How to use

AnnotatedObjectImpl

in

uk.ac.ebi.intact.model

/**
 * Returns a cloned version of the current object.
 *
 * @return a cloned version of the current Experiment with following exceptions. <ul> <li>Interactions are not
 *         cloned. The interactions for the cloned experiment is empty</li> <li>New components but with the same
 *         proteins. The new components has the cloned interaction as their interaction.</li> </ul>
 *
 * @throws CloneNotSupportedException
 */
@Override
public Object clone() throws CloneNotSupportedException {
  Experiment copy = ( Experiment ) super.clone();
  // Not copying any interactions.
  copy.interactions = new ArrayList<Interaction>();
  return copy;
}

public boolean equals(Object o) {
  if ( this == o ) {
    return true;
  }
  if ( !( o instanceof Institution ) ) {
    return false;
  }
  if ( !super.equals( o ) ) {
    return false;
  }
  Institution that = (Institution) o;
  return true;
}

  @Override
  public String toString() {
    return this.getAc() + "; owner=" + this.getOwner().getAc()
        + "; name=" + this.shortLabel + "; fullname=" + fullName;
  }
}

AnnotatedObjectImpl copy = ( AnnotatedObjectImpl ) super.clone();
Collection<T> xrefs = getXrefs();
Collection<A> aliases = getAliases();
for ( Xref xref : getXrefs() ) {
  Xref xrefClone = ( Xref ) xref.clone();
  xrefClone.setParent( copy );
  copiedXrefs.add( xrefClone );
copy.setXrefs( copiedXrefs );
for ( Alias alias : getAliases() ) {
  Alias aliasClone = ( Alias ) alias.clone();
  aliasClone.setParent( copy );
  copiedAliases.add( ( Alias ) alias.clone() );
copy.setAliases( copiedAliases );

  if ( !shortLabel.equals( annotatedObject.getShortLabel() ) ) {
    return false;
  if ( annotatedObject.getShortLabel() != null ) {
    return false;
  if ( !fullName.equals( annotatedObject.getFullName() ) ) {
    return false;
  if ( annotatedObject.getFullName() != null ) {
    return false;
if (IntactCore.isInitialized(getXrefs()) &&
    IntactCore.isInitialized(annotatedObject.getXrefs()) &&
    !CollectionUtils.isEqualCollection( getXrefs(), annotatedObject.getXrefs() )) {
  return false;
if (IntactCore.isInitialized(getAnnotations()) &&
    IntactCore.isInitialized(annotatedObject.getAnnotations()) &&
    !CollectionUtils.isEqualCollection( getAnnotations(), annotatedObject.getAnnotations() )) {
  return false;
if (IntactCore.isInitialized(getAliases()) &&
    IntactCore.isInitialized(annotatedObject.getAliases()) &&
    !CollectionUtils.isEqualCollection( getAliases(), annotatedObject.getAliases() )) {
  return false;

@OneToMany( mappedBy = "parent", cascade = {CascadeType.PERSIST, CascadeType.REMOVE} )
@Override
public Collection<BioSourceXref> getXrefs() {
  return super.getXrefs();
}

@OneToMany( mappedBy = "parent", cascade = {CascadeType.PERSIST, CascadeType.REMOVE} )
@Override
public Collection<BioSourceAlias> getAliases() {
  return super.getAliases();
}

@ManyToMany( cascade = {CascadeType.PERSIST, CascadeType.REMOVE, CascadeType.MERGE, CascadeType.REFRESH, CascadeType.DETACH})
@JoinTable(
    name = "ia_cvobject2annot",
    joinColumns = {@JoinColumn( name = "cvobject_ac" )},
    inverseJoinColumns = {@JoinColumn( name = "annotation_ac" )}
)
@Override
public Collection<Annotation> getAnnotations() {
  return super.getAnnotations();
}

