/** * Adds a description as the concatenation of the comments to a concept. * * @param c * ONDEXConcept to modify * @param e * BioPAX Level2Element */ public void addDescription(ONDEXConcept c, Level2Element e) { // construct description as concatenation StringBuffer comment = new StringBuffer(); for (String part : e.getCOMMENT()) { comment.append(part); comment.append("\n"); } c.setDescription(comment.toString()); }
evidencetype); else c.setDescription(desc);
concept.setDescription(description.getText());
concept.setDescription(text); return text;
false); if (node.getComment() != null) concept.setDescription(node.getComment()); if (node.getSynonym().size() > 0) { Iterator<String> i = node.getSynonym().iterator();
false); if (node.getComment() != null) concept.setDescription(node.getComment()); if (node.getSynonym().size() > 0) { Iterator<String> i = node.getSynonym().iterator();
false); if (node.getComment() != null) concept.setDescription(node.getComment()); if (node.getSynonym().size() > 0) { Iterator<String> i = node.getSynonym().iterator();
false); if (node.getComment() != null) concept.setDescription(node.getComment()); if (node.getSynonym().size() > 0) { Iterator<String> i = node.getSynonym().iterator();
ONDEXConcept g = graph.getFactory().createConcept(ecID, dataSourceJGI, ccEnzyme, etIMPD); if (!catalyticActivity.equals("\\N")) g.setDescription(catalyticActivity); g.createConceptAccession(ecID, dataSourceEC, false); g.createConceptName(definition, true); g.setAnnotation(pathwayType); if (!pathwayClass.equals("\\N")) g.setDescription(pathwayClass); parsedKeggIDs.put(pathwayKegg, g.getId());
concept.setDescription(compartment.getNotesString());
concept.setDescription(compartment.getNotesString());
speciesC.setDescription(species.getNotesString());
speciesC.setDescription(species.getNotesString());
nc.setDescription(c.getDescription());
/** * 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()); }
reactionC.setDescription(reaction.getNotesString());
reactionC.setDescription(reaction.getNotesString());
.setDescription(copySourceConcept.getDescription());