public String getValue(ONDEXEntity cOrr) throws InvalidOndexEntityException { if(AbstractConcept.class.isAssignableFrom(cOrr.getClass())){ return ((ONDEXConcept)cOrr).getPID(); } if(AbstractRelation.class.isAssignableFrom(cOrr.getClass())){ return ((ONDEXRelation)cOrr).getKey().toString(); } throw new InvalidOndexEntityException(cOrr.getClass()+": is not an Ondex class for which a pid or key is known"); }
@Override public boolean isValid(ONDEXRelation relation, EvidencePathNode<ONDEXConcept, ONDEXRelation, State> path) { boolean priorCondition = super.isValid(relation, path); if (priorCondition) { if (treatment == EdgeTreatment.BIDIRECTIONAL) return true; ONDEXConcept concept = path.getEntity(); boolean isOutgoing = relation.getKey().getFromID() == concept.getId(); if (isOutgoing && treatment == EdgeTreatment.FORWARD) { return true; } else if (isOutgoing && treatment == EdgeTreatment.BACKWARD) { return relation.getKey().getFromID() == relation.getKey().getToID(); //ban loops else ok } } return false; }
relations.put(relation.getKey(), relation);
if (relation.getKey().getFromID() == relation.getKey().getToID()) { continue; if (directionIsToRoot && relation.getKey().getFromID() == possibleConcept.getId()) { } else if (!directionIsToRoot && relation.getKey().getToID() == possibleConcept.getId()) { } else if (directionIsToRoot && relation.getKey().getToID() == possibleConcept.getId()) { } else if (!directionIsToRoot && relation.getKey().getFromID() == possibleConcept.getId()) {
if (relation.getOfType().getId().equals(rt)) { ONDEXConcept targetConcept = null; if (relation.getKey().getFromID() == queryConcept.getId()) { targetConcept = relation.getToConcept(); } else if (relation.getKey().getToID() == queryConcept.getId()) { targetConcept = relation.getFromConcept(); } else {
if (relation.getKey().getFromID() != relation.getKey().getToID()) { ONDEXConcept from = relation.getFromConcept(); ONDEXConcept to = relation.getToConcept(); if (cRelation.getOfType().equals(rt)) { Integer from = cRelation.getKey().getFromID(); Integer to = cRelation.getKey().getToID(); && !relationAdded.contains(cRelation.getKey())) { cRelation.addTag(conceptContext); countrelations++; relationAdded.add(cRelation.getKey()); } else { ONDEXConcept targetConcept = null;
if (ec.getKey().getFromID() == protein.getId()) { GraphElementManipulation.changeRelationVertex(graph, ec.getToConcept(), protein, ec); } else {
RelationKey key = relation.getKey();
myKey = berkeley.convert(r.getKey()); } else if (o instanceof ONDEXConcept) { ONDEXConcept c = (ONDEXConcept) o;