How to use

searchXrefs

method

in

uk.ac.ebi.intact.model.util.AnnotatedObjectUtils

public static <X extends Xref> X getPsiMiIdentityXref(AnnotatedObject<X, ?> annotatedObject) {
  if (annotatedObject == null) {
    throw new NullPointerException("annotatedObject should not be null");
  }
  X psiMiXref = null;
  Collection<X> identityXrefs = AnnotatedObjectUtils.searchXrefs(annotatedObject, CvDatabase.PSI_MI_MI_REF, CvXrefQualifier.IDENTITY_MI_REF);
  if (!identityXrefs.isEmpty()) {
    psiMiXref = identityXrefs.iterator().next();
  }
  return psiMiXref;
}

if (log.isDebugEnabled()) log.debug("Populating identifier for: "+cvObject.getShortLabel());
Collection<CvObjectXref> miIdXrefs = AnnotatedObjectUtils.searchXrefs(cvObject, CvDatabase.PSI_MI_MI_REF, CvXrefQualifier.IDENTITY_MI_REF);

public static <X extends Xref> X getPsiMiIdentityXref(AnnotatedObject<X, ?> annotatedObject) {
  if (annotatedObject == null) {
    throw new NullPointerException("annotatedObject should not be null");
  }
  X psiMiXref = null;
  Collection<X> identityXrefs = AnnotatedObjectUtils.searchXrefs(annotatedObject, CvDatabase.PSI_MI_MI_REF, CvXrefQualifier.IDENTITY_MI_REF);
  if (!identityXrefs.isEmpty()) {
    psiMiXref = identityXrefs.iterator().next();
  }
  return psiMiXref;
}

listOfXrefLists.add(searchXrefs(ao, xrefFilter));

listOfXrefLists.add(searchXrefs(ao, xrefFilter));

/**
 * Search for all Xrefs having Xref with the given CvDatabase.
 *
 * @param ao the non null AnnotatedObject to search on.
 * @param db the non null CvDatabase filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static Collection<Xref> searchXrefs(AnnotatedObject ao, CvDatabase db) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (db == null) {
    throw new NullPointerException("CvDatabase must not be null.");
  }
  CvObjectFilterGroup cvFilterGroup = new CvObjectFilterGroup();
  cvFilterGroup.addIncludedCvObject(db);
  return searchXrefs(ao, new XrefCvFilter(cvFilterGroup));
}

/**
 * Search for all Xrefs having Xref with the given CvDatabase.
 *
 * @param ao the non null AnnotatedObject to search on.
 * @param db the non null CvDatabase filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static Collection<Xref> searchXrefs(AnnotatedObject ao, CvDatabase db) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (db == null) {
    throw new NullPointerException("CvDatabase must not be null.");
  }
  CvObjectFilterGroup cvFilterGroup = new CvObjectFilterGroup();
  cvFilterGroup.addIncludedCvObject(db);
  return searchXrefs(ao, new XrefCvFilter(cvFilterGroup));
}

/**
 * Search for all Xrefs having Xref with the given CvDatabase MI.
 *
 * @param ao   the non null AnnotatedObject to search on.
 * @param dbMi the non null CvDatabase filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static <X extends Xref> Collection<X> searchXrefsByDatabase(AnnotatedObject<X, ?> ao, String dbMi) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (dbMi == null) {
    throw new NullPointerException("dbMi must not be null.");
  }
  CvObjectFilterGroup cvFilterGroup = new CvObjectFilterGroup();
  cvFilterGroup.addIncludedIdentifier(dbMi);
  return searchXrefs(ao, new XrefCvFilter(cvFilterGroup));
}

/**
 * Search for all Xrefs having Xref with the given CvDatabase MI.
 *
 * @param ao   the non null AnnotatedObject to search on.
 * @param dbMi the non null CvDatabase filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static <X extends Xref> Collection<X> searchXrefsByDatabase(AnnotatedObject<X, ?> ao, String dbMi) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (dbMi == null) {
    throw new NullPointerException("dbMi must not be null.");
  }
  CvObjectFilterGroup cvFilterGroup = new CvObjectFilterGroup();
  cvFilterGroup.addIncludedIdentifier(dbMi);
  return searchXrefs(ao, new XrefCvFilter(cvFilterGroup));
}

/**
 * Search for all Xrefs having Xref with the given CvXrefQualifier.
 *
 * @param ao          the non null AnnotatedObject to search on.
 * @param qualifierMi the non null CvXrefQualifier filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static <X extends Xref> Collection<X> searchXrefsByQualifier(AnnotatedObject<X, ?> ao, String qualifierMi) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (qualifierMi == null) {
    throw new NullPointerException("qualifierMi must not be null.");
  }
  CvObjectFilterGroup cvFilterGroup = new CvObjectFilterGroup();
  cvFilterGroup.addIncludedIdentifier(qualifierMi);
  return searchXrefs(ao, new XrefCvFilter(new CvObjectFilterGroup(), cvFilterGroup));
}

