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ProteinInteractorChecker.getProtein
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How to use
getProtein
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ProteinInteractorChecker

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ProteinInteractorChecker.getProtein (Showing top 6 results out of 315)

origin: uk.ac.ebi.intact.app/data-conversion

  /**
   * Get an Intact Protein out of a ProteinInteractorTag.
   *
   * @param proteinParticipant
   *
   * @return the IntAct Protein correcponding to the given ProteinParticipantTag.
   */
  private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) {

    final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();

    OrganismTag organism = proteinInteractor.getOrganism();
    BioSource bioSource = null;
    if ( organism != null ) {
      bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
    }

    String proteinId = proteinInteractor.getPrimaryXref().getId();
    String db = proteinInteractor.getPrimaryXref().getDb();

//        System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" +
//                            proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" );

    return ProteinInteractorChecker.getProtein( proteinId, db, bioSource );
  }
}
origin: uk.ac.ebi.intact.util/data-conversion

  /**
   * Get an Intact Protein out of a ProteinInteractorTag.
   *
   * @param proteinParticipant
   *
   * @return the IntAct Protein correcponding to the given ProteinParticipantTag.
   */
  private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) {

    final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();

    OrganismTag organism = proteinInteractor.getOrganism();
    BioSource bioSource = null;
    if ( organism != null ) {
      bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
    }

    String proteinId = proteinInteractor.getPrimaryXref().getId();
    String db = proteinInteractor.getPrimaryXref().getDb();

//        System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" +
//                            proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" );

    return ProteinInteractorChecker.getProtein( proteinId, db, bioSource );
  }
}
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

  /**
   * Get an Intact Protein out of a ProteinInteractorTag.
   *
   * @param proteinParticipant
   *
   * @return the IntAct Protein correcponding to the given ProteinParticipantTag.
   */
  private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) {

    final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();

    OrganismTag organism = proteinInteractor.getOrganism();
    BioSource bioSource = null;
    if ( organism != null ) {
      bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
    }

    String proteinId = proteinInteractor.getPrimaryXref().getId();
    String db = proteinInteractor.getPrimaryXref().getDb();

//        System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" +
//                            proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" );

    return ProteinInteractorChecker.getProtein( proteinId, db, bioSource );
  }
}
origin: uk.ac.ebi.intact.util/data-conversion

final String proteinId = proteinInteractor.getPrimaryXref().getId();
final String db = proteinInteractor.getPrimaryXref().getDb();
final ProteinHolder proteinHolder = ProteinInteractorChecker.getProtein( proteinId, db, bioSource );
final CvComponentRole role = RoleChecker.getCvComponentRole( proteinParticipant.getRole() );
origin: uk.ac.ebi.intact.app/data-conversion

final String proteinId = proteinInteractor.getPrimaryXref().getId();
final String db = proteinInteractor.getPrimaryXref().getDb();
final ProteinHolder proteinHolder = ProteinInteractorChecker.getProtein( proteinId, db, bioSource );
final CvComponentRole role = RoleChecker.getCvComponentRole( proteinParticipant.getRole() );
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

final String proteinId = proteinInteractor.getPrimaryXref().getId();
final String db = proteinInteractor.getPrimaryXref().getDb();
final ProteinHolder proteinHolder = ProteinInteractorChecker.getProtein( proteinId, db, bioSource );
final CvExperimentalRole expRole = RoleChecker.getCvExperimentalRole( proteinParticipant.getRole() );
CvBiologicalRole bioRole = RoleChecker.getDefaultCvBiologicalRole();
uk.ac.ebi.intact.application.dataConversion.psiUpload.checkerProteinInteractorCheckergetProtein

Javadoc

Search a protein in the cache

Popular methods of ProteinInteractorChecker

  • buildID
    Build an identifier for the cache
  • check
  • checkCvInteractorType
  • createXref
  • filterByTaxid
    Remove from a collection of Protein all those that are not related to the given taxid.
  • getIntactProtein
    Get Protein from IntAct from its ID. If this is ID refers to (1) a protein, we send back a Protein o
  • getOrCreateNonUniprotProtein
    In case of Non uniprot protein, we check if it already exist in IntAct (based on biosource, primaryi
  • hasMultipleBioSource
    Check if the set of proteins is related to more than one biosource.
  • isSpliceVariant
    Answer the question: is that protein a Splice Variant ? One (quick) way is to check if the shortlabe

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