public String getRefseq() { return this.refseq != null ? this.refseq.getId() : null; }
public void writeIdentifier(Xref identifier) throws IOException { if (identifier != null){ // write db first escapeAndWriteString(identifier.getDatabase().getShortName()); // write xref separator writer.write(MitabUtils.XREF_SEPARATOR); // write id escapeAndWriteString(identifier.getId()); // write version if (identifier.getVersion() != null){ writer.write(identifier.getVersion()); } } }
/** * Method to know if a Xref is a potential identifier. * It can be an identity xref or a secondary xref. * @param ref : the Xref * @return true if the Xref has a qualifier identity or secondary-ac */ public static boolean isXrefAnIdentifier(Xref ref){ if (ref == null || ref.getQualifier() == null){ return false; } String qualifierMI = ref.getQualifier().getMIIdentifier(); if (qualifierMI != null){ return (Xref.IDENTITY_MI.equals(qualifierMI) || Xref.SECONDARY_MI.equals(qualifierMI)); } else { String qualifier = ref.getQualifier().getShortName(); return (Xref.IDENTITY.equalsIgnoreCase(qualifier) || Xref.SECONDARY.equalsIgnoreCase(qualifier)); } }
CvTerm database = ref.getDatabase(); return ref.getId().equals(id); return ref.getId().equals(id);
CvTerm database1 = xref.getDatabase(); String mi1 = database1.getMIIdentifier(); hashcode = 31 * hashcode + xref.getId().hashCode(); CvTerm qualifier = xref.getQualifier(); if (qualifier != null){ String qualifierMi = qualifier.getMIIdentifier();
CvTerm database1 = xref.getDatabase(); String mi1 = database1.getMIIdentifier(); hashcode = 31 * hashcode + xref.getId().hashCode(); hashcode = 31 * hashcode + (xref.getVersion() != null ? xref.getVersion().hashCode():0); CvTerm qualifier = xref.getQualifier(); if (qualifier != null){ String qualifierMi = qualifier.getMIIdentifier();
if (ref.getDatabase().getMIIdentifier() != null && !dbMiRefs.isEmpty()) { if (!dbMiRefs.contains( ref.getDatabase().getMIIdentifier() )){ continue; else if (!dbRefs.contains( ref.getDatabase().getShortName() )){ continue; if ( ref.getQualifier() == null ) { continue; else if (ref.getQualifier().getMIIdentifier() != null && !typeMiRefs.isEmpty()){ if ( !typeMiRefs.contains( ref.getQualifier().getMIIdentifier() )){ continue; else if (!typeRefs.contains( ref.getQualifier().getShortName() )){ continue;
/** * Return the proper instance of the interactor if the database is recognized (the interactor will be returned on the first database which is recognized). It returns null otherwise. * @param xrefs : identifiers * @param name : name * @return the proper instance of the interactor if the database is recognized (the interactor will be returned on the first database which is recognized). It returns null otherwise. */ public Interactor createInteractorFromIdentityXrefs(Collection<? extends Xref> xrefs, String name){ Interactor interactor = null; Iterator<? extends Xref> xrefsIterator = xrefs.iterator(); while (interactor == null && xrefsIterator.hasNext()){ interactor = createInteractorFromDatabase(xrefsIterator.next().getDatabase(), name); } return interactor; }
CvTerm qualifier = ref.getQualifier(); if (qualifier == null){ return false; return ref.getId().equals(id); return ref.getId().equals(id);
String version1 = externalIdentifier1.getVersion(); String version2 = externalIdentifier2.getVersion();
if (xRef.getDatabase() != null){ String dbAc = xRef.getDatabase().getMIIdentifier(); String accession = xRef.getId();
CvTerm database1 = xref1.getDatabase(); CvTerm database2 = xref2.getDatabase(); String mi1 = database1.getMIIdentifier(); String mi2 = database2.getMIIdentifier(); String id1 = xref1.getId(); String id2 = xref2.getId(); CvTerm qualifier1 = xref1.getQualifier(); CvTerm qualifier2 = xref2.getQualifier();
/** * For each cross reference of this XrefContainer, collects all respective cross reference type(s) and * check if the dependencies are correct. * * @param container to check on. * @return a collection of validator messages. * if we fail to retreive the MI Ontology. */ public Collection<ValidatorMessage> check( Experiment container) throws ValidatorException { Collection<ValidatorMessage> messages = Collections.EMPTY_LIST; // Collect the db references Collection<Xref> databaseReferences = container.getXrefs(); if (!databaseReferences.isEmpty()){ messages = new ArrayList<ValidatorMessage>(); for ( Xref reference : databaseReferences) { MiContext context = RuleUtils.buildContext(reference, "database cross reference"); context.addAssociatedContext(RuleUtils.buildContext(container, "experiment")); // build a context in case of error messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) ); } } return messages; }
private String buildDbList( Collection<Xref> identities ) { StringBuilder sb = new StringBuilder( 128 ); for ( Iterator<Xref> dbReferenceIterator = identities.iterator(); dbReferenceIterator.hasNext(); ) { Xref ref = dbReferenceIterator.next(); final String db = ref.getDatabase().getShortName(); final String dbAc = ref.getDatabase().getMIIdentifier(); if( db != null && db.length() > 0 ) { sb.append( db ).append(" ,"); } else if( dbAc != null && dbAc.length() > 0 ) { sb.append( dbAc ).append(" ,"); } } int length = sb.length(); if( length > 0 ) { length = length - 2; // gets rid of the last comma } return sb.substring( 0, length ); }
String version1 = xref1.getVersion(); String version2 = xref2.getVersion();
/** * * @param ref * @param interactor * @return an array of String : first the database, then the interactorId */ public static String[] extractInteractorId(Xref ref, Interactor interactor){ String interactorId = null; String db = null; if (ref != null){ interactorId = JSONValue.escape(ref.getId()); db = JSONValue.escape(ref.getDatabase().getShortName()); } else{ interactorId = Integer.toString(UnambiguousExactInteractorBaseComparator.hashCode(interactor)); db = "generated"; } return new String[]{db, interactorId}; }
public String getImexId() { return this.imexId != null ? this.imexId.getId() : null; }
CvTerm database1 = xref1.getDatabase(); CvTerm database2 = xref2.getDatabase(); String mi1 = database1.getMIIdentifier(); String mi2 = database2.getMIIdentifier(); String id1 = xref1.getId(); String id2 = xref2.getId(); CvTerm qualifier1 = xref1.getQualifier(); CvTerm qualifier2 = xref2.getQualifier(); if (qualifier1 == null && qualifier2 == null){ return EQUAL;
CvTerm database1 = externalIdentifier1.getDatabase(); String mi = database1.getMIIdentifier(); String mod = database1.getMODIdentifier(); hashcode = 31 * hashcode + externalIdentifier1.getId().hashCode(); hashcode = 31 * hashcode + (externalIdentifier1.getVersion() != null ? externalIdentifier1.getVersion().hashCode() : 0);
messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) ); messages.addAll( mapping.check( reference.getDatabase(), reference.getQualifier(), context, this ) );