org.sigpath.datamodel
Class ChemicalImpl

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

All Implemented Interfaces:

InstanceCallbacks, Chemical, Collectable, SigPathEntity

Direct Known Subclasses:

BioPolymerImpl, ComplexImpl, NamedChemical, SmallMoleculeImpl

public class ChemicalImpl
extends SigPathEntityImpl
implements Chemical

Represents a chemical compound, either protein, DNA, complex, or small molecule. Subclasses are provided which classify Chemicals into more specific categories.

Version:

$Revision: 9227 $

Author:

Fabien Campagne

Field Summary

Fields inherited from class org.sigpath.datamodel.SigPathEntityImpl

forwardReferences

Constructor Summary

	ChemicalImpl()
protected	ChemicalImpl(SigPathFactory factory)
protected	ChemicalImpl(SigPathFactory factory, String spid)

Method Summary

void	addBecomesInfo(BecomesInfo info) Add information about one chemical that this chemical can become.
void	addComesFromInfo(ComesFromInfo info) Add information about one chemical that this chemical can come from.
boolean	contains(Chemical part) Does the chemical contain this part.
Collection	getBecomes() Gets information about the chemicals that this chemical becomes.
Collection	getComesFrom() Gets information about the chemical that this chemical comes from
Set	getForwardReferences() Chemicals do not reference other entities and always return an empty set.
Organism	getOrganism() Returns the organism which produces this chemical.
Set	involvedIn() Returns a Set of Reactions/EnzymaticReactions with which this Chemical is involved with
boolean	isBackgroundInformation() Is this chemical background information.
void	jdoPreDelete()
void	setInvolvedIn(EnzymaticReaction er, boolean state) Adds/Removes an EnzymaticReaction to the Set of reactions/enzymaticReactions this Chemical is involvedIn
void	setInvolvedIn(EnzymaticReaction er, boolean state, SigPathFactory factory)
void	setInvolvedIn(NamedChemicalInteraction nci, boolean state) Makes or destroys the "involved in" association to a Named Chemical Interaction.
void	setInvolvedIn(Reaction reaction, boolean state) Adds/Removes a Reaction to the Set of reactions/enzymaticReactions this Chemical is involvedIn
void	setInvolvedIn(Reaction reaction, boolean state, SigPathFactory factory)
void	setOrganism(Organism o) Sets the organism which produces this chemical.

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.SigPathEntity

addAlias, addAliases, addReview, addUserComment, changeAlias, getAliases, getAliasesCollection, getAliasesIterator, getChangeLog, getCombinedStringLength, getComments, getDescription, getExternalReferences, 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

ChemicalImpl

public ChemicalImpl()

ChemicalImpl

protected ChemicalImpl(SigPathFactory factory)

ChemicalImpl

protected ChemicalImpl(SigPathFactory factory,
                       String spid)

Method Detail

getBecomes

public Collection getBecomes()

Gets information about the chemicals that this chemical becomes.

Specified by:

getBecomes in interface Chemical

Returns:

Collection of BecomesInfo instances.

See Also:

BecomesInfo

getComesFrom

public Collection getComesFrom()

Gets information about the chemical that this chemical comes from

Specified by:

getComesFrom in interface Chemical

Returns:

Collection of ComesFromInfo instances.

See Also:

ComesFromInfo

getOrganism

public Organism getOrganism()

Returns the organism which produces this chemical.

Specified by:

getOrganism in interface Chemical

contains

public boolean contains(Chemical part)

Does the chemical contain this part. A complex contains each monomer and their parts, and other molecules contains themselves.

Specified by:

contains in interface Chemical

Returns:

True if the entity contains this part. False otherwise.

setOrganism

public void setOrganism(Organism o)

Sets the organism which produces this chemical.

Specified by:

setOrganism in interface Chemical

involvedIn

public Set involvedIn()

Returns a Set of Reactions/EnzymaticReactions with which this Chemical is involved with

Specified by:

involvedIn in interface Chemical

Returns:

Set of Reactions/EnzymaticReactions

setInvolvedIn

public void setInvolvedIn(Reaction reaction,
                          boolean state)

Adds/Removes a Reaction to the Set of reactions/enzymaticReactions this Chemical is involvedIn

Specified by:

setInvolvedIn in interface Chemical

Parameters:

reaction - Reaction with which this Chemical is involved in

state - boolean value of adding or removing reaction from the list of reactions/enzymaticReactions this Chemical is involved in.

See Also:

Chemical.involvedIn()

setInvolvedIn

public void setInvolvedIn(EnzymaticReaction er,
                          boolean state)

Adds/Removes an EnzymaticReaction to the Set of reactions/enzymaticReactions this Chemical is involvedIn

Specified by:

setInvolvedIn in interface Chemical

Parameters:

er - EnzymaticReaction with which this Chemical is involved in

state - boolean value of adding or removing er from the list of reactions/enzymaticReactions this Chemical is involved in.

See Also:

Chemical.involvedIn()

setInvolvedIn

public void setInvolvedIn(NamedChemicalInteraction nci,
                          boolean state)

Description copied from interface: Chemical

Makes or destroys the "involved in" association to a Named Chemical Interaction. Involved in association describes the fact that the chemical a is/is not involved in the interaction nci. a.setInvolvedIn(er, "true") means that the chemical a is involved in nci. In this case, involvedIn() will return a collection that contains nci.

Specified by:

setInvolvedIn in interface Chemical

Parameters:

nci - NamedChemicalInteraction in which this chemical is involved.

state - True when the chemical is involved in the Named Chemical Interaction, False otherwise.

See Also:

Chemical.involvedIn()

isBackgroundInformation

public boolean isBackgroundInformation()

Description copied from interface: Chemical

Is this chemical background information. A chemical is background information if it not the result of the transformation of another chemical described in sigpath. Background information is usually imported from other biological databases than SigPath, and have appropriate links (database, accession codes pairs).

Specified by:

isBackgroundInformation in interface Chemical

addBecomesInfo

public void addBecomesInfo(BecomesInfo info)

Add information about one chemical that this chemical can become. This method is not part of the interface. It is reserved for SigPath's use. BecomesInfo will be regenerated automatically from reaction data. clearBecomes() should be called before new targets are added with addBecomesInfo().

addComesFromInfo

public void addComesFromInfo(ComesFromInfo info)

Add information about one chemical that this chemical can come from. This method is not part of the interface. It is reserved for SigPath's use. ComesFromInfo will be regenerated automatically from reaction data. clearComesFrom() should be called before new targets are added with addComesFrom().

setInvolvedIn

public void setInvolvedIn(Reaction reaction,
                          boolean state,
                          SigPathFactory factory)

setInvolvedIn

public void setInvolvedIn(EnzymaticReaction er,
                          boolean state,
                          SigPathFactory factory)

getForwardReferences

public Set getForwardReferences()

Chemicals do not reference other entities and always return an empty set.

Specified by:

getForwardReferences in interface SigPathEntity

Returns:

Empty set.

jdoPreDelete

public void jdoPreDelete()

Specified by:

jdoPreDelete in interface InstanceCallbacks

Overrides:

jdoPreDelete in class SigPathEntityImpl