Package psidev.psi.mi.jami.model.impl

Class DefaultBioactiveEntity

java.lang.Object

psidev.psi.mi.jami.model.impl.DefaultInteractor

psidev.psi.mi.jami.model.impl.DefaultMolecule

psidev.psi.mi.jami.model.impl.DefaultBioactiveEntity

All Implemented Interfaces:

BioactiveEntity, Interactor, Molecule

Direct Known Subclasses:

MitabBioactiveEntity, XmlBioactiveEntity, XmlBioactiveEntity, XmlBioactiveEntity

public class DefaultBioactiveEntity
extends DefaultMolecule
implements BioactiveEntity

Default implementation for bioactive entity Notes: The equals and hashcode methods have NOT been overridden because the BioactiveEntity object is a complex object. To compare BioactiveEntity objects, you can use some comparators provided by default: - DefaultBioactiveEntityComparator - UnambiguousBioactiveEntityComparator - DefaultExactBioactiveEntityComparator - UnambiguousExactBioactiveEntityComparator - BioactiveEntityComparator

Since:

24/01/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from interface psidev.psi.mi.jami.model.BioactiveEntity

BIOACTIVE_ENTITY, BIOACTIVE_ENTITY_MI, POLYSACCHARIDE, POLYSACCHARIDE_MI, SMALL_MOLECULE, SMALL_MOLECULE_MI

Fields inherited from interface psidev.psi.mi.jami.model.Interactor

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

Constructor Summary

Constructors

Constructor	Description
DefaultBioactiveEntity(String name)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, String uniqueChebi)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, CvTerm type)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, CvTerm type, String uniqueChebi)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, CvTerm type, Organism organism)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, String uniqueChebi)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, Organism organism)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, Organism organism, String uniqueChebi)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, CvTerm type)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, CvTerm type, Organism organism)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, CvTerm type, Organism organism, String uniqueChebi)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, Organism organism)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, Organism organism, String uniqueChebi)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, Organism organism, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, Xref uniqueId)	Constructor for DefaultBioactiveEntity.

Method Summary

Modifier and Type	Method	Description
protected void	clearPropertiesLinkedToChecksums()	clearPropertiesLinkedToChecksums
protected void	clearPropertiesLinkedToIdentifiers()
String	getChebi()	Getter for the field chebi.
Xref	getPreferredIdentifier()	getPreferredIdentifier
String	getSmile()	Getter for the field smile.
String	getStandardInchi()	Getter for the field standardInchi.
String	getStandardInchiKey()	Getter for the field standardInchiKey.
protected void	initialiseChecksums()	initialiseChecksums
protected void	initialiseIdentifiers()	initialiseIdentifiers
protected void	processAddedChecksumEvent(Checksum added)	processAddedChecksumEvent
protected void	processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	processRemovedChecksumEvent(Checksum removed)	processRemovedChecksumEvent
protected void	processRemovedIdentifierEvent(Xref removed)
void	setChebi(String id)	Sets the CHEBI identifier.
void	setInteractorType(CvTerm interactorType)	Sets the interactor type of this bioactive entity.
void	setSmile(String smile)	Sets the smile of this small molecule.
void	setStandardInchi(String inchi)	Sets the standard InChI.
void	setStandardInchiKey(String key)	Sets the standard InChI key .
String	toString()

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultInteractor

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getPreferredName, getShortName, getXrefs, initialiseAliases, initialiseAliasesWith, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksumsWith, initialiseIdentifiersWith, initialiseXrefs, initialiseXrefsWith, setFullName, setOrganism, setShortName

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.model.Interactor

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getPreferredName, getShortName, getXrefs, setFullName, setOrganism, setShortName

Constructor Detail

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              CvTerm type)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              CvTerm type)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              CvTerm type,
                              Organism organism)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              CvTerm type,
                              Organism organism)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              CvTerm type,
                              Xref uniqueId)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              CvTerm type,
                              Xref uniqueId)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              CvTerm type,
                              Organism organism,
                              Xref uniqueId)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              CvTerm type,
                              Organism organism,
                              Xref uniqueId)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              CvTerm type,
                              String uniqueChebi)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueChebi - a String object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              CvTerm type,
                              Organism organism,
                              String uniqueChebi)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueChebi - a String object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              CvTerm type,
                              Organism organism,
                              String uniqueChebi)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueChebi - a String object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              Organism organism)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

organism - a Organism object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              Organism organism)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              Xref uniqueId)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

uniqueId - a Xref object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              Xref uniqueId)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              Organism organism,
                              Xref uniqueId)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              Organism organism,
                              Xref uniqueId)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              String uniqueChebi)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

uniqueChebi - a String object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              Organism organism,
                              String uniqueChebi)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

organism - a Organism object.

uniqueChebi - a String object.

