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ProteinParticipantTag.getFeatures
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How to use
getFeatures
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinParticipantTag

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinParticipantTag.getFeatures (Showing top 9 results out of 315)

origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

  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
  }
}
origin: uk.ac.ebi.intact.util/data-conversion

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

  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
  }
}
origin: uk.ac.ebi.intact.util/data-conversion

if ( psiComponent.hasFeature() ) {
  sb.append( ", Feature[" );
  for ( Iterator iterator3 = psiComponent.getFeatures().iterator(); iterator3.hasNext(); )
origin: uk.ac.ebi.intact.app/data-conversion

if ( psiComponent.hasFeature() ) {
  sb.append( ", Feature[" );
  for ( Iterator iterator3 = psiComponent.getFeatures().iterator(); iterator3.hasNext(); )
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

if ( psiComponent.hasFeature() ) {
  sb.append( ", Feature[" );
  for ( Iterator iterator3 = psiComponent.getFeatures().iterator(); iterator3.hasNext(); )
origin: uk.ac.ebi.intact.util/data-conversion

Collection features = proteinParticipant.getFeatures();
for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) {
  FeatureTag featureTag = (FeatureTag) iterator.next();
origin: uk.ac.ebi.intact.app/data-conversion

Collection features = proteinParticipant.getFeatures();
for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) {
  FeatureTag featureTag = (FeatureTag) iterator.next();
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

Collection features = proteinParticipant.getFeatures();
for ( Iterator iterator = features.iterator(); iterator.hasNext(); ) {
  FeatureTag featureTag = (FeatureTag) iterator.next();
uk.ac.ebi.intact.application.dataConversion.psiUpload.modelProteinParticipantTaggetFeatures

Popular methods of ProteinParticipantTag

  • <init>
  • getClusteredFeatures
    Produce a map that represents a clustering of the features. That method is there to help with PSI ve
  • getExpressedIn
  • getFeatureId
    Get from a feature object the primaryId of an Xref having the given database.
  • getProteinInteractor
  • getRole
  • hasFeature
    Checks if a feature has an Xref with the given primaryId and database.

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