@SuppressWarnings({"unchecked", "unused"})
public final JSONObject innerMap() throws ParseException {
final JSONObject json = new JSONObject();
String key;
Object value;
key = objectKey();
jj_consume_token(EQUALS);
value = value();
json.put(key, value);
key = null;
value = null;
label_1:
while (true) {
switch (jj_nt.kind) {
case SLASH:;
break;
default:
jj_la1[1] = jj_gen;
break label_1;
}
jj_consume_token(SLASH);
jj_consume_token(COMMA);
key = objectKey();
jj_consume_token(EQUALS);
value = value();
json.put(key, value);
key = null;
value = null;
}
{
if (true) return json;
}
throw new Error("Missing return statement in function");
}
@SuppressWarnings({"unused", "unchecked"})
public final JSONObject object() throws ParseException {
final JSONObject json = new JSONObject();
String key;
Object value;
key = objectKey();
jj_consume_token(EQUALS);
value = value();
json.put(key, value);
key = null;
value = null;
label_2:
while (true) {
if (jj_2_1(2)) {;
} else {
break label_2;
}
jj_consume_token(COMMA);
key = objectKey();
jj_consume_token(EQUALS);
value = value();
json.put(key, value);
key = null;
value = null;
}
{
if (true) return json;
}
throw new Error("Missing return statement in function");
}
public void registrarUsuario() {
String dato = "";
JSONParser parser = new JSONParser();
try {
while (true) {
dato = dis.readUTF();
String usuario = "";
String contraseña = "";
String contra = "";
if (dato.equals("Usuario")) {
while (true) {
usuario = dis.readUTF();
if (usuario != null) {
JSONObject user = new JSONObject();
user.put(usuario, null);
FileWriter escribir = new FileWriter("texto.txt");
BufferedWriter bw = new BufferedWriter(escribir);
PrintWriter pw = new PrintWriter(bw);
pw.write(user.toJSONString());
pw.close();
bw.close();
while (true) {
contra = dis.readUTF();
if (contra.equals("Contraseña")) {
while (true) {
contraseña = dis.readUTF();
if (contraseña != null) {
Object obj = parser.parse(new FileReader("texto.txt"));
JSONObject asignaPass = (JSONObject) obj;
asignaPass.put(usuario, contra);
FileWriter escribir2 = new FileWriter("texto.txt");
BufferedWriter bw2 = new BufferedWriter(escribir2);
PrintWriter pw2 = new PrintWriter(bw2);
pw2.write(asignaPass.toJSONString());
bw2.newLine();
pw2.close();
bw2.close();
break;
}
}
break;
}
}
break;
}
}
break;
}
}
} catch (Exception e) {
}
}
/**
* Sends command to retrieve phones list.
*
* @return is command successful.
*/
@SuppressWarnings("unchecked")
private boolean getPhoneList() {
JSONObject obj = new JSONObject();
try {
obj.put("class", "phones");
obj.put("function", "getlist");
return send(obj);
} catch (Exception e) {
logger.error("Error retrieving phones");
return false;
}
}
protected void processRequest(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
response.setContentType("text/html;charset=UTF-8");
PrintWriter out = response.getWriter();
try {
Class.forName("com.mysql.jdbc.Driver").newInstance();
Connection con =
DriverManager.getConnection(Utility.connection, Utility.username, Utility.password);
String email = request.getParameter("email_id");
String number = "";
boolean exists = false;
String user_name = "";
int user_id = -1;
String str1 = "SELECT USER_ID,NAME,PHONE_NUMBER FROM USERS WHERE EMAIL_ID=?";
PreparedStatement prep1 = con.prepareStatement(str1);
prep1.setString(1, email);
ResultSet rs1 = prep1.executeQuery();
if (rs1.next()) {
exists = true;
user_id = rs1.getInt("USER_ID");
user_name = rs1.getString("NAME");
number = rs1.getString("PHONE_NUMBER");
}
int verification = 0;
JSONObject data = new JSONObject();
if (exists) {
verification = (int) (Math.random() * 9535641 % 999999);
System.out.println("Number " + number + "\nVerification: " + verification);
SMSProvider.sendSMS(
number, "Your One Time Verification Code for PeopleConnect Is " + verification);
}
data.put("user_name", user_name);
data.put("user_id", user_id);
data.put("verification_code", "" + verification);
data.put("phone_number", number);
String toSend = data.toJSONString();
out.print(toSend);
System.out.println(toSend);
} catch (Exception e) {
e.printStackTrace();
} finally {
out.close();
}
}
/**
* Send needed command for features.
