uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinParticipantTag.getProteinInteractor java code examples

Common ways to obtain ProteinParticipantTag

private void myMethod () {
 ProteinParticipantTag p =Iterator iterator;(ProteinParticipantTag) iterator.next()
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}

Object o = (Object) iterator.next();
if ( o instanceof ProteinParticipantTag ) {
  uniprotID = ( (ProteinParticipantTag) o ).getProteinInteractor().getPrimaryXref().getId();

Object o = (Object) iterator.next();
if ( o instanceof ProteinParticipantTag ) {
  uniprotID = ( (ProteinParticipantTag) o ).getProteinInteractor().getPrimaryXref().getId();

Object o = (Object) iterator.next();
if ( o instanceof ProteinParticipantTag ) {
  uniprotID = ( (ProteinParticipantTag) o ).getProteinInteractor().getPrimaryXref().getId();

  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
  }
}

ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next();
sb.append( NEW_LINE ).append( '[' );
sb.append( psiComponent.getProteinInteractor().getPrimaryXref().getId() );
sb.append( ", " );
sb.append( psiComponent.getRole() );

ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next();
sb.append( NEW_LINE ).append( '[' );
sb.append( psiComponent.getProteinInteractor().getPrimaryXref().getId() );
sb.append( ", " );
sb.append( psiComponent.getRole() );

ProteinParticipantTag psiComponent = (ProteinParticipantTag) iterator2.next();
sb.append( NEW_LINE ).append( '[' );
sb.append( psiComponent.getProteinInteractor().getPrimaryXref().getId() );
sb.append( ", " );
sb.append( psiComponent.getRole() );

ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();
String uniprotID = null;
String taxid = null;

ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();
String uniprotID = null;
String taxid = null;

ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();
String uniprotID = null;
String taxid = null;

  /**
   * 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 );
  }
}

public static void persist( final ProteinParticipantTag proteinParticipant,
              final Interaction interaction ) throws IntactException {
  ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();

public static void persist( final ProteinParticipantTag proteinParticipant,
              final Interaction interaction ) throws IntactException {
  ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();

public static void persist( final ProteinParticipantTag proteinParticipant,
              final Interaction interaction ) throws IntactException {
  ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();

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.
getFeatures
getRole
hasFeature
Checks if a feature has an Xref with the given primaryId and database.

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How to use getProteinInteractormethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinParticipantTag

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinParticipantTag.getProteinInteractor (Showing top 18 results out of 315)

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