public Interactor createInteractor( int taxid, String db, String id, String txt ) { CrossReference cr = new CrossReferenceImpl( db, id, txt ); final Interactor interactor = buildInteractor(); interactor.setIdentifiers( createList( cr ) ); Organism o = new OrganismImpl( taxid ); interactor.setOrganism( o ); return interactor; }
protected void populateInteractor(Interactor source, Interactor target) { if (target != null && source != null){ target.getAlternativeIdentifiers().addAll(source.getAlternativeIdentifiers()); target.getAliases().addAll(source.getAliases()); if ( !target.hasOrganism() ) { target.setOrganism(new OrganismImpl()); } if( source.hasOrganism() ) { target.getOrganism().getIdentifiers().addAll(source.getOrganism().getIdentifiers()); } target.getAnnotations().addAll(source.getAnnotations()); target.getBiologicalRoles().addAll(source.getBiologicalRoles()); target.getChecksums().addAll(source.getChecksums()); target.getFeatures().addAll(source.getFeatures()); target.getInteractorTypes().addAll(source.getInteractorTypes()); target.getParticipantIdentificationMethods().addAll(source.getParticipantIdentificationMethods()); target.getStoichiometry().addAll(source.getStoichiometry()); target.getXrefs().addAll(source.getXrefs()); } } }
psiInteractorA.setAlternativeIdentifiers(psiAlternativeIdentifierA); psiInteractorA.setAliases(psiAliasA); psiInteractorA.setOrganism(psiOrganismA); psiInteractorB.setAlternativeIdentifiers(psiAlternativeIdentifierB); psiInteractorB.setAliases(psiAliasB); psiInteractorB.setOrganism(psiOrganismB);
psiInteractorA.setAlternativeIdentifiers(psiAlternativeIdentifierA); psiInteractorA.setAliases(psiAliasA); psiInteractorA.setOrganism(psiOrganismA); psiInteractorB.setAlternativeIdentifiers(psiAlternativeIdentifierB); psiInteractorB.setAliases(psiAliasB); psiInteractorB.setOrganism(psiOrganismB);
tabInteractor.setOrganism(new OrganismImpl(organismXrefs));
public Interactor createProteinInteractorRandom() { final Interactor interactor = buildInteractor(); interactor.setAliases( createAliasRandom( boundRandom( 1, 4 ), "uniprotkb" ) ); interactor.setAlternativeIdentifiers( createUniprotCrossReferenceList( boundRandom( 0, 4 ) ) ); interactor.setIdentifiers( createList( createCrossReference( "uniprotkb", randomUniprotAc() ) ) ); interactor.setOrganism( ( Organism ) pickRandom( organisms ) ); return interactor; }
Organism bioSourceField = organismConverter.intactToMitab(interactor.getBioSource()); mitabInteractor.setOrganism(bioSourceField);
interactorA.setAlternativeIdentifiers(splitCrossReferences(line[PsimiTabColumns.ALTID_INTERACTOR_A.ordinal()])); interactorA.setAliases(splitAliases(line[PsimiTabColumns.ALIAS_INTERACTOR_A.ordinal()])); interactorA.setOrganism(splitOrganism(line[PsimiTabColumns.TAXID_A.ordinal()])); interactorB.setAlternativeIdentifiers(splitCrossReferences(line[PsimiTabColumns.ALTID_INTERACTOR_B.ordinal()])); interactorB.setAliases(splitAliases(line[PsimiTabColumns.ALIAS_INTERACTOR_B.ordinal()])); interactorB.setOrganism(splitOrganism(line[PsimiTabColumns.TAXID_B.ordinal()]));