How to use

getTags

method

in

net.sourceforge.ondex.core.ONDEXConcept

@Override
public Set<ONDEXConcept> getTags() {
  return parent.getTags();
}

@Override
public boolean accepts() {
  for (ONDEXConcept n : entities) {
    if (!n.getTags().isEmpty())
      return true;
  }
  return false;
}

@Override
public boolean accepts() {
  for (ONDEXConcept n : entities) {
    if (!n.getTags().isEmpty())
      return true;
  }
  return false;
}

  public HashSet<ONDEXConcept> getNonRedundant(ONDEXConcept acTo, ONDEXConcept acFrom){
    HashSet<ONDEXConcept> nonRedundantConcepts = new HashSet<ONDEXConcept>();
    for (ONDEXConcept concept : acFrom.getTags()){
      if (acTo != null &&  acTo.getTags().contains(concept) == false )
        nonRedundantConcepts.add(concept);
      else if(acTo == null){
        nonRedundantConcepts.add(concept);
      }
    }
    return nonRedundantConcepts;
  }
}

  public HashSet<ONDEXConcept> getNonRedundant(ONDEXConcept acTo, ONDEXConcept acFrom){
    HashSet<ONDEXConcept> nonRedundantConcepts = new HashSet<ONDEXConcept>();
    for (ONDEXConcept concept : acFrom.getTags()){
      if (acTo != null &&  acTo.getTags().contains(concept) == false )
        nonRedundantConcepts.add(concept);
      else if(acTo == null){
        nonRedundantConcepts.add(concept);
      }
    }
    return nonRedundantConcepts;
  }
}

  public HashSet<ONDEXConcept> getNonRedundant(ONDEXConcept acTo, ONDEXConcept acFrom){
    HashSet<ONDEXConcept> nonRedundantConcepts = new HashSet<ONDEXConcept>();
    for (ONDEXConcept concept : acFrom.getTags()){
      if (acTo != null && !acTo.getTags().contains(concept))
        nonRedundantConcepts.add(concept);
      else if(acTo == null){
        nonRedundantConcepts.add(concept);
      }
    }
    return nonRedundantConcepts;
  }
}

  public HashSet<ONDEXConcept> getNonRedundant(ONDEXConcept acTo, ONDEXConcept acFrom){
    HashSet<ONDEXConcept> nonRedundantConcepts = new HashSet<ONDEXConcept>();
    for (ONDEXConcept concept : acFrom.getTags()){
      if (acTo != null &&  acTo.getTags().contains(concept) == false )
        nonRedundantConcepts.add(concept);
      else if(acTo == null){
        nonRedundantConcepts.add(concept);
      }
    }
    return nonRedundantConcepts;
  }
}

/**
 * Copies a context list from on concept to another concept
 * @param acFrom
 * @param acTo
 */
public void copyContext(ONDEXConcept acTo, Set<ONDEXConcept> acFrom){
  for (ONDEXConcept concept : acFrom) {
    if (!acTo.getTags().contains(concept)) {
      acTo.addTag(concept);
    }
  }
}
/**

/**
 * Copies a context list from on concept to another concept
 * @param acFrom
 * @param acTo
 */
public void copyContext(ONDEXConcept acTo, Set<ONDEXConcept> acFrom){
  for (ONDEXConcept concept : acFrom) {
    if (acTo.getTags().contains(concept) == false) {
      acTo.addTag(concept);
    }
  }
}
/**

/**
 * Copies a context list from on concept to another concept
 * @param acFrom
 * @param acTo
 */
public void copyContext(ONDEXConcept acTo, Set<ONDEXConcept> acFrom){
  Iterator<ONDEXConcept> concepts = acFrom.iterator();
  while(concepts.hasNext()){
    ONDEXConcept concept = concepts.next();
    if ( acTo.getTags().contains(concept) == false )
      acTo.addTag(concept);
  }
}
/**

