net.sourceforge.ondex.core.ONDEXConcept.getTags java code examples

Common ways to obtain ONDEXConcept

private void myMethod () {
 ONDEXConcept o =ONDEXRelation r;r.getToConcept()
ONDEXRelation r;r.getFromConcept()
ONDEXGraph graph;graph.getConcept(id)
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}

@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);
      }
    }
  }
}

Popular methods of ONDEXConcept

getId
createAttribute
createConceptAccession
Creates a new ConceptAccession with the given accession, the information which DataSource it belongs
createConceptName
Creates a new ConceptName with the given name and the information if this name is preferred. Then ad
getOfType
getConceptAccessions
getElementOf
Returns the DataSource, which this AbstractConcept belongs to.
getPID
Returns the parser id of this instance of AbstractConcept.
getConceptNames
Returns all ConceptNames contained in the list of ConceptNames.
getAttribute
getConceptName
Returns a ConceptName or null if unsuccessful for a given name or null if unsuccessful.
getAnnotation
Returns the annotation of this instance of AbstractConcept.

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Top 12 Jupyter Notebook Extensions

How to use getTagsmethodin net.sourceforge.ondex.core.ONDEXConcept

Best Java code snippets using net.sourceforge.ondex.core.ONDEXConcept.getTags (Showing top 20 results out of 315)

How to use
getTags
method
in
net.sourceforge.ondex.core.ONDEXConcept