public static Xref createXrefIdentity(String primaryId, String dbMi, String dbName) { Xref xref = new Xref(); xref.setPrimaryRef(createDbReference(primaryId, dbMi, dbName, "MI:0356", "identity")); return xref; }
public static Bibref createBibref(String publicationId, String dbAc, String dbName) { DbReference dbReference = createDbReference(publicationId, dbAc, dbName, "MI:0358", "primary-reference"); Xref xref = new Xref(dbReference); return new Bibref(xref); }
public static Xref createXref(String primaryId, String dbMi, String dbName, String qualifierMi, String qualifierName) { Xref xref = new Xref(); xref.setPrimaryRef(createDbReference(primaryId, dbMi, dbName, qualifierMi, qualifierName)); return xref; }
public psidev.psi.mi.xml.model.Xref fromJaxb( psidev.psi.mi.xml253.jaxb.XrefType jXref ) { if ( jXref == null ) { throw new IllegalArgumentException( "You must give a non null JAXB Xref." ); } psidev.psi.mi.xml.model.Xref mXref = new psidev.psi.mi.xml.model.Xref(); // Initialise the model reading the Jaxb object // 1. set attributes mXref.setPrimaryRef( dbReferenceConverter.fromJaxb( jXref.getPrimaryRef() ) ); // 2. set encapsulated objects for ( DbReferenceType jRef : jXref.getSecondaryReves() ) { mXref.getSecondaryRef().add( dbReferenceConverter.fromJaxb( jRef ) ); } return mXref; }
public psidev.psi.mi.xml.model.Xref fromJaxb( psidev.psi.mi.xml254.jaxb.Xref jXref ) { if ( jXref == null ) { throw new IllegalArgumentException( "You must give a non null JAXB Xref." ); } psidev.psi.mi.xml.model.Xref mXref = new psidev.psi.mi.xml.model.Xref(); // Initialise the model reading the Jaxb object // 1. set attributes mXref.setPrimaryRef( dbReferenceConverter.fromJaxb( jXref.getPrimaryRef() ) ); // 2. set encapsulated objects for ( DbReference jRef : jXref.getSecondaryReves() ) { mXref.getSecondaryRef().add( dbReferenceConverter.fromJaxb( jRef ) ); } return mXref; }
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; } }
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; }
Iterator<DbReference> iteratorDb = disjunction.iterator(); Xref expRef = new Xref(iteratorDb.next());
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; }
names.setShortLabel(IntactConverterUtils.AUTH_CONF_MI); psidev.psi.mi.xml.model.Xref xref = new psidev.psi.mi.xml.model.Xref(); 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();
primaryRef.setRefTypeAc(IDENTITY_REF); xref = new Xref(primaryRef);
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; }
Xref xref = new Xref(); boolean found = false;
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);
Xref xref = new Xref();
rangeRef.setRefTypeAc("MI:0356"); Xref xref = new Xref(); xref.setPrimaryRef(rangeRef);
Xref xref = new Xref(); xref.setPrimaryRef(new DbReference(CvDatabase.PUBMED, CvDatabase.PUBMED_MI_REF, publication.getShortLabel(), CvXrefQualifier.PRIMARY_REFERENCE, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF)); bibref.setXref(xref);