libSBML Perl API
libSBML 5.10.0 Perl API
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Class Hierarchy
Go to the graphical class hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level
1
2
3
4
5
]
►
C
ASTBase
C
ASTNode
{core} Abstract Syntax Tree (AST) representation of a mathematical expression
C
CompPkgNamespaces
{comp} Extension of
SBMLNamespaces
for the SBML Level 3 'comp' package
C
ConversionOption
{core} Class of object that encapsulates a conversion option
C
ConversionProperties
{core} Class of object that encapsulates the properties of an SBML converter
C
CVTerm
{core} Representation of MIRIAM-compliant controlled vocabulary annotation
C
Date
{core} Representation of MIRIAM-compliant dates used in
ModelHistory
C
doc_about_mathml_semantic_annotations
The
<semantics>
element is a MathML 2.0 construct that can be used to associate additional information with a MathML construct
C
doc_additional_typecode_details
C
doc_algebraicrule_setting_lv
C
doc_astnode_types
C
doc_base_units
C
doc_compartment_both_size_and_volume
C
doc_compartment_units
C
doc_compartmenttype_setting_lv
C
doc_config_for_reading_zipped_files
C
doc_config_for_writing_zipped_files
C
doc_constraint_setting_lv
C
doc_cvterm_common_description
C
doc_date_string_format
C
doc_delay_setting_lv
C
doc_delay_units
C
doc_errorlog_what_are_severities
C
doc_event_setting_lv
C
doc_event_using_useValuesFromTriggerTime
C
doc_eventassignment_units
C
doc_id_syntax
C
doc_initialassignment_units
C
doc_kineticlaw_units
C
doc_localparameter_units
C
doc_note_assignmentRule_setting_lv
C
doc_note_charge_deprecated
C
doc_note_compartment_setting_lv
C
doc_note_compartment_volume
C
doc_note_eventassignment_setting_lv
C
doc_note_functiondefinition_setting_lv
C
doc_note_initialassignment_setting_lv
C
doc_note_kineticlaw_setting_lv
C
doc_note_localparameter_setting_lv
C
doc_note_mathml_semantic_annotations_uncommon
C
doc_note_model_setting_lv
C
doc_note_modifierspeciesreference_setting_lv
C
doc_note_object_is_copied
C
doc_note_parameter_about_constant
C
doc_note_parameter_setting_lv
C
doc_note_priority_only_l3
C
doc_note_priority_setting_lv
C
doc_note_raterule_setting_lv
C
doc_note_reaction_setting_lv
C
doc_note_sbmlreader_error_handling
C
doc_note_spatial_dimensions_as_double
C
doc_note_species_setting_lv
C
doc_note_species_units
C
doc_note_speciesreference_setting_lv
C
doc_note_speciestype_setting_lv
C
doc_note_stoichiometrymath_availability
C
doc_note_stoichiometrymath_setting_lv
C
doc_note_timeunits_substanceunits
C
doc_note_unassigned_unit_are_not_a_default
C
doc_note_unit_analysis_depends_on_model
C
doc_note_unit_inference_depends_on_model
C
doc_note_unit_setting_lv
C
doc_note_unitdefinition_setting_lv
C
doc_rule_level_1
C
doc_rule_units
C
doc_rules_general_summary
C
doc_sbase_what_is_user_data
C
doc_sbml_error_code_ranges
C
doc_sbml_error_table
C
doc_sbmldocument_default_level
C
doc_sbmldocument_default_version
C
doc_sbmlnamespaces_what_is_it
C
doc_sbmlreader_if_compressed
C
doc_summary_of_string_math
C
doc_summary_of_string_math_l3
C
doc_warning_delay_math_literals
C
doc_warning_event_timeUnits
C
doc_warning_eventassignment_math_literals
C
doc_warning_initialassignment_math_literals
C
doc_warning_kineticlaw_math_literals
C
doc_warning_L1_math_string_syntax
C
doc_warning_modifying_structure
C
doc_warning_reaction_cant_ignore_fast
C
doc_warning_rule_math_literals
C
doc_warning_species_spatialSizeUnits
C
doc_warning_typecodes_not_unique
C
doc_warning_unit_offset_only_l2v1
C
doc_warning_useValuesFromTriggerTime
C
doc_what_are_annotations
C
doc_what_are_cvterms
C
doc_what_are_notes
C
doc_what_are_plugins
C
doc_what_are_sbmlnamespaces
C
doc_what_are_typecodes
C
doc_what_is_astnode
C
doc_what_is_listof
C
doc_what_is_metaid
C
doc_what_is_metaidref
C
doc_what_is_SBMLDocument
C
doc_what_is_sid
C
doc_what_is_sidref
C
doc_what_is_unitsidref
►
C
std::exception
STL class
►
C
std::logic_error
STL class
►
C
std::invalid_argument
STL class
C
SBMLConstructorException
{core} Class of exceptions thrown by constructors of some libSBML objects
C
SBMLExtensionException
