uk.ac.ebi.intact.model.AnnotatedObject.getAliases java code examples

private static void logPersistence(AnnotatedObject<?,?> ao) {
  if (log.isDebugEnabled()) {
    log.debug("\t\t\tPersisted with AC: " + ao.getAc());
    if (!ao.getXrefs().isEmpty()) {
      log.debug("\t\t\tXrefs: " + ao.getXrefs().size());
      for (Xref xref : ao.getXrefs()) {
        log.debug("\t\t\t\t"+xref);
      }
    }
    if (!ao.getAliases().isEmpty()) {
      log.debug("\t\t\tAliases: " + ao.getAliases().size());
      for (Alias alias: ao.getAliases()) {
        log.debug("\t\t\t\t"+alias);
      }
    }
    if (!ao.getAnnotations().isEmpty()) {
      log.debug("\t\t\tAnnotations: " + ao.getAnnotations().size());
      for (Annotation annot: ao.getAnnotations()) {
        log.debug("\t\t\t\t"+annot);
      }
    }
  }
}

/**
 * Prints the label, ac, and the counts of some attributes (xrefs, aliases and annotations) of an AnnotatedObject
 * @param ao Annotated object to prints
 *
 * @since 1.8.0
 */
public static String annotatedObjectToString(AnnotatedObject ao, boolean showAttributesCount) {
  Class clazz = CgLibUtil.removeCglibEnhanced(ao.getClass());
  StringBuilder sb = new StringBuilder();
  sb.append(clazz.getSimpleName()).append("{label=").append(ao.getShortLabel()).append(", ac=").append(ao.getAc());
  if (showAttributesCount) {
    String xrefsCount = "[not initialized]";
    String aliasCount = "[not initialized]";
    String annotationsCount = "[not initialized]";
    if (IntactCore.isInitialized(ao.getXrefs())) {
      xrefsCount = String.valueOf(ao.getXrefs().size());
    }
    if (IntactCore.isInitialized(ao.getAliases())) {
      aliasCount = String.valueOf(ao.getAliases().size());
    }
    if (IntactCore.isInitialized(ao.getAnnotations())) {
      annotationsCount = String.valueOf(ao.getAnnotations().size());
    }
    sb.append(", xrefCount=").append(xrefsCount).append(", aliasCount=").append(aliasCount).append(", annotationsCount=").append(annotationsCount);
  }
  sb.append("}");
  return sb.toString();
}

public static Collection<Alias> getAliasByType(AnnotatedObject<?, ?> annotatedObject, String miOrLabel) {
  Collection<Alias> matchingAliases = new ArrayList<Alias>();
  for (Alias alias : annotatedObject.getAliases()) {
    if (alias.getCvAliasType() != null
        && (
        alias.getCvAliasType().getIdentifier().equals(miOrLabel)
            ||
            alias.getCvAliasType().getShortLabel().equals(miOrLabel))
        ) {
      matchingAliases.add(alias);
    }
  }
  return matchingAliases;
}

/**
 * Prints the label, ac, and the counts of some attributes (xrefs, aliases and annotations) of an AnnotatedObject
 * @param ao Annotated object to prints
 *
 * @since 1.8.0
 */
public static String annotatedObjectToString(AnnotatedObject ao, boolean showAttributesCount) {
  Class clazz = CgLibUtil.removeCglibEnhanced(ao.getClass());
  StringBuilder sb = new StringBuilder();
  sb.append(clazz.getSimpleName()).append("{label=").append(ao.getShortLabel()).append(", ac=").append(ao.getAc());
  if (showAttributesCount) {
    String xrefsCount = "[not initialized]";
    String aliasCount = "[not initialized]";
    String annotationsCount = "[not initialized]";
    if (IntactCore.isInitialized(ao.getXrefs())) {
      xrefsCount = String.valueOf(ao.getXrefs().size());
    }
    if (IntactCore.isInitialized(ao.getAliases())) {
      aliasCount = String.valueOf(ao.getAliases().size());
    }
    if (IntactCore.isInitialized(ao.getAnnotations())) {
      annotationsCount = String.valueOf(ao.getAnnotations().size());
    }
    sb.append(", xrefCount=").append(xrefsCount).append(", aliasCount=").append(aliasCount).append(", annotationsCount=").append(annotationsCount);
  }
  sb.append("}");
  return sb.toString();
}

public static Collection<Alias> getAliasByType(AnnotatedObject<?, ?> annotatedObject, String miOrLabel) {
  Collection<Alias> matchingAliases = new ArrayList<Alias>();
  for (Alias alias : annotatedObject.getAliases()) {
    if (alias.getCvAliasType() != null
        && (
        alias.getCvAliasType().getIdentifier().equals(miOrLabel)
            ||
            alias.getCvAliasType().getShortLabel().equals(miOrLabel))
        ) {
      matchingAliases.add(alias);
    }
  }
  return matchingAliases;
}

