uk.ac.ebi.intact.model.util.AnnotatedObjectUtils.searchXrefs java code examples

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}

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));
}

Javadoc

Search for all Xrefs having Xref with both the given CvDatabase and CvXrefQualifier MIs.

Popular methods of AnnotatedObjectUtils

getAliasClassType
Gets the generic Xref type for an AnnotatedObject class
getXrefClassType
Gets the generic Xref type for an AnnotatedObject class
findAnnotationByTopicMiOrLabel
Finds an Annotations with a topic that has an MI or label equal to the value provided
getParameterizedType
prepareShortLabel
Trims a shortlabel if it is too long to be inserted in the database.
areCollectionEqual
Method to compare Annotation, Xref and Aliases collections
containSameAliases
containSameAnnotations
containSameCollections
Checks if two given annotated objects contain the same set of annotations, xrefs and aliases
containSameXrefs
containTheSameXrefs
Check if the passed annotated objects contain the same set of filtered Xrefs.
createUniqueString
Creates unique strings for Annotations,Xrefs and aliases.

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How to use searchXrefsmethodin uk.ac.ebi.intact.model.util.AnnotatedObjectUtils

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