for XMLElements |
| XMLAttributes.h | XMLAttributes are a list of name/value pairs for XML elements |
| XMLBuffer.cpp | |
| XMLBuffer.h | |
| XMLConstructorException.cpp | XMLConstructorException an exception thrown by XML classes |
| XMLConstructorException.h | XMLConstructorException an exception thrown by XML classes |
| XMLError.cpp | Represents errors (and messages) encountered during an XML parse |
| XMLError.h | Represents errors (and messages) encountered during an XML parse |
| XMLErrorLog.cpp | Stores errors (and messages) encountered while processing XML |
| XMLErrorLog.h | Stores errors (and messages) encountered while processing XML |
| XMLExtern.h | Defines LIBLAX_EXTERN |
| XMLFileBuffer.cpp | |
| XMLFileBuffer.h | |
| XMLHandler.cpp | |
| XMLHandler.h | |
| XMLInputStream.cpp | |
| XMLInputStream.h | XMLInputStream |
| XMLLogOverride.cpp | Utility class implementing a temporary override the severity on error logs |
| XMLLogOverride.h | Utility class implementing a temporary override the severity on error logs |
| XMLMemoryBuffer.cpp | |
| XMLMemoryBuffer.h | |
| XMLNamespaces.cpp | A list of XMLNamespace declarations (URI/prefix pairs) |
| XMLNamespaces.h | A list of XMLNamespace declarations (URI/prefix pairs) |
| XMLNode.cpp | A node in an XML document tree |
| XMLNode.h | Class definition of XMLNode, a node in an XML document tree |
| XMLOutputStream.cpp | |
| XMLOutputStream.h | XMLOutputStream |
| XMLParser.cpp | |
| XMLParser.h | |
| XMLToken.cpp | A unit of XML syntax, either an XML element or text |
| XMLToken.h | A unit of XML syntax, either an XML element or text |
| XMLTokenizer.cpp | |
| XMLTokenizer.h | |
| XMLTriple.cpp | Stores an XML namespace triple |
| XMLTriple.h | Stores an XML namespace triple |
| AlgebraicRule.cpp | Implementations of AlgebraicRule |
| AlgebraicRule.h | Definitions of AlgebraicRule |
| AssignmentRule.cpp | Implementations of AssignmentRule |
| AssignmentRule.h | Definitions of AssignmentRule |
| Compartment.cpp | Implementations of Compartment and ListOfCompartments |
| Compartment.h | Definitions of Compartment and ListOfCompartments |
| CompartmentType.cpp | Implementation of CompartmentType and ListOfCompartmentTypes |
| CompartmentType.h | Definitions of CompartmentType and ListOfCompartmentTypes |
| Constraint.cpp | Implementations of Constraint and ListOfConstraints |
| Constraint.h | Definitions of Constraint and ListOfConstraints |
| Delay.cpp | Implementation of Delay |
| Delay.h | Definition of Delay |
| Event.cpp | Implementations of Event and ListOfEvents |
| Event.h | Definitions of Event and ListOfEvents |
| EventAssignment.cpp | Implementation of EventAssignment |
| EventAssignment.h | Definition of EventAssignment and ListOfEventAssignments |
| ExpectedAttributes.cpp | Implementation of ExpectedAttributes, the class allowing the specification of attributes to expect |
| ExpectedAttributes.h | Definition of ExpectedAttributes, the class allowing the specification of attributes to expect |
| FunctionDefinition.cpp | Implementation of FunctionDefinition and ListOfFunctionDefinitions |
| FunctionDefinition.h | Definitions of FunctionDefinition and ListOfFunctionDefinitions |
| InitialAssignment.cpp | Implementation of InitialAssignment and ListOfInitialAssignments |
| InitialAssignment.h | Definitions of InitialAssignment and ListOfInitialAssignments |
| KineticLaw.cpp | Implementation of KineticLaw |
| KineticLaw.h | Definition of KineticLaw |
| ListOf.cpp | Wraps List and inherits from SBase |
| ListOf.h | |
| LocalParameter.cpp | Implementations of LocalLocalParameter and ListOfLocalLocalParameters |
| LocalParameter.h | Definitions of LocalParameter and ListOfLocalParameters |
| Model.cpp | Implementation of Model |
| Model.h | Definition of Model |