An exception class for
SBMLExtensionException
C
XMLConstructorException
{core} Class of exceptions thrown by constructors of some libSBML objects
C
FbcPkgNamespaces
{fbc} Extension of
SBMLNamespaces
for the SBML Level 3 'fbc' package
C
FormulaTokenizer_t
{core} used to track the state of tokenizing a string
C
L3ParserSettings
{core} A helper class for controlling the behavior of the text-string formula parser
C
LayoutPkgNamespaces
{layout} Extension of
SBMLNamespaces
for the SBML Level 3 'layout' package
C
List
{core} Simple, plain, generic lists, and associated list utilities
C
ModelCreator
{core} Representation of MIRIAM-compliant model creator data used in
ModelHistory
C
ModelHistory
{core} Representation of MIRIAM-compliant model history data
C
QualPkgNamespaces
{qual} Extension of
SBMLNamespaces
for the SBML Level 3 'qual' package
C
RDFAnnotationParser
{core} Read/write/manipulate RDF annotations stored in SBML annotation elements
►
C
SBase
{core} Implementation of SBase, the base class of most SBML objects
C
Association
{fbc} Implementation of the 'fbc' proposed package Association construct
C
BoundingBox
{layout} Representation of a bounding box
C
Compartment
{core} Implementation of SBML's Compartment construct
C
CompartmentType
{core} Implementation of SBML's Level 2's CompartmentType construct
►
C
CompBase
{comp} A convenience subclass of “comp” package SBase-derived classes
C
ExternalModelDefinition
{comp} Implementation of the ExternalModelDefinition construct from the “comp” package
►
C
SBaseRef
{comp} Implementation of the SBaseRef construct from the “comp” package
C
Deletion
{comp} Implementation of the Deletion construct from the “comp” package
C
Port
{comp} Implementation of the Port construct from the “comp” package
►
C
Replacing
{comp} A convenience subclass of the ReplacedElement and ReplacedBy constructs from the “comp” package
C
ReplacedBy
{comp} Implementation of the ReplacedBy construct from the “comp” package
C
ReplacedElement
{comp} Implementation of the ReplacedElement construct from the “comp” package
C
Submodel
{comp} Implementation of the Submodel construct from the “comp” package
C
Constraint
{core} Implementation of SBML's Constraint construct
C
Curve
{layout} The
Curve
class describes how to connect elements in a diagram defined with the use of the “layout” package
C
DefaultTerm
{qual} The
DefaultTerm
class for the Qualitative Models package
C
Delay
{core} Implementation of SBML's Delay construct for Event
C
Dimensions
{layout} The Dimensions class describes the overall 2D or 3D shape of a “layout” package object
C
Event
{core} Implementation of SBML's Event construct
C
EventAssignment
{core} Implementation of SBML's EventAssignment construct for Event
C
FluxBound
{fbc} Implementation of the 'fbc' package FluxBound construct
C
FluxObjective
{fbc} Implementation of the 'fbc' package FluxObjective construct
C
FunctionDefinition
{core} Implementation of SBML's FunctionDefinition construct
C
FunctionTerm
{qual} The
FunctionTerm
class for the Qualitative Models package
C
GeneAssociation
{fbc} Implementation of the 'fbc' package GeneAssociation construct
►
C
GraphicalObject
{layout} The basic “layout” package element for storing layout information
C
CompartmentGlyph
{layout} Representation of a compartment glyph
C
GeneralGlyph
{layout} The GeneralGlyph is used by the “layout” package to represent any SBML object
C
ReactionGlyph
{layout} The ReactionGlyph is used to represent
Reaction
elements in the layout
C
ReferenceGlyph
{layout} The ReferenceGlyph is used by the “layout” package to connect a
GraphicalObject
and a
GeneralGlyph
C
SpeciesGlyph
{layout} The SpeciesGlyph represents a
Species
in the “layout” package
C
SpeciesReferenceGlyph
{layout} A SpeciesReferenceGlyph represents a reactant or product from a
Reaction
in the “layout” package
C
TextGlyph
{layout} The TextGlyph class describes the position and dimension of text labels in the “layout” package
C
InitialAssignment
{core} Implementation of SBML's InitialAssignment construct
C
Input
{qual} The
Input
