private DbReference createSecondaryRef(CrossReference secondaryIdentifier) { String database = secondaryIdentifier.getDatabase(); String id = secondaryIdentifier.getIdentifier(); return new DbReference(id, database); }
public static DbReference createDbReference(String primaryId, String dbAc, String dbName, String refTypeAc, String refTypeName) { DbReference dbRef = new DbReference(); dbRef.setId(primaryId); dbRef.setDbAc(dbAc); dbRef.setDb(dbName); dbRef.setRefType(refTypeName); dbRef.setRefTypeAc(refTypeAc); return dbRef; }
public Xref imexPrimaryFromMitab( CrossReference ref ) { Xref imex = null; if (ref != null && ref.getIdentifier() != null && ref.getDatabase() != null){ String db = ref.getDatabase(); String id = ref.getIdentifier(); DbReference primaryRef = new DbReference(id, db); primaryRef.setRefType("imex-primary"); primaryRef.setRefTypeAc("MI:0662"); if (db.equals("imex")) primaryRef.setDbAc("MI:0670"); imex = new Xref(primaryRef); } return imex; } }
private boolean extractPrimaryRefFromExperiment(Experiment intactObject, Bibref bibref) { if (!intactObject.getXrefs().isEmpty()){ Collection<uk.ac.ebi.intact.model.Xref> primaryRefs = searchXrefs(intactObject, CvDatabase.PUBMED_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, isCheckInitializedCollections()); if (primaryRefs.isEmpty()){ primaryRefs = searchXrefs(intactObject, CvDatabase.DOI_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, isCheckInitializedCollections()); } if (!primaryRefs.isEmpty()){ Iterator<uk.ac.ebi.intact.model.Xref> iterator = primaryRefs.iterator(); uk.ac.ebi.intact.model.Xref primaryRef = iterator.next(); Xref xref = new Xref(); xref.setPrimaryRef(new DbReference(primaryRef.getCvDatabase().getShortLabel(), primaryRef.getCvDatabase().getIdentifier(), primaryRef.getPrimaryId(), primaryRef.getCvXrefQualifier().getShortLabel(), primaryRef.getCvXrefQualifier().getIdentifier())); bibref.setXref(xref); while (iterator.hasNext()){ primaryRef = iterator.next(); xref.getSecondaryRef().add(new DbReference(primaryRef.getCvDatabase().getShortLabel(), primaryRef.getCvDatabase().getIdentifier(), primaryRef.getPrimaryId(), primaryRef.getCvXrefQualifier().getShortLabel(), primaryRef.getCvXrefQualifier().getIdentifier())); } return true; } } return false; }
public Bibref fromMitab( CrossReference ref ) { Bibref bibref = null; if (ref != null && ref.getIdentifier() != null && ref.getDatabase() != null){ String db = ref.getDatabase(); String id = ref.getIdentifier(); DbReference primaryRef = new DbReference(id, db); primaryRef.setRefType("primary-reference"); primaryRef.setRefTypeAc("MI:0358"); if (db.equals("pubmed")) primaryRef.setDbAc("MI:0446"); Xref xref = new Xref(primaryRef); bibref = new Bibref(xref); } return bibref; }
private static <T extends CvType> T createUnspecifiedRole( Class<T> roleClass ) { T role; try { role = roleClass.newInstance(); } catch ( Exception e ) { throw new RuntimeException( e ); } Names names = new Names(); names.setShortLabel(CvExperimentalRole.UNSPECIFIED); names.setFullName(CvExperimentalRole.UNSPECIFIED); role.setNames( names ); Xref xref = new Xref(); String unspecifiedRoleMiRef = CvExperimentalRole.UNSPECIFIED_PSI_REF; DbReference dbRef = new DbReference( unspecifiedRoleMiRef, CvDatabase.PSI_MI ); dbRef.setRefType( CvXrefQualifier.IDENTITY ); dbRef.setRefTypeAc( CvXrefQualifier.IDENTITY_MI_REF ); dbRef.setDbAc( CvDatabase.PSI_MI_MI_REF ); xref.setPrimaryRef( dbRef ); role.setXref( xref ); return role; }
xref.setPrimaryRef(new DbReference(CvDatabase.PSI_MI, CvDatabase.PSI_MI_MI_REF, IntactConverterUtils.AUTH_CONF_MI, CvXrefQualifier.IDENTITY, CvXrefQualifier.IDENTITY_MI_REF)); Unit unit = new Unit(); unit.setNames(names);
String id = tabCv.getIdentifier(); DbReference primaryRef = new DbReference(id, PSI_MI); primaryRef.setDbAc(PSI_MI_REF); primaryRef.setRefType(IDENTITY);