| ModifierSpeciesReference.cpp | Implementation of ModifierSpeciesReference |
| ModifierSpeciesReference.h | Definitions of ModifierSpeciesReference |
| Parameter.cpp | Implementations of Parameter and ListOfParameters |
| Parameter.h | Definitions of Parameter and ListOfParameters |
| Priority.cpp | Implementation of Priority |
| Priority.h | Definition of Priority |
| RateRule.cpp | Implementations of RateRule |
| RateRule.h | Definitions of RateRule |
| Reaction.cpp | Implementations of Reaction and ListOfReactions |
| Reaction.h | Definitions of Reaction and ListOfReactions |
| Rule.cpp | Implementations of Rule and ListOfRules |
| Rule.h | Definitions of Rule and ListOfRules |
| SBase.cpp | Implementation of SBase, the base object of all SBML objects |
| SBase.h | Definition of SBase, the base object of all SBML objects |
| SBMLConstructorException.cpp | Implementation of SBMLConstructorException, the exception class for constructor exceptions |
| SBMLConstructorException.h | Definition of SBMLConstructorException, the exception class for constructor exceptions |
| SBMLConvert.cpp | Performs conversion between SBML levels |
| SBMLDocument.cpp | Implementation of the top-level container for an SBML Model and associated data |
| SBMLDocument.h | Top-level container for an SBML Model and associated data |
| SBMLError.cpp | Represents SBML errors and other diagnostics |
| SBMLError.h | Represents SBML errors and other diagnostics |
| SBMLErrorLog.cpp | Stores errors (and messages) encountered while processing SBML |
| SBMLErrorLog.h | Stores errors (and messages) encountered while processing SBML |
| SBMLErrorTable.h | Represents SBML errors and other diagnostics |
| SBMLNamespaces.cpp | SBMLNamespaces class to store level/version and namespace |
| SBMLNamespaces.h | SBMLNamespaces class to store level/version and namespace |
| SBMLReader.cpp | Reads an SBML Document into memory |
| SBMLReader.h | Reads an SBML Document into memory |
| SBMLTransforms.cpp | Transform functions |
| SBMLTransforms.h | |
| SBMLTypeCodes.cpp | Enumeration to identify SBML objects at runtime |
| SBMLTypeCodes.h | Enumeration to identify SBML objects at runtime |
| SBMLTypes.h | Include all SBML types in a single header file |
| SBMLVisitor.cpp | Visitor Design Pattern for the SBML object tree |
| SBMLVisitor.h | Visitor Design Pattern for the SBML object tree |
| SBMLWriter.cpp | Writes an SBML Document to file or in-memory string |
| SBMLWriter.h | Writes an SBML Document to file or in-memory string |
| SBO.cpp | SBO utility functions |
| SBO.h | SBO utility Function |
| SimpleSpeciesReference.cpp | Implementation of SimpleSpeciesReference |
| SimpleSpeciesReference.h | Definitions of SimpleSpeciesReference |
| Species.cpp | Implementations of Species and ListOfSpecies |
| Species.h | Definitions of Species and ListOfSpecies |
| SpeciesReference.cpp | Implementation of SpeciesReference and ListOfSpeciesReferences |
| SpeciesReference.h | Definitions of SpeciesReference and ListOfSpeciesReferences |
| SpeciesType.cpp | Implementation of SpeciesType and ListOfSpeciesTypes |
| SpeciesType.h | Definitions of SpeciesType and ListOfSpeciesType |
| StoichiometryMath.cpp | Implementation of StoichiometryMath |
| StoichiometryMath.h | Definition of StoichiometryMath |
| SyntaxChecker.cpp | Syntax checking functions |
| SyntaxChecker.h | Syntax checking functions |
| Trigger.cpp | Implementation of Trigger |
| Trigger.h | Definition of Trigger |
| Unit.cpp | Implementations of Unit and ListOfUnits |
| Unit.h | Definitions of Unit and ListOfUnits |
| UnitDefinition.cpp | Implementations of SBML's UnitDefinition and ListOfUnitDefinitions |
| UnitDefinition.h | Definitions of UnitDefinition and ListOfUnitDefinitions |
| UnitKind.c | SBML UnitKind enumeration |
| UnitKind.h | Definition of SBML's UnitKind enumeration |