How to use

getShortLabel

method

in

uk.ac.ebi.intact.model.AnnotatedObject

/**
 * Returns the list of labels for the annotated objects provided
 *
 * @param intactObjects list of annotated objects
 *
 * @return a list of labels
 */
public static List<String> labelList( Collection<? extends AnnotatedObject> intactObjects ) {
  List<String> labels = new ArrayList<String>( intactObjects.size() );
  for ( AnnotatedObject io : intactObjects ) {
    labels.add( io.getShortLabel() );
  }
  return labels;
}

/**
 * Returns the list of labels for the annotated objects provided
 *
 * @param intactObjects list of annotated objects
 *
 * @return a list of labels
 */
public static List<String> labelList( Collection<? extends AnnotatedObject> intactObjects ) {
  List<String> labels = new ArrayList<String>( intactObjects.size() );
  for ( AnnotatedObject io : intactObjects ) {
    labels.add( io.getShortLabel() );
  }
  return labels;
}

/**
 * Returns the list of labels for the annotated objects provided
 *
 * @param intactObjects list of annotated objects
 *
 * @return a list of labels
 */
public static List<String> labelList( Collection<? extends AnnotatedObject> intactObjects ) {
  List<String> labels = new ArrayList<String>( intactObjects.size() );
  for ( AnnotatedObject io : intactObjects ) {
    labels.add( io.getShortLabel() );
  }
  return labels;
}

@Override
public void visitAnnotatedObject(AnnotatedObject annotatedObject) {
  currentNode.setUserObject(annotatedObject.getClass().getSimpleName()+": "+annotatedObject.getShortLabel());
}

@Override
public void visitAnnotatedObject(AnnotatedObject annotatedObject) {
  currentNode.setUserObject(annotatedObject.getClass().getSimpleName()+": "+annotatedObject.getShortLabel());
}

@Override
public void visitAnnotatedObject(AnnotatedObject annotatedObject) {
  ps.println(indentation()+annotatedObject.getClass().getSimpleName()+": "+annotatedObject.getShortLabel());
}

@Override
public void visitAnnotatedObject(AnnotatedObject annotatedObject) {
  ps.println(indentation()+annotatedObject.getClass().getSimpleName()+": "+annotatedObject.getShortLabel());
}

private <T extends AnnotatedObject> void warnIfInteractionDuplicate( T ao, T managedObject ) {
  if ( log.isWarnEnabled() && ao instanceof Interaction ) {
    Interaction newInteraction = ( Interaction ) ao;
    Interaction existingInteraction = ( Interaction ) managedObject;
    String newImexId = InteractionUtils.getImexIdentifier( newInteraction );
    String existingImexId = InteractionUtils.getImexIdentifier( existingInteraction );
    log.warn( "An AC already exists for this interaction. Possibly a duplicate? : Existing [" + managedObject.getAc() + ", " + managedObject.getShortLabel() + ", " + existingImexId + "] - " +
        "New [-, " + ao.getShortLabel() + ", " + newImexId + "]. The existing interaction will be updated" );
  }
}

private <T extends AnnotatedObject> void warnIfInteractionDuplicate( T ao, T managedObject ) {
  if ( log.isWarnEnabled() && ao instanceof Interaction ) {
    Interaction newInteraction = ( Interaction ) ao;
    Interaction existingInteraction = ( Interaction ) managedObject;
    String newImexId = InteractionUtils.getImexIdentifier( newInteraction );
    String existingImexId = InteractionUtils.getImexIdentifier( existingInteraction );
    log.warn( "An AC already exists for this interaction. Possibly a duplicate? : Existing [" + managedObject.getAc() + ", " + managedObject.getShortLabel() + ", " + existingImexId + "] - " +
        "New [-, " + ao.getShortLabel() + ", " + newImexId + "]. The existing interaction will be updated" );
  }
}