/** * TODO comment this * * @param interactionAc * @param sourceReference * @return primaryReference of these interaction. */ private DbReference getPrimaryRef(CrossReference interactionAc, CrossReference sourceReference) { DbReference primaryRef = null; // set references if (interactionAc != null) { String id = interactionAc.getIdentifier(); String db = interactionAc.getDatabase(); primaryRef = new DbReference(id, db); if (sourceReference != null) { primaryRef.setDbAc(sourceReference.getIdentifier()); } primaryRef.setRefType("identity"); primaryRef.setRefTypeAc("MI:0356"); } return primaryRef; }
acRef = new DbReference( db, dbMi, ac, CvXrefQualifier.IDENTITY, CvXrefQualifier.IDENTITY_MI_REF );
DbReference dbRef = new DbReference();
acRef = new DbReference( db, dbMi, ac, CvXrefQualifier.IDENTITY, CvXrefQualifier.IDENTITY_MI_REF );
DbReference dbRef = new DbReference(); dbRef.setDb(PSI_MI); dbRef.setDbAc(PSI_MI_REF); DbReference dbRef = new DbReference(); dbRef.setId(crossReference.getIdentifier()); dbRef.setDb(crossReference.getDatabase());
public psidev.psi.mi.xml.model.DbReference fromJaxb( psidev.psi.mi.xml253.jaxb.DbReferenceType jDbReference ) { if ( jDbReference == null ) { throw new IllegalArgumentException( "You must give a non null JAXB DbReference." ); } psidev.psi.mi.xml.model.DbReference mDbReference = new psidev.psi.mi.xml.model.DbReference(); // Initialise the model reading the Jaxb object // 1. set attributes mDbReference.setDb( jDbReference.getDb() ); mDbReference.setDbAc( jDbReference.getDbAc() ); mDbReference.setId( jDbReference.getId() ); mDbReference.setRefType( jDbReference.getRefType() ); mDbReference.setRefTypeAc( jDbReference.getRefTypeAc() ); mDbReference.setSecondary( jDbReference.getSecondary() ); mDbReference.setVersion( jDbReference.getVersion() ); return mDbReference; }
xref.setPrimaryRef(new DbReference(primaryRef.getCvDatabase().getShortLabel(), primaryRef.getCvDatabase().getIdentifier(), primaryRef.getPrimaryId(), primaryRef.getCvXrefQualifier().getShortLabel(), primaryRef.getCvXrefQualifier().getIdentifier())); bibref.setXref(xref); xref.getSecondaryRef().add(new DbReference(primaryRef.getCvDatabase().getShortLabel(), primaryRef.getCvDatabase().getIdentifier(), primaryRef.getPrimaryId(), primaryRef.getCvXrefQualifier().getShortLabel(), primaryRef.getCvXrefQualifier().getIdentifier()));
public psidev.psi.mi.xml.model.DbReference fromJaxb( psidev.psi.mi.xml254.jaxb.DbReference jDbReference ) { if ( jDbReference == null ) { throw new IllegalArgumentException( "You must give a non null JAXB DbReference." ); } psidev.psi.mi.xml.model.DbReference mDbReference = new psidev.psi.mi.xml.model.DbReference(); // Initialise the model reading the Jaxb object // 1. set attributes mDbReference.setDb( jDbReference.getDb() ); mDbReference.setDbAc( jDbReference.getDbAc() ); mDbReference.setId( jDbReference.getId() ); mDbReference.setRefType( jDbReference.getRefType() ); mDbReference.setRefTypeAc( jDbReference.getRefTypeAc() ); mDbReference.setSecondary( jDbReference.getSecondary() ); mDbReference.setVersion( jDbReference.getVersion() ); return mDbReference; }
DbReference dbRef = new DbReference(); dbRef.setDb(PSI_MI); dbRef.setDbAc(PSI_MI_REF); DbReference dbRef = new DbReference(); dbRef.setId(crossReference.getIdentifier()); dbRef.setDb(crossReference.getDatabase());
names.setFullName("unspecified role"); DbReference dbRef = new DbReference(); dbRef.setDb(PSIMI); dbRef.setDbAc(PSIMI_MI); names.setFullName("unspecified role"); DbReference dbRef = new DbReference(); dbRef.setDb(PSIMI); dbRef.setDbAc(PSIMI_MI); DbReference dbRef = new DbReference(); dbRef.setDb(PSIMI); dbRef.setDbAc(PSIMI_MI); DbReference dbRef = new DbReference(); dbRef.setDb(PSIMI); dbRef.setDbAc(PSIMI_MI); DbReference dbRef = new DbReference(); dbRef.setId(participantIdentificationMethod.getIdentifier()); dbRef.setDb(participantIdentificationMethod.getDatabase());
DbReference rangeRef = new DbReference(); rangeRef.setDb("psi-mi"); rangeRef.setDbAc("MI:0488");
xref.setPrimaryRef(new DbReference(CvDatabase.PUBMED, CvDatabase.PUBMED_MI_REF, publication.getShortLabel(), CvXrefQualifier.PRIMARY_REFERENCE, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF)); bibref.setXref(xref); isBibRefSet = true;