/**
 * Retrieves the aliases from an AnnotatedObject, initializing them if necessary.
 *
 * @param ao The annotated object instance with possibly non-initialized aliases
 * @return The returned aliases are ensured to be initialized
 * @since 2.4.0
 */
public static Collection<? extends Alias> ensureInitializedAliases(AnnotatedObject<?, ?> ao) {
  Collection<? extends Alias> aliases;
  if (IntactCore.isInitialized(ao.getAliases())) {
    aliases = ao.getAliases();
  } else {
    aliases = IntactContext.getCurrentInstance().getDaoFactory().getAliasDao(AnnotatedObjectUtils.getAliasClassType(ao.getClass()))
        .getByParentAc(ao.getAc());
  }
  return aliases;
}

/**
 * Retrieves the aliases from an AnnotatedObject, initializing them if necessary.
 *
 * @param ao The annotated object instance with possibly non-initialized aliases
 * @return The returned aliases are ensured to be initialized
 * @since 2.4.0
 */
public static Collection<? extends Alias> ensureInitializedAliases(AnnotatedObject<?, ?> ao) {
  Collection<? extends Alias> aliases;
  if (IntactCore.isInitialized(ao.getAliases())) {
    aliases = ao.getAliases();
  } else {
    aliases = IntactContext.getCurrentInstance().getDaoFactory().getAliasDao(AnnotatedObjectUtils.getAliasClassType(ao.getClass()))
        .getByParentAc(ao.getAc());
  }
  return aliases;
}

if (IntactCore.isInitializedAndDirty(ao.getAliases())) {
  for ( Alias alias : ao.getAliases() ) {
    synchedAliases.add( synchronizeAlias( alias, ao ) );
  ao.getAliases().clear();
  ao.getAliases().addAll(synchedAliases);
} else {
  synchedAliases = ao.getAliases();

private static List<SearchItem> searchItemsForAnnotatedObject( AnnotatedObject<? extends Xref, ? extends Alias> ao, boolean includeAliases ) {
  List<SearchItem> searchItems = new ArrayList<SearchItem>();
  searchItems.add( new SearchItem( ao.getAc(), ao.getAc(), ao.getClass().getName(), "ac" ) );
  searchItems.add( new SearchItem( ao.getAc(), ao.getShortLabel(), ao.getClass().getName(), "shortlabel" ) );
  if ( ao.getFullName() != null ) {
    searchItems.add( new SearchItem( ao.getAc(), ao.getFullName(), ao.getClass().getName(), "fullname" ) );
  }
  if ( includeAliases ) {
    for ( Alias alias : ao.getAliases() ) {
      if ( alias.getCvAliasType() != null ) {
        searchItems.add( new SearchItem( ao.getAc(), alias.getName(), ao.getClass().getName(), alias.getCvAliasType().getShortLabel() ) );
      } else {
        log.warn( "Couldn't insert SearchItem for Alias, as it cvAliasType is null: " + alias.getName() );
      }
    }
  }
  return searchItems;
}

protected <X extends Xref, A extends Alias> void copyAnotatedObjectCommons( AnnotatedObject<X, A> source,
                                      AnnotatedObject<X, A> target ) {
  // if the source does not have an AC, we should not update the target shortLabel, fullName and owner
  // as it does not make much sense
  //if (source.getAc() != null) {
    copyProperty(source, "shortLabel", target);
    copyProperty(source, "fullName", target);
    copyProperty(source, "owner", target);
  //}
  copyXrefCollection( source.getXrefs(), target.getXrefs() );
  copyAliasCollection( source.getAliases(), target.getAliases(), source, target );
  copyAnnotationCollection( source.getAnnotations(), target.getAnnotations() );
}

private <T extends AnnotatedObject> void initializeCommonsIfNecessary(T ao, T managedObject) {
  if (IntactCore.isInitialized(ao.getXrefs()))
    IntactCore.initialize(managedObject.getXrefs());
  if (IntactCore.isInitialized(ao.getAnnotations()))
    IntactCore.initialize(managedObject.getAnnotations());
  if (IntactCore.isInitialized(ao.getAliases())) {
    IntactCore.initialize(managedObject.getAliases());
  }
}

/**
 * Initializes the AnnotatedObject collections (xrefs, aliases, annotations).
 *
 * @param ao The annotatedObject
 */
public static void initializeAnnotatedObject(AnnotatedObject ao) {
  initialize(ao.getXrefs());
  initialize(ao.getAliases());
  initialize(ao.getAnnotations());
}

