de.unirostock.sems.bives.ds.rn

Class ReactionNetworkSubstance

java.lang.Object

de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity

de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstance

All Implemented Interfaces:

GraphEntity

public class ReactionNetworkSubstance
extends ReactionNetworkEntity

The Class ReactionNetworkSubstance representing a substance in a reaction network.

Author:

Martin Scharm

Field Summary

Fields inherited from class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity

docA, docB, id, labelA, labelB, singleDoc

Fields inherited from interface de.unirostock.sems.bives.ds.GraphEntity

DELETE, INSERT, MODIFIED, UNMODIFIED

Constructor Summary

Constructors

Constructor and Description
ReactionNetworkSubstance(ReactionNetwork rn, String labelA, String labelB, de.unirostock.sems.xmlutils.ds.DocumentNode docA, de.unirostock.sems.xmlutils.ds.DocumentNode docB, ReactionNetworkCompartment compartmentA, ReactionNetworkCompartment compartmentB) Instantiates a new substance in a reaction network.

Method Summary

Modifier and Type	Method and Description
ReactionNetworkCompartment	getCompartment() Gets the compartment.
String	getSBO() Gets the SBOTerm describing this substance.
void	setCompartmentA(ReactionNetworkCompartment compartment) Sets the compartment in original version.
void	setCompartmentB(ReactionNetworkCompartment compartment) Sets the compartment in modified version.

Methods inherited from class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity

getA, getB, getId, getLabel, getModification, setDocA, setDocB, setLabelA, setLabelB, setSingleDocument

Methods inherited from class java.lang.Object

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

Constructor Detail

ReactionNetworkSubstance

public ReactionNetworkSubstance(ReactionNetwork rn,
                                String labelA,
                                String labelB,
                                de.unirostock.sems.xmlutils.ds.DocumentNode docA,
                                de.unirostock.sems.xmlutils.ds.DocumentNode docB,
                                ReactionNetworkCompartment compartmentA,
                                ReactionNetworkCompartment compartmentB)

Instantiates a new substance in a reaction network.

Parameters:

rn - the reaction network

labelA - the label of that compartment in the original document

labelB - the label of that compartment in the modified document

docA - the original document

docB - the modified document

compartmentA - the compartment a

compartmentB - the compartment b

Method Detail

setCompartmentA

public void setCompartmentA(ReactionNetworkCompartment compartment)

Sets the compartment in original version.

Parameters:

compartment - the compartment in original version

setCompartmentB

public void setCompartmentB(ReactionNetworkCompartment compartment)

Sets the compartment in modified version.

Parameters:

compartment - the compartment in modified version

getCompartment

public ReactionNetworkCompartment getCompartment()

Gets the compartment. Will return:

• the original compartment, if it's the same compartment as in the modified version
• null, otherwise

Returns:

the compartment

getSBO

public String getSBO()

Gets the SBOTerm describing this substance.

Returns:

the SBOTerm