/** * @param fromConcept * @param toConcept * @param ofType * @param evidence * @return * @see net.sourceforge.ondex.core.ONDEXGraph#createRelation(net.sourceforge.ondex.core.ONDEXConcept, * net.sourceforge.ondex.core.ONDEXConcept, * net.sourceforge.ondex.core.RelationType, java.util.Collection) */ public ONDEXRelation createRelation(ONDEXConcept fromConcept, ONDEXConcept toConcept, RelationType ofType, Collection<EvidenceType> evidence) { return og.createRelation(fromConcept, toConcept, ofType, evidence); }
List<EvidenceType> v = new ArrayList<EvidenceType>(1); v.add(evidencetype); return g.createRelation(fromConcept, toConcept, ofType, v);
graph.createRelation(cluster.get(i), cluster.get(j), clusterRel, evidence);
continue; ONDEXRelation relation = graph.createRelation(fromConcept, reaction, createRT(graph, MetaData.RT_CONSUMED_BY), etypes); continue; ONDEXRelation relation = graph.createRelation(fromConcept, reaction, createRT(graph, MetaData.RT_PRODUCED_BY), etypes); continue; ONDEXRelation relation = graph.createRelation(reaction, toConcept, createRT(graph, MetaData.RT_REGULATED_BY), etypes);
ONDEXRelation r = og.createRelation(fromConcept, toConcept, rt, evidences);
/** * Transfers all relations that the old concept takes part into to the new * concept. * * @param oldC * old ONDEXConcept * @param newC * new ONDEXConcept */ private void transferRelations(ONDEXConcept oldC, ONDEXConcept newC) { // iterate over all relations of old concept for (ONDEXRelation oldR : graph.getRelationsOfConcept(oldC)) { ONDEXRelation newR = null; if (oldR.getFromConcept().equals(oldC)) { // old concept is from concept newR = graph.createRelation(newC, oldR.getToConcept(), oldR.getOfType(), oldR.getEvidence()); } else if (oldR.getToConcept().equals(oldC)) { // old concept is to concept newR = graph.createRelation(oldR.getFromConcept(), newC, oldR.getOfType(), oldR.getEvidence()); } // transfer context old to new for (ONDEXConcept c : oldR.getTags()) { newR.addTag(c); } } }
/** * This method will create a copy of the original relation between the * concepts specified. * * @param graph * - graph where this things live * @param from * - source concept of the copied relation * @param to * - target concept of the copied relation * @param r * - relation that will be copied */ public static void copyRelation(ONDEXGraph graph, ONDEXConcept from, ONDEXConcept to, ONDEXRelation r) { ONDEXRelation nr = null; Collection<EvidenceType> evidence = r.getEvidence(); Collection<ONDEXConcept> tags = new HashSet<ONDEXConcept>(r.getTags()); Collection<Attribute> rgdss = r.getAttributes(); nr = graph.createRelation(from, to, r.getOfType(), evidence); for (ONDEXConcept tag : tags) nr.addTag(tag); for (Attribute rattribute : rgdss) { cloneAttributeWithAttName(graph, r, nr, rattribute.getOfType()); } }
newR = graph.createRelation(newC, oldR.getToConcept(), oldR.getOfType(), oldR.getEvidence()); break; case TO: newR = graph.createRelation(oldR.getFromConcept(), newC, oldR.getOfType(), oldR.getEvidence()); break; default:
nr = graph.getRelation(copyTarget, copyTarget, r.getOfType()); if (nr == null) nr = graph.createRelation(copyTarget, copyTarget, r.getOfType(), evidence); } else { r.getOfType()); if (nr == null) nr = graph.createRelation(copyTarget, r.getToConcept(), r.getOfType(), evidence); } else { r.getOfType()); if (nr == null) nr = graph.createRelation(r.getFromConcept(), copyTarget, r.getOfType(), evidence);
graph.createRelation(path.head(), path.tail(), typeToAdd, evidenceTypes);
/** * Clone relation with having a new RelationType. * * @param oldR * old ONDEXRelation * @param newRT * new RelationType to use * @return new ONDEXRelation */ public ONDEXRelation clone(ONDEXRelation oldR, RelationType newRT) { // first clone concept with new ConceptClass ONDEXRelation newR = graph.getRelation(oldR.getFromConcept(), oldR.getToConcept(), oldR.getOfType()); if (newR == null) graph.createRelation(oldR.getFromConcept(), oldR.getToConcept(), oldR.getOfType(), oldR.getEvidence()); // copies everything else copyEverythingElse(oldR, newR); return newR; }
newRelation = graph.createRelation(newFrom, newTo, relation.getOfType(), relation.getEvidence());
@Override public void start() throws Exception { Set<ONDEXConcept> conceptsWithNT = graph.getConceptsOfAttributeName(graph.getMetaData().getAttributeName("NA")); Set<ONDEXConcept> conceptsWithProteins = graph.getConceptsOfAttributeName(graph.getMetaData().getAttributeName("AA")); DecypherAlignment dcAlign = new DecypherAlignment( net.sourceforge.ondex.config.Config.ondexDir, getArguments().getUniqueValue(PROGRAM_DIR_ARG).toString(), 0, //cutff 0f, //% 0001f, //evalue 0, //bitscore Integer.MAX_VALUE, //max alignments false); Collection<Match> hits = dcAlign.query(graph, conceptsWithNT, conceptsWithProteins, BLASTAlignmentProgram.ALGO_BLASTX); RelationType h_s_s = graph.getMetaData().getRelationType("h_s_s"); EvidenceType ev = graph.getMetaData().createEvidenceType("BLASTx", "BLASTx", "BLASTx"); Set<EvidenceType> evs = new HashSet<EvidenceType>(); for (Match hit : hits) { //you might prefer to build an index query-->Hit if you want to take the best n ONDEXConcept query = graph.getConcept(hit.getQueryId()); ONDEXConcept hitTarget = graph.getConcept(hit.getTargetId()); ONDEXRelation relation = graph.createRelation(query, hitTarget, h_s_s, evs); //add some properties to the relations...etc } }
ONDEXRelation r = graph.createRelation(from, to, rtInteracts, evidences);
RelationType newRt = nomd.getRelationType(rt.getId()); ONDEXRelation newRelation = newGraph.createRelation(newFrom, newTo, newRt, ets); assert newRelation != null : "new relation was not created in new graph";
nr = graph.createRelation(nc, nc, r.getOfType(), evidence); } else { if (r.getFromConcept().equals(c)) { nr = graph.createRelation(nc, r.getToConcept(), r.getOfType(), evidence); } else { nr = graph.createRelation(r.getFromConcept(), nc, r.getOfType(), evidence);
ONDEXRelation newr = graph.createRelation(to, from, rt, r.getEvidence());