class for the Qualitative Models package
C
KineticLaw
{core} Implementation of SBML's KineticLaw construct
C
Layout
{layout} Each
Layout
object stores a set of layout information for objects in the
Model
►
C
LineSegment
{layout} The representation of a line in the “layout” package
C
CubicBezier
{layout} A CubicBezier represents a smooth curve in the “layout” package
►
C
ListOf
{core} Parent class for libSBML's "ListOfXYZ" classes
C
ListOfCompartmentGlyphs
{layout} Implementation of the ListOfCompartmentGlyphs construct from the “layout” package
C
ListOfCompartments
{core} Implementation of SBML Level 2's ListOfCompartments construct
C
ListOfCompartmentTypes
{core} Implementation of SBML's ListOfCompartmentTypes construct
C
ListOfConstraints
{core} Implementation of SBML's ListOfConstraints construct
C
ListOfDeletions
{comp} Implementation of the ListOfDeletions construct from the “comp” package
C
ListOfEventAssignments
{core} Implementation of SBML's ListOfEventAssignments construct
C
ListOfEvents
{core} Implementation of SBML's ListOfEvents construct
C
ListOfExternalModelDefinitions
{comp} Implementation of the ListOfExternalModelDefinitions construct from the “comp” package
C
ListOfFluxBounds
{fbc} Implementation of the ListOfFluxBounds construct from the 'fbc' package
C
ListOfFluxObjectives
{fbc} Implementation of the 'fbc' package ListOfFluxObjectives construct
C
ListOfFunctionDefinitions
{core} Implementation of SBML's ListOfFunctionDefinitions construct
C
ListOfFunctionTerms
{qual} Implementation of the ListOfFunctionTerms construct from the 'qual' package
C
ListOfGeneAssociations
{fbc} Implementation of the 'fbc' package suggested ListOfGeneAssociations annotation construct
C
ListOfGraphicalObjects
{layout} Implementation of the ListOfAdditionalGraphicalObjects construct from the “layout” package
C
ListOfInitialAssignments
{core} Implementation of SBML's ListOfInitialAssignments construct
C
ListOfInputs
{qual} Implementation of the ListOfInputs construct from the 'qual' package
C
ListOfLayouts
{layout} Implementation of the * ListOfLayouts construct from the “layout” package
C
ListOfLineSegments
{layout} Implementation of the ListOfLineSegments construct from the 'layout' package
C
ListOfModelDefinitions
{comp} Implementation of the ListOfModelDefinitions construct from the “comp” package
C
ListOfObjectives
{fbc} Implementation of the ListOfObjectives construct from the 'fbc' package
C
ListOfOutputs
{qual} Implementation of the ListOfOutputs construct from the 'qual' package
►
C
ListOfParameters
{core} Implementation of SBML's ListOfParameters construct
C
ListOfLocalParameters
{core} Implementation of SBML Level 3's ListOfLocalParameters construct
C
ListOfPorts
{comp} Implementation of the ListOfPorts construct from the “comp” package
C
ListOfQualitativeSpecies
{qual} Implementation of the ListOfQualitativeSpecies construct from the 'qual' package
C
ListOfReactionGlyphs
{layout} Implementation of the ListOfReactionGlyphs construct from the “layout” package
C
ListOfReactions
{core} Implementation of SBML's ListOfReactions construct
C
ListOfReferenceGlyphs
{layout} Implementation of the ListOfReferenceGlyphs construct from the “layout” package
C
ListOfReplacedElements
{comp} Implementation of the ListOfReplacedElements construct from the “comp” package
C
ListOfRules
{core} Implementation of SBML's ListOfRules construct
C
ListOfSpecies
{core} Implementation of SBML Level 2's ListOfSpecies construct
C
ListOfSpeciesGlyphs
{layout} Implementation of the ListOfSpeciesGlyphs construct from the “layout” package
C
ListOfSpeciesReferenceGlyphs
{layout} Implementation of the ListOfSpeciesReferenceGlyphs construct from the “layout” package
C
ListOfSpeciesReferences
{core} Implementation of SBML's ListOfSpeciesReferences construct
C
ListOfSpeciesTypes
{core} Implementation of SBML's ListOfSpeciesTypes construct
C
ListOfSubmodels
{comp} Implementation of the ListOfSubmodels construct from the “comp” package
C
ListOfTextGlyphs
{layout} Implementation of the ListOfTextGlyphs construct from the “layout” package
C
ListOfTransitions
