| src | |
| sbml | |
| annotation | |
| CVTerm.cpp | CVTerm_t I/O |
| CVTerm.h | Definition of a CVTerm_t class for adding annotations to a Model_t |
| Date.cpp | Date_t I/O |
| Date.h | Date_t I/O |
| ModelCreator.cpp | ModelCreator_t I/O |
| ModelCreator.h | ModelCreator_t I/O |
| ModelHistory.cpp | ModelHistory_t I/O |
| ModelHistory.h | ModelHistory_t 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 |
| conversion | |
| ConversionOption.cpp | Implementation of ConversionOption_t, the class encapsulating conversion options |
| ConversionOption.h | Definition of ConversionOption_t, the class encapsulating conversion options |
| ConversionProperties.cpp | Implemenentation of ConversionProperties_t, the class encapsulating conversion configuration |
| ConversionProperties.h | Definition of ConversionProperties_t, the class encapsulating conversion configuration |
| ExpressionAnalyser.cpp | Implementation of ExpressionAnalyser_t |
| ExpressionAnalyser.h | Definition of ExpressionAnalyser_t, a class for analysing expressions |
| RegisterConverters.cpp | Registers all available converters |
| SBMLConverter.cpp | Implementation of SBMLConverter_t, the base class of package extensions |
| SBMLConverter.h | Definition of SBMLConverter_t, the base class for SBML conversion |
| SBMLConverterRegister.h | |
| SBMLConverterRegistry.cpp | Implementation of SBMLConverterRegistry_t, a registry of available converters |
| SBMLConverterRegistry.h | Definition of SBMLConverterRegistry_t, a registry of available converters |
| SBMLConverterTypes.h | Definition of SBMLConverterTypes |
| SBMLFunctionDefinitionConverter.cpp | Implementation of SBMLFunctionDefinitionConverter_t, a converter replacing function definitions |
| SBMLFunctionDefinitionConverter.h | Definition of SBMLFunctionDefinitionConverter_t, a converter replacing function definitions |
| SBMLIdConverter.cpp | Implementation of SBMLIdConverter_t, a converter renaming SIds |
| SBMLIdConverter.h | Definition of SBMLIdConverter_t, a converter renaming SIds |
| SBMLInferUnitsConverter.cpp | Implementation of SBMLInferUnitsConverter_t |
| SBMLInferUnitsConverter.h | Definition of SBMLInferUnitsConverter_t, infers units for parameters |
| SBMLInitialAssignmentConverter.cpp | Implementation of SBMLInitialAssignmentConverter_t, a converter inlining initial assignments |
| SBMLInitialAssignmentConverter.h | Definition of SBMLInitialAssignmentConverter_t, a converter inlining function definitions |
| SBMLLevel1Version1Converter.cpp | Implementation of SBMLLevel1Version1Converter_t |
| SBMLLevel1Version1Converter.h | Definition of SBMLLevel1Version1Converter_t |
| SBMLLevelVersionConverter.cpp | Implementation of SBMLLevelVersionConverter_t, the base class of package extensions |
| SBMLLevelVersionConverter.h | Definition of SBMLLevelVersionConverter_t, the base class for SBML conversion |
| SBMLLocalParameterConverter.cpp | Implementation of SBMLLocalParameterConverter_t, a converter replacing local parameters with global ones |
| SBMLLocalParameterConverter.h | Definition of SBMLLocalParameterConverter_t, a converter replacing local parameters with global ones |
| SBMLRateOfConverter.cpp | Implementation of SBMLRateOfConverter_t, a converter changing 'rateOf' into functionDefinition |
| SBMLRateOfConverter.h | Definition of SBMLRateOfConverter_t, a converter changing reactions into rate rules |
| SBMLRateRuleConverter.cpp | Implementation of SBMLRateRuleConverter_t, a converter from raterule to reaction |
| SBMLRateRuleConverter.h | Definition of SBMLRateRuleConverter_t, a converter from raterule to reaction |
| SBMLReactionConverter.cpp | Implementation of SBMLReactionConverter_t, a converter changing reactions into rate rules |
| SBMLReactionConverter.h | Definition of SBMLReactionConverter_t, a converter changing reactions into rate rules |
| SBMLRuleConverter.cpp | Implementation of SBMLRuleConverter_t, a converter sorting rules |
