Package psidev.psi.mi.jami.utils

Class InteractorUtils

java.lang.Object

psidev.psi.mi.jami.utils.InteractorUtils

public class InteractorUtils
extends Object

Factory for interactors

Since:

11/02/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
InteractorUtils()

Method Summary

Modifier and Type	Method	Description
static BioactiveEntity	createBioactiveEntityChebi(String name, String chebi)	createBioactiveEntityChebi
static BioactiveEntity	createBioactiveEntitySmile(String name, String smile)	createBioactiveEntitySmile
static BioactiveEntity	createBioactiveEntityStandardInchi(String name, String standard)	createBioactiveEntityStandardInchi
static BioactiveEntity	createBioactiveEntityStandardInchiKey(String name, String key)	createBioactiveEntityStandardInchiKey
static Gene	createGeneEnsembl(String name, String identity)	createGeneEnsembl
static Gene	createGeneEnsemblGenomes(String name, String identity)	createGeneEnsemblGenomes
static Gene	createGeneEntrezGene(String name, String identity)	createGeneEntrezGene
static Gene	createGeneRefseq(String name, String identity)	createGeneRefseq
static NucleicAcid	createNucleicAcidDdbjEmblGenbank(String name, String identity)	createNucleicAcidDdbjEmblGenbank
static NucleicAcid	createNucleicAcidRefseq(String name, String identity)	createNucleicAcidRefseq
static Polymer	createPolymer(String name, String sequence)	createPolymer
static Protein	createProteinGeneName(String name, String geneName)	createProteinGeneName
static Protein	createProteinRefseq(String name, String refseq)	createProteinRefseq
static Protein	createProteinRogid(String name, String rogid)	createProteinRogid
static Protein	createProteinUniprot(String name, String uniprot)	createProteinUniprot
static Interactor	createUnknownBasicInteractor()	createUnknownBasicInteractor
static boolean	doesInteractorHaveType(Interactor interactor, String typeId, String typeName)	To know if an interactor have a specific interactor type.

Methods inherited from class java.lang.Object

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

Constructor Detail

InteractorUtils

public InteractorUtils()

Method Detail

createUnknownBasicInteractor

public static Interactor createUnknownBasicInteractor()

createUnknownBasicInteractor

Returns:

a Interactor object.

doesInteractorHaveType

public static boolean doesInteractorHaveType(Interactor interactor,
                                             String typeId,
                                             String typeName)

To know if an interactor have a specific interactor type.

Parameters:

interactor - a Interactor object.

typeId - a String object.

typeName - a String object.

Returns:

true if the interactor has the type with given name/identifier

createProteinUniprot

public static Protein createProteinUniprot(String name,
                                           String uniprot)

createProteinUniprot

Parameters:

name - a String object.

uniprot - a String object.

Returns:

a Protein object.

createProteinRefseq

public static Protein createProteinRefseq(String name,
                                          String refseq)

createProteinRefseq

Parameters:

name - a String object.

refseq - a String object.

Returns:

a Protein object.

createProteinGeneName

public static Protein createProteinGeneName(String name,
                                            String geneName)

createProteinGeneName

Parameters:

name - a String object.

geneName - a String object.

Returns:

a Protein object.

createProteinRogid

public static Protein createProteinRogid(String name,
                                         String rogid)

createProteinRogid

Parameters:

name - a String object.

rogid - a String object.

Returns:

a Protein object.

createBioactiveEntityChebi

public static BioactiveEntity createBioactiveEntityChebi(String name,
                                                         String chebi)

createBioactiveEntityChebi

Parameters:

name - a String object.

chebi - a String object.

Returns:

a BioactiveEntity object.

createBioactiveEntitySmile

public static BioactiveEntity createBioactiveEntitySmile(String name,
                                                         String smile)

createBioactiveEntitySmile

Parameters:

name - a String object.

smile - a String object.

Returns:

a BioactiveEntity object.

createBioactiveEntityStandardInchi

public static BioactiveEntity createBioactiveEntityStandardInchi(String name,
                                                                 String standard)

createBioactiveEntityStandardInchi

Parameters:

name - a String object.

standard - a String object.

Returns:

a BioactiveEntity object.

createBioactiveEntityStandardInchiKey

public static BioactiveEntity createBioactiveEntityStandardInchiKey(String name,
                                                                    String key)

createBioactiveEntityStandardInchiKey

Parameters:

name - a String object.

key - a String object.

Returns:

a BioactiveEntity object.

createNucleicAcidDdbjEmblGenbank

public static NucleicAcid createNucleicAcidDdbjEmblGenbank(String name,
                                                           String identity)

createNucleicAcidDdbjEmblGenbank

Parameters:

name - a String object.

identity - a String object.

Returns:

a NucleicAcid object.

createNucleicAcidRefseq

public static NucleicAcid createNucleicAcidRefseq(String name,
                                                  String identity)

createNucleicAcidRefseq

Parameters:

name - a String object.

identity - a String object.

Returns:

a NucleicAcid object.

createGeneRefseq

public static Gene createGeneRefseq(String name,
                                    String identity)

createGeneRefseq

Parameters:

name - a String object.

identity - a String object.

Returns:

a Gene object.

createGeneEnsembl

public static Gene createGeneEnsembl(String name,
                                     String identity)

createGeneEnsembl

Parameters:

name - a String object.

identity - a String object.

Returns:

a Gene object.

createGeneEnsemblGenomes

public static Gene createGeneEnsemblGenomes(String name,
                                            String identity)

createGeneEnsemblGenomes

Parameters:

name - a String object.

identity - a String object.

Returns:

a Gene object.

createGeneEntrezGene

public static Gene createGeneEntrezGene(String name,
                                        String identity)

createGeneEntrezGene

Parameters:

name - a String object.

identity - a String object.

Returns:

a Gene object.

createPolymer

public static Polymer createPolymer(String name,
                                    String sequence)

createPolymer

Parameters:

name - a String object.

sequence - a String object.

Returns:

a Polymer object.