de.unirostock.sems.bives.ds.rn

Class ReactionNetworkReaction

java.lang.Object

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

de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction

All Implemented Interfaces:

GraphEntity

public class ReactionNetworkReaction
extends ReactionNetworkEntity

The Class ReactionNetworkReaction representing a reaction 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
ReactionNetworkReaction(ReactionNetwork rn, String labelA, String labelB, de.unirostock.sems.xmlutils.ds.DocumentNode docA, de.unirostock.sems.xmlutils.ds.DocumentNode docB, ReactionNetworkCompartment compartmentA, ReactionNetworkCompartment compartmentB, boolean reversible) Instantiates a new ReactionNetwork reaction.

Method Summary

Modifier and Type	Method and Description
void	addInputA(ReactionNetworkSubstance subst, SBOTerm sbo) Add a reactant of this reaction in its original version.
void	addInputB(ReactionNetworkSubstance subst, SBOTerm sbo) Add a reactant of this reaction in its modified version.
void	addModA(ReactionNetworkSubstance subst, SBOTerm sbo) Adds the modifier of this reaction in its original version.
void	addModB(ReactionNetworkSubstance subst, SBOTerm sbo) Add a modifier of this reaction in its modified version.
void	addOutputA(ReactionNetworkSubstance subst, SBOTerm sbo) Add a product of this reaction in its original version.
void	addOutputB(ReactionNetworkSubstance subst, SBOTerm sbo) Add a product of this reaction in its modified version.
ReactionNetworkCompartment	getCompartment() Gets the compartment.
Collection<ReactionNetworkSubstanceRef>	getInputs() Gets the reactants.
int	getModification() Gets the modification of this entity.
Collection<ReactionNetworkSubstanceRef>	getModifiers() Gets the modifiers.
Collection<ReactionNetworkSubstanceRef>	getOutputs() Gets the products.
String	getSBO() Gets the sbo.
boolean	isReversible() Checks if is reversible.
void	setCompartmentA(ReactionNetworkCompartment compartment) Sets the compartment in original version.
void	setCompartmentB(ReactionNetworkCompartment compartment) Sets the compartment in modified version.
void	setSingleDocument() Sets the single document flag.

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

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

Methods inherited from class java.lang.Object

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

Constructor Detail

ReactionNetworkReaction

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

Instantiates a new ReactionNetwork reaction.

Parameters:

rn - the reaction network

labelA - the label of that reaction in the original document

labelB - the label of that reaction in the modified document

docA - the original document

docB - the modified document

compartmentA - the compartment a

compartmentB - the compartment b

reversible - the reversible flag

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
• the compartment all substances involved in this reactions are from, if all substances originate from the same compartment
• null, otherwise

Returns:

the compartment

addInputA

public void addInputA(ReactionNetworkSubstance subst,
                      SBOTerm sbo)

Add a reactant of this reaction in its original version.

Parameters:

subst - the substance

sbo - the SBOTerm describing the interaction

addOutputA

public void addOutputA(ReactionNetworkSubstance subst,
                       SBOTerm sbo)

Add a product of this reaction in its original version.

Parameters:

subst - the substance

sbo - the SBOTerm describing the interaction

addModA

public void addModA(ReactionNetworkSubstance subst,
                    SBOTerm sbo)
             throws BivesUnsupportedException

Adds the modifier of this reaction in its original version.

Parameters:

subst - the substance

sbo - the SBOTerm describing the modification

Throws:

BivesUnsupportedException - if one edges contains two types of modifications

addInputB

public void addInputB(ReactionNetworkSubstance subst,
                      SBOTerm sbo)

Add a reactant of this reaction in its modified version.

Parameters:

subst - the substance

sbo - the SBOTerm describing the interaction

addOutputB

public void addOutputB(ReactionNetworkSubstance subst,
                       SBOTerm sbo)

Add a product of this reaction in its modified version.

Parameters:

subst - the substance

sbo - the SBOTerm describing the interaction

addModB

public void addModB(ReactionNetworkSubstance subst,
                    SBOTerm sbo)
             throws BivesUnsupportedException

Add a modifier of this reaction in its modified version.

Parameters:

subst - the substance

sbo - the SBOTerm describing the modification

Throws:

BivesUnsupportedException - if one edges contains two types of modifications

getInputs

public Collection<ReactionNetworkSubstanceRef> getInputs()

Gets the reactants.

Returns:

the reactants

getOutputs

public Collection<ReactionNetworkSubstanceRef> getOutputs()

Gets the products.

Returns:

the products

getModifiers

public Collection<ReactionNetworkSubstanceRef> getModifiers()

Gets the modifiers.

Returns:

the modifiers

getSBO

public String getSBO()

Gets the sbo.

Returns:

the sbo

isReversible

public boolean isReversible()

Checks if is reversible.

Returns:

true, if is reversible

setSingleDocument

public void setSingleDocument()

Sets the single document flag.

Overrides:

setSingleDocument in class ReactionNetworkEntity

getModification

public int getModification()

Description copied from class: ReactionNetworkEntity

Gets the modification of this entity.

Overrides:

getModification in class ReactionNetworkEntity

Returns:

the modification