| SBMLRuleConverter.h | Definition of SBMLRuleConverter_t, a converter sorting rules |
| SBMLStripPackageConverter.cpp | Implementation of SBMLStripPackageConverter_t, the base class of package extensions |
| SBMLStripPackageConverter.h | Definition of SBMLStripPackageConverter_t, the base class for SBML conversion |
| SBMLUnitsConverter.cpp | Implementation of SBMLUnitsConverter_t, for converting units to SI |
| SBMLUnitsConverter.h | Definition of SBMLUnitsConverter_t, for converting units to SI |
| extension | |
| ASTBasePlugin.cpp | |
| ASTBasePlugin.h | |
| ISBMLExtensionNamespaces.cpp | |
| ISBMLExtensionNamespaces.h | |
| SBaseExtensionPoint.cpp | Implementation of SBaseExtensionPoint_t |
| SBaseExtensionPoint.h | Definition of SBaseExtensionPoint_t |
| SBasePlugin.cpp | Implementation of SBasePlugin_t, the base class of extension entities plugged in SBase_t derived classes in the SBML Core package |
| SBasePlugin.h | Definition of SBasePlugin_t, the base class of extension entities plugged in SBase_t derived classes in the SBML Core package |
| SBasePluginCreator.h | Template class for SBasePlugin_t-based classes |
| SBasePluginCreatorBase.cpp | Implementation of SBasePluginCreatorBase_t, the base class of SBasePlugin_t creator classes |
| SBasePluginCreatorBase.h | Definition of SBasePluginCreatorBase_t, the base class of SBasePlugin_t creator classes |
| SBMLDocumentPlugin.cpp | Implementation of SBMLDocumentPlugin_t, the derived class of SBasePlugin_t |
| SBMLDocumentPlugin.h | Definition of SBMLDocumentPlugin_t, the derived class of SBasePlugin_t |
| SBMLDocumentPluginNotRequired.cpp | Implementation of SBMLDocumentPluginNotRequired_t, the plugin class of layout package for the Model_t element |
| SBMLDocumentPluginNotRequired.h | Definition of SBMLDocumentPluginNotRequired_t, the plugin class of layout package for the SBMLDocument_t element, whose 'required' attribute must be 'false' |
| SBMLExtension.cpp | Implementation of SBMLExtension_t, the base class of package extensions |
| SBMLExtension.h | Definition of SBMLExtension_t, the core component of SBML package extension |
| SBMLExtensionException.cpp | SBMLExtensionException_t 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_t 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_t, 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_t, a registry of available DefinitionURLs |
| DefinitionURLRegistry.h | Definition of DefinitionURLRegistry_t, 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 |
| extension | |
| CompExtension.cpp | Implementation of CompExtension_t, the core module of comp package |
| CompExtension.h | Definition of CompExtension_t, the core module of comp package |
| CompModelPlugin.cpp | Implementation of CompModelPlugin_t, the plugin class of comp package for the SBase_t element |
| CompModelPlugin.h | Definition of CompModelPlugin_t, the plugin class of comp package for the Model_t element |
| CompSBasePlugin.cpp | Implementation of CompSBasePlugin_t, the plugin class of comp package for the SBase_t element |
| CompSBasePlugin.h | Definition of CompSBasePlugin_t, the plugin class of comp package for the Model_t element |
| CompSBMLDocumentPlugin.cpp | Implementation of CompSBMLDocumentPlugin_t, the plugin class of comp package for the SBase_t element |
| CompSBMLDocumentPlugin.h | Definition of CompSBMLDocumentPlugin_t, the plugin class of comp package for the Model_t element |
| sbml | |
| CompBase.cpp | Implementation of CompBase_t, the base class of extension entities plugged in SBase_t derived classes in the SBML Core package |
| CompBase.h | Definition of CompBase_t, the base class of extension entities plugged in SBase_t derived classes in the SBML Core package |
| Deletion.cpp | Implementation of Deletion_t, the SBaseRef_t derived class of deletions package |
| Deletion.h | Definition of Deletion_t, the SBase_t derived class of deletions package |
| ExternalModelDefinition.cpp | Implementation of ExternalModelDefinition_t, the SBase_t-derived class of the comp package |