DefaultBioactiveEntity

public DefaultBioactiveEntity(String name,
                              String fullName,
                              Organism organism,
                              String uniqueChebi)

Constructor for DefaultBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueChebi - a String object.

Method Detail

initialiseIdentifiers

protected void initialiseIdentifiers()

initialiseIdentifiers

Overrides:

initialiseIdentifiers in class DefaultInteractor

initialiseChecksums

protected void initialiseChecksums()

initialiseChecksums

Overrides:

initialiseChecksums in class DefaultInteractor

getPreferredIdentifier

public Xref getPreferredIdentifier()

getPreferredIdentifier

Return the first chebi identifier if provided, otherwise the first identifier in the list of identifiers

Specified by:

getPreferredIdentifier in interface Interactor

Overrides:

getPreferredIdentifier in class DefaultInteractor

Returns:

the first identifier in the list of identifiers or null if the list is empty

getChebi

public String getChebi()

Getter for the field chebi.

Specified by:

getChebi in interface BioactiveEntity

Returns:

a String object.

setChebi

public void setChebi(String id)

Sets the CHEBI identifier. It will remove the old chebi identifier from the collection of identifiers and replace it with the new chebi identifier. If the new chebi identifier is null, all the existing chebi identifiers will be removed from the collection of identifiers

Specified by:

setChebi in interface BioactiveEntity

Parameters:

id - : CHEBI identifier

getSmile

public String getSmile()

Getter for the field smile.

Specified by:

getSmile in interface BioactiveEntity

Returns:

a String object.

setSmile

public void setSmile(String smile)

Sets the smile of this small molecule. It will remove the old smile from the collection of checksums and replace it with the new smile. If the new smile is null, all the existing smiles will be removed from the collection of checksums

Specified by:

setSmile in interface BioactiveEntity

Parameters:

smile - : the smile

getStandardInchiKey

public String getStandardInchiKey()

Getter for the field standardInchiKey.

Specified by:

getStandardInchiKey in interface BioactiveEntity

Returns:

a String object.

setStandardInchiKey

public void setStandardInchiKey(String key)

Sets the standard InChI key . It will remove the old standard inchi key from the collection of checksums and replace it with the new standard inchi key. If the new standard inchi key is null, all the existing standard inchi keys will be removed from the collection of checksums

Specified by:

setStandardInchiKey in interface BioactiveEntity

Parameters:

key - : the standard inchi key

getStandardInchi

public String getStandardInchi()

Getter for the field standardInchi.

Specified by:

getStandardInchi in interface BioactiveEntity

Returns:

a String object.

setStandardInchi

public void setStandardInchi(String inchi)

Sets the standard InChI. It will remove the old standard inchi from the collection of checksums and replace it with the new standard inchi. If the new standard is null, all the existing standard inchi will be removed from the collection of checksums

Specified by:

setStandardInchi in interface BioactiveEntity

Parameters:

inchi - : the standard InChI

processAddedChecksumEvent

protected void processAddedChecksumEvent(Checksum added)

processAddedChecksumEvent

Parameters:

added - a Checksum object.

processRemovedChecksumEvent

protected void processRemovedChecksumEvent(Checksum removed)

processRemovedChecksumEvent

Parameters:

removed - a Checksum object.

clearPropertiesLinkedToChecksums

protected void clearPropertiesLinkedToChecksums()

clearPropertiesLinkedToChecksums

processAddedIdentifierEvent

protected void processAddedIdentifierEvent(Xref added)

processAddedIdentifierEvent

Parameters:

added - a Xref object.

processRemovedIdentifierEvent

protected void processRemovedIdentifierEvent(Xref removed)

processRemovedIdentifierEvent

Parameters:

removed - a Xref object.

clearPropertiesLinkedToIdentifiers

protected void clearPropertiesLinkedToIdentifiers()

setInteractorType

public void setInteractorType(CvTerm interactorType)

Sets the interactor type of this bioactive entity. If the given interactorType is null, it sets the interactorType to 'bioactive entity'(MI:1100)

Specified by:

setInteractorType in interface Interactor

Overrides:

setInteractorType in class DefaultInteractor

Parameters:

interactorType - : molecule type

toString

public String toString()

Overrides:

toString in class DefaultInteractor