@Override
public String process(File page, Map<String, String> query) {
JSONObject jo = new JSONObject();
jo.put("cr", "not found");
if (graphs.containsKey(query.get("graphName")) && query.containsKey("sk")) {
jo.put("cr", query.get("sk") + " not found");
CortexGraph cg = graphs.get(query.get("graphName"));
CortexKmer ck = new CortexKmer(query.get("sk"));
CortexRecord cr = cg.findRecord(ck);
if (cr != null) {
String text = cr.toString();
if (ck.isFlipped()) {
String info = query.get("sk");
for (int coverage : cr.getCoverages()) {
info += " " + coverage;
}
for (String edge : cr.getEdgeAsStrings()) {
info += " " + SequenceUtils.reverseComplement(edge);
}
text = info;
}
String sampleName = cg.getColor(0).getSampleName();
if (LINKS != null && !LINKS.isEmpty()) {
for (CortexLinksMap link : LINKS) {
if (sampleName.equals(link.getCortexLinks().getColor(0).getSampleName())) {
if (link.containsKey(ck)) {
CortexLinksRecord clr = link.get(ck);
int cov = 0;
for (CortexJunctionsRecord cjr : clr.getJunctions()) {
cov += cjr.getCoverage(0);
}
text += " (" + cov + " links)";
}
}
}
}
jo.put("cr", text);
}
}
return jo.toString();
}
public CtxVertex(String kmer, int pos, VertexType vt, CortexRecord cr) {
this.kmer = kmer;
this.pos = pos + kmer.length() - 1;
this.vertexType = vt;
this.missingFromGraph = (cr == null);
this.cov = (cr == null) ? 0 : cr.getCoverage(0);
}