How to use

setAnnotation

method

in

net.sourceforge.ondex.core.ONDEXConcept

concept.setAnnotation(text);
return text;

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

concept.setAnnotation(annotation.getText());

@Override
public void nodeToConcept(AbstractNode node) {
  Reaction reaction = (Reaction) node;
  ONDEXConcept concept = graph.getFactory().createConcept(
      reaction.getUniqueId(), dataSourceMetaC, ccReaction, etIMPD);
  if (reaction.getBalancedState() != null)
    concept.setAnnotation(reaction.getBalancedState());
  concept.createConceptName(constructFormula(reaction), false);
  if (reaction.getDeltaGo() != null) {
    concept.createAttribute(deltaGo, reaction.getDeltaGo(), false);
  }
  
  if (reaction.getDirection() != null) {
    concept.setAnnotation(reaction.getDirection());
  }
  reaction.setConcept(concept);
}

c.setAnnotation(value);

concept.setAnnotation(newAnno);
concept.setAnnotation(newDesc);

g.createConceptName(pathwayKegg, true);
if (!pathwayType.equals("\\N"))
  g.setAnnotation(pathwayType);
if (!pathwayClass.equals("\\N"))
  g.setDescription(pathwayClass);

@Override
public void nodeToConcept(AbstractNode node) {
  Reaction reaction = (Reaction) node;
  ONDEXConcept concept = graph.getFactory().createConcept(
      reaction.getUniqueId(), dataSourceAraC, ccReaction, etIMPD);
  if (reaction.getBalancedState() != null)
    concept.setAnnotation(reaction.getBalancedState());
  concept.createConceptName(constructFormula(reaction), false);
  if (reaction.getDeltaGo() != null) {
    concept.createAttribute(deltaGo, reaction.getDeltaGo(), false);
  }
  reaction.setConcept(concept);
}

c.setAnnotation(molecularFormula);

@Override
public void nodeToConcept(AbstractNode node) {
  Reaction reaction = (Reaction) node;
  ONDEXConcept concept = graph.getFactory().createConcept(
      reaction.getUniqueId(), dataSourceMetaC, ccReaction, etIMPD);
  if (reaction.getBalancedState() != null)
    concept.setAnnotation(reaction.getBalancedState());
  concept.createConceptName(constructFormula(reaction), false);
  if (reaction.getDeltaGo() != null) {
    concept.createAttribute(deltaGo, reaction.getDeltaGo(), false);
  }
  reaction.setConcept(concept);
}

@Override
public void nodeToConcept(AbstractNode node) {
  Reaction reaction = (Reaction) node;
  ONDEXConcept concept = graph.getFactory().createConcept(
      reaction.getUniqueId(), dataSourceBioC, ccReaction, etIMPD);
  if (reaction.getBalancedState() != null)
    concept.setAnnotation(reaction.getBalancedState());
  concept.createConceptName(constructFormula(reaction), false);
  if (reaction.getDeltaGo() != null) {
    concept.createAttribute(deltaGo, reaction.getDeltaGo(), false);
  }
  reaction.setConcept(concept);
}

nc.setAnnotation(c.getAnnotation());

/**
 * 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());
}

copyTargetConcept.setAnnotation(copySourceConcept.getAnnotation());