primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() ); primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() );
primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() ); primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() );
primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() ); primaryXref.getId(), primaryXref.getSecondary(), primaryXref.getVersion() );
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 ); } }
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 ); } }
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 ); } }
XrefChecker.getCvDatabase( bibRef.getDb() ), bibRef.getId(), bibRef.getSecondary(), bibRef.getVersion(), ControlledVocabularyRepository.getPrimaryXrefQualifier() ); XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), ControlledVocabularyRepository.getSeeAlsoXrefQualifier() ); XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), null );
XrefChecker.getCvDatabase( bibRef.getDb() ), bibRef.getId(), bibRef.getSecondary(), bibRef.getVersion(), ControlledVocabularyRepository.getPrimaryXrefQualifier() ); XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), ControlledVocabularyRepository.getSeeAlsoXrefQualifier() ); XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), null );
XrefChecker.getCvDatabase( bibRef.getDb() ), bibRef.getId(), bibRef.getSecondary(), bibRef.getVersion(), ControlledVocabularyRepository.getPrimaryXrefQualifier() ); XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), ControlledVocabularyRepository.getSeeAlsoXrefQualifier() ); XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), null );
XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier );
XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier );
XrefChecker.getCvDatabase( xrefTag.getDb() ), xrefTag.getId(), xrefTag.getSecondary(), xrefTag.getVersion(), qualifier );