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

Class SBMLSpeciesReference

java.lang.Object

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

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

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

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

public class SBMLSpeciesReference
extends SBMLSimpleSpeciesReference

The Class SBMLSpeciesReference representing a link to a species.

Author:

Martin Scharm

Field Summary

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

documentNode, sbmlModel

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

id, name, species

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
String	report()	Typeset this reference.
String	reportDelete()	Report a delete.
String	reportInsert()	Report an insert.
String	reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt, SBMLSpeciesReference a, SBMLSpeciesReference b)	Report the modifications of this species reference.

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.SBMLGenericObject

getDocumentNode, getModel

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

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

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

getSpecies, reportModification

Constructor Detail

SBMLSpeciesReference

public SBMLSpeciesReference(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
                            SBMLModel sbmlModel)
                     throws BivesSBMLParseException

Instantiates a new SBML species reference.

Parameters:

documentNode - the document node encoding this entity in the corresponding XML tree

sbmlModel - the corresponding SBML model

Throws:

BivesSBMLParseException - the bives sbml parse exception

Method Detail

reportModification

public String reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt,
                                 SBMLSpeciesReference a,
                                 SBMLSpeciesReference b)

Report the modifications of this species reference.

Parameters:

conMgmt - the connection manager

a - the original species reference

b - the modified species reference

Returns:

the string

reportInsert

public String reportInsert()

Description copied from class: SBMLSimpleSpeciesReference

Report an insert.

Overrides:

reportInsert in class SBMLSimpleSpeciesReference

Returns:

the string

reportDelete

public String reportDelete()

Description copied from class: SBMLSimpleSpeciesReference

Report a delete.

Overrides:

reportDelete in class SBMLSimpleSpeciesReference

Returns:

the string

report

public String report()

Description copied from class: SBMLSimpleSpeciesReference

Typeset this reference.

Overrides:

report in class SBMLSimpleSpeciesReference

Returns:

the string