/**
 * Copies a context list from on concept to another concept
 * @param acFrom
 * @param acTo
 */
public void copyContext(ONDEXConcept acTo, Set<ONDEXConcept> acFrom){
  Iterator<ONDEXConcept> concepts = acFrom.iterator();
  while(concepts.hasNext()){
    ONDEXConcept concept = concepts.next();
    if ( acTo.getTags().contains(concept) == false )
      acTo.addTag(concept);
  }
}
/**

/**
 * Shows all other members of all the contexts that the selected concept(s)
 * are members of
 * 
 * @param viewer
 */
public static void showRelevantContexts(OVTK2PropertiesAggregator viewer) {
  ONDEXJUNGGraph graph = viewer.getONDEXJUNGGraph();
  Set<ONDEXConcept> contexts = new HashSet<ONDEXConcept>();
  for (ONDEXConcept c : viewer.getPickedNodes().toArray(new ONDEXConcept[0])) {
    contexts.addAll(c.getTags());
  }
  for (ONDEXConcept contextConcept : contexts) {
    graph.setVisibility(graph.getConceptsOfTag(contextConcept), true);
    graph.setVisibility(graph.getRelationsOfTag(contextConcept), true);
  }
}

/**
 * Shows all other members of all the contexts that the selected concept(s)
 * are members of, if the contexts are of particular class
 * 
 * @param viewer
 * @param contextClasses
 */
public static void showRelevantContextsByTypes(OVTK2PropertiesAggregator viewer, String... contextClasses) {
  ONDEXJUNGGraph graph = viewer.getONDEXJUNGGraph();
  Set<ONDEXConcept> contexts = new HashSet<ONDEXConcept>();
  Set<ConceptClass> selectedClasses = new HashSet<ConceptClass>();
  for (String s : contextClasses) {
    createCC(viewer.getONDEXJUNGGraph(), s);
  }
  for (ONDEXConcept c : viewer.getPickedNodes().toArray(new ONDEXConcept[0])) {
    for (ONDEXConcept candidate : c.getTags()) {
      if (selectedClasses.contains(candidate.getOfType()))
        contexts.add(candidate);
    }
  }
  for (ONDEXConcept contextConcept : contexts) {
    graph.setVisibility(graph.getConceptsOfTag(contextConcept), true);
    graph.setVisibility(graph.getRelationsOfTag(contextConcept), true);
  }
}

  @Override
  public void pointerToRelation(AbstractNode node) {
    HashSet<ONDEXRelation> relations = new HashSet<ONDEXRelation>();
    Compound compound = (Compound) node;
    for (AbstractNode abstractNode : compound.getCofactorOf()) {
      // Compound (cofactor of)=> Enzyme
      relations.add(graph.getFactory().createRelation(abstractNode.getConcept(), compound.getConcept(), rtCofectorOf, etIMPD));
    }
    for( ONDEXRelation relation: relations ){
      for (ONDEXConcept c : node.getConcept().getTags()){
        relation.addTag(c);
      }
    }/*
    for( AbstractNode n: compound.getCofactorOf()){
      Set<ONDEXConcept> toConcepts = node.getConcept().getContext(s);
      while( toConcepts.hasNext() ){
        ONDEXConcept toContext = toConcepts.next();
        if ( !n.getConcept().getContext(s).contains(toContext) )
          n.getConcept().addContext(toContext);
      }
    }*/
    
  }
}

  @Override
  public void pointerToRelation(AbstractNode node) {
    HashSet<ONDEXRelation> relations = new HashSet<ONDEXRelation>();
    Compound compound = (Compound) node;
    for (AbstractNode abstractNode : compound.getCofactorOf()) {
      // Compound (cofactor of)=> Enzyme
      relations.add(graph.getFactory().createRelation(abstractNode.getConcept(), compound.getConcept(), rtCofectorOf, etIMPD));
    }
    for( ONDEXRelation relation: relations ){
      for (ONDEXConcept c : node.getConcept().getTags()){
        relation.addTag(c);
      }
    }/*
    for( AbstractNode n: compound.getCofactorOf()){
      Set<ONDEXConcept> toConcepts = node.getConcept().getContext(s);
      while( toConcepts.hasNext() ){
        ONDEXConcept toContext = toConcepts.next();
        if ( !n.getConcept().getContext(s).contains(toContext) )
          n.getConcept().addContext(toContext);
      }
    }*/
    
