/**
* takes a query object and calls the appropriate sub component that answers the given query
*
* @param query the query that has to be answered
* @return a string in the answer exchange format that will be sent to the frontend
*/
public static String handleQuery(Query query) {
// interval search
String answer;
if (query.x_Search == null) {
// check if necessary fields are given
if (query.i_Start == -1 || query.i_End == -1) {
// query.response_format = "Wrong interval given";
return "Wrong interval given";
} else if (query.s_Chromosome == -1) {
// query.response_format = "No chromosome given";
return "No chromosome given";
} else if (query.s_Source == -1) {
// query.response_format = "No source given";
return "No source given";
}
// correct query format
else {
// Send query to IndexController
// Translation from query to intervalst.query
// needs to be unified
/*
short s_SourceNo=(short)0;
if (query.source.equals("dbSNP")) {
s_SourceNo = (short) 0;
}
if (query.source.equals("1000GenomesProject")){
s_SourceNo =(short) 1;
}
*/
Query[] q_Query = {query};
QueryAnswer temp_answer = indexController.answerQuery(q_Query);
answer = answerQuery(temp_answer);
/*
// byte temp = query.chromosome.get();
// byte[] b={temp};
//CRITICAL PART. change query format into intervallst.query . answerquery throws nullpointer
byte[] b=new byte[0];
byte[] c=new byte[0];
int i=query.position[0];
int j=query.position[1];
IntervalST.Query intervalst_query=new IntervalST.Query(1,i,j,s_SourceNo,Integer.toString(query.chromosome).getBytes(),null,null);
IntervalST.Query[] queries={intervalst_query};
IntervalST.Answer x_Result=indexController.answerQuery(queries);
System.out.println("Length of AnswerList: "+x_Result.x_List.size());
if (query.hasDetail) {
String sequence = Chromosome_reader.retrieve_sequence(i,j,Integer.toString(query.chromosome));
}
return query;
*/
}
}
// gene name search
else {
// test for prefix query
if (query.b_isPrefix) {
/*
// This needs to be replaced!
String[] genenames = GeneTranslator.completeGeneName(query.search);
*/
String[] genenames = {"FOXP2", "FOXP4"};
JSONObject obj = new JSONObject();
obj.put("source", query.s_Source);
obj.put("chromosome", query.s_Chromosome);
JSONArray names = new JSONArray();
for (int i = 0; i < genenames.length; i++) {
names.add(genenames[i]);
}
obj.put("prefix", names);
StringWriter out = new StringWriter();
try {
obj.writeJSONString(out);
} catch (IOException e) {
e.printStackTrace();
}
answer = out.toString();
} else {
if (query.x_Search == "getInitialSources") {
System.out.println("getInitialSources");
return null;
} else {
String[] interval = GeneTranslator.translateToIntervall(query.x_Search);
JSONObject pos_obj = new JSONObject();
JSONObject obj = new JSONObject();
pos_obj.put("from", Integer.valueOf(interval[0]));
pos_obj.put("to", Integer.valueOf(interval[1]));
obj.put("search", query.x_Search);
obj.put("position", pos_obj);
StringWriter out = new StringWriter();
try {
obj.writeJSONString(out);
} catch (IOException e) {
e.printStackTrace();
}
answer = out.toString();
}
}
}
// queryID_pool.add(query.queryID);
return answer;
}
