How to use

getPrimaryId

method

in

uk.ac.ebi.intact.model.InteractorXref

  public int compare(InteractorXref o1, InteractorXref o2) {
    return o1.getPrimaryId().compareTo(o2.getPrimaryId());
  }
};

  public int compare(InteractorXref o1, InteractorXref o2) {
    return o1.getPrimaryId().compareTo(o2.getPrimaryId());
  }
};

  public int compare(InteractorXref o1, InteractorXref o2) {
    return o1.getPrimaryId().toLowerCase().compareTo(o2.getPrimaryId().toLowerCase());
  }
});

  public int compare(InteractorXref o1, InteractorXref o2) {
    return o1.getPrimaryId().toLowerCase().compareTo(o2.getPrimaryId().toLowerCase());
  }
});

@Override
public ProteinUpdateError createInvalidCollectionOfParentsError(String proteinAc, UpdateError errorLabel, Collection<InteractorXref> isoformParents, Collection<InteractorXref> chainParents) {
  InvalidCollectionOfParents error = new InvalidCollectionOfParents(null, proteinAc, errorLabel);
  for (InteractorXref ref : isoformParents){
    error.getIsoformParents().add(ref.getPrimaryId());
  }
  for (InteractorXref ref : chainParents){
    error.getChainParents().add(ref.getPrimaryId());
  }
  return error;
}

@Override
public ProteinUpdateError createMultiUniprotIdentitiesError(String proteinAc, Collection<InteractorXref> identities) {
  MultiUniprotIdentities error = new MultiUniprotIdentities(null, proteinAc);
  for (InteractorXref ref : identities){
    error.getUniprotIdentities().add(ref.getPrimaryId());
  }
  return error;
}

public PersistentProteinEvent(ProteinUpdateProcess process, Protein protein){
  super(process);
  this.proteinAc = protein != null ? protein.getAc() : null;
  InteractorXref uniprotXref = ProteinUtils.getUniprotXref(protein);
  if (uniprotXref != null){
    this.uniprotAc = uniprotXref.getPrimaryId();
  }
  else {
    this.uniprotAc = null;
  }
  this.message = null;
}

/**
 * Retreives Imex identifier stored in the Xrefs.
 *
 * @param interaction the interaction to search on.
 * @return an imex id or null if not found.
 */
public static String getImexIdentifier(Interaction interaction) {
  if (interaction == null) {
    throw new IllegalArgumentException("You must give a non null interaction");
  }
  for (InteractorXref xref : interaction.getXrefs()) {
    if (CvDatabase.IMEX_MI_REF.equals(xref.getCvDatabase().getIdentifier())) {
      return xref.getPrimaryId();
    }
  }
  // Could not find an IMEx id
  return null;
}

/**
 * Retreives Imex identifier stored in the Xrefs.
 *
 * @param interaction the interaction to search on.
 * @return an imex id or null if not found.
 */
public static String getImexIdentifier(Interaction interaction) {
  if (interaction == null) {
    throw new IllegalArgumentException("You must give a non null interaction");
  }
  for (InteractorXref xref : interaction.getXrefs()) {
    if (CvDatabase.IMEX_MI_REF.equals(xref.getCvDatabase().getIdentifier())) {
      return xref.getPrimaryId();
    }
  }
  // Could not find an IMEx id
  return null;
}

/**
 * Gets the Interactor Identifiers for that interaction
 *
 * @since 1.7.2
 */
public static List<String> getInteractorPrimaryIDs(Interaction interaction) {
  final Collection<Component> components = interaction.getComponents();
  List<String> ids = new ArrayList<String>(components.size());
  for (Component component : components) {
    Interactor interactor = component.getInteractor();
    final Collection<InteractorXref> idXrefs = XrefUtils.getIdentityXrefs(interactor);
    if (idXrefs.size() > 0) {
      final Iterator<InteractorXref> iterator = idXrefs.iterator();
      ids.add(iterator.next().getPrimaryId());
      if (log.isDebugEnabled()) {
        if (iterator.hasNext()) {
          log.debug("Interaction contains interactor with more than one identities. Interaction: " + interaction.getShortLabel() + "(" + interaction.getAc() + ") " +
              " - Xrefs: " + idXrefs);
        }
      }
    }
  }
  return ids;
}

/**
 * Gets the Interactor Identifiers for that interaction
 *
 * @since 1.7.2
 */
public static List<String> getInteractorPrimaryIDs(Interaction interaction) {
  final Collection<Component> components = interaction.getComponents();
  List<String> ids = new ArrayList<String>(components.size());
  for (Component component : components) {
    Interactor interactor = component.getInteractor();
    final Collection<InteractorXref> idXrefs = XrefUtils.getIdentityXrefs(interactor);
    if (idXrefs.size() > 0) {
      final Iterator<InteractorXref> iterator = idXrefs.iterator();
      ids.add(iterator.next().getPrimaryId());
      if (log.isDebugEnabled()) {
        if (iterator.hasNext()) {
          log.debug("Interaction contains interactor with more than one identities. Interaction: " + interaction.getShortLabel() + "(" + interaction.getAc() + ") " +
              " - Xrefs: " + idXrefs);
        }
      }
    }
  }
  return ids;
}