{qual} Implementation of the ListOfTransitions construct from the 'qual' package
C
ListOfUnitDefinitions
{core} Implementation of SBML's ListOfUnitDefinitions construct
C
ListOfUnits
{core} Implementation of SBML's ListOfUnits construct
►
C
Model
{core} Implementation of SBML's Model construct
C
ModelDefinition
{comp} Implementation of the ModelDefinition construct from the “comp” package
C
Objective
{fbc} Implementation of the 'fbc' package Objective construct
C
Output
{qual} The
Output
class for the Qualitative Models package
►
C
Parameter
{core} Implementation of SBML's Parameter construct
C
LocalParameter
{core} Implementation of SBML Level 3's LocalParameter construct
C
Point
{layout} The representation of a point in the “layout” package
C
Priority
{core} Implementation of SBML Level 3's Priority construct for
Event
C
QualitativeSpecies
{qual} The
QualitativeSpecies
class for the Qualitative Models package
C
Reaction
{core} Implementation of SBML's Reaction construct
►
C
Rule
{core} Implementation of SBML's Rule construct
C
AlgebraicRule
{core} Implementation of SBML's AlgebraicRule construct
C
AssignmentRule
{core} Implementation of SBML's AssignmentRule construct
C
RateRule
{core} Implementation of SBML's RateRule construct
C
SBMLDocument
{core} Container for an SBML document and interface for global operations on SBML documents
►
C
SimpleSpeciesReference
{core} Implementation of SBML's SimpleSpeciesReference construct
C
ModifierSpeciesReference
{core} Implementation of SBML's ModifierSpeciesReference construct
C
SpeciesReference
{core} Implementation of SBML's SpeciesReference construct
C
Species
{core} Implementation of SBML's Species construct
C
SpeciesType
{core} Implementation of SBML Level 2's SpeciesType construct
C
StoichiometryMath
{core} Implementation of SBML Level 2's StoichiometryMath construct
C
Transition
{qual} The
Transition
class for the Qualitative Models package
C
Trigger
{core} Implementation of SBML's Trigger construct for Event
C
Unit
{core} Implementation of SBML's Unit construct
C
UnitDefinition
{core} Implementation of SBML's UnitDefinition construct
C
SBaseExtensionPoint
{core} Representation of an extension point of SBML's package extension
►
C
SBasePlugin
{core} Representation of a plug-in object of SBML's package extension
►
C
CompSBasePlugin
{comp} Implementation of the “comp” package extention to the SBase construct
C
CompModelPlugin
{comp} Implementation of the “comp” package extention to the Model construct
C
FbcModelPlugin
{fbc} Implementation of the 'fbc' package extention to the Model construct
C
FbcSpeciesPlugin
{fbc} Implementation of the 'fbc' package extention to the Species construct
C
LayoutModelPlugin
{layout} Implementation of the 'layout' package extention to the Model construct
C
LayoutSpeciesReferencePlugin
{layout} Implementation of the 'layout' package extention to the SpeciesReference construct
C
QualModelPlugin
{qual} Implementation of the 'qual' package extention to the Model construct
►
C
SBMLDocumentPlugin
{core} Template class for the SBMLDocument Plugin class needed by all packages
C
CompSBMLDocumentPlugin
{comp} Implementation of the “comp” package extention to the SBMLDocument construct
C
FbcSBMLDocumentPlugin
{fbc} Implementation of the 'fbc' package extention to the SBMLDocument construct
C
LayoutSBMLDocumentPlugin
{layout} Implementation of the 'layout' package extention to the SBMLDocument construct
C
QualSBMLDocumentPlugin
{qual} Implementation of the 'qual' package extention to the SBMLDocument construct
C
SBMLDocumentPluginNotRequired
{core} Template class for the SBMLDocument Plugin class for non-required packages
►
C
SBasePluginCreatorBase
{core} Base class of SBasePluginCreator
C
SBasePluginCreator< SBasePluginType, SBMLExtensionType >
{core} Template class of SBasePlugin
►
C
SBMLConverter
{core} Base class for SBML converters
C
CobraToFbcConverter
{fbc} Implementation of a COBRA to SBML Level 3 'fbc' package converter
C
CompFlatteningConverter
{comp} Flattening converter for the “comp” package
C
FbcToCobraConverter
