How to use

getConceptName

method

in

net.sourceforge.ondex.core.ONDEXConcept

@Override
public ConceptName getConceptName(String name) throws NullValueException,
    EmptyStringException {
  return parent.getConceptName(name);
}

ConceptName cn = concept.getConceptName();
if (cn != null) {
  defaultName = cn.getName();

@Override
public ConceptName getConceptName() {
  return parent.getConceptName();
}

ConceptName cn = concept.getConceptName();
if (cn != null)
  name = concept.getConceptName().getName();
else {

public static String getName(ONDEXConcept c, String prefix){
  String name;
  ConceptName cn = c.getConceptName();
  if(cn != null ){
    name = c.getConceptName().getName();
    if(name == null || name.trim().equals("")){
      name = prefix+c.getId();
    }
  }
  else{
    name = prefix+c.getId();    
  }
  return name;
}
 

/**
 * helper method to extract a usable concept name.
 * 
 * @param c
 *            a concept.
 * @return a usable name.
 */
private String extractName(ONDEXConcept c) {
  String str = "";
  if (c.getConceptName() != null)
    str = c.getConceptName().getName();
  if (str.trim().length() == 0)
    str = c.getPID();
  if (str.trim().length() == 0)
    str = c.getId() + "";
  return str;
}

  public void filter(Set<ONDEXConcept> ov) throws NullValueException, EmptyStringException, AccessDeniedException{
     for(ONDEXConcept c : ov){
       boolean addToset = true;
       for(ConceptAttributeChecker chk :conditions.values()){
         if(!chk.check(c)){
           addToset = false;
           break;
         }
       }
       System.err.println("Deleted: "+c.getConceptName().getName());
       if(addToset)graph.deleteConcept(c.getId());
     }
  }
}

ConceptName name = abstractConcept.getConceptName();
if (name != null) {
  builder.append(name.getName());

/**
 * Returns a JLabel for the concept
 */
@Override
public Object getElementAt(int index) {
  JLabel label = null;
  if (index > -1) {
    ONDEXConcept ac = concepts.get(index);
    String name = null;
    ConceptName cn = ac.getConceptName();
    if (cn != null)
      name = cn.getName();
    else
      name = String.valueOf(ac.getId());
    label = new JLabel(name);
    label.setName(String.valueOf(ac.getId()));
    label.setToolTipText("(" + ac.getId() + ") " + ac.getDescription());
  }
  return label;
}

/**
 * Creates a name on concept only if it does not already exists
 * 
 * @param target
 *            - relation
 * @param newName
 *            - attribute to create
 * @throws AccessDeniedException
 * @throws EmptyStringException
 * @throws NullValueException
 */
public static void addNewName(ONDEXConcept target, ConceptName newName)
    throws NullValueException, EmptyStringException,
    AccessDeniedException {
  if (target.getConceptName(newName.getName()) == null)
    target.createConceptName(newName.getName(), false);
}

/**
 * Create a name for concepts
 * 
 * @param c
 *            ONDEXConcept
 * @return normalised name
 */
private String getDefaultNameForConcept(ONDEXConcept c) {
  String name = null;
  // this is the preferred concept name
  ConceptName cn = c.getConceptName();
  // use accessions as alternatives
  Set<ConceptAccession> accs = c.getConceptAccessions();
  if (cn != null && cn.getName().trim().length() > 0)
    name = cn.getName().trim();
  else if (accs.size() > 0)
    for (ConceptAccession acc : accs) {
      if (acc.getAccession().trim().length() > 0) {
        if (acc.getElementOf().equals(c.getElementOf())) {
          // prefer native accession
          name = acc.getAccession().trim();
          break;
        }
        name = acc.getAccession().trim();
      }
    }
  else
    name = "null";
  return name;
}

@Override
public Object getCellEditorValue() {
  // this is value returned by default editor
  String newName = super.getCellEditorValue().toString();
  if (name == null) {
    // construct new CN with defaults
    if (newName.trim().length() > 0)
      name = concept.createConceptName(newName, false);
  } else {
    // existing CN check name update
    if (!newName.equals(name.getName())) {
      // delete old one
      ConceptName old = concept.getConceptName(name.getName());
      concept.deleteConceptName(name.getName());
      // keep preferred setting and create non empty name
      if (newName.trim().length() > 0)
        name = concept.createConceptName(newName, old.isPreferred());
      else
        // clear existing concept name from table
        name = null;
    }
  }
  // return concept name instead of string
  return name;
}

ConceptName cn = c.getConceptName();

ConceptName cn = c.getConceptName();

/**
 * Tries to get the most worthwhile identifier for the concept
 * 
 * @param c
 *            - concept
 * @return - some id (in order of decreasing preference: name, pid,
 *         description, concepts class+is)
 */
private static String getSomething(ONDEXConcept c) {
  if (c.getConceptName() != null) {
    return c.getConceptName().getName();
  }
  if (c.getPID() != null && c.getPID().equals("")) {
    return c.getPID();
  }
  if (c.getDescription() != null && c.getDescription().equals("")) {
    return c.getDescription();
  }
  return "[" + c.getOfType().getId() + " " + c.getId() + "]";
}

/**
 * Constructs the local name of a given concept.
 * 
 * @param c
 *            ONDEXConcept
 * @return String
 */
private String getLocalName(ONDEXConcept c) {
  String local = String.valueOf(c.getId());
  if (concat) {
    // check if preferred name is present
    ConceptName preferredName = c.getConceptName();
    if (preferredName != null) {
      local = local + ": " + quote(preferredName.getName());
    } else {
      // use PID as fall-back
      local = local + ": " + quote(c.getPID());
    }
  }
  return local;
}

if(ac.getConceptName(symbol) == null){
  ac.createConceptName(symbol, true);

if(ac.getConceptName(symbol) == null){
  ac.createConceptName(symbol, true);

/**
 * Creates new form NewJFrame1
 */
public SetSelector() throws Exception {
  if (OVTK2Desktop.getDesktopResources().getSelectedViewer() == null) {
    return;
  }
  OVTK2Desktop.getInstance().getDesktopResources().getParentPane().add(this);
  graph = OVTK2Desktop.getDesktopResources().getSelectedViewer().getONDEXJUNGGraph();
  initComponents();
  this.setVisible(true);
  this.setTitle("Show tagget sets for members");
  DefaultListModel listModel = new DefaultListModel();
  lSets.setModel(listModel);
  for (ONDEXConcept c : graph.getConceptsOfConceptClass(MdHelper.createCC(graph, "Superset"))) {
    JCheckBox check = new JCheckBox(c.getConceptName().getName());
    supersets.put(check, c);
    listModel.addElement(check);
  }
  System.err.println("Set selectior initialized.");
}

String value = c.getConceptName().getName();
for (ONDEXConcept d : cluster) {
  d.createAttribute(an, value, false);