/**
 * Retreives Imex identifier stored in the Xrefs.
 *
 * @param interaction the interaction to search on.
 * @return an imex id or null if not found.
 */
public static String getImexIdentifier( Interaction interaction ) {
  if ( interaction == null ) {
    throw new IllegalArgumentException( "You must give a non null interaction" );
  }
  for ( InteractorXref xref : interaction.getXrefs() ) {
    CvObjectXref idCvDatabase = CvObjectUtils.getPsiMiIdentityXref( xref.getCvDatabase() );
    if ( idCvDatabase.getPrimaryId().equals( CvDatabase.IMEX_MI_REF ) ) {
      return xref.getPrimaryId();
    }
  }
  // Could not find an IMEx id
  return null;
}

protected ProteinImpl getProteinTranscriptsMasterProtein( Protein proteinTranscript, String cvXRefQualifier) {
  if ( proteinTranscript == null ) {
    throw new NullPointerException( "proteinTranscript must not be null." );
  }
  if ( cvXRefQualifier == null ) {
    throw new NullPointerException( "The Cv Xref qualifier must not be null." );
  }
  String masterProtAc = null;
  for (InteractorXref xref : proteinTranscript.getXrefs()) {
    if (xref.getCvXrefQualifier() != null && cvXRefQualifier.equals(xref.getCvXrefQualifier().getIdentifier())) {
      if (masterProtAc == null) {
        masterProtAc = xref.getPrimaryId();
      } else {
        throw new IntactException("This protein transcript contains more than one "+cvXRefQualifier+" xrefs: "+proteinTranscript.getShortLabel() );
      }
    }
  }
  // search protein by AC
  return getByAc(masterProtAc);
}

protected ProteinImpl getProteinTranscriptsMasterProtein( Protein proteinTranscript, String cvXRefQualifier) {
  if ( proteinTranscript == null ) {
    throw new NullPointerException( "proteinTranscript must not be null." );
  }
  if ( cvXRefQualifier == null ) {
    throw new NullPointerException( "The Cv Xref qualifier must not be null." );
  }
  String masterProtAc = null;
  for (InteractorXref xref : proteinTranscript.getXrefs()) {
    if (xref.getCvXrefQualifier() != null && cvXRefQualifier.equals(xref.getCvXrefQualifier().getIdentifier())) {
      if (masterProtAc == null) {
        masterProtAc = xref.getPrimaryId();
      } else {
        throw new IntactException("This protein transcript contains more than one "+cvXRefQualifier+" xrefs: "+proteinTranscript.getShortLabel() );
      }
    }
  }
  // search protein by AC
  return getByAc(masterProtAc);
}

/**
 * Get the uniprot primary ID from Protein and Splice variant.
 *
 * @param protein the Protein for which we want the uniprot ID.
 *
 * @return the uniprot ID as a String or null if none is found (should not occur)
 */
public String getUniprotID(final Protein protein) {
  if (protAcToUniprotIdCache.containsKey(protein.getAc())) {
    return protAcToUniprotIdCache.get(protein.getAc());
  }
  String uniprotId = null;
  Collection<InteractorXref> xrefs = protein.getXrefs();
  for (InteractorXref xref : xrefs) {
    if (getUniprot().getIdentifier().equals(xref.getCvDatabase().getIdentifier()) &&
        getIdentity().equals(xref.getCvXrefQualifier())) {
      uniprotId = xref.getPrimaryId();
      break;
    }
  }
  protAcToUniprotIdCache.put(protein.getAc(), uniprotId);
  return uniprotId;
}

@Override
@Transactional( "update" )
public void onDeadProteinFound(DeadUniprotEvent evt) throws ProcessorException {
  // reattach the updateProcess to the entity manager
  ProteinUpdateProcess updateProcess = IntactUpdateContext.getCurrentInstance().getUpdateFactory().getEntityManager().merge(this.updateProcess);
  Protein protein = evt.getProtein();
  String identity = evt.getUniprotIdentityXref() != null ? evt.getUniprotIdentityXref().getPrimaryId() : null;
  Collection<InteractorXref> deletedXrefs = evt.getDeletedXrefs();
  DeadProteinEvent proteinEvt = new DeadProteinEvent(updateProcess, protein, identity);
  if (deletedXrefs != null && !deletedXrefs.isEmpty()){
    proteinEvt.addDeletedReferencesFromXref(deletedXrefs);
  }
  IntactUpdateContext.getCurrentInstance().getUpdateFactory().getDeadProteinEventDao().persist(proteinEvt);
}