| ExternalModelDefinition.h | Definition of ExternalModelDefinition_t, the SBase_t derived class of the comp package |
| ListOfDeletions.cpp | Implementation of ListOfDeletions_t |
| ListOfDeletions.h | Definition of ListOfDeletions_t, the SBase_t derived class of deletions package |
| ListOfExternalModelDefinitions.cpp | Implementation of ListOfExternalModelDefinitions_t |
| ListOfExternalModelDefinitions.h | Definition of ListOfExternalModelDefinitions_t, the SBase_t derived class of the Hierarchial Model Defintions package |
| ListOfModelDefinitions.cpp | Implementation of ListOfModelDefinitions_t from the comp package |
| ListOfModelDefinitions.h | Definition of ListOfModelDefinitions_t, the SBase_t derived class of modelDefinitions package |
| ListOfPorts.cpp | Implementation of ListOfPorts_t |
| ListOfPorts.h | Definition of ListOfPorts_t, the SBase_t derived class of ports package |
| ListOfReplacedElements.cpp | Implementation of ListOfReplacedElements_t from the comp package |
| ListOfReplacedElements.h | Definition of ListOfReplacedElements_t, the SBase_t derived class of replacedElements package |
| ListOfSubmodels.cpp | Implementation of ListOfSubmodels_t |
| ListOfSubmodels.h | Definition of ListOfSubmodels_t, the SBase_t derived class of submodels package |
| ModelDefinition.cpp | Implementation of ModelDefinition_t, the SBase_t-derived class of the comp package |
| ModelDefinition.h | Definition of ModelDefinition_t, the SBase_t derived class of the comp package |
| Port.cpp | Implementation of Port_t, the SBase_t-derived class of the comp package |
| Port.h | Definition of Port_t, the SBase_t derived class of the comp package |
| ReplacedBy.cpp | Implementation of ReplacedBy_t, the SBaseRef_t derived class of the comp package |
| ReplacedBy.h | Definition of ReplacedBy_t, the Replacing_t-derived class of the comp package |
| ReplacedElement.cpp | Implementation of ReplacedElement_t, the SBaseRef_t derived class of replacedElements package |
| ReplacedElement.h | Definition of ReplacedElement_t, the SBase_t derived class of replacedElements package |
| Replacing.cpp | Implementation of Replacing_t, the SBaseRef_t derived class of Replacings package |
| Replacing.h | Definition of Replacing_t, the SBaseRef_t-derived class of the comp package |
| SBaseRef.cpp | Implementation of SBaseRef_t, the SBase_t-derived class of the comp package |
| SBaseRef.h | Definition of SBaseRef_t, the SBase_t derived class of the comp package |
| Submodel.cpp | Implementation of Submodel_t, the SBase_t-derived class of the comp package |
| Submodel.h | Definition of Submodel_t, the SBase_t 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_t, the file system based resolver for SBML Documents |
| SBMLFileResolver.h | A file-based resolver for SBML Documents |
| SBMLResolver.cpp | Implementation of SBMLResolver_t, the base class of package extensions |
| SBMLResolver.h | Definition of SBMLResolver_t, the base class for resolving SBML documents |
| SBMLResolverRegistry.cpp | Implementation of SBMLResolverRegistry_t, a registry of available resolvers |
| SBMLResolverRegistry.h | Definition of SBMLResolverRegistry_t, a registry of available resolvers |
| SBMLUri.cpp | Implementation of SBMLUri_t, the utility class for handling uris |
| SBMLUri.h | Definition of SBMLUri_t, 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 |
| 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_t, the core module of fbc package |
| FbcExtension.h | Definition of FbcExtension_t, the core module of fbc package |
| FbcModelPlugin.cpp | Implementation of FbcModelPlugin_t, the plugin class of the fbc package for the Model_t element |
| FbcModelPlugin.h | Definition of FbcModelPlugin_t, the plugin class of fbc package for the Model_t element |
| FbcReactionPlugin.cpp | Implementation of the FbcReactionPlugin_t class |
| FbcReactionPlugin.h | Implementation of the FbcReactionPlugin_t class |
