Package de.unirostock.sems.bives.cellml.parser

Class CellMLReaction

java.lang.Object

de.unirostock.sems.bives.cellml.parser.CellMLEntity

de.unirostock.sems.bives.cellml.parser.CellMLReaction

All Implemented Interfaces:

de.unirostock.sems.bives.algorithm.DiffReporter

public class CellMLReaction
extends CellMLEntity
implements de.unirostock.sems.bives.algorithm.DiffReporter

The Class CellMLReaction representing a reaction defined in a CellML model.

Author:

Martin Scharm

Field Summary

Fields inherited from class de.unirostock.sems.bives.cellml.parser.CellMLEntity

model

Constructor Summary

Constructors

Constructor	Description
CellMLReaction(CellMLModel model, CellMLComponent component, de.unirostock.sems.xmlutils.ds.DocumentNode node)	Instantiates a new CellML reaction.

Method Summary

Modifier and Type	Method	Description
CellMLComponent	getComponent()	Gets the component defining this reaction.
List<CellMLReactionSubstance>	getSubstances()	Gets the substances taking part in the reaction.
boolean	isReversible()	Checks if this reaction is reversible.
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 de.unirostock.sems.bives.cellml.parser.CellMLEntity

associateRdfDescription, flagMetaModifcations, getDocumentNode, getMetaId, getModel, getRdfBlocks, getRdfDescriptions, setMetaId, setModel

Methods inherited from class java.lang.Object

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

Constructor Detail

CellMLReaction

public CellMLReaction(CellMLModel model,
                      CellMLComponent component,
                      de.unirostock.sems.xmlutils.ds.DocumentNode node)
               throws de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                      BivesCellMLParseException,
                      de.unirostock.sems.bives.exception.BivesLogicalException

Instantiates a new CellML reaction.

Parameters:

model - the model defining this reaction

component - the component this reaction belongs to

node - the corresponding document node in the XML tree

Throws:

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

BivesCellMLParseException - the bives cell ml parse exception

de.unirostock.sems.bives.exception.BivesLogicalException

Method Detail

getSubstances

public List<CellMLReactionSubstance> getSubstances()

Gets the substances taking part in the reaction.

Returns:

the substances

getComponent

public CellMLComponent getComponent()

Gets the component defining this reaction.

Returns:

the component

isReversible

public boolean isReversible()

Checks if this reaction is reversible.

Returns:

true, if is reversible

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