Class SBMLSpecies

  • All Implemented Interfaces:
    de.unirostock.sems.bives.algorithm.DiffReporter

    public class SBMLSpecies
    extends SBMLGenericIdNameObject
    implements de.unirostock.sems.bives.algorithm.DiffReporter
    The Class SBMLSpecies representing a species in an SBML document.
    Author:
    Martin Scharm
    • Constructor Detail

      • SBMLSpecies

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

      • getInitialAmount

        public double getInitialAmount()
        Returns the initial amount of this species or null if not defined.
        Returns:
        the initial amount
      • getInitialConcentration

        public double getInitialConcentration()
        Returns the initial concentration of this species or null if not defined.
        Returns:
        the initial concentration
      • getCompartment

        public SBMLCompartment getCompartment()
        Gets the compartment that hosts this species.
        Returns:
        the compartment
      • canHaveAssignmentRule

        public boolean canHaveAssignmentRule()
        Is this species allowed to have an assignment rule.
        Returns:
        true, if allowed
      • canBeReactantOrProduct

        public boolean canBeReactantOrProduct()
        Can this species take part in a reaction as a reactant or product?
        Returns:
        true, if that is possible
      • isConstant

        public boolean isConstant()
        Checks if this species is constant.
        Returns:
        true, if it is constant
      • hasBoundaryCondition

        public boolean hasBoundaryCondition()
        Checks for a boundary condition.
        Returns:
        true, if successful
      • hasOnlySubstanceUnits

        public boolean hasOnlySubstanceUnits()
        Checks if this species has only substance units.
        Returns:
        true, if it has only substance units
      • reportModification

        public de.unirostock.sems.bives.markup.MarkupElement reportModification​(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt,
                                                                                de.unirostock.sems.bives.algorithm.DiffReporter docA,
                                                                                de.unirostock.sems.bives.algorithm.DiffReporter docB)
        Specified by:
        reportModification in interface de.unirostock.sems.bives.algorithm.DiffReporter
      • reportInsert

        public de.unirostock.sems.bives.markup.MarkupElement reportInsert()
        Specified by:
        reportInsert in interface de.unirostock.sems.bives.algorithm.DiffReporter
      • reportDelete

        public de.unirostock.sems.bives.markup.MarkupElement reportDelete()
        Specified by:
        reportDelete in interface de.unirostock.sems.bives.algorithm.DiffReporter