How to use

getAttributes

method

in

net.sourceforge.ondex.core.ONDEXConcept

@Override
public Set<Attribute> getAttributes() {
  return parent.getAttributes();
}

/**
 * Return all of attribute names of the concepts
 * contained in the collection
 *
 * @param cs
 * @return set of attribute names
 */
public static Set<AttributeName> getConceptAttNames(Collection<ONDEXConcept> cs) {
  Set<AttributeName> result = new HashSet<AttributeName>();
  for (ONDEXConcept c : cs) {
    for (Attribute g : c.getAttributes()) {
      result.add(g.getOfType());
    }
  }
  return result;
}

/**
 * Return all of attribute names of the concepts
 * contained in the collection
 *
 * @param cs
 * @return set of attribute names
 */
public static Set<AttributeName> getConceptAttNames(Collection<ONDEXConcept> cs) {
  Set<AttributeName> result = new HashSet<AttributeName>();
  for (ONDEXConcept c : cs) {
    for (Attribute g : c.getAttributes()) {
      result.add(g.getOfType());
    }
  }
  return result;
}

  private void step() {
    boolean match = false;
    next = null;
    while (!match && view.hasNext()) {
      ONDEXConcept r = view.next();
      List<String> gds = new ArrayList<String>();
      for (Attribute g : r.getAttributes()) {
        String name = g.getOfType().getId();
        if (validArgs.contains(name))
          gds.add(name);
      }
      if (gds.size() > 0) {
        match = true;
        next = gds.toArray(new String[gds.size()]);
      }
    }
  }
}

/**
 * Populates given combo box with list of AttributeNames for visible
 * concepts.
 * 
 * @param box
 *            JComboBox to fill
 */
private void populateComboBox(JComboBox box) {
  Set<AttributeName> ans = new HashSet<AttributeName>();
  for (ONDEXConcept n : graph.getVertices()) {
    for (Attribute g : n.getAttributes()) {
      if (!AppearanceSynchronizer.attr
          .contains(g.getOfType().getId()))
        ans.add(g.getOfType());
    }
  }
  box.removeAllItems();
  box.addItem("None");
  if (ans.size() > 0) {
    AttributeName[] array = ans.toArray(new AttributeName[0]);
    Arrays.sort(array);
    for (AttributeName an : array) {
      box.addItem(an);
    }
    box.revalidate();
  }
}

Set<Attribute> attributes = ac.getAttributes();

for (Attribute attribute : c.getAttributes()) {
  ArrayKey<Object> accessionKey = new ArrayKey<Object>(new Object[]{attribute.getOfType(), attribute.getValue()});
  gdsToConceptIndexBuider.addEntry(accessionKey, c.getId());

/**
 * Copies all Attribute from old concept to new concept.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newC
 *            new ONDEXConcept
 */
private void copyGDS(ONDEXConcept oldC, ONDEXConcept newC) {
  // iterate over all old Attribute
  for (Attribute attribute : oldC.getAttributes()) {
    // clone old Attribute on new concept
    newC.createAttribute(attribute.getOfType(), attribute.getValue(), attribute.isDoIndex());
  }
}

  public void run() {
    // just being paranoid
    cleanPopups();
    if (showMouseOver && vv.isShowing() && onNode && n.equals(currentNode) && !activePopups.containsKey(n)) {
      ConceptClass cc = n.getOfType();
      if (cc.getId().equals("Comp") || (cc.getSpecialisationOf() != null && cc.getSpecialisationOf().getId().equals("Comp"))) {
        for (Attribute attr : n.getAttributes()) {
          Object o = attr.getValue();
          if (o instanceof ChemicalStructure) {
            // use Attribute Editor as a hack
            JComponent c = AttributePanel.findEditor(attr);
            if (c != null) {
              c.setBorder(BorderFactory.createEtchedBorder());
              c.setPreferredSize(new Dimension(150, 150));
              Point location = calculatePopupLocation(c);
              // show popup
              PopupFactory popupFactory = PopupFactory.getSharedInstance();
              Popup popup = popupFactory.getPopup(vv, c, location.x, location.y);
              // just being paranoid
              if (!activePopups.containsKey(n)) {
                activePopups.put(n, popup);
                popup.show();
              }
            }
          }
        }
      }
    }
  }
}, 500);

for (ONDEXConcept concept : graph.getConcepts()) {
  for (Attribute attribute : concept.getAttributes()) {

public void parseLine(String[] data) throws FileNotFoundException, IOException {
  ONDEXConcept exp = lookup.lookupExperiment(data[0]);
  if (exp.getAttributes().size() == 0) {
    exp.createAttribute(ecoCont, data[1], false);
    exp.createAttribute(ecoTest, data[2], false);
    exp.createAttribute(cell, data[3], false);
    exp.createAttribute(age, data[5], false);
    exp.createAttribute(treatments, data[8], false);
    exp.createAttribute(description, data[7], false);
    exp.createAttribute(hormoneTreat, data[4], false);
    exp.createAttribute(hormoneConc, data[6], false);
  }
  createHormoneContext(data[4], exp);
}

for (Attribute attribute : c.getAttributes()) {
  if (attribute.getOfType().equals(at)) {
    propagate(toKeep, c, 0);

for (Attribute attribute : ac.getAttributes()) {
  if(attribute.getOfType().getId().equals("AA") ||
      attribute.getOfType().getId().equals("NA")){

for (Attribute attribute : ac.getAttributes()) {
  if(attribute.getOfType().getId().equals("AA") ||
      attribute.getOfType().getId().equals("NA")){

for (Attribute attribute : concept.getAttributes()) {
  if(attribute.getOfType().getId().equals("AA") ||
      attribute.getOfType().getId().equals("NA")){

for (Attribute attribute : conceptToClone.getAttributes()) {
  AttributeName att = attribute.getOfType();
  AttributeName newAtt = nomd.getAttributeName(att.getId());

for (Attribute attribute : c.getAttributes()) {
  nc.createAttribute(attribute.getOfType(), attribute.getValue(),
      attribute.isDoIndex());

/**
 * Copies all of the attributes from one concept to another (only if they do
 * not already exist at target)
 * 
 * @param from
 *            - concept to copy from
 * @param to
 *            - concept to copy to
 * @throws AccessDeniedException
 * @throws NullValueException
 * @throws EmptyStringException
 */
public static void copyConceptAttributes(ONDEXConcept from, ONDEXConcept to)
    throws NullValueException, AccessDeniedException,
    EmptyStringException {
  for (EvidenceType et : from.getEvidence())
    addNewEvidence(to, et);
  for (ConceptAccession ca : from.getConceptAccessions())
    addNewAccession(to, ca);
  for (ConceptName cn : from.getConceptNames())
    addNewName(to, cn);
  for (Attribute attribute : from.getAttributes())
    addNewAttribute(to, attribute);
  if (from.getAnnotation() != null && to.getDescription() == null)
    to.setAnnotation(from.getAnnotation());
  if (from.getDescription() != null && to.getDescription() == null)
    to.setDescription(from.getDescription());
}

for (Attribute attribute : copySourceConcept.getAttributes()) {
  copyTargetConcept.createAttribute(attribute.getOfType(),
      attribute.getValue(), attribute.isDoIndex());

Set<Attribute> attribute = c.getAttributes();
if (prettyPrint)
  xmlw.writeCharacters(newline);