/**
 * Search for all Xrefs having Xref with the given CvXrefQualifier.
 *
 * @param ao          the non null AnnotatedObject to search on.
 * @param qualifierMi the non null CvXrefQualifier filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static <X extends Xref> Collection<X> searchXrefsByQualifier(AnnotatedObject<X, ?> ao, String qualifierMi) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (qualifierMi == null) {
    throw new NullPointerException("qualifierMi must not be null.");
  }
  CvObjectFilterGroup cvFilterGroup = new CvObjectFilterGroup();
  cvFilterGroup.addIncludedIdentifier(qualifierMi);
  return searchXrefs(ao, new XrefCvFilter(new CvObjectFilterGroup(), cvFilterGroup));
}

Collection<Xref> xrefs = AnnotatedObjectUtils.searchXrefs( spliceVariant, isoformParent );

/**
 * Search for all Xrefs having Xref with both the given CvDatabase and CvXrefQualifier MIs.
 *
 * @param ao          the non null AnnotatedObject to search on.
 * @param dbMi        the non null CvDatabase filter.
 * @param qualifierMi the non null CvXrefQualifier filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static <X extends Xref> Collection<X> searchXrefs(AnnotatedObject<X, ?> ao, String dbMi, String qualifierMi) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (dbMi == null) {
    throw new NullPointerException("dbMi must not be null.");
  }
  CvObjectFilterGroup databaseCvFilterGroup = new CvObjectFilterGroup();
  databaseCvFilterGroup.addIncludedIdentifier(dbMi);
  CvObjectFilterGroup qualifierCvFilterGroup = new CvObjectFilterGroup();
  qualifierCvFilterGroup.addIncludedIdentifier(qualifierMi);
  return searchXrefs(ao, new XrefCvFilter(databaseCvFilterGroup, qualifierCvFilterGroup));
}

/**
 * Search for all Xrefs having Xref with the given CvXrefQualifier.
 *
 * @param ao the non null AnnotatedObject to search on.
 * @param qu the non null CvXrefQualifier filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static Collection<Xref> searchXrefs(AnnotatedObject ao, CvXrefQualifier qu) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (qu == null) {
    throw new NullPointerException("CvXrefQualifier must not be null.");
  }
  CvObjectFilterGroup cvFilterGroup = new CvObjectFilterGroup();
  cvFilterGroup.addIncludedCvObject(qu);
  return searchXrefs(ao, new XrefCvFilter(new CvObjectFilterGroup(), cvFilterGroup));
}

/**
 * Search for all Xrefs having Xref with both the given CvDatabase and CvXrefQualifier.
 *
 * @param ao the non null AnnotatedObject to search on.
 * @param db the non null CvDatabase filter.
 * @param qu the non null CvXrefQualifier filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static Collection<Xref> searchXrefs(AnnotatedObject ao, CvDatabase db, CvXrefQualifier qu) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (db == null) {
    throw new NullPointerException("CvDatabase must not be null.");
  }
  if (qu == null) {
    throw new NullPointerException("CvXrefQualifier must not be null.");
  }
  CvObjectFilterGroup cvFilterGroup = new CvObjectFilterGroup();
  cvFilterGroup.addIncludedCvObject(db);
  CvObjectFilterGroup qualifierCvFilterGroup = new CvObjectFilterGroup();
  qualifierCvFilterGroup.addIncludedCvObject(qu);
  return searchXrefs(ao, new XrefCvFilter(cvFilterGroup, qualifierCvFilterGroup));
}

/**
 * Search for all Xrefs having Xref with the given CvXrefQualifier.
 *
 * @param ao the non null AnnotatedObject to search on.
 * @param qu the non null CvXrefQualifier filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static Collection<Xref> searchXrefs(AnnotatedObject ao, CvXrefQualifier qu) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (qu == null) {
    throw new NullPointerException("CvXrefQualifier must not be null.");
  }
  CvObjectFilterGroup cvFilterGroup = new CvObjectFilterGroup();
  cvFilterGroup.addIncludedCvObject(qu);
  return searchXrefs(ao, new XrefCvFilter(new CvObjectFilterGroup(), cvFilterGroup));
}

