/**
* parses an answer object into the json exchange format for an answer
*
* @param answer the answer object that should be translated
* @return json string in the exchange format between frontend and middleware
*/
public static String answerQuery(QueryAnswer answer) {
JSONObject obj = new JSONObject();
obj.put("source", answer.source);
// add chromosome attribute to json answer
obj.put("chromosome", answer.chromosome);
JSONObject from_to = new JSONObject();
from_to.put("from", answer.position[0]);
from_to.put("to", answer.position[1]);
obj.put("position", from_to);
String response;
if (answer.hasDetail) {
JSONObject details = new JSONObject();
details.put("refseq", answer.refseq);
// create json_array for found mutations
JSONArray mutations_array = new JSONArray();
for (IntervalST.Mutation x : answer.mutations) {
// json object for single mutation, that was found
JSONObject mut = new JSONObject();
// name of mutation, need to convert from byte array to string
mut.put("name", new String(x.b_RefName));
// json object for position of mutation's interval, with "to" and "from" as attributes
JSONObject mut_pos = new JSONObject();
mut_pos.put("from", x.i_Low);
mut_pos.put("to", x.i_High);
mut.put("position", mut_pos);
// json object for metadata
JSONObject meta = new JSONObject();
// json object for gender
JSONObject gender = new JSONObject();
// -1 for no filter on gender, 0 for male and 1 for female
if (x.s_Gender == -1) {
gender.put("m", true);
gender.put("w", true);
} else if (x.s_Gender == 0) {
gender.put("m", true);
gender.put("w", false);
} else if (x.s_Gender == 1) {
gender.put("m", false);
gender.put("w", true);
} else {
gender = null;
}
meta.put("gender", gender);
// add country
meta.put("origin", IndexController.getCountry(x.s_Country));
// downloadtime
meta.put("downloadtime", x.s_Date);
// add metadata json object to mutation json object
mut.put("metadata", meta);
// add sequence of basis pairs, first need to convert integer to string
if (answer.chromosome == 23) {
mut.put("mutationseq", Chromosome_reader.retrieve_sequence(x.i_Low, x.i_High, "X"));
} else if (answer.chromosome == 24) {
mut.put("mutationseq", Chromosome_reader.retrieve_sequence(x.i_Low, x.i_High, "Y"));
} else if (answer.chromosome == 25) {
mut.put("mutationseq", Chromosome_reader.retrieve_sequence(x.i_Low, x.i_High, "MT"));
} else {
mut.put(
"mutationseq",
Chromosome_reader.retrieve_sequence(x.i_Low, x.i_High, answer.chromosome.toString()));
}
// add json object for mutation x to json array for all mutations that were found
mutations_array.add(mut);
}
details.put("mutations", mutations_array);
obj.put("details", details);
StringWriter out = new StringWriter();
try {
obj.writeJSONString(out);
} catch (IOException e) {
e.printStackTrace();
}
response = out.toString();
} else {
obj.put("details", null);
// function to count occurrences of mutations in subintervals
Integer[] counts = count_mutations(answer);
JSONArray mutation_counts = new JSONArray();
for (int i = 0; i < counts.length; i++) {
mutation_counts.add(counts[i]);
}
obj.put("graph", mutation_counts);
StringWriter out = new StringWriter();
try {
obj.writeJSONString(out);
} catch (IOException e) {
e.printStackTrace();
}
response = out.toString();
}
if (response != null) {
return response;
} else {
return "Something went wrong while creating answer";
}
}
