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)

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}

  /**
   * 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 );
  }
}

  /**
   * 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 );
  }
}

  /**
   * 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 );
  }
}

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() );

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() );

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();

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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How to use getProteinmethodin 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)

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