  @Override
  public int hashCode() {
    return 29 * super.hashCode();
  }
}

@Deprecated
protected AnnotatedObjectImpl( String shortLabel, Institution owner ) {
  this(shortLabel);
  setOwner(owner);
}

  @Override
  public String toString() {
    return this.getClass().getSimpleName()+"{ac="+this.getAc() + "; name=" + this.shortLabel + "; fullname=" + fullName+"}";
  }
}

AnnotatedObjectImpl copy = ( AnnotatedObjectImpl ) super.clone();
Collection<T> xrefs = getXrefs();
Collection<A> aliases = getAliases();
for ( Xref xref : getXrefs() ) {
  Xref xrefClone = ( Xref ) xref.clone();
  xrefClone.setParent( copy );
  copiedXrefs.add( xrefClone );
copy.setXrefs( copiedXrefs );
for ( Alias alias : getAliases() ) {
  Alias aliasClone = ( Alias ) alias.clone();
  aliasClone.setParent( copy );
  copiedAliases.add( ( Alias ) alias.clone() );
copy.setAliases( copiedAliases );

  if ( !shortLabel.equals( annotatedObject.getShortLabel() ) ) {
    return false;
  if ( annotatedObject.getShortLabel() != null ) {
    return false;
  if ( !fullName.equals( annotatedObject.getFullName() ) ) {
    return false;
  if ( annotatedObject.getFullName() != null ) {
    return false;
if (IntactCore.isInitialized(getXrefs()) &&
    IntactCore.isInitialized(annotatedObject.getXrefs()) &&
    !CollectionUtils.isEqualCollection( getXrefs(), annotatedObject.getXrefs() )) {
  return false;
if (IntactCore.isInitialized(getAnnotations()) &&
    IntactCore.isInitialized(annotatedObject.getAnnotations()) &&
    !CollectionUtils.isEqualCollection( getAnnotations(), annotatedObject.getAnnotations() )) {
  return false;
if (IntactCore.isInitialized(getAliases()) &&
    IntactCore.isInitialized(annotatedObject.getAliases()) &&
    !CollectionUtils.isEqualCollection( getAliases(), annotatedObject.getAliases() )) {
  return false;

@OneToMany( mappedBy = "parent", cascade = {CascadeType.ALL}, orphanRemoval = true )
public Collection<InstitutionXref> getXrefs() {
  return super.getXrefs();
}

@OneToMany( mappedBy = "parent", cascade = {CascadeType.ALL}, orphanRemoval = true)
public Collection<InstitutionAlias> getAliases() {
  return super.getAliases();
}

@ManyToMany( cascade = {CascadeType.PERSIST} )
@JoinTable(
    name = "ia_pub2annot",
    joinColumns = {@JoinColumn( name = "publication_ac" )},
    inverseJoinColumns = {@JoinColumn( name = "annotation_ac" )}
)
@Override
public Collection<Annotation> getAnnotations() {
  return super.getAnnotations();
}

public int hashCode() {
  return 31*super.hashCode();
}

@Deprecated
protected AnnotatedObjectImpl( String shortLabel, Institution owner ) {
  this(shortLabel);
  setOwner(owner);
}

  @Override
  public String toString() {
    return this.getClass().getSimpleName()+"{ac="+this.getAc() + "; name=" + this.shortLabel + "; fullname=" + fullName+"}";
  }
}

AnnotatedObjectImpl copy = ( AnnotatedObjectImpl ) super.clone();
Collection<T> xrefs = getXrefs();
Collection<A> aliases = getAliases();
for ( Xref xref : getXrefs() ) {
  Xref xrefClone = ( Xref ) xref.clone();
  xrefClone.setParent( copy );
  copiedXrefs.add( xrefClone );
copy.setXrefs( copiedXrefs );
for ( Alias alias : getAliases() ) {
  Alias aliasClone = ( Alias ) alias.clone();
  aliasClone.setParent( copy );
  copiedAliases.add( ( Alias ) alias.clone() );
copy.setAliases( copiedAliases );