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

Class SBMLSimpleSpeciesReference

java.lang.Object

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

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

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

Direct Known Subclasses:

SBMLSpeciesReference

public class SBMLSimpleSpeciesReference
extends SBMLSBase

The Class SBMLSimpleSpeciesReference representing a link to a species (mainly for modifiers, parent class for substrates and products).

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field	Description
protected String	id	The id of this species reference.
protected String	name	The name.
protected SBMLSpecies	species	The species it is linking to.

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

documentNode, sbmlModel

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
SBMLSpecies	getSpecies()	Gets the corresponding species.
String	report()	Typeset this reference.
String	reportDelete()	Report a delete.
String	reportInsert()	Report an insert.
String	reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt, SBMLSimpleSpeciesReference a, SBMLSimpleSpeciesReference b)	Report modification between two versions 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

Field Detail

id

protected String id

The id of this species reference.

name

protected String name

The name.

species

protected SBMLSpecies species

The species it is linking to.

Constructor Detail

SBMLSimpleSpeciesReference

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

Instantiates a new SBML simple species reference.

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

getSpecies

public SBMLSpecies getSpecies()

Gets the corresponding species.

Returns:

the species

reportModification

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

Report modification between two versions of this species reference.

Parameters:

conMgmt - the connection manager

a - the original reference

b - the modified reference

Returns:

the textual representation of this modification

reportInsert

public String reportInsert()

Report an insert.

Returns:

the string

reportDelete

public String reportDelete()

Report a delete.

Returns:

the string

report

public String report()

Typeset this reference.

Returns:

the string