org.sigpath.datamodel
Interface Complex

All Superinterfaces:

Chemical, Collectable, MacroMolecule, SigPathEntity

All Known Implementing Classes:

ComplexImpl

public interface Complex
extends MacroMolecule

Represents a complex of Chemicals. A Complex can represent a protein/protein interaction complex, a protein/lipid complex, a protein/DNA complex, etc. This is possible as the the complex is defined as an aggregate of Chemicals.

Version:

$Revision: 5731 $

Author:

Fabien Campagne

Method Summary

void	addMonomer(Chemical chemical) Adds a monomer to this complex.
void	addMonomer(Chemical chemical, int stoechiometry) Adds a monomer to this complex.
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 fully-defined value of this complex.
void	setFullyDefined(boolean fullyDefined) Indicate whether or not this Complex has been fully defined.

Methods inherited from interface org.sigpath.datamodel.Chemical

contains, 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

Method Detail

getComponents

Collection getComponents()

Returns the components of this complex.

addMonomer

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.

addMonomer

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.

Parameters:

chemical - Chemical to be added to this complex.

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

getStoechiometry

int getStoechiometry(Chemical chem)

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.

isFullyDefined

boolean isFullyDefined()

Returns the fully-defined value of this complex. True indicates all components are fully defined. False indicates NOT all components are fully defined, and changes (addition or removal) may be made to the components in the future.

setFullyDefined

void setFullyDefined(boolean fullyDefined)

Indicate whether or not this Complex has been fully defined.

Parameters:

fullyDefined -