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

Class SBMLUnitDefinition

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.SBMLUnitDefinition

All Implemented Interfaces:

de.unirostock.sems.bives.algorithm.DiffReporter, de.unirostock.sems.bives.markup.Markup

public class SBMLUnitDefinition
extends SBMLGenericIdNameObject
implements de.unirostock.sems.bives.algorithm.DiffReporter, de.unirostock.sems.bives.markup.Markup

The Class SBMLUnitDefinition.

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
SBMLUnitDefinition(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode, SBMLModel sbmlModel)	Instantiates a new SBML unit definition.
SBMLUnitDefinition(String name, SBMLModel sbmlModel)	Instantiates a new SBML base unit.

Method Summary

Modifier and Type	Method	Description
boolean	isBaseUnit()	Checks if this is a base unit.
String	markup()
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

SBMLUnitDefinition

public SBMLUnitDefinition(String name,
                          SBMLModel sbmlModel)
                   throws BivesSBMLParseException

Instantiates a new SBML base unit.

Parameters:

name - the name of the unit

sbmlModel - the SBML model

Throws:

BivesSBMLParseException - the bives sbml parse exception

SBMLUnitDefinition

public SBMLUnitDefinition(de.unirostock.sems.xmlutils.ds.DocumentNode documentNode,
                          SBMLModel sbmlModel)
                   throws BivesSBMLParseException,
                          de.unirostock.sems.bives.exception.BivesDocumentConsistencyException

Instantiates a new SBML unit definition.

Parameters:

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

sbmlModel - the SBML model

Throws:

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

Method Detail

isBaseUnit

public boolean isBaseUnit()

Checks if this is a base unit.

Returns:

true, if it is a base unit

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

markup

public String markup()

Specified by:

markup in interface de.unirostock.sems.bives.markup.Markup