de.unirostock.sems.bives.ds.rn

Class ReactionNetworkSubstanceRef

java.lang.Object

de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef

All Implemented Interfaces:

GraphEntity

public class ReactionNetworkSubstanceRef
extends Object
implements GraphEntity

The Class ReactionNetworkSubstanceRef representing a reference to a ReactionNetworkSubstance.

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field and Description
SBOTerm	modTermA The optional modification terms in original doc.
SBOTerm	modTermB The optional modification terms in modified doc.
protected boolean	singleDoc The single doc flag if in single-doc-operation-mode.
ReactionNetworkSubstance	subst The substance.

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

DELETE, INSERT, MODIFIED, UNMODIFIED

Constructor Summary

Constructors

Constructor and Description
ReactionNetworkSubstanceRef(ReactionNetworkSubstance subst, boolean flagA, boolean flagB, SBOTerm modTermA, SBOTerm modTermB) Instantiates a new substance reference.

Method Summary

Modifier and Type	Method and Description
int	getModification() Gets the modification.
String	getModTerm() Gets the modifier term.
String	getSBO() Gets the SBOTerm.
ReactionNetworkSubstance	getSubstance() Gets the referenced substance.
void	setFlagA(boolean flagA) Sets the existence flag for the original version.
void	setFlagB(boolean flagB) Sets the existence flag for the modified version.
void	setSboA(SBOTerm modTermA) Sets the SBOTerm as defined in the original version.
void	setSboB(SBOTerm modTermB) Sets the SBOTerm as defined in the modified version.
void	setSingleDocument() Sets the single document flag.

Methods inherited from class java.lang.Object

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

Field Detail

subst

public ReactionNetworkSubstance subst

The substance.

modTermA

public SBOTerm modTermA

The optional modification terms in original doc.

modTermB

public SBOTerm modTermB

The optional modification terms in modified doc.

singleDoc

protected boolean singleDoc

The single doc flag if in single-doc-operation-mode.

Constructor Detail

ReactionNetworkSubstanceRef

public ReactionNetworkSubstanceRef(ReactionNetworkSubstance subst,
                                   boolean flagA,
                                   boolean flagB,
                                   SBOTerm modTermA,
                                   SBOTerm modTermB)
                            throws BivesUnsupportedException

Instantiates a new substance reference.

Parameters:

subst - the substance

flagA - the existence flag for the original version

flagB - the existence flag for the modified version

modTermA - the modification type in the original version

modTermB - the modification type in the original version

Throws:

BivesUnsupportedException

Method Detail

setSboA

public void setSboA(SBOTerm modTermA)
             throws BivesUnsupportedException

Sets the SBOTerm as defined in the original version.

Parameters:

modTermA - the SBOTerm of version A

Throws:

BivesUnsupportedException - indicating that this edge has two different modification properties.

setSboB

public void setSboB(SBOTerm modTermB)
             throws BivesUnsupportedException

Sets the SBOTerm as defined in the modified version.

Parameters:

modTermB - the SBOTerm of version B

Throws:

BivesUnsupportedException - indicating that this edge has two different modification properties.

getSubstance

public ReactionNetworkSubstance getSubstance()

Gets the referenced substance.

Returns:

the substance

setFlagA

public void setFlagA(boolean flagA)

Sets the existence flag for the original version.

Parameters:

flagA - the flag for doc A

setFlagB

public void setFlagB(boolean flagB)

Sets the existence flag for the modified version.

Parameters:

flagB - the flag for doc B

getSBO

public String getSBO()

Gets the SBOTerm.

Returns:

the SBOTerm

getModTerm

public String getModTerm()

Gets the modifier term.

Returns:

the modifier term

getModification

public int getModification()

Gets the modification.

Returns:

the modification

setSingleDocument

public void setSingleDocument()

Sets the single document flag.