org.sigpath.datamodel
Class ComplexImpl

java.lang.Object
  org.sigpath.datamodel.lset.CollectableImpl
      org.sigpath.datamodel.SigPathEntityImpl
          org.sigpath.datamodel.ChemicalImpl
              org.sigpath.datamodel.ComplexImpl

All Implemented Interfaces:

InstanceCallbacks, Chemical, Complex, Collectable, MacroMolecule, SigPathEntity

public class ComplexImpl
extends ChemicalImpl
implements Complex

Implements Complex.

Version:

$Revision: 7329 $

Author:

Fabien Campagne

Field Summary

Fields inherited from class org.sigpath.datamodel.SigPathEntityImpl

forwardReferences

Constructor Summary

	ComplexImpl() Default constructor.
protected	ComplexImpl(SigPathFactory factory)
protected	ComplexImpl(SigPathFactory factory, String spid)

Method Summary

void	addMonomer(Chemical chemical) Adds a monomer to this complex.
void	addMonomer(Chemical chemical, int stoechiometry) Adds a monomer to this complex.
boolean	contains(Chemical part) Does the chemical contain this part.
Collection	getComponents() Returns the components of this complex.
int	getStoechiometry(Chemical chem) Returns the stoechiometry of the chemical in the complex.
boolean	isFullyDefined() Returns the fullyDefined value of this complex.
void	setFullyDefined(boolean fullyDefined) Sets the fullyDefined value of this complex.

Methods inherited from class org.sigpath.datamodel.ChemicalImpl

addBecomesInfo, addComesFromInfo, getBecomes, getComesFrom, getForwardReferences, getOrganism, involvedIn, isBackgroundInformation, jdoPreDelete, setInvolvedIn, setInvolvedIn, setInvolvedIn, setInvolvedIn, setInvolvedIn, setOrganism

Methods inherited from class org.sigpath.datamodel.SigPathEntityImpl

addAlias, addAliases, addAliases, addReview, addUserComment, changeAlias, getAliases, getAliasesCollection, getAliasesIterator, getChangeLog, getCombinedStringLength, getComments, getDescription, getExternalReferences, getLiteratureReferences, getName, getReviews, getSpid, getUserComments, isExportable, isIndexed, jdoPostLoad, jdoPreClear, jdoPreStore, removeAlias, removeAliases, removeReviews, setAliases, setAliasesCollection, setChangeLog, setComments, setDescription, setExportable, setForwardReferences, setIndexed, setName, setSpid

Methods inherited from class org.sigpath.datamodel.lset.CollectableImpl

createCollectionsSet, getCollections

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.sigpath.datamodel.Chemical

getBecomes, getComesFrom, getOrganism, involvedIn, isBackgroundInformation, setInvolvedIn, setInvolvedIn, setInvolvedIn, setOrganism

Methods inherited from interface org.sigpath.datamodel.SigPathEntity

addAlias, addAliases, addReview, addUserComment, changeAlias, getAliases, getAliasesCollection, getAliasesIterator, getChangeLog, getCombinedStringLength, getComments, getDescription, getExternalReferences, getForwardReferences, getLiteratureReferences, getName, getReviews, getSpid, getUserComments, isExportable, removeAlias, removeAliases, removeReviews, setAliases, setAliasesCollection, setChangeLog, setComments, setDescription, setExportable, setName, setSpid

Methods inherited from interface org.sigpath.datamodel.lset.Collectable

getCollections

Constructor Detail

ComplexImpl

public ComplexImpl()

Default constructor.

ComplexImpl

protected ComplexImpl(SigPathFactory factory)

ComplexImpl

protected ComplexImpl(SigPathFactory factory,
                      String spid)

Method Detail

getComponents

public Collection getComponents()

Returns the components of this complex.

Specified by:

getComponents in interface Complex

addMonomer

public void addMonomer(Chemical chemical)

Adds a monomer to this complex. Use this to add one monomer to a complex when the stoechiometry of the monomer in the complex is 1.

Specified by:

addMonomer in interface Complex

Parameters:

chemical - The chemical to add to this complex

addMonomer

public void addMonomer(Chemical chemical,
                       int stoechiometry)

Adds a monomer to this complex. Use this to add one monomer to a complex when the stoechiometry of the monomer can be more than 1 in the complex.

Specified by:

addMonomer in interface Complex

Parameters:

chemical - Chemical to be added to this complex.

stoechiometry - Stoechiometry of the monomer in the complex. (1+ are valid values for the stoechiometry).

contains

public boolean contains(Chemical part)

Does the chemical contain this part. A complex contains each monomer and their parts.

Specified by:

contains in interface Chemical

Overrides:

contains in class ChemicalImpl

Returns:

True if the entity contains this part. False otherwise.

getStoechiometry

public int getStoechiometry(Chemical chem)

Description copied from interface: Complex

Returns the stoechiometry of the chemical in the complex. This is the number of time the chemical appears at the first level of this complex. in complex A.A.A.B, stoechiometry of A is 3 and stoechiometry of B is 1. In a recursive complexe such as (A.B).A.A.B, only the first level is considered. Therefore, stoechiometry of A is 2, stoechiometry of B is 1, and stoechiometry of A.B is 1.

Specified by:

getStoechiometry in interface Complex

isFullyDefined

public boolean isFullyDefined()

Returns the fullyDefined value of this complex.

Specified by:

isFullyDefined in interface Complex

Returns:

true if the complex is fully defined

setFullyDefined

public void setFullyDefined(boolean fullyDefined)

Sets the fullyDefined value of this complex.

Specified by:

setFullyDefined in interface Complex