*
* @param astid param from previous command.
* @param xivoUserId param from previous command.
* @return is command successful.
*/
@SuppressWarnings("unchecked")
private boolean sendFeatures(String astid, String xivoUserId) {
if (connection == null || astid == null || xivoUserId == null) return false;
JSONObject obj = new JSONObject();
try {
obj.put("class", "featuresget");
obj.put("userid", astid + "/" + xivoUserId);
return send(obj);
} catch (Exception e) {
logger.error("Error send features get command", e);
return false;
}
}
/**
* Sends password command.
*
* @param sessionId the session id from previous command.
* @param password the password to authorize.
* @return is command successful.
*/
@SuppressWarnings("unchecked")
private boolean authorize(String sessionId, String password) {
if (connection == null || sessionId == null || password == null) return false;
JSONObject obj = new JSONObject();
try {
obj.put("class", "login_pass");
obj.put("hashedpassword", Sha1Crypto.encode(sessionId + ":" + password));
return send(obj);
} catch (Exception e) {
logger.error("Error login with password", e);
return false;
}
}
/**
* Performs a test by sending HTTP Gets to the URL, and records the number of bytes returned. Each
* test results are documented and displayed in standard out with the following information:
*
* <p>URL - The source URL of the test REQ CNT - How many times this test has run START - The
* start time of the last test run STOP - The stop time of the last test run THREAD - The thread
* id handling this test case RESULT - The result of the test. Either the number of bytes returned
* or an error message.
*/
private void doTest() {
String result = "";
this.reqCount++;
// Connect and run test steps
Date startTime = new Date();
try {
ClientResource client = new ClientResource(this.myURL);
// place order
JSONObject json = new JSONObject();
json.put("payment", "quarter");
json.put("action", "place-order");
client.post(new JsonRepresentation(json), MediaType.APPLICATION_JSON);
// Get Gumball Count
Representation result_string = client.get();
JSONObject json_count = new JSONObject(result_string.getText());
result = Integer.toString((int) json_count.get("count"));
} catch (Exception e) {
result = e.toString();
} finally {
Date stopTime = new Date();
// Print Report of Result:
System.out.println(
"======================================\n"
+ "URL => "
+ this.myURL
+ "\n"
+ "REQ CNT => "
+ this.reqCount
+ "\n"
+ "START => "
+ startTime
+ "\n"
+ "STOP => "
+ stopTime
+ "\n"
+ "THREAD => "
+ Thread.currentThread().getName()
+ "\n"
+ "RESULT => "
+ result
+ "\n");
}
}
/**
* Sends login command.
*
* @param capalistParam param from previous command.
* @return is command successful.
