All Classes and Interfaces
Class
Description
This interface provides options for connecting to the ADB database.
This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
BiGGCVTermAnnotator<T extends org.sbml.jsbml.SBase>
Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
This class provides a connection to the BiGG database.
Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
Represents a BiGG identifier used to uniquely identify various biological entities
such as reactions, metabolites, and genes within the BiGG database.
This class is responsible for annotating an SBML
Model with relevant metadata and references.This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers.
This class is responsible for annotating SBML models using data from the BiGG database.
This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
The
CombineArchive class provides functionality to create a COMBINE archive from an SBML document.This class is responsible for polishing the properties of a compartment in an SBML model to ensure
compliance with standards and completeness.
A collection of helpful functions for dealing with SBML data structures.
IAnnotateSBases<SBMLElement extends org.sbml.jsbml.SBase>
The
IdentifiersOrg class serves as a central hub for managing and processing identifiers related to the MIRIAM registry.The
IdentifiersOrgRegistryParser class is a singleton that provides functionality to parse the MIRIAM registry
from a JSON file and convert it into a Miriam object.IFixSBases<SBMLElement extends org.sbml.jsbml.SBase>
IPolishSBases<SBMLElement extends org.sbml.jsbml.SBase>
For more information about COBRA model fields, see the following
Supplementary
Material.
This class provides functionality to polish an SBML (Systems Biology Markup Language) document.
Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings.
This class provides methods to polish and validate SBML reactions according to specific rules and patterns.
Possible FileTypes of input file
From ...:
This class is responsible for ensuring that all necessary
UnitDefinitions and Units are correctly
defined and present in the SBML model.The
UpdateListener class implements the TreeNodeChangeListener to monitor and respond to changes
within an SBML model's structure.