/**
 * Search for all Xrefs having Xref with both the given CvDatabase and CvXrefQualifier.
 *
 * @param ao the non null AnnotatedObject to search on.
 * @param db the non null CvDatabase filter.
 * @param qu the non null CvXrefQualifier filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static Collection<Xref> searchXrefs(AnnotatedObject ao, CvDatabase db, CvXrefQualifier qu) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (db == null) {
    throw new NullPointerException("CvDatabase must not be null.");
  }
  if (qu == null) {
    throw new NullPointerException("CvXrefQualifier must not be null.");
  }
  CvObjectFilterGroup cvFilterGroup = new CvObjectFilterGroup();
  cvFilterGroup.addIncludedCvObject(db);
  CvObjectFilterGroup qualifierCvFilterGroup = new CvObjectFilterGroup();
  qualifierCvFilterGroup.addIncludedCvObject(qu);
  return searchXrefs(ao, new XrefCvFilter(cvFilterGroup, qualifierCvFilterGroup));
}

/**
 * Search for all Xrefs having Xref with both the given CvDatabase and CvXrefQualifier MIs.
 *
 * @param ao          the non null AnnotatedObject to search on.
 * @param dbMi        the non null CvDatabase filter.
 * @param qualifierMi the non null CvXrefQualifier filter.
 * @return a non null Collection of Xref, may be empty.
 */
public static <X extends Xref> Collection<X> searchXrefs(AnnotatedObject<X, ?> ao, String dbMi, String qualifierMi) {
  if (ao == null) {
    throw new NullPointerException("AnnotatedObject must not be null.");
  }
  if (dbMi == null) {
    throw new NullPointerException("dbMi must not be null.");
  }
  CvObjectFilterGroup databaseCvFilterGroup = new CvObjectFilterGroup();
  databaseCvFilterGroup.addIncludedIdentifier(dbMi);
  CvObjectFilterGroup qualifierCvFilterGroup = new CvObjectFilterGroup();
  qualifierCvFilterGroup.addIncludedIdentifier(qualifierMi);
  return searchXrefs(ao, new XrefCvFilter(databaseCvFilterGroup, qualifierCvFilterGroup));
}

/**
 * Get the Xref identities for an interactor, allowing the exclude the identities that come from the IMEx partners (intact, mint and dip)
 *
 * @param interactor
 * @param excludeIdentitiesFromImexPartners
 *
 * @return
 */
public static List<InteractorXref> getIdentityXrefs(Interactor interactor, boolean excludeIdentitiesFromImexPartners) {
  CvObjectFilterGroup qualifierFilterGroup = new CvObjectFilterGroup();
  qualifierFilterGroup.addIncludedIdentifier(CvXrefQualifier.IDENTITY_MI_REF);
  CvObjectFilterGroup databaseFilterGroup = new CvObjectFilterGroup();
  if (excludeIdentitiesFromImexPartners) {
    // TODO this has to be maintained in case we get new IMEx partners
    // TODO a work around could be to load the list of MI identities of all institutions present in the repository
    databaseFilterGroup.addExcludedIdentifier(CvDatabase.INTACT_MI_REF);
    databaseFilterGroup.addExcludedIdentifier(CvDatabase.MINT_MI_REF);
    databaseFilterGroup.addExcludedIdentifier(CvDatabase.DIP_MI_REF);
  }
  return AnnotatedObjectUtils.searchXrefs(interactor, new XrefCvFilter(databaseFilterGroup, qualifierFilterGroup));
}

/**
 * Get the Xref identities for an interactor, allowing the exclude the identities that come from the IMEx partners (intact, mint and dip)
 *
 * @param interactor
 * @param excludeIdentitiesFromImexPartners
 *
 * @return
 */
public static List<InteractorXref> getIdentityXrefs(Interactor interactor, boolean excludeIdentitiesFromImexPartners) {
  CvObjectFilterGroup qualifierFilterGroup = new CvObjectFilterGroup();
  qualifierFilterGroup.addIncludedIdentifier(CvXrefQualifier.IDENTITY_MI_REF);
  CvObjectFilterGroup databaseFilterGroup = new CvObjectFilterGroup();
  if (excludeIdentitiesFromImexPartners) {
    // TODO this has to be maintained in case we get new IMEx partners
    // TODO a work around could be to load the list of MI identities of all institutions present in the repository
    databaseFilterGroup.addExcludedIdentifier(CvDatabase.INTACT_MI_REF);
    databaseFilterGroup.addExcludedIdentifier(CvDatabase.MINT_MI_REF);
    databaseFilterGroup.addExcludedIdentifier(CvDatabase.DIP_MI_REF);
  }
  return AnnotatedObjectUtils.searchXrefs(interactor, new XrefCvFilter(databaseFilterGroup, qualifierFilterGroup));
}