| FbcSBasePlugin.cpp | Implementation of the FbcSBasePlugin_t class |
| FbcSBasePlugin.h | Definition of the FbcSBasePlugin_t class |
| FbcSBMLDocumentPlugin.cpp | Implementation of the FbcSBMLDocumentPlugin_t class |
| FbcSBMLDocumentPlugin.h | Implementation of the FbcSBMLDocumentPlugin_t class |
| FbcSpeciesPlugin.cpp | Implementation of FbcSpeciesPlugin_t, the plugin class of the fbc package for the Species_t element |
| FbcSpeciesPlugin.h | Definition of FbcSpeciesPlugin_t, the plugin class of the fbc package for the Species_t element |
| sbml | |
| Association.cpp | Implementation of Association_t, the contents of a GeneAssociation_t |
| Association.h | Definition of Association_t, the contents of a GeneAssociation_t |
| FbcAnd.cpp | Implementation of the FbcAnd_t class |
| FbcAnd.h | Implementation of the FbcAnd_t class |
| FbcAssociation.cpp | Implementation of the FbcAssociation_t class |
| FbcAssociation.h | Implementation of the FbcAssociation_t class |
| FbcOr.cpp | Implementation of the FbcOr_t class |
| FbcOr.h | Implementation of the FbcOr_t class |
| FluxBound.cpp | Implementation of FluxBound_t, the SBase_t derived class of the fbc package |
| FluxBound.h | Definition of FluxBound_t, the SBase_t derived class of the fbc package |
| FluxObjective.cpp | Implementation of the FluxObjective_t class |
| FluxObjective.h | Definition of FluxObjective_t, the SBase_t derived class of the fbc package |
| GeneAssociation.cpp | Implementation of GeneAssociation_t, the SBase_t derived class of the fbc package |
| GeneAssociation.h | Definition of GeneAssociation_t, the SBase_t derived class of the fbc package |
| GeneProduct.cpp | Implementation of the GeneProduct_t class |
| GeneProduct.h | Implementation of the GeneProduct_t class |
| GeneProductAssociation.cpp | Implementation of the GeneProductAssociation_t class |
| GeneProductAssociation.h | Implementation of the GeneProductAssociation_t class |
| GeneProductRef.cpp | Implementation of the GeneProductRef_t class |
| GeneProductRef.h | Implementation of the GeneProductRef_t class |
| KeyValuePair.cpp | Implementation of the KeyValuePair_t class |
| KeyValuePair.h | Definition of the KeyValuePair_t class |
| ListOfKeyValuePairs.cpp | Implementation of the ListOfKeyValuePairs_t class |
| ListOfKeyValuePairs.h | Definition of the ListOfKeyValuePairs_t class |
| ListOfUserDefinedConstraintComponents.cpp | Implementation of the ListOfUserDefinedConstraintComponents_t class |
| ListOfUserDefinedConstraintComponents.h | Definition of the ListOfUserDefinedConstraintComponents_t class |
| ListOfUserDefinedConstraints.cpp | Implementation of the ListOfUserDefinedConstraints_t class |
| ListOfUserDefinedConstraints.h | Definition of the ListOfUserDefinedConstraints_t class |
| Objective.cpp | Implementation of the Objective_t class |
| Objective.h | Definition of Objective_t, the SBase_t derived class of the fbc package |
| UserDefinedConstraint.cpp | Implementation of the UserDefinedConstraint_t class |
| UserDefinedConstraint.h | Definition of the UserDefinedConstraint_t class |
| UserDefinedConstraintComponent.cpp | Implementation of the UserDefinedConstraintComponent_t class |
| UserDefinedConstraintComponent.h | Definition of the UserDefinedConstraintComponent_t 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_t |
| GroupsExtension.h | Definition of GroupsExtension_t |
| GroupsModelPlugin.cpp | Implementation of the GroupsModelPlugin_t class |
| GroupsModelPlugin.h | Definition of the GroupsModelPlugin_t class |
| GroupsSBMLDocumentPlugin.cpp | Implementation of the GroupsSBMLDocumentPlugin_t class |
| GroupsSBMLDocumentPlugin.h | Definition of the GroupsSBMLDocumentPlugin_t class |
| sbml | |
| Group.cpp | Implementation of the Group_t class |
| Group.h | Definition of the Group_t class |
| ListOfGroups.cpp | Implementation of the ListOfGroups_t class |
| ListOfGroups.h | Definition of the ListOfGroups_t class |