*/
@SuppressWarnings("unchecked")
private boolean sendCapas(JSONArray capalistParam) {
if (connection == null || capalistParam == null || capalistParam.isEmpty()) return false;
JSONObject obj = new JSONObject();
try {
obj.put("class", "login_capas");
obj.put("capaid", capalistParam.get(0));
obj.put("lastconnwins", "false");
obj.put("loginkind", "agent");
obj.put("state", "");
return send(obj);
} catch (Exception e) {
logger.error("Error login", e);
return false;
}
}
/** @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response) */
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException, MongoException, DuplicateKeyException,
UnknownHostException {
// TODO Auto-generated method stub
doGet(request, response);
StringBuilder buffer = new StringBuilder();
BufferedReader reader = request.getReader();
String uname = request.getParameter("username");
String password = request.getParameter("password");
String email = request.getParameter("email");
System.out.println(uname + " " + password + " " + email);
/*String line;
while((line=reader.readLine())!=null){
buffer.append(line);
}
String data = buffer.toString();
System.out.println(data);
data = "{\"p\":\"N\",\"c\":\"W\"}";*/
// System.out.println(data);
// JSONObject params = (JSONObject)JSON.parse(data);
JSONObject params = new JSONObject();
params.put("username", uname);
params.put("password", password);
BasicDBObject user1 = new BasicDBObject(params);
for (Object key : params.keySet().toArray()) {
user1.put(key.toString(), params.get(key));
}
// System.out.println(user1.toJson());
MongoClientURI uri =
new MongoClientURI("mongodb://*****:*****@ds035014.mongolab.com:35014/vikas2");
MongoClient client = new MongoClient(uri);
DB db = client.getDB(uri.getDatabase());
DBCollection users = db.getCollection("users");
users.insert(user1);
response.setHeader("Access-Control-Allow-Origin", "*");
response.setHeader("Access-Control-Allow-Methods", "POST");
response.setHeader("Access-Control-Allow-Headers", "Content-Type");
response.setHeader("Access-Control-Max-Age", "86400");
}
private JSONObject createNewUser(int gameId) {
int userId;
JSONObject jObj = new JSONObject();
JSONObject action = new JSONObject();
Random randomNum = new Random();
userId = randomNum.nextInt(max_users) + 1;
while (userIds[userId] == true) {
userId = randomNum.nextInt(max_users) + 1;
}
userIds[userId] = true;
try {
jObj.put("game", gameId);
action.put("actionType", "gameStart");
action.put("actionNumber", 1);
jObj.put("action", action);
jObj.put("user", "u" + userId);
} catch (JSONException e) {
System.out.println("could not put");
}
gameRecord.put(gameId, new GameInfo("u" + userId, userId));
return jObj;
}
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws IOException {
response.setContentType("text/plain");
PrintWriter writer = response.getWriter();
String q = request.getParameter("q");
if (q == null) {
writer.println("ERROR: q has no value.");
writer.close();
return;
}
ResultBundle[] results = Map.getResults(q.toLowerCase());
writer.println("STATUS: " + results.length + " results for the query " + q + "!");
for (ResultBundle rb : results) {
JSONObject j = new JSONObject();
j.put("thumbnail", rb.getThumbnail());
j.put("title", rb.getTitle());
j.put("description", rb.getDescription());
j.put("url", rb.getUrl());
writer.println(j.toString());
}
writer.close();
}
@RequestMapping(
value = "/getCityApi",
method = {RequestMethod.GET, RequestMethod.POST})
public String getCityApi(
HttpServletRequest request,
@RequestParam(value = "locationname") String locationname,
ModelMap model) {
Map<Object, Object> map = new HashMap<Object, Object>();
JSONArray jSONArray = new JSONArray();
try {
String status = "active";
List<City> cityList = cityService.getCityApi(locationname, status);
if (cityList != null && cityList.size() > 0) {
for (int i = 0; i < cityList.size(); i++) {
City city = (City) cityList.get(i);
String cityName = (String) city.getCity();
String stateName = (String) city.getState();
int ID = (Integer) (city.getId());
JSONObject jSONObject = new JSONObject();
jSONObject.put("id", ID);
jSONObject.put("text", cityName);
jSONArray.put(jSONObject);
}
utilities.setSuccessResponse(response, jSONArray.toString());
} else {
throw new ConstException(ConstException.ERR_CODE_NO_DATA, ConstException.ERR_MSG_NO_DATA);
}
} catch (Exception ex) {
logger.error("getCity :" + ex.getMessage());
utilities.setErrResponse(ex, response);
}
model.addAttribute("model", jSONArray.toString());
return "home";
}
private JSONObject moveUser(int gameCount) {
Random randomNum = new Random();
GameInfo gameInfo;
JSONObject jObj = new JSONObject();
JSONObject action = new JSONObject();
JSONObject coords = new JSONObject();
int game;
int xCoord;
int yCoord;
int addPoints;
// Gets random number to denote which game to use action on
game = getRandomGame(gameCount);
xCoord = randomNum.nextInt(20) + 1;
yCoord = randomNum.nextInt(20) + 1;
addPoints = randomNum.nextInt(41) - 20;
gameInfo = gameRecord.get(game);
gameInfo.addPoints(addPoints);
gameInfo.incrementCount();
try {
jObj.put("game", game);
coords.put("x", xCoord);
coords.put("y", yCoord);
action.put("actionType", