public static String getPsiReference( CvObject cv ) { if ( cv == null ) { throw new IllegalArgumentException( "the given CvObject must not be null." ); } for ( Iterator iterator = cv.getXrefs().iterator(); iterator.hasNext(); ) { Xref xref = (Xref) iterator.next(); if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) { return xref.getPrimaryId(); } } return null; } }
public static String getPsiReference( CvObject cv ) { if ( cv == null ) { throw new IllegalArgumentException( "the given CvObject must not be null." ); } for ( Iterator iterator = cv.getXrefs().iterator(); iterator.hasNext(); ) { Xref xref = (Xref) iterator.next(); if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) { return xref.getPrimaryId(); } } return null; } }
public static String getPsiReference( CvObject cv ) { if ( cv == null ) { throw new IllegalArgumentException( "the given CvObject must not be null." ); } for ( Iterator iterator = cv.getXrefs().iterator(); iterator.hasNext(); ) { Xref xref = (Xref) iterator.next(); if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) { return xref.getPrimaryId(); } } return null; } }
private boolean hasPsiXref( AnnotatedObject annotatedObject, String psiId ) { boolean hasIt = false; if ( psiId == null ) { return false; } for ( Iterator iterator = annotatedObject.getXrefs().iterator(); iterator.hasNext() && false == hasIt; ) { Xref xref = (Xref) iterator.next(); if ( xref.getCvDatabase().getShortLabel().equals( CvDatabase.PSI_MI ) ) { if ( psiId.equals( xref.getPrimaryId() ) ) { hasIt = true; } } } return hasIt; }
private boolean hasPsiXref( AnnotatedObject annotatedObject, String psiId ) { boolean hasIt = false; if ( psiId == null ) { return false; } for ( Iterator iterator = annotatedObject.getXrefs().iterator(); iterator.hasNext() && false == hasIt; ) { Xref xref = (Xref) iterator.next(); if ( xref.getCvDatabase().getShortLabel().equals( CvDatabase.PSI_MI ) ) { if ( psiId.equals( xref.getPrimaryId() ) ) { hasIt = true; } } } return hasIt; }
private boolean hasPsiXref( AnnotatedObject annotatedObject, String psiId ) { boolean hasIt = false; if ( psiId == null ) { return false; } for ( Iterator iterator = annotatedObject.getXrefs().iterator(); iterator.hasNext() && false == hasIt; ) { Xref xref = (Xref) iterator.next(); if ( xref.getCvDatabase().getShortLabel().equals( CvDatabase.PSI_MI ) ) { if ( psiId.equals( xref.getPrimaryId() ) ) { hasIt = true; } } } return hasIt; }
public UpdatedCrossReference(Xref ref, UpdateStatus status){ super(); if (ref != null){ this.database = ref.getCvDatabase() != null ? ref.getCvDatabase().getAc() : null; this.identifier = ref.getPrimaryId(); this.qualifier = ref.getCvXrefQualifier() != null ? ref.getCvXrefQualifier().getAc() : null; } else { this.database = null; this.identifier = null; this.qualifier = null; } this.status = status != null ? status : UpdateStatus.none; this.parent = null; }
public static <X extends Xref> X getIdentityXref(AnnotatedObject<X, ?> annotatedObject, String databaseMi) { for (X xref : annotatedObject.getXrefs()) { CvXrefQualifier qualifier = xref.getCvXrefQualifier(); CvDatabase database = xref.getCvDatabase(); String qualMi; String dbMi; if (qualifier != null && database != null && (qualMi = qualifier.getIdentifier()) != null && (dbMi = database.getIdentifier()) != null && qualMi.equals(CvXrefQualifier.IDENTITY_MI_REF) && dbMi.equals(databaseMi)) { return xref; } } return null; }