{fbc} Implementation of a SBML Level 3 'fbc' package to COBRA converter
C
SBMLFunctionDefinitionConverter
{core} SBML converter for replacing function definitions
C
SBMLIdConverter
{core} SBML converter for replacing SIds
C
SBMLInferUnitsConverter
{core} SBML converter for inferring the units of parameters
C
SBMLInitialAssignmentConverter
{core} SBML converter for replacing initial assignments
C
SBMLLevelVersionConverter
{core} SBML converter for transforming documents from one Level+Version to another
C
SBMLLocalParameterConverter
{core} SBML converter for replacing SIds
C
SBMLReactionConverter
{core} SBML converter for replacing reactions with rate rules
C
SBMLRuleConverter
{core} SBML converter for reordering rules and assignments in a model
C
SBMLStripPackageConverter
{core} SBML converter for removing packages
C
SBMLUnitsConverter
{core} SBML converter to convert a model's units to SI units
C
SBMLConverterRegistry
{core} Registry of all SBML converters
►
C
SBMLExtension
{core} The core component of SBML's package extension
C
CompExtension
{comp} The core module of the “comp” package extension
C
FbcExtension
{fbc} The core module of the 'fbc' package extension
C
LayoutExtension
{layout} The core module of the 'layout' package extension
C
QualExtension
{qual} The core module of the 'qual' package extension
C
SBMLExtensionRegister< SBMLExtensionType >
{core} Template class for registering an extension package to the
SBMLExtensionRegistry
class
C
SBMLExtensionRegistry
{core} Registry class in which extension packages are registered
►
C
SBMLNamespaces
{core} Class to store SBML Level, Version and namespace information
C
SBMLExtensionNamespaces< SBMLExtensionType >
{core} Class to store the Level, Version and XML namespace information of an SBML extension package
C
SBMLReader
{core} Methods for reading SBML from files and text strings
►
C
SBMLResolver
{comp} Base class for SBML resolvers
C
SBMLFileResolver
{comp} A resolver for documents stored on a file system
C
SBMLResolverRegistry
{comp} Registry of all SBML resolvers
C
SBMLUri
{comp} utility class for handling URIs
►
C
SBMLValidator
{core} Base class for SBML validators
C
SBMLInternalValidator
{core} Implementation of basic SBML consistency checks and other validations
C
SBMLVisitor
{core} Support class for performing operations on SBML objects
C
SBMLWriter
{core} Methods for writing SBML to files and text strings
C
SBO
{core} Methods for interacting with Systems Biology Ontology terms
C
SyntaxChecker
{core} Methods for checking syntax of SBML identifiers and other strings
C
Token_t
{core} Structure used to store a token returned by
FormulaTokenizer_nextToken()
►
C
Validator
{core} Entry point for libSBML's implementation of SBML validation rules
C
CompValidator
{comp} Entry point for libSBML's implementation of SBML validation rules for the “comp” package
C
FbcValidator
{fbc} Entry point for libSBML's implementation of SBML validation rules for 'fbc'
C
LayoutValidator
{layout} Entry point for libSBML's implementation of SBML validation rules for the “layout” package
C
QualValidator
{qual} Entry point for libSBML's implementation of SBML validation rules for 'qual'
C
VConstraint
{core} Helper class for implementing SBML validation and consistency-checking
C
XMLAttributes
{core} Representation of attributes on an XML node
►
C
XMLError
{core} Representation of errors, warnings and other diagnostics
C
SBMLError
{core} Representation of errors, warnings and other diagnostics
►
C
XMLErrorLog
{core} Log of errors and other events encountered while processing an XML file or data stream
C
SBMLErrorLog
{core} Log of errors and other events encountered during SBML processing
C
XMLLogOverride
{core} Utility class implementing a temporary override the severity on error logs
C
XMLNamespaces
{core} Representation of XML Namespaces
►
C
XMLToken
{core} Representation of a token in an XML stream
C
XMLNode
{core} Representation of a node in an XML document tree
C
XMLTriple
{core} Representation of a qualified XML name
Visit
SBML.org
for more information about SBML and libSBML.