  }
}

  @Override
  public void pointerToRelation(AbstractNode node) {
    HashSet<ONDEXRelation> relations = new HashSet<ONDEXRelation>();
    Compound compound = (Compound) node;
    for (AbstractNode abstractNode : compound.getCofactorOf()) {
      // Compound (cofactor of)=> Enzyme
      relations.add(graph.getFactory().createRelation(abstractNode.getConcept(), compound.getConcept(), rtCofectorOf, etIMPD));
    }
    for( ONDEXRelation relation: relations ){
      for (ONDEXConcept c : node.getConcept().getTags()){
        relation.addTag(c);
      }
    }/*
    for( AbstractNode n: compound.getCofactorOf()){
      Set<ONDEXConcept> toConcepts = node.getConcept().getContext(s);
      while( toConcepts.hasNext() ){
        ONDEXConcept toContext = toConcepts.next();
        if ( !n.getConcept().getContext(s).contains(toContext) )
          n.getConcept().addContext(toContext);
      }
    }*/
    
  }
}

  @Override
  public void pointerToRelation(AbstractNode node) {
    HashSet<ONDEXRelation> relations = new HashSet<ONDEXRelation>();
    Compound compound = (Compound) node;
    for (AbstractNode abstractNode : compound.getCofactorOf()) {
      // Compound (cofactor of)=> Enzyme
      relations.add(graph.getFactory().createRelation(abstractNode.getConcept(), compound.getConcept(), rtCofectorOf, etIMPD));
    }
    for( ONDEXRelation relation: relations ){
      for(ONDEXConcept c : node.getConcept().getTags()){
        relation.addTag(c);
      }
    }/*
    for( AbstractNode n: compound.getCofactorOf()){
      Set<ONDEXConcept> toConcepts = node.getConcept().getContext(s);
      while( toConcepts.hasNext() ){
        ONDEXConcept toContext = toConcepts.next();
        if ( !n.getConcept().getContext(s).contains(toContext) )
          n.getConcept().addContext(toContext);
      }
    }*/
    
  }
}

/**
 * Copies all context information from old concept to new concept and
 * updates context references on other entities.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newC
 *            new ONDEXConcept
 */
private void copyContext(ONDEXConcept oldC, ONDEXConcept newC) {
  // add new concept to same references as old concept
  for (ONDEXConcept c : graph.getConceptsOfTag(oldC)) {
    c.addTag(newC);
  }
  for (ONDEXRelation r : graph.getRelationsOfTag(oldC)) {
    r.addTag(newC);
  }
  // transfer context from old concept to new concept
  for (ONDEXConcept c : oldC.getTags()) {
    newC.addTag(c);
  }
}

@Override
protected void doAction() {
  for (ONDEXConcept c : entities) {
    for (ONDEXConcept concept : c.getTags()) {
      // first set concepts visible
      for (ONDEXConcept ctxt : viewer.getONDEXJUNGGraph().getConceptsOfTag(concept)) {
        viewer.getONDEXJUNGGraph().setVisibility(ctxt, true);
      }
      // second set relations visible
      for (ONDEXRelation r : viewer.getONDEXJUNGGraph().getRelationsOfTag(concept)) {
        viewer.getONDEXJUNGGraph().setVisibility(r, true);
      }
    }
  }
}

@Override
protected void doAction() {
  for (ONDEXConcept vertex : entities) {
    ONDEXConcept c = vertex;
    for (ONDEXConcept concept : c.getTags()) {
      // first set relations invisible
      for (ONDEXRelation r : viewer.getONDEXJUNGGraph().getRelationsOfTag(concept)) {
        viewer.getONDEXJUNGGraph().setVisibility(r, false);
      }
      // second set concepts invisible
      for (ONDEXConcept c2 : viewer.getONDEXJUNGGraph().getConceptsOfTag(concept)) {
        viewer.getONDEXJUNGGraph().setVisibility(c2, false);
      }
    }
  }
}