public static <X extends Xref> X getIdentityXref(AnnotatedObject<X, ?> annotatedObject, String databaseMi) { for (X xref : annotatedObject.getXrefs()) { CvXrefQualifier qualifier = xref.getCvXrefQualifier(); CvDatabase database = xref.getCvDatabase(); String qualMi; String dbMi; if (qualifier != null && database != null && (qualMi = qualifier.getIdentifier()) != null && (dbMi = database.getIdentifier()) != null && qualMi.equals(CvXrefQualifier.IDENTITY_MI_REF) && dbMi.equals(databaseMi)) { return xref; } } return null; }
@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()+")"); }
/** * * @param xref the xref to check * @return */ private boolean xrefPointsToOwnAc(Xref xref) { if (xref.getPrimaryId().startsWith(config.getAcPrefix())) { return true; } else { for (InstitutionXref institutionXref : IntactContext.getCurrentInstance().getInstitution().getXrefs()) { if (institutionXref.getPrimaryId().equals(xref.getCvDatabase().getIdentifier())) { return true; } } return false; } }
@Override public void visitXref(Xref xref) { currentNode.setUserObject("Xref: "+xref.getPrimaryId()+" / Database="+ DebugUtil.cvObjectToSimpleString(xref.getCvDatabase())+ ", Qualifier="+DebugUtil.cvObjectToSimpleString(xref.getCvXrefQualifier())); }
@Override public void visitXref(Xref xref) { currentNode.setUserObject("Xref: "+xref.getPrimaryId()+" / Database="+ DebugUtil.cvObjectToSimpleString(xref.getCvDatabase())+ ", Qualifier="+DebugUtil.cvObjectToSimpleString(xref.getCvXrefQualifier())); }
protected void fixPubmedReferenceAsIdentityToPrimaryRef(Xref xref) { if (CvDatabase.PUBMED_MI_REF.equals(xref.getCvDatabase().getIdentifier()) && CvXrefQualifier.IDENTITY_MI_REF.equals(xref.getCvXrefQualifier().getIdentifier())) { CvXrefQualifier primaryRef = CvObjectUtils.createCvObject(xref.getOwner(), CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE); xref.setCvXrefQualifier(primaryRef); 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); } }
private String getMiReference( CvObject cv ) { for ( Xref xref : cv.getXrefs() ) { if ( getPsi().equals( xref.getCvDatabase() ) ) { if ( getIdentity().equals( xref.getCvXrefQualifier() ) ) { return xref.getPrimaryId(); } } } return null; }
protected void traverseXref(Xref xref, IntactVisitor... visitors) { if (xref == null) return; for (IntactVisitor visitor : visitors) { visitor.visitXref(xref); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(xref)) { return; } traverse(xref.getCvXrefQualifier(), visitors); traverse(xref.getCvDatabase(), visitors); traverse(xref.getOwner(), visitors); }
protected void traverseXref(Xref xref, IntactVisitor... visitors) { if (xref == null) return; for (IntactVisitor visitor : visitors) { visitor.visitXref(xref); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(xref)) { return; } traverse(xref.getCvXrefQualifier(), visitors); traverse(xref.getCvDatabase(), visitors); traverse(xref.getOwner(), visitors); }
private Xref synchronizeXref( Xref xref, AnnotatedObject parent ) { if (xref.getAc() != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getXrefDao().getByAc(xref.getAc()); } xref.setCvDatabase( synchronize( xref.getCvDatabase() ) ); xref.setCvXrefQualifier( synchronize( xref.getCvXrefQualifier() ) ); xref.setParent(parent); if (xref.getAc() == null && xref.getAc() != null) { annotatedObjectsToPersist.put(keyBuilder.keyForXref(xref), xref); } return xref; }
private Xref synchronizeXref( Xref xref, AnnotatedObject parent ) { if (xref.getAc() != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getXrefDao().getByAc(xref.getAc()); } xref.setCvDatabase( synchronize( xref.getCvDatabase() ) ); xref.setCvXrefQualifier( synchronize( xref.getCvXrefQualifier() ) ); xref.setParent(parent); if (xref.getAc() == null && xref.getAc() != null) { annotatedObjectsToPersist.put(keyBuilder.keyForXref(xref), xref); } return xref; }