| ListOfMembers.cpp | Implementation of the ListOfMembers_t class |
| ListOfMembers.h | Definition of the ListOfMembers_t class |
| Member.cpp | Implementation of the Member_t class |
| Member.h | Definition of the Member_t 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_t |
| GroupsValidator.h | Definition of GroupsValidator_t |
| layout | |
| common | |
| LayoutExtensionTypes.h | Include all SBML types of layout extension in a single header file |
| layoutfwd.h | C Structure declarations for SBML Layout_t |
| extension | |
| LayoutExtension.cpp | Implementation of LayoutExtension_t, the core module of layout package |
| LayoutExtension.h | Definition of LayoutExtension_t, the core module of layout package |
| LayoutModelPlugin.cpp | Implementation of LayoutModelPlugin_t, the plugin class of layout package for the Model_t element |
| LayoutModelPlugin.h | Definition of LayoutModelPlugin_t, the plugin class of layout package for Model_t element |
| LayoutSBMLDocumentPlugin.cpp | Implementation of the LayoutSBMLDocumentPlugin_t class |
| LayoutSBMLDocumentPlugin.h | Implementation of the LayoutSBMLDocumentPlugin_t class |
| LayoutSpeciesReferencePlugin.cpp | Implementation of LayoutSpeciesReferencePlugin_t, the plugin object of layout package (Level2) for the SpeciesReference_t and ModifierSpeciesReference_t elements |
| LayoutSpeciesReferencePlugin.h | Definition of LayoutSpeciesReferencePlugin_t, the plugin class of layout package (Level2) for the SpeciesReference_t and ModifierSpeciesReference_t elements |
| sbml | |
| BoundingBox.cpp | Implementation of BoundingBox_t for SBML Layout_t |
| BoundingBox.h | Definition of BoundingBox_t for SBML Layout_t |
| CompartmentGlyph.cpp | Implementation of CompartmentGlyph_t for SBML Layout_t |
| CompartmentGlyph.h | Definition of CompartmentGlyph_t for SBML Layout_t |
| CubicBezier.cpp | Implementation of CubicBezier_t for SBML Layout_t |
| CubicBezier.h | Definition of CubicBezier_t for SBML Layout_t |
| Curve.cpp | Implementation of Curve_t for SBML Layout_t |
| Curve.h | Definition of Curve_t for SBML Layout_t |
| Dimensions.cpp | Implementation of Dimensions_t for SBML Layout_t |
| Dimensions.h | Definition of Dimensions_t for SBML Layout_t |
| GeneralGlyph.cpp | Implementation of GeneralGlyph_t for SBML Layout_t |
| GeneralGlyph.h | Definition of GeneralGlyph_t for SBML Layout_t |
| GraphicalObject.cpp | Implementation of GraphicalObject_t for SBML Layout_t |
| GraphicalObject.h | Definition of GraphicalObject_t for SBML Layout_t |
| Layout.cpp | Implementation of Layout_t for SBML Layout_t |
| Layout.h | Definition of Layout_t for SBML Layout_t |
| LineSegment.cpp | Implementation of LineSegment_t for SBML Layout_t |
| LineSegment.h | Definition of LineSegment_t for SBML Layout_t |
| Point.cpp | Implementation of Point_t for SBML Layout_t |
| Point.h | Definition of Point_t for SBML Layout_t |
| ReactionGlyph.cpp | Implementation of ReactionGlyph_t for SBML Layout_t |
| ReactionGlyph.h | Definition of ReactionGlyph_t for SBML Layout_t |
| ReferenceGlyph.cpp | Implementation of ReferenceGlyph_t for SBML Layout_t |
| ReferenceGlyph.h | Definition of ReferenceGlyph_t for SBML Layout_t |
| SpeciesGlyph.cpp | Implementation of SpeciesGlyph_t for SBML Layout_t |
| SpeciesGlyph.h | Definition of SpeciesGlyph_t for SBML Layout_t |
| SpeciesReferenceGlyph.cpp | Implementation of SpeciesReferenceGlyph_t for SBML Layout_t |
| SpeciesReferenceGlyph.h | Definition of SpeciesReferenceGlyph_t for SBML Layout_t |
| SpeciesReferenceRole.h | Definition of SpeciesReferenceRole enum for SBML Layout_t |
| TextGlyph.cpp | Implementation of TextGlyph_t for SBML Layout_t |
| TextGlyph.h | Definition of TextGlyph_t for SBML Layout_t |
| util | |
| LayoutAnnotation.cpp | Layout_t annotation I/O |
| LayoutAnnotation.h | Layout_t annotation I/O |
| LayoutUtilities.cpp | Implementation of some methods used by many of the layout files |
| LayoutUtilities.h | Definition of LayoutUtilities for SBML Layout_t |