protected Key keyForAnnotatedObject(AnnotatedObject annotatedObject) {
  Class normalizedClass = CgLibUtil.removeCglibEnhanced(annotatedObject.getClass());
  return new Key(normalizedClass.getSimpleName() + ":" + annotatedObject.getShortLabel());
}

public AnnotatedObjectStatsUnit(AnnotatedObject ao) {
  this.shortLabel = ao.getShortLabel();
  this.ac = ao.getAc();
  this.type = CgLibUtil.removeCglibEnhanced(ao.getClass());
}

protected Key keyForAnnotatedObject(AnnotatedObject annotatedObject) {
  Class normalizedClass = CgLibUtil.removeCglibEnhanced(annotatedObject.getClass());
  return new Key(normalizedClass.getSimpleName() + ":" + annotatedObject.getShortLabel());
}

public AnnotatedObjectStatsUnit(AnnotatedObject ao) {
  this.shortLabel = ao.getShortLabel();
  this.ac = ao.getAc();
  this.type = CgLibUtil.removeCglibEnhanced(ao.getClass());
}

/**
 * Create a shortlabel element containing the shortlabel of the given AnnotatatedObject.
 *
 * @param session
 * @param parent  the names element, not null.
 * @param object  the annotatedObject from which we get the shortlabel, not null.
 */
protected void createShortlabel( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  // shortlabel is mandatory in the IntAct API.
  Element shortlabel = session.createElement( "shortLabel" );
  Text shortlabelText = session.createTextNode( object.getShortLabel() );
  shortlabel.appendChild( shortlabelText );
  parent.appendChild( shortlabel );
}

/**
 * Create a shortlabel element containing the shortlabel of the given AnnotatatedObject.
 *
 * @param session
 * @param parent  the names element, not null.
 * @param object  the annotatedObject from which we get the shortlabel, not null.
 */
protected void createShortlabel( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  // shortlabel is mandatory in the IntAct API.
  Element shortlabel = session.createElement( "shortLabel" );
  Text shortlabelText = session.createTextNode( object.getShortLabel() );
  shortlabel.appendChild( shortlabelText );
  parent.appendChild( shortlabel );
}

public SimplifiedAnnotatedObject( AnnotatedObject annotatedObject ) {
  this.ac = annotatedObject.getAc();
  this.shortLabel = annotatedObject.getShortLabel();
  this.created = annotatedObject.getCreated();
}

public SimplifiedAnnotatedObject( AnnotatedObject annotatedObject ) {
  this.ac = annotatedObject.getAc();
  this.shortLabel = annotatedObject.getShortLabel();
  this.created = annotatedObject.getCreated();
}

public SimplifiedAnnotatedObject( AnnotatedObject annotatedObject ) {
  this.ac = annotatedObject.getAc();
  this.shortLabel = annotatedObject.getShortLabel();
  this.created = annotatedObject.getCreated();
}

private void insertSearchItemForAnnotatedObject( AnnotatedObject<? extends Xref, ? extends Alias> ao, boolean includeAliases ) {
  if ( log.isDebugEnabled() ) {
    log.debug( "Inserting SearchItems for AnnotatedObject: " + ao.getShortLabel() + " (" + ao.getAc() + ")" );
  }
  for ( SearchItem searchItem : searchItemsForAnnotatedObject( ao, includeAliases ) ) {
    if ( log.isDebugEnabled() ) {
      log.debug( "\t" + searchItem );
    }
    IntactContext.getCurrentInstance().getDataContext().getDaoFactory()
        .getSearchItemDao().persist( searchItem );
  }
}

private void deleteSearchItemsForAnnotatedObject( AnnotatedObject<? extends Xref, ? extends Alias> ao ) {
  if ( log.isDebugEnabled() ) {
    log.debug( "Deleting SearchItems for AnnotatedObject: " + ao.getShortLabel() + " (" + ao.getAc() + ")" );
  }
  IntactContext.getCurrentInstance().getDataContext().getDaoFactory()
      .getSearchItemDao().deleteByAc( ao.getAc() );
}