  /**
   * Get the uniprot primary ID from Protein and Splice variant.
   *
   * @param protein the Protein for which we want the uniprot ID.
   *
   * @return the uniprot ID as a String or null if none is found (should not occur)
   */
  public String getUniprotPrimaryAc(final Protein protein) {

    if (protAcToUniprotIdCache.containsKey(protein.getAc())) {
      return protAcToUniprotIdCache.get(protein.getAc());
    }

    String uniprotId = null;

    Collection<InteractorXref> xrefs = protein.getXrefs();

    for (InteractorXref xref : xrefs) {
      if (getUniprot().equals(xref.getCvDatabase()) &&
          getIdentity().equals(xref.getCvXrefQualifier())) {
        uniprotId = xref.getPrimaryId();
        break;
      }
    }

    protAcToUniprotIdCache.put(protein.getAc(), uniprotId);

    return uniprotId;
  }
}

protected void fixSourceReferenceXrefsIfNecessary(Interaction interaction) {
  InteractorXref xrefToFix = null;
  if( ConverterContext.getInstance().isAutoFixInteractionSourceReference() ) {
    // Look up source reference xref and only try to fix identity if there is no source ref present.
    // if the qualifier is identity, we will check if the owner identity MI is the same as the database MI
    for (InteractorXref xref : interaction.getXrefs()) {
      if (xref.getCvXrefQualifier() != null &&
          getInstitutionPrimaryId() != null &&
          getInstitutionPrimaryId().equals( xref.getPrimaryId() ) &&
          !CvXrefQualifier.SOURCE_REFERENCE_MI_REF.equals(xref.getCvXrefQualifier().getIdentifier())) {
        xrefToFix = xref;
        break;
      }
    }
    if ( xrefToFix != null ) {
      log.warn("Interaction identity xref found pointing to the source database. It should be of type 'source-reference'. Will be fixed automatically: "+xrefToFix);
      CvXrefQualifier sourceReference = CvObjectUtils.createCvObject(interaction.getOwner(), CvXrefQualifier.class, CvXrefQualifier.SOURCE_REFERENCE_MI_REF, CvXrefQualifier.SOURCE_REFERENCE);
      xrefToFix.setCvXrefQualifier(sourceReference);
      addMessageToContext(MessageLevel.WARN, "Interaction identity xref found pointing to the source database. It should be of type 'source-reference'. Fixed.", true);
    }
  }
}

@Override
@Transactional( "update" )
public void onInvalidIntactParent(InvalidIntactParentFoundEvent evt) throws ProcessorException {
  // reattach the updateProcess to the entity manager
  ProteinUpdateProcess updateProcess = IntactUpdateContext.getCurrentInstance().getUpdateFactory().getEntityManager().merge(this.updateProcess);
  Protein protein = evt.getProtein();
  String newParentAc = evt.getNewParentAc();
  String oldParentAc = evt.getOldParentAc();
  InteractorXref uniprotXref = ProteinUtils.getUniprotXref(evt.getProtein());
  String uniprotAc= uniprotXref != null ? uniprotXref.getPrimaryId() : null;
  IntactTranscriptUpdateEvent protEvt = new IntactTranscriptUpdateEvent(updateProcess, protein, uniprotAc, oldParentAc, newParentAc);
  IntactUpdateContext.getCurrentInstance().getUpdateFactory().getIntactTranscriptEventDao().persist(protEvt);
}

@Override
@Transactional( "update" )
public void onSecondaryAcsFound(UpdateCaseEvent evt) throws ProcessorException {
  // reattach the updateProcess to the entity manager
  ProteinUpdateProcess updateProcess = IntactUpdateContext.getCurrentInstance().getUpdateFactory().getEntityManager().merge(this.updateProcess);
  Collection<Protein> secondaryProteins = evt.getSecondaryProteins();
  Collection<ProteinTranscript> secondaryIsoforms = evt.getSecondaryIsoforms();
  Collection<XrefUpdaterReport> secondaryXrefReports = evt.getXrefUpdaterReports();
  for (Protein prot : secondaryProteins){
    InteractorXref oldPrimary = ProteinUtils.getUniprotXref(prot);
    String oldAc = oldPrimary != null ? oldPrimary.getPrimaryId() : null;
    SecondaryProteinEvent protEvt = new SecondaryProteinEvent(updateProcess, prot, oldAc, evt.getProtein().getPrimaryAc());
    IntactUpdateContext.getCurrentInstance().getUpdateFactory().getSecondaryProteinEventDao().persist(protEvt);
  }
  for (ProteinTranscript protTrans : secondaryIsoforms){
    Protein prot = protTrans.getProtein();
    InteractorXref oldPrimary = ProteinUtils.getUniprotXref(prot);
    String oldAc = oldPrimary != null ? oldPrimary.getPrimaryId() : null;
    SecondaryProteinEvent protEvt = new SecondaryProteinEvent(updateProcess, prot, oldAc, protTrans.getUniprotVariant().getPrimaryAc());
    IntactUpdateContext.getCurrentInstance().getUpdateFactory().getSecondaryProteinEventDao().persist(protEvt);
  }
}