How to use
check
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.check (Showing top 6 results out of 315)

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}

  public static void check( final ProteinParticipantTag proteinParticipant,
               final UpdateProteinsI proteinFactory,
               final BioSourceFactory bioSourceFactory ) {

    final String role = proteinParticipant.getRole();
    RoleChecker.check( role );

    final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();
    ProteinInteractorChecker.check( proteinInteractor, proteinFactory, bioSourceFactory );

    final Collection features = proteinParticipant.getFeatures();
    for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) {
      FeatureTag feature = (FeatureTag) iterator.next();

      FeatureChecker.ckeck( feature );
    }

    // check feature clustering (specific to PSI version 1)
    try {
      proteinParticipant.getClusteredFeatures();
    } catch ( IllegalArgumentException iae ) {
      MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while checking if the feature were clusterizable: " +
                                    iae.getMessage() ) );
    }

    // TODO check isOverExpressed
    // TODO check isTaggedProtein: as we have to create a Feature having CvFeatureType(tagged-protein) with undetermined range
  }
}

  public static void check( final ProteinParticipantTag proteinParticipant,
               final UpdateProteinsI proteinFactory,
               final BioSourceFactory bioSourceFactory ) {

    final String role = proteinParticipant.getRole();
    RoleChecker.check( role );

    final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();
    ProteinInteractorChecker.check( proteinInteractor, proteinFactory, bioSourceFactory );

    final Collection features = proteinParticipant.getFeatures();
    for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) {
      FeatureTag feature = (FeatureTag) iterator.next();

      FeatureChecker.ckeck( feature );
    }

    // check feature clustering (specific to PSI version 1)
    try {
      proteinParticipant.getClusteredFeatures();
    } catch ( IllegalArgumentException iae ) {
      MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while checking if the feature were clusterizable: " +
                                    iae.getMessage() ) );
    }

    // TODO check isOverExpressed
    // TODO check isTaggedProtein: as we have to create a Feature having CvFeatureType(tagged-protein) with undetermined range
  }
}

  public static void check( final ProteinParticipantTag proteinParticipant,
               final UpdateProteinsI proteinFactory,
               final BioSourceFactory bioSourceFactory ) {

    final String role = proteinParticipant.getRole();
    RoleChecker.check( role );

    final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();
    ProteinInteractorChecker.check( proteinInteractor, proteinFactory, bioSourceFactory );

    final Collection features = proteinParticipant.getFeatures();
    for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) {
      FeatureTag feature = (FeatureTag) iterator.next();

      FeatureChecker.ckeck( feature );
    }

    // check feature clustering (specific to PSI version 1)
    try {
      proteinParticipant.getClusteredFeatures();
    } catch ( IllegalArgumentException iae ) {
      MessageHolder.getInstance().addCheckerMessage( new Message( "An error occured while checking if the feature were clusterizable: " +
                                    iae.getMessage() ) );
    }

    // TODO check isOverExpressed
    // TODO check isTaggedProtein: as we have to create a Feature having CvFeatureType(tagged-protein) with undetermined range
  }
}

ProteinInteractorChecker.check( proteinInteractor, proteinFactory, bioSourceFactory );

ProteinInteractorChecker.check( proteinInteractor, proteinFactory, bioSourceFactory );

ProteinInteractorChecker.check( proteinInteractor, proteinFactory, bioSourceFactory );

Popular methods of ProteinInteractorChecker

buildID
Build an identifier for the cache
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
getProtein
Search a protein in the cache
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 checkmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ProteinInteractorChecker

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

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