| validator | |
| LayoutConsistencyValidator.cpp | |
| LayoutConsistencyValidator.h | |
| LayoutIdentifierConsistencyValidator.cpp | |
| LayoutIdentifierConsistencyValidator.h | |
| LayoutSBMLError.h | Implementation of the LayoutSBMLError class |
| LayoutSBMLErrorTable.h | |
| LayoutValidator.cpp | Implementation of the LayoutValidator_t class |
| LayoutValidator.h | Implementation of the LayoutValidator_t class |
| multi | |
| common | |
| MultiExtensionTypes.h | : Implementation of the MultiExtensionTypes class |
| multifwd.h | : Implementation of the multifwd class |
| extension | |
| MultiASTPlugin.cpp | Implementation of MultiASTPlugin_t, the plugin class of multi package for the AST element |
| MultiASTPlugin.h | Definition of MultiASTPlugin_t, the plugin class of multi package for the AST element |
| MultiCompartmentPlugin.cpp | : Implementation of the MultiCompartmentPlugin_t class |
| MultiCompartmentPlugin.h | : Implementation of the MultiCompartmentPlugin_t class |
| MultiExtension.cpp | : Implementation of the MultiExtension_t class |
| MultiExtension.h | : Implementation of the MultiExtension_t class |
| MultiListOfReactionsPlugin.cpp | : Implementation of the MultiListOfReactionsPlugin_t class |
| MultiListOfReactionsPlugin.h | : Implementation of the MultiListOfReactionsPlugin_t class |
| MultiModelPlugin.cpp | : Implementation of the MultiModelPlugin_t class |
| MultiModelPlugin.h | : Implementation of the MultiModelPlugin_t class |
| MultiSBMLDocumentPlugin.cpp | : Implementation of the MultiSBMLDocumentPlugin_t class |
| MultiSBMLDocumentPlugin.h | : Implementation of the MultiSBMLDocumentPlugin_t class |
| MultiSimpleSpeciesReferencePlugin.cpp | : Implementation of the MultiSimpleSpeciesReferencePlugin_t class |
| MultiSimpleSpeciesReferencePlugin.h | : Implementation of the MultiSimpleSpeciesReferencePlugin_t class |
| MultiSpeciesPlugin.cpp | : Implementation of the MultiSpeciesPlugin_t class |
| MultiSpeciesPlugin.h | : Implementation of the MultiSpeciesPlugin_t class |
| MultiSpeciesReferencePlugin.cpp | : Implementation of the MultiSpeciesReferencePlugin_t class |
| MultiSpeciesReferencePlugin.h | : Implementation of the MultiSpeciesReferencePlugin_t class |
| sbml | |
| BindingSiteSpeciesType.cpp | : Implementation of the BindingSiteSpeciesType_t class |
| BindingSiteSpeciesType.h | : Implementation of the BindingSiteSpeciesType_t class |
| CompartmentReference.cpp | : Implementation of the CompartmentReference_t class |
| CompartmentReference.h | : Implementation of the CompartmentReference_t class |
| InSpeciesTypeBond.cpp | : Implementation of the InSpeciesTypeBond_t class |
| InSpeciesTypeBond.h | : Implementation of the InSpeciesTypeBond_t class |
| IntraSpeciesReaction.cpp | : Implementation of the IntraSpeciesReaction_t class |
| IntraSpeciesReaction.h | : Implementation of the IntraSpeciesReaction_t class |
| MultiSpeciesType.cpp | : Implementation of the MultiSpeciesType_t class |
| MultiSpeciesType.h | : Implementation of the MultiSpeciesType_t class |
| OutwardBindingSite.cpp | : Implementation of the OutwardBindingSite_t class |
| OutwardBindingSite.h | : Implementation of the OutwardBindingSite_t class |
| PossibleSpeciesFeatureValue.cpp | : Implementation of the PossibleSpeciesFeatureValue_t class |
| PossibleSpeciesFeatureValue.h | : Implementation of the PossibleSpeciesFeatureValue_t class |
| SpeciesFeature.cpp | : Implementation of the SpeciesFeature_t class |
| SpeciesFeature.h | : Implementation of the SpeciesFeature_t class |
| SpeciesFeatureType.cpp | : Implementation of the SpeciesFeatureType_t class |
| SpeciesFeatureType.h | : Implementation of the SpeciesFeatureType_t class |
| SpeciesFeatureValue.cpp | : Implementation of the SpeciesFeatureValue_t class |
| SpeciesFeatureValue.h | : Implementation of the SpeciesFeatureValue_t class |
| SpeciesTypeComponentIndex.cpp | : Implementation of the SpeciesTypeComponentIndex_t class |
