Package de.unirostock.sems.bives.sbml.parser

Class SBMLSpecies

java.lang.Object

de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

de.unirostock.sems.bives.sbml.parser.SBMLSBase

de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

de.unirostock.sems.bives.sbml.parser.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

Field Summary

Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

id, name

Fields inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

documentNode, sbmlModel

Constructor Summary

Constructors

Constructor	Description
SBMLSpecies(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel)	Instantiates a new SBML species.

Method Summary

Modifier and Type	Method	Description
boolean	canBeReactantOrProduct()	Can this species take part in a reaction as a reactant or product?
boolean	canHaveAssignmentRule()	Is this species allowed to have an assignment rule.
SBMLCompartment	getCompartment()	Gets the compartment that hosts this species.
double	getInitialAmount()	Returns the initial amount of this species or null if not defined.
double	getInitialConcentration()	Returns the initial concentration of this species or null if not defined.
boolean	hasBoundaryCondition()	Checks for a boundary condition.
boolean	hasOnlySubstanceUnits()	Checks if this species has only substance units.
boolean	isConstant()	Checks if this species is constant.
de.unirostock.sems.bives.markup.MarkupElement	reportDelete()
de.unirostock.sems.bives.markup.MarkupElement	reportInsert()
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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject

getID, getName, getNameAndId, getNameOrId

Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject

getDocumentNode, getModel

Methods inherited from class de.unirostock.sems.bives.sbml.parser.SBMLSBase

addOntologyLink, flagMetaModifcations, getAnnotation, getMetaId, getNotes, getOntologyLinks, getSBOTerm

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