Package psidev.psi.mi.jami.utils

Class ExperimentUtils

java.lang.Object

psidev.psi.mi.jami.utils.ExperimentUtils

public class ExperimentUtils
extends Object

Factory for experiment

Since:

11/02/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
ExperimentUtils()

Method Summary

Modifier and Type	Method	Description
static Experiment	createBasicExperimentForComplexes()	createBasicExperimentForComplexes
static Experiment	createBasicExperimentForComplexes(int taxid)	createBasicExperimentForComplexes
static Experiment	createBasicExperimentForComplexes(int taxid, String name)	createBasicExperimentForComplexes
static Experiment	createBasicExperimentForModelledInteractions()	createBasicExperimentForModelledInteractions
static NamedExperiment	createExperiment(String name, String pubmedId, CvTerm interactionDetectionMethod, Organism hostOrganism)	createExperiment
static Experiment	createExperiment(String pubmedId, CvTerm interactionDetectionMethod, Organism hostOrganism)	createExperiment
static Experiment	createExperimentWithoutPublication()	createExperimentWithoutPublication
static Experiment	createUnknownBasicExperiment()	createUnknownBasicExperiment
static CvTerm	extractMostCommonParticipantDetectionMethodFrom(Experiment exp)	Compare all participant identification methods in all participant evidences from all the interactions evidences.
static String	getDoiId(Experiment exp)	getDoiId
static Xref	getDoiReference(Experiment exp)	getDoiReference
static String	getPubmedId(Experiment exp)	getPubmedId
static Xref	getPubmedReference(Experiment exp)	getPubmedReference

Methods inherited from class java.lang.Object

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

Constructor Detail

ExperimentUtils

public ExperimentUtils()

Method Detail

createUnknownBasicExperiment

public static Experiment createUnknownBasicExperiment()

createUnknownBasicExperiment

Returns:

a Experiment object.

createExperimentWithoutPublication

public static Experiment createExperimentWithoutPublication()

createExperimentWithoutPublication

Returns:

a Experiment object.

createBasicExperimentForModelledInteractions

public static Experiment createBasicExperimentForModelledInteractions()

createBasicExperimentForModelledInteractions

Returns:

a Experiment object.

createBasicExperimentForComplexes

public static Experiment createBasicExperimentForComplexes()

createBasicExperimentForComplexes

Returns:

a Experiment object.

createBasicExperimentForComplexes

public static Experiment createBasicExperimentForComplexes(int taxid)

createBasicExperimentForComplexes

Parameters:

taxid - a int.

Returns:

a Experiment object.

createBasicExperimentForComplexes

public static Experiment createBasicExperimentForComplexes(int taxid,
                                                           String name)

createBasicExperimentForComplexes

Parameters:

taxid - a int.

name - a String object.

Returns:

a Experiment object.

getPubmedId

public static String getPubmedId(Experiment exp)

getPubmedId

Parameters:

exp - a Experiment object.

Returns:

a String object.

getDoiId

public static String getDoiId(Experiment exp)

getDoiId

Parameters:

exp - a Experiment object.

Returns:

a String object.

getPubmedReference

public static Xref getPubmedReference(Experiment exp)

getPubmedReference

Parameters:

exp - a Experiment object.

Returns:

a Xref object.

getDoiReference

public static Xref getDoiReference(Experiment exp)

getDoiReference

Parameters:

exp - a Experiment object.

Returns:

a Xref object.

createExperiment

public static Experiment createExperiment(String pubmedId,
                                          CvTerm interactionDetectionMethod,
                                          Organism hostOrganism)

createExperiment

Parameters:

pubmedId - a String object.

interactionDetectionMethod - a CvTerm object.

hostOrganism - a Organism object.

Returns:

a Experiment object.

createExperiment

public static NamedExperiment createExperiment(String name,
                                               String pubmedId,
                                               CvTerm interactionDetectionMethod,
                                               Organism hostOrganism)

createExperiment

Parameters:

name - a String object.

pubmedId - a String object.

interactionDetectionMethod - a CvTerm object.

hostOrganism - a Organism object.

Returns:

a NamedExperiment object.

extractMostCommonParticipantDetectionMethodFrom

public static CvTerm extractMostCommonParticipantDetectionMethodFrom(Experiment exp)

Compare all participant identification methods in all participant evidences from all the interactions evidences.

Parameters:

exp - a Experiment object.

Returns:

the most frequent participant identification method (first one if several have same frequency), null if no participant identification methods