| SpeciesTypeComponentIndex.h | : Implementation of the SpeciesTypeComponentIndex_t class |
| SpeciesTypeComponentMapInProduct.cpp | : Implementation of the SpeciesTypeComponentMapInProduct_t class |
| SpeciesTypeComponentMapInProduct.h | : Implementation of the SpeciesTypeComponentMapInProduct_t class |
| SpeciesTypeInstance.cpp | : Implementation of the SpeciesTypeInstance_t class |
| SpeciesTypeInstance.h | : Implementation of the SpeciesTypeInstance_t class |
| SubListOfSpeciesFeatures.cpp | : Implementation of the SubListOfSpeciesFeatures_t class |
| SubListOfSpeciesFeatures.h | : Implementation of the SubListOfSpeciesFeatures_t 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_t class |
| MultiValidator.h | : Implementation of the MultiValidator_t 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_t, the core module of qual package |
| QualExtension.h | Definition of QualExtension_t, the core module of qual package |
| QualModelPlugin.cpp | Implementation of QualModelPlugin_t, the plugin class of qual package for the Model_t element |
| QualModelPlugin.h | Definition of QualModelPlugin_t, the plugin class of qual package for the Model_t element |
| QualSBMLDocumentPlugin.cpp | Implementation of QualSBMLDocumentPlugin_t, the plugin class of qual package for the SBase_t element |
| QualSBMLDocumentPlugin.h | Implementation of the QualSBMLDocumentPlugin_t class |
| sbml | |
| DefaultTerm.cpp | Implementation of the DefaultTerm_t class |
| DefaultTerm.h | Implementation of the DefaultTerm_t class |
| FunctionTerm.cpp | Implementation of the FunctionTerm_t class |
| FunctionTerm.h | Implementation of the FunctionTerm_t class |
| Input.cpp | Implementation of the Input_t class |
| Input.h | Implementation of the Input_t class |
| Output.cpp | Implementation of the Output_t class |
| Output.h | Implementation of the Output_t class |
| QualitativeSpecies.cpp | Implementation of the QualitativeSpecies_t class |
| QualitativeSpecies.h | Implementation of the QualitativeSpecies_t class |
| Transition.cpp | Implementation of the Transition_t class |
| Transition.h | Implementation of the Transition_t 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_t class |
| 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_t, the validator for all internal validation performed by libSBML |
| SBMLInternalValidator.h | Definition of SBMLInternalValidator_t, the validator for all internal validation performed by libSBML |
| SBMLValidator.cpp | Implementation of SBMLValidator_t, the base class for user callable SBML validators |
| SBMLValidator.h | Definition of SBMLValidator_t, 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_t Constraints |
| VConstraint.h | Base class for all SBML Validator_t 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_t are a list of name/value pairs for XMLElements |
| XMLAttributes.h | XMLAttributes_t are a list of name/value pairs for XML elements |
| XMLBuffer.cpp | |
| XMLBuffer.h | |
| XMLConstructorException.cpp | XMLConstructorException_t an exception thrown by XML classes |
| XMLConstructorException.h | XMLConstructorException_t 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_t |
| 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_t, a node in an XML document tree |
| XMLOutputStream.cpp | |
| XMLOutputStream.h | XMLOutputStream_t |
| 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_t |
| AlgebraicRule.h | Definitions of AlgebraicRule_t |
| AssignmentRule.cpp | Implementations of AssignmentRule_t |
| AssignmentRule.h | Definitions of AssignmentRule_t |
| Compartment.cpp | Implementations of Compartment_t and ListOfCompartments_t |
| Compartment.h | Definitions of Compartment_t and ListOfCompartments_t |
| CompartmentType.cpp | Implementation of CompartmentType_t and ListOfCompartmentTypes_t |
| CompartmentType.h | Definitions of CompartmentType_t and ListOfCompartmentTypes_t |
| Constraint.cpp | Implementations of Constraint_t and ListOfConstraints_t |
