Class SBMLModel


  • public class SBMLModel
    extends SBMLSBase
    The Class SBMLModel representing a model encoded in SBML.
    Author:
    Martin Scharm
    • Constructor Detail

      • SBMLModel

        public SBMLModel​(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
                         SBMLDocument sbmlDocument)
                  throws BivesSBMLParseException,
                         de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
        Instantiates a new SBML model.
        Parameters:
        documentNode - the document node encoding this entity in the corresponding XML tree
        sbmlDocument - the SBML document
        Throws:
        BivesSBMLParseException - the bives sbml parse exception
        de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception
    • Method Detail

      • getOntologyMappings

        public HashMap<String,​List<SBMLSBase>> getOntologyMappings()
        Gets the ontology mappings which group entities by there pointers into ontologies.
        Returns:
        the ontology mappings
      • getUnitDefinition

        public SBMLUnitDefinition getUnitDefinition​(String kind)
        Gets the unit definition.
        Parameters:
        kind - the kind
        Returns:
        the unit definition
      • getCompartmentType

        public SBMLCompartmentType getCompartmentType​(String id)
        Gets the compartment type.
        Parameters:
        id - the id
        Returns:
        the compartment type
      • getCompartment

        public SBMLCompartment getCompartment​(String id)
        Gets the compartment.
        Parameters:
        id - the id
        Returns:
        the compartment
      • getSpecies

        public SBMLSpecies getSpecies​(String id)
        Gets the species.
        Parameters:
        id - the id
        Returns:
        the species
      • getSpeciesType

        public SBMLSpeciesType getSpeciesType​(String id)
        Gets the species type.
        Parameters:
        id - the id
        Returns:
        the species type
      • getParameter

        public SBMLParameter getParameter​(String id)
        Gets a specific parameter.
        Parameters:
        id - the id of the parameter
        Returns:
        the parameter
      • registerSpeciesReference

        public void registerSpeciesReference​(String id,
                                             SBMLSimpleSpeciesReference ref)
        Registers a species reference.
        Parameters:
        id - the id of the species reference
        ref - the reference
      • getSpeciesReference

        public SBMLSimpleSpeciesReference getSpeciesReference​(String id)
        Gets the species reference.
        Parameters:
        id - the id of the species reference
        Returns:
        the species reference
      • getReaction

        public SBMLReaction getReaction​(String id)
        Gets a specific reaction.
        Parameters:
        id - the id of the reaction
        Returns:
        the reaction
      • getConstraints

        public List<SBMLConstraint> getConstraints()
        Gets the constraints.
        Returns:
        the constraints
      • getInitialAssignments

        public List<SBMLInitialAssignment> getInitialAssignments()
        Gets the initial assignments.
        Returns:
        the initial assignments
      • getEvents

        public List<SBMLEvent> getEvents()
        Gets the events.
        Returns:
        the events
      • getRules

        public List<SBMLRule> getRules()
        Gets the rules.
        Returns:
        the rules
      • getID

        public String getID()
        Gets the id of the model.
        Returns:
        the id
      • getName

        public String getName()
        Gets the name of the model.
        Returns:
        the name
      • mapNode

        public void mapNode​(de.unirostock.sems.xmlutils.ds.DocumentNode node,
                            SBMLSBase sbase)
        Map node model node to its entity.
        Parameters:
        node - the document node in the corresponding XML tree
        sbase - the entity to get mapped
      • getFromNode

        public SBMLSBase getFromNode​(de.unirostock.sems.xmlutils.ds.TreeNode node)
        Gets an entity given its tree node.
        Parameters:
        node - the node in the XML tree
        Returns:
        the entity registered for this node
      • getFromMetaId

        public SBMLSBase getFromMetaId​(String metaId)
        Gets an entity given its meta id.
        Parameters:
        metaId - the meta id
        Returns:
        the entity registered for this meta id
      • getDocument

        public SBMLDocument getDocument()
        Gets the SBML document.
        Returns:
        the document
      • resolveSymbole

        public SBMLSBase resolveSymbole​(String symbol)
        Deprecated.
        as of version 1.3.6, replaced by resolveSymbol(String)
        Resolve certain symbol.
        Parameters:
        symbol - the symbol
        Returns:
        the SBMLS base
      • resolveSymbol

        public SBMLSBase resolveSymbol​(String symbol)
        Resolve certain symbol.
        Parameters:
        symbol - the symbol
        Returns:
        the SBMLS base
      • getSidName

        public static String getSidName​(SBMLSBase ref)
        Gets the SId.
        Parameters:
        ref - the ref
        Returns:
        the sid name