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; } }
/** * 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; }
protected void fixPubmedReferenceAsIdentityToPrimaryRef(DbReference dbRef) { if (((dbRef.getDbAc() != null && CvDatabase.PUBMED_MI_REF.equals(dbRef.getDbAc())) || (dbRef.getDbAc() == null && CvDatabase.PUBMED.equals(dbRef.getDb().toLowerCase()))) && (( dbRef.getRefTypeAc() != null && CvXrefQualifier.IDENTITY_MI_REF.equals(dbRef.getRefTypeAc())) || ( dbRef.getRefTypeAc() == null && CvXrefQualifier.IDENTITY.equals(dbRef.getRefType().toLowerCase())))) { dbRef.setRefTypeAc(CvXrefQualifier.PRIMARY_REFERENCE_MI_REF); dbRef.setRefType(CvXrefQualifier.PRIMARY_REFERENCE); final ConverterMessage converterMessage = new ConverterMessage(MessageLevel.WARN, "Incorrect cross refernece to Pubmed that had qualifier 'identity'. Changed to 'primary-reference", ConverterContext.getInstance().getLocation().getCurrentLocation()); converterMessage.setAutoFixed(true); ConverterContext.getInstance().getReport().getMessages().add(converterMessage); } }
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; }
dbRef.setDbAc(PSI_MI_REF); dbRef.setId(crossReference.getIdentifier()); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); } else if (database.equals(CHEBI)) { dbRef.setDbAc(CHEBI_MI); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); } else if (database.equals(INTACT)) { dbRef.setDbAc(INTACT_MI); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF);
primaryRef.setRefType(IDENTITY); primaryRef.setRefTypeAc(IDENTITY_REF);
dbRef.setDbAc(PSI_MI_REF); dbRef.setId(crossReference.getIdentifier()); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); } else if (database.equals(CHEBI)) { dbRef.setDbAc(CHEBI_MI); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); } else if (database.equals(INTACT)) { dbRef.setDbAc(INTACT_MI); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF);
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; }
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; }
dbRef.setRefType(CvXrefQualifier.PRIMARY_REFERENCE); dbRef.setRefTypeAc(CvXrefQualifier.PRIMARY_REFERENCE_MI_REF); dbRef.setRefType(intactObject.getCvXrefQualifier().getShortLabel());
primaryReferece.setRefType(IDENTITY); primaryReferece.setRefTypeAc(IDENTITY_REF); } else if (primaryDatabase.equals(CHEBI)) { primaryReferece.setDbAc(CHEBI_MI); primaryReferece.setRefType(IDENTITY); primaryReferece.setRefTypeAc(IDENTITY_REF); } else if (primaryDatabase.equals(INTACT)) { primaryReferece.setDbAc(INTACT_MI); primaryReferece.setRefType(IDENTITY); primaryReferece.setRefTypeAc(IDENTITY_REF); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); interactorTypeXref = new Xref(dbRef); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); interactorTypeXref = new Xref(dbRef); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); interactorTypeXref = new Xref(dbRef); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); interactorTypeXref = new Xref(dbRef);
dbRef.setDbAc(PSIMI_MI); dbRef.setId(UNSPECIFIED_ROLE); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); dbRef.setDbAc(PSIMI_MI); dbRef.setId(UNSPECIFIED_ROLE); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); dbRef.setDbAc(PSIMI_MI); dbRef.setId(FEATURE_TYPE); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); dbRef.setDbAc(PSIMI_MI); dbRef.setId(participantIdentificationMethod.getIdentifier()); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF); dbRef.setRefType(IDENTITY); dbRef.setRefTypeAc(IDENTITY_REF);
rangeRef.setDb("psi-mi"); rangeRef.setDbAc("MI:0488"); rangeRef.setRefType("identity"); rangeRef.setRefTypeAc("MI:0356");