Package psidev.psi.mi.jami.tab.extension.factory

Class MitabInteractorFactory

java.lang.Object

psidev.psi.mi.jami.factory.DefaultInteractorFactory

psidev.psi.mi.jami.tab.extension.factory.MitabInteractorFactory

All Implemented Interfaces:

InteractorFactory

public class MitabInteractorFactory
extends DefaultInteractorFactory

The MITAB extension of the InteractorFactory

Since:

18/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MitabInteractorFactory()	Constructor for MitabInteractorFactory.

Method Summary

Modifier and Type	Method	Description
MitabBioactiveEntity	createBioactiveEntity(String name, CvTerm type)	Creates a new BioactiveEntity with the name and interactor type
MitabComplex	createComplex(String name, CvTerm type)	Creates a new Complex with the name and interactor type
MitabGene	createGene(String name)	Creates a new Gene with the name
MitabInteractor	createInteractor(String name, CvTerm type)	Creates a default interactor from the name and interactor type
Interactor	createInteractorFromInteractorTypes(Collection<MitabCvTerm> types, String name)	Return the proper instance of the interactor if at least one type is recognized (always take the first recognized type).
MitabInteractorPool	createInteractorSet(String name, CvTerm type)	Creates an interactor pool from the name and interactor type
MitabNucleicAcid	createNucleicAcid(String name, CvTerm type)	Creates a new NucleicAcid with the name and interactor type
MitabPolymer	createPolymer(String name, CvTerm type)	Creates a new Polymer with the name and interactor type
MitabProtein	createProtein(String name, CvTerm type)	Creates a new Protein with the name and interactor type

Methods inherited from class psidev.psi.mi.jami.factory.DefaultInteractorFactory

createInteractorFromDatabase, createInteractorFromIdentityXrefs, createInteractorFromInteractorType, createInteractorFromRecognizedCategory, extractCvTermFromKey, initialiseDeterministicInteractorMaps, loadProperties

Methods inherited from class java.lang.Object

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

Constructor Detail

MitabInteractorFactory

public MitabInteractorFactory()

Constructor for MitabInteractorFactory.

Method Detail

createProtein

public MitabProtein createProtein(String name,
                                  CvTerm type)

Creates a new Protein with the name and interactor type Creates a new Protein with the name and interactor type

Specified by:

createProtein in interface InteractorFactory

Overrides:

createProtein in class DefaultInteractorFactory

Parameters:

name - : short name

type - : interactor type

Returns:

created protein

createNucleicAcid

public MitabNucleicAcid createNucleicAcid(String name,
                                          CvTerm type)

Creates a new NucleicAcid with the name and interactor type Creates a new NucleicAcid with the name and interactor type

Specified by:

createNucleicAcid in interface InteractorFactory

Overrides:

createNucleicAcid in class DefaultInteractorFactory

Parameters:

name - : short name

type - : interactor type

Returns:

created nucleic acid

createGene

public MitabGene createGene(String name)

Creates a new Gene with the name Creates a new Gene with the name

Specified by:

createGene in interface InteractorFactory

Overrides:

createGene in class DefaultInteractorFactory

Parameters:

name - : name

Returns:

created gene

createComplex

public MitabComplex createComplex(String name,
                                  CvTerm type)

Creates a new Complex with the name and interactor type Creates a new Complex with the name and interactor type

Specified by:

createComplex in interface InteractorFactory

Overrides:

createComplex in class DefaultInteractorFactory

Parameters:

name - : short name

type - : interactor type

Returns:

created complex

createBioactiveEntity

public MitabBioactiveEntity createBioactiveEntity(String name,
                                                  CvTerm type)

Creates a new BioactiveEntity with the name and interactor type Creates a new BioactiveEntity with the name and interactor type

Specified by:

createBioactiveEntity in interface InteractorFactory

Overrides:

createBioactiveEntity in class DefaultInteractorFactory

Parameters:

name - : short name

type - : interactor type

Returns:

created bioactive entity

createPolymer

public MitabPolymer createPolymer(String name,
                                  CvTerm type)

Creates a new Polymer with the name and interactor type Creates a new Polymer with the name and interactor type

Specified by:

createPolymer in interface InteractorFactory

Overrides:

createPolymer in class DefaultInteractorFactory

Parameters:

name - : short name

type - : interactor type

Returns:

created polymer

createInteractor

public MitabInteractor createInteractor(String name,
                                        CvTerm type)

Creates a default interactor from the name and interactor type Creates a default interactor from the name and interactor type

Specified by:

createInteractor in interface InteractorFactory

Overrides:

createInteractor in class DefaultInteractorFactory

Parameters:

name - : short name

type - : interactor type

Returns:

created default interactor

createInteractorSet

public MitabInteractorPool createInteractorSet(String name,
                                               CvTerm type)

Creates an interactor pool from the name and interactor type Creates an interactor pool from the name and interactor type

Specified by:

createInteractorSet in interface InteractorFactory

Overrides:

createInteractorSet in class DefaultInteractorFactory

Parameters:

name - : short name

type - : interactor type

Returns:

created interactor pool

createInteractorFromInteractorTypes

public Interactor createInteractorFromInteractorTypes(Collection<MitabCvTerm> types,
                                                      String name)

Return the proper instance of the interactor if at least one type is recognized (always take the first recognized type). It returns null otherwise.

Parameters:

types - a Collection object.

name - a String object.

Returns:

the proper instance of the interactor if at least one type (always take the first recognized type) is recognized. It returns null otherwise.