| Constraint.h | Definitions of Constraint_t and ListOfConstraints_t |
| Delay.cpp | Implementation of Delay_t |
| Delay.h | Definition of Delay_t |
| Event.cpp | Implementations of Event_t and ListOfEvents_t |
| Event.h | Definitions of Event_t and ListOfEvents_t |
| EventAssignment.cpp | Implementation of EventAssignment_t |
| EventAssignment.h | Definition of EventAssignment_t and ListOfEventAssignments_t |
| 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_t and ListOfFunctionDefinitions_t |
| FunctionDefinition.h | Definitions of FunctionDefinition_t and ListOfFunctionDefinitions_t |
| InitialAssignment.cpp | Implementation of InitialAssignment_t and ListOfInitialAssignments_t |
| InitialAssignment.h | Definitions of InitialAssignment_t and ListOfInitialAssignments_t |
| KineticLaw.cpp | Implementation of KineticLaw_t |
| KineticLaw.h | Definition of KineticLaw_t |
| ListOf.cpp | Wraps List_t and inherits from SBase_t |
| ListOf.h | |
| LocalParameter.cpp | Implementations of LocalLocalParameter and ListOfLocalLocalParameters |
| LocalParameter.h | Definitions of LocalParameter_t and ListOfLocalParameters_t |
| Model.cpp | Implementation of Model_t |
| Model.h | Definition of Model_t |
| ModifierSpeciesReference.cpp | Implementation of ModifierSpeciesReference_t |
| ModifierSpeciesReference.h | Definitions of ModifierSpeciesReference_t |
| Parameter.cpp | Implementations of Parameter_t and ListOfParameters_t |
| Parameter.h | Definitions of Parameter_t and ListOfParameters_t |
| Priority.cpp | Implementation of Priority_t |
| Priority.h | Definition of Priority_t |
| RateRule.cpp | Implementations of RateRule_t |
| RateRule.h | Definitions of RateRule_t |
| Reaction.cpp | Implementations of Reaction_t and ListOfReactions_t |
| Reaction.h | Definitions of Reaction_t and ListOfReactions_t |
| Rule.cpp | Implementations of Rule_t and ListOfRules_t |
| Rule.h | Definitions of Rule_t and ListOfRules_t |
| SBase.cpp | Implementation of SBase_t, the base object of all SBML objects |
| SBase.h | Definition of SBase_t, the base object of all SBML objects |
| SBMLConstructorException.cpp | Implementation of SBMLConstructorException_t, the exception class for constructor exceptions |
| SBMLConstructorException.h | Definition of SBMLConstructorException_t, 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_t and associated data |
| SBMLDocument.h | Top-level container for an SBML Model_t 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_t class to store level/version and namespace |
| SBMLNamespaces.h | SBMLNamespaces_t 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_t utility functions |
| SBO.h | SBO_t utility Function |
| SimpleSpeciesReference.cpp | Implementation of SimpleSpeciesReference_t |
| SimpleSpeciesReference.h | Definitions of SimpleSpeciesReference_t |
| Species.cpp | Implementations of Species_t and ListOfSpecies_t |
| Species.h | Definitions of Species_t and ListOfSpecies_t |
| SpeciesReference.cpp | Implementation of SpeciesReference_t and ListOfSpeciesReferences_t |
| SpeciesReference.h | Definitions of SpeciesReference_t and ListOfSpeciesReferences_t |
| SpeciesType.cpp | Implementation of SpeciesType_t and ListOfSpeciesTypes_t |
| SpeciesType.h | Definitions of SpeciesType_t and ListOfSpeciesType |
| StoichiometryMath.cpp | Implementation of StoichiometryMath_t |
| StoichiometryMath.h | Definition of StoichiometryMath_t |
| SyntaxChecker.cpp | Syntax checking functions |
| SyntaxChecker.h | Syntax checking functions |
| Trigger.cpp | Implementation of Trigger_t |
| Trigger.h | Definition of Trigger_t |
| Unit.cpp | Implementations of Unit_t and ListOfUnits_t |
| Unit.h | Definitions of Unit_t and ListOfUnits_t |
| UnitDefinition.cpp | Implementations of SBML's UnitDefinition_t and ListOfUnitDefinitions_t |
| UnitDefinition.h | Definitions of UnitDefinition_t and ListOfUnitDefinitions_t |
| UnitKind.c | SBML UnitKind enumeration |
| UnitKind.h | Definition of SBML's UnitKind enumeration |