/**
 * Initializes the AnnotatedObject collections (xrefs, aliases, annotations).
 *
 * @param ao The annotatedObject
 */
public static void initializeAnnotatedObject(AnnotatedObject ao) {
  initialize(ao.getXrefs());
  initialize(ao.getAliases());
  initialize(ao.getAnnotations());
}

private <T extends AnnotatedObject> void initializeCommonsIfNecessary(T ao, T managedObject) {
  if (IntactCore.isInitialized(ao.getXrefs()))
    IntactCore.initialize(managedObject.getXrefs());
  if (IntactCore.isInitialized(ao.getAnnotations()))
    IntactCore.initialize(managedObject.getAnnotations());
  if (IntactCore.isInitialized(ao.getAliases())) {
    IntactCore.initialize(managedObject.getAliases());
  }
}

protected <X extends Xref, A extends Alias> void copyAnotatedObjectCommons( AnnotatedObject<X, A> source,
                                      AnnotatedObject<X, A> target ) {
  // if the source does not have an AC, we should not update the target shortLabel, fullName and owner
  // as it does not make much sense
  //if (source.getAc() != null) {
    copyProperty(source, "shortLabel", target);
    copyProperty(source, "fullName", target);
    copyProperty(source, "owner", target);
  //}
  copyXrefCollection( source.getXrefs(), target.getXrefs() );
  copyAliasCollection( source.getAliases(), target.getAliases(), source, target );
  copyAnnotationCollection( source.getAnnotations(), target.getAnnotations() );
}

protected void traverseAnnotatedObjectCommon(AnnotatedObject ao, IntactVisitor ... visitors) {
  traverse(ao.getAnnotations(), visitors);
  traverse(ao.getAliases(), visitors);
  traverse(ao.getXrefs(), visitors);
  // check if this element has been traversed already, to avoid cyclic recursion
  if (recursionChecker.isAlreadyTraversed(ao)) {
    return;
  }
  traverse(ao.getOwner(), visitors);
}

protected void traverseAnnotatedObjectCommon(AnnotatedObject ao, IntactVisitor ... visitors) {
  traverse(ao.getAnnotations(), visitors);
  traverse(ao.getAliases(), visitors);
  traverse(ao.getXrefs(), visitors);
  // check if this element has been traversed already, to avoid cyclic recursion
  if (recursionChecker.isAlreadyTraversed(ao)) {
    return;
  }
  traverse(ao.getOwner(), visitors);
}

  return IntactCore.isInitialized(parent.getAnnotations());
} else if (child instanceof Alias) {
  return IntactCore.isInitialized(parent.getAliases());
} else {
  throw new IllegalArgumentException("Unexpected combination parent/child - Parent: " +

public static void populateNames( AnnotatedObject<?, ?> annotatedObject, NamesContainer namesContainer, AliasConverter aliasConverter ) {
  Names names = namesContainer.getNames();
  if ( names == null ) {
    names = new Names();
  }
  String shortLabel = annotatedObject.getShortLabel();
  String fullName = annotatedObject.getFullName();
  names.setShortLabel( shortLabel );
  names.setFullName( fullName );
  if ( !ConverterContext.getInstance().getInteractorConfig().isExcludeInteractorAliases() ) {
    Collection<? extends Alias> aliases;
    if (aliasConverter.isCheckInitializedCollections()){
      aliases = IntactCore.ensureInitializedAliases(annotatedObject);
    }
    else {
      aliases = annotatedObject.getAliases();
    }
    for ( Alias alias : aliases) {
      names.getAliases().add( aliasConverter.intactToPsi( alias ) );
    }
  }
  namesContainer.setNames( names );
}

@Override
protected void saveOrUpdateAttributes( T intactObject ) throws PersisterException {
  if ( intactObject == null ) {
    throw new NullPointerException( "intactObject" );
  }
  InstitutionPersister institutionPersister = InstitutionPersister.getInstance();
  institutionPersister.saveOrUpdate( intactObject.getOwner() );
  CvObjectPersister cvPersister = CvObjectPersister.getInstance();
  for ( Xref xref : intactObject.getXrefs() ) {
    cvPersister.saveOrUpdate( xref.getCvDatabase() );
    if ( xref.getCvXrefQualifier() != null ) {
      cvPersister.saveOrUpdate( xref.getCvXrefQualifier() );
    }
    institutionPersister.saveOrUpdate( xref.getOwner() );
  }
  for ( Alias alias : intactObject.getAliases() ) {
    if ( alias.getCvAliasType() != null ) {
      cvPersister.saveOrUpdate( alias.getCvAliasType() );
    }
    institutionPersister.saveOrUpdate( alias.getOwner() );
  }
  
  for ( Annotation annotation : intactObject.getAnnotations() ) {
    if ( annotation.getCvTopic() != null ) {
      cvPersister.saveOrUpdate( annotation.getCvTopic() );
    }
    institutionPersister.saveOrUpdate( annotation.getOwner() );
  }
}

How to use getAliasesmethodin uk.ac.ebi.intact.model.AnnotatedObject

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How to use
getAliases
method
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uk.ac.ebi.intact.model.AnnotatedObject