@Override public String toString() { final StringBuffer sb = new StringBuffer(150); sb.append("Xref"); sb.append("{cvDatabase=").append(cvDatabase.getShortLabel()); sb.append(", cvXrefQualifier=").append((cvXrefQualifier == null ? "-" : cvXrefQualifier.getShortLabel())); sb.append(", primaryId='").append(primaryId).append('\''); sb.append(", secondaryId='").append((secondaryId == null ? "-" : secondaryId)).append('\''); sb.append(", dbRelease='").append((dbRelease == null ? "-" : dbRelease)).append('\''); sb.append('}'); return sb.toString(); }
@Override public String toString() { final StringBuffer sb = new StringBuffer(150); sb.append("Xref"); sb.append("{cvDatabase=").append(cvDatabase.getShortLabel()); sb.append(", cvXrefQualifier=").append((cvXrefQualifier == null ? "-" : cvXrefQualifier.getShortLabel())); sb.append(", primaryId='").append(primaryId).append('\''); sb.append(", secondaryId='").append((secondaryId == null ? "-" : secondaryId)).append('\''); sb.append(", dbRelease='").append((dbRelease == null ? "-" : dbRelease)).append('\''); sb.append('}'); return sb.toString(); }
@Override public String toString() { final StringBuffer sb = new StringBuffer( 150 ); sb.append( "Xref" ); sb.append( "{cvDatabase=" ).append( cvDatabase.getShortLabel() ); sb.append( ", cvXrefQualifier=" ).append( ( cvXrefQualifier == null ? "-" : cvXrefQualifier.getShortLabel() ) ); sb.append( ", primaryId='" ).append( primaryId ).append( '\'' ); sb.append( ", secondaryId='" ).append( ( secondaryId == null ? "-" : secondaryId ) ).append( '\'' ); sb.append( ", dbRelease='" ).append( ( dbRelease == null ? "-" : dbRelease ) ).append( '\'' ); sb.append( '}' ); return sb.toString(); }
@Override public boolean equals( Object o ) { if ( this == o ) return true; if ( !( o instanceof Xref ) ) return false; final Xref xref = ( Xref ) o; if (!getClass().equals(xref.getClass())) return false; if ( !primaryId.equals( xref.primaryId ) ) return false; if ( cvDatabase != null ) { if ( !cvDatabase.getShortLabel().equals( xref.cvDatabase.getShortLabel() ) ) return false; } if ( cvXrefQualifier != null ? !cvXrefQualifier.getShortLabel().equals( xref.cvXrefQualifier.getShortLabel() ) : xref.cvXrefQualifier != null ) return false; if ( dbRelease != null ? !dbRelease.equals( xref.dbRelease ) : xref.dbRelease != null ) return false; return true; }
/** * Returns the Identity xref. * This method does not take into account that a cvObject can have several identity xref, therefore it will be * deprecated and will disappear from version 1.7 use instead : getPsiMiIdentityXref from the * uk.ac.ebi.intact.model.util.CvObjectUtils method. * It will throw an IllegalStateException if one CvObject is found 2 identity xref. * * @return the Identity xref or null if there is no Identity xref found. */ @Transient @Deprecated public Xref getIdentityXref() { List<Xref> xrefs = new ArrayList<Xref>(); for ( Xref xref : getXrefs() ) { CvXrefQualifier xq = xref.getCvXrefQualifier(); if ( ( xq != null ) && CvXrefQualifier.IDENTITY.equals( xq.getShortLabel() ) ) { xrefs.add( xref ); } if ( xrefs.size() > 1 ) { throw new IllegalStateException( "This cv has 2 xref identities. Can not decide on witch one to return" ); } } return xrefs.get( 0 ); } } // end CvObject
/** * * @param qualifier : the qualifier of the cross reference * @return true if the qualifier is 'identity' */ private boolean isIdentityCrossReference(CvXrefQualifier qualifier){ if (qualifier.getIdentifier() != null){ if (qualifier.getIdentifier().equals(CvXrefQualifier.IDENTITY_MI_REF)){ return true; } } else { if (qualifier.getShortLabel().equals(CvXrefQualifier.IDENTITY)){ return true; } } return false; }
private boolean isAnIdentityOrSecondaryCrossReference(CvXrefQualifier qualifier){ if (qualifier == null){ return false; } if (qualifier.getIdentifier() != null){ if (qualifier.getIdentifier().equals(CvXrefQualifier.IDENTITY_MI_REF) || qualifier.getIdentifier().equals(CvXrefQualifier.SECONDARY_AC_MI_REF)){ return true; } } else { if (qualifier.getShortLabel() != null){ if (qualifier.getShortLabel().equals(CvXrefQualifier.IDENTITY) || qualifier.getShortLabel().equals(CvXrefQualifier.SECONDARY_AC)){ return true; } } else if (qualifier.getFullName() != null){ if (qualifier.getFullName().equals("identical object")){ return true; } } } return false; }
private void writeXrefs(StringBuffer createdXrefs, Collection<CvObjectXref> refs) { int index = 0; int size = refs.size(); if (refs.isEmpty()){ createdXrefs.append(EMPTY_VALUE); } else { for (CvObjectXref ref : refs){ createdXrefs.append(ref.getCvDatabase().getShortLabel()); createdXrefs.append(":"); createdXrefs.append(ref.getPrimaryId()); createdXrefs.append(":"); createdXrefs.append(ref.getCvXrefQualifier().getShortLabel()); if (index < size - 1){ createdXrefs.append(", "); } index ++; } } }
