How to use

getAnnotation

method

in

net.sourceforge.ondex.core.ONDEXConcept

@Override
public String getAnnotation() {
  return parent.getAnnotation();
}

public String getValue(ONDEXEntity cOrr) throws InvalidOndexEntityException {
  if(AbstractConcept.class.isAssignableFrom(cOrr.getClass())){
    return ((ONDEXConcept)cOrr).getAnnotation();
  }
  throw new InvalidOndexEntityException(cOrr.getClass()+": is not an Ondex class for which annotation is known");
}

public String assembleLine(ONDEXConcept c1, Set<ONDEXConcept> additional,
    ONDEXConcept c2, RelationType rt, Set<ONDEXConcept> other) {
  StringBuffer buf = new StringBuffer();
  buf.append(c1.getPID());
  buf.append("\t");
  buf.append(additional);
  buf.append("\t");
  if (c1.getAnnotation().contains("irreversible")) {
    buf.append("irreversible");
  } else if (c1.getAnnotation().contains("reversible")) {
    buf.append("reversible");
  } else {
    buf.append("unknown");
  }
  buf.append("\t");
  buf.append(c2.getPID());
  buf.append("\t");
  buf.append(rt.getId());
  buf.append("\t");
  buf.append(other);
  buf.append("\n");
  return buf.toString();
}

public String getName(ONDEXConcept ac) {
  String label = "";
  // get first preferred name as label
  for (ConceptName cn : ac.getConceptNames()) {
    if (cn.isPreferred()) {
      label = cn.getName();
      break;
    }
  }
  // next try annotation
  if (label == null || label.trim().length() == 0) {
    label = ac.getAnnotation();
  }
  // next try description
  if (label == null || label.trim().length() == 0) {
    label = ac.getDescription();
  }
  // next try pid
  if (label == null || label.trim().length() == 0) {
    label = ac.getPID();
  }
  // last resort to concept id
  if (label == null || label.trim().length() == 0) {
    label = String.valueOf(ac.getId());
  }
  return label;
}

else if (c.getAnnotation().length() > 0)
  name = c.getAnnotation().trim();
else if (c.getDescription().length() > 0)
  name = c.getDescription().trim();

else if (c.getAnnotation().length() > 0)
  name = c.getAnnotation().trim();
else if (c.getDescription().length() > 0)
  name = c.getDescription().trim();

for (ONDEXConcept c : concepts.get(key)) {
  String anno = "";
  if (c.getAnnotation() != null)
    anno = c.getAnnotation();
  String desc = "";
  if (c.getDescription() != null)

defaultName = concept.getAnnotation();

else if (concept.getAnnotation() != null)
  name = concept.getAnnotation();
else if (concept.getDescription() != null)
  name = concept.getDescription();

/**
 * Clone concept with having a new DataSource.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newDataSource
 *            new DataSource to use
 * @return new ONDEXConcept
 */
public ONDEXConcept clone(ONDEXConcept oldC, DataSource newDataSource) {
  // first clone concept with new DataSource
  ONDEXConcept newC = graph.createConcept(oldC.getPID(), oldC.getAnnotation(), oldC.getDescription(), newDataSource, oldC.getOfType(), oldC.getEvidence());
  // copies everything else
  copyEverythingElse(oldC, newC);
  return newC;
}

/**
 * Clone concept with having a new PID.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newPID
 *            new PID to use
 * @return new ONDEXConcept
 */
public ONDEXConcept clone(ONDEXConcept oldC, String newPID) {
  // first clone concept with new PID
  ONDEXConcept newC = graph.createConcept(newPID, oldC.getAnnotation(), oldC.getDescription(), oldC.getElementOf(), oldC.getOfType(), oldC.getEvidence());
  // copies everything else
  copyEverythingElse(oldC, newC);
  return newC;
}

/**
 * Clone concept with having a new ConceptClass.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newCC
 *            new ConceptClass to use
 * @return new ONDEXConcept
 */
public ONDEXConcept clone(ONDEXConcept oldC, ConceptClass newCC) {
  // first clone concept with new ConceptClass
  ONDEXConcept newC = graph.createConcept(oldC.getPID(), oldC.getAnnotation(), oldC.getDescription(), oldC.getElementOf(), newCC, oldC.getEvidence());
  // copies everything else
  copyEverythingElse(oldC, newC);
  return newC;
}

concept.setAnnotation(concept.getAnnotation() + " URL:" + dbLink.getAccession());
continue;

/**
 * Initialises table data with the given ONDEXGraph.
 * 
 * @param graph
 *            ONDEXGraph to extract concepts from
 */
public ConceptPanel(ONDEXGraph graph) {
  Object[][] data = new Object[graph.getConcepts().size()][];
  int i = 0;
  for (ONDEXConcept concept : graph.getConcepts()) {
    // first entry in table row is concept itself
    Object[] row = { concept, concept.getPID(), concept.getAnnotation(), concept.getDescription(), concept.getElementOf(), concept.getOfType(), concept.getEvidence() };
    data[i] = row;
    i++;
  }
  // initialise table model and populate table
  DefaultTableModel model = new DefaultTableModel();
  model.setDataVector(data, header);
  table = new ConceptTable(model, graph);
  // add table to panel
  this.setLayout(new GridLayout(1, 1));
  this.add(new JScrollPane(table));
  Util.calcColumnWidths(table, 150);
}

String anno = ac.getAnnotation();
if (isMatching(p, search, anno))
  found = true;

String anno = ac.getAnnotation();
if (isMatching(p, anno))
  found = true;

/**
 * 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());
}

if (copySourceConcept.getAnnotation() != null)
  copyTargetConcept.setAnnotation(copySourceConcept.getAnnotation());

String anno = conceptToClone.getAnnotation();

Resource cR = model.createResource(ONDEXRdf.conceptToUri(graphURI, c));
cRap(cR, model.createProperty(ONDEXRdf.annotationUri), c.getAnnotation());
for(ConceptAccession ca : c.getConceptAccessions()) {
  cR.addProperty(model.createProperty(ONDEXRdf.conceptAccessionUri), ca.getAccession());