public static void check( ) { initialise( ); }
if ( ControlledVocabularyRepository.getIdentityQualifier().equals( xref.getCvXrefQualifier() ) ) ControlledVocabularyRepository.getNoUniprotUpdateTopic() ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); proteinType.addAnnotation( annotation );
bibRef.getSecondary(), bibRef.getVersion(), ControlledVocabularyRepository.getPrimaryXrefQualifier() ); xrefTag.getSecondary(), xrefTag.getVersion(), ControlledVocabularyRepository.getSeeAlsoXrefQualifier() );
Xref xref = (Xref) iterator.next(); if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) { if ( ControlledVocabularyRepository.getPrimaryXrefQualifier().equals( xref.getCvXrefQualifier() ) ) {
CvXrefQualifier identity = ControlledVocabularyRepository.getIdentityQualifier();
CvAliasType geneNameAliasType = ControlledVocabularyRepository.getGeneNameAliasType(); if ( geneNameAliasType != null ) { for ( Iterator iterator = protein.getAliases().iterator(); iterator.hasNext() && geneName == null; ) {
if ( confidence != null ) { final CvTopic authorConfidence = ControlledVocabularyRepository.getAuthorConfidenceTopic();
ControlledVocabularyRepository.check( );
if ( ControlledVocabularyRepository.getIdentityQualifier().equals( xref.getCvXrefQualifier() ) ) ControlledVocabularyRepository.getNoUniprotUpdateTopic() ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); proteinType.addAnnotation( annotation );
bibRef.getSecondary(), bibRef.getVersion(), ControlledVocabularyRepository.getPrimaryXrefQualifier() ); xrefTag.getSecondary(), xrefTag.getVersion(), ControlledVocabularyRepository.getSeeAlsoXrefQualifier() );
Xref xref = (Xref) iterator.next(); if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) { if ( ControlledVocabularyRepository.getPrimaryXrefQualifier().equals( xref.getCvXrefQualifier() ) ) {
private static void createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref ); } }
CvAliasType geneNameAliasType = ControlledVocabularyRepository.getGeneNameAliasType(); if ( geneNameAliasType != null ) { for ( Iterator iterator = protein.getAliases().iterator(); iterator.hasNext() && geneName == null; ) {
if ( confidence != null ) { final CvTopic authorConfidence = ControlledVocabularyRepository.getAuthorConfidenceTopic();
ControlledVocabularyRepository.check( );
if ( ControlledVocabularyRepository.getIdentityQualifier().equals( xref.getCvXrefQualifier() ) ) ControlledVocabularyRepository.getNoUniprotUpdateTopic() ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); proteinType.addAnnotation( annotation );
bibRef.getSecondary(), bibRef.getVersion(), ControlledVocabularyRepository.getPrimaryXrefQualifier() ); xrefTag.getSecondary(), xrefTag.getVersion(), ControlledVocabularyRepository.getSeeAlsoXrefQualifier() );
Xref xref = (Xref) iterator.next(); if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) { if ( ControlledVocabularyRepository.getPrimaryXrefQualifier().equals( xref.getCvXrefQualifier() ) ) {
private static void createXref( Protein protein, XrefTag xrefTag, boolean identity ) throws IntactException { CvXrefQualifier qualifier = null; if ( identity ) { qualifier = ControlledVocabularyRepository.getIdentityQualifier(); } CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() ); if ( database == null ) { // failed to find the database, skip the Xref creation } else { InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(), database, xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier ); protein.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref ); } }
public static void check( ) { initialise( ); }