private boolean isAnIdentityOrSecondaryCrossReference(CvXrefQualifier qualifier){ if (qualifier == null){ return false; } if (qualifier.getIdentifier() != null){ if (qualifier.getIdentifier().equals(CvXrefQualifier.IDENTITY_MI_REF) || qualifier.getIdentifier().equals(CvXrefQualifier.SECONDARY_AC_MI_REF)){ return true; } } else { if (qualifier.getShortLabel() != null){ if (qualifier.getShortLabel().equals(CvXrefQualifier.IDENTITY) || qualifier.getShortLabel().equals(CvXrefQualifier.SECONDARY_AC)){ return true; } } else if (qualifier.getFullName() != null){ if (qualifier.getFullName().equals("identical object")){ return true; } } } return false; }
/** * Retreive a pubmed ID from an IntAct experience. <br> That information should be found in Xref( CvDatabase( pubmed * ), CvXrefQualifier( primary-reference ) ). * * @param experiment the experiment from which we try to retreive the pubmedId. * * @return the pubmedId as a String or null if none were found. */ private static String getPubmedId( Experiment experiment ) { if ( experiment == null ) { return null; } // TODO use the helper to get the real CV term instead of comparing shortlabel. String pubmedId = null; for ( Iterator iterator = experiment.getXrefs().iterator(); iterator.hasNext() && pubmedId == null; ) { Xref xref = (Xref) iterator.next(); if ( CvDatabase.PUBMED.equals( xref.getCvDatabase().getShortLabel() ) ) { if ( CvXrefQualifier.PRIMARY_REFERENCE.equals( xref.getCvXrefQualifier().getShortLabel() ) ) { pubmedId = xref.getPrimaryId(); } } } return pubmedId; }
@Override public void visitXref(Xref xref) { ps.println(indentation()+"Xref: "+xref.getPrimaryId()+" (db: "+xref.getCvDatabase().getShortLabel()+", qual: "+xref.getCvXrefQualifier().getShortLabel()+")"); }
@Override public void visitXref(Xref xref) { ps.println(indentation()+"Xref: "+xref.getPrimaryId()+" (db: "+xref.getCvDatabase().getShortLabel()+", qual: "+xref.getCvXrefQualifier().getShortLabel()+")"); }
private boolean hasAnIdentityCrossReference(CvObject cvObject){ if (cvObject.getXrefs() != null){ if (!cvObject.getXrefs().isEmpty()){ for (Xref ref : cvObject.getXrefs()){ CvXrefQualifier qualifier = ref.getCvXrefQualifier(); if (qualifier.getAc() != null){ if (qualifier.getAc().equals("MI:0356")){ return true; } } else { if (qualifier.getShortLabel().equals("identity") || qualifier.getFullName().equals("identical object")){ return true; } } } } } return false; }
private boolean hasAnIdentityCrossReference(CvObject cvObject){ if (cvObject.getXrefs() != null){ if (!cvObject.getXrefs().isEmpty()){ for (Xref ref : cvObject.getXrefs()){ CvXrefQualifier qualifier = ref.getCvXrefQualifier(); if (qualifier.getAc() != null){ if (qualifier.getAc().equals("MI:0356")){ return true; } } else { if (qualifier.getShortLabel().equals("identity") || qualifier.getFullName().equals("identical object")){ return true; } } } } } return false; }
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 Collection<Field> fieldsForXref(Xref xref) { Collection<Field> fields = new ArrayList<Field>(); Field primaryIdField = new Field(); primaryIdField.setName("Primary ID"); primaryIdField.setValue(xref.getPrimaryId()); fields.add(primaryIdField); Field dbField = new Field(); dbField.setName("Xref Database Name"); dbField.setValue(xref.getCvDatabase().getShortLabel()); fields.add(dbField); Field qualField = new Field(); qualField.setName("Xref Qualifier Name"); if (xref.getCvXrefQualifier() != null) { qualField.setValue(xref.getCvXrefQualifier().getShortLabel()); } else { qualField.setValue(""); } fields.add(qualField); return fields; }
qualMi = CvXrefQualifier.PRIMARY_REFERENCE.equalsIgnoreCase(xref.getCvXrefQualifier().getShortLabel());
qualMi = CvXrefQualifier.PRIMARY_REFERENCE.equalsIgnoreCase(xref.getCvXrefQualifier().getShortLabel());
public CrossReference createCrossReference(Xref xref, boolean withText) { CrossReference ref = null; String db = xref.getCvDatabase() != null ? xref.getCvDatabase().getShortLabel() : DATABASE_UNKNOWN; String id = xref.getPrimaryId(); if (id != null && db != null) { String secondaryId = (withText && xref.getSecondaryId() != null) ? xref.getSecondaryId() : null; String cvXrefQualifier = (withText && xref.getCvXrefQualifier() != null) ? xref.getCvXrefQualifier().getShortLabel() : null; if (secondaryId != null) { ref = new CrossReferenceImpl(db, id, secondaryId); } else if (cvXrefQualifier != null) { ref = new CrossReferenceImpl(db, id, cvXrefQualifier); } else { ref = new CrossReferenceImpl(db, id, null); } } return ref; } }
if (qualifierFilterGroup != null) { String qualId = CvObjectUtils.getIdentity(xref.getCvXrefQualifier()); if (qualId == null) xref.getCvXrefQualifier().getShortLabel();