uk.ac.ebi.intact.application.dataConversion.psiUpload.model.XrefTag.getSecondary java code examples

Common ways to obtain XrefTag

private void myMethod () {
 XrefTag x =Iterator iterator;(XrefTag) iterator.next()
Conversion.psiUpload.parser.XrefParser XrefParser;Element root;XrefParser.processPrimaryRef(root)
Conversion.psiUpload.model.CellTypeTag cellTypeTag;cellTypeTag.getPsiDefinition()
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}

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 );

Popular methods of XrefTag

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How to use getSecondarymethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.model.XrefTag

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.model.XrefTag.getSecondary (Showing top 12 results out of 315)

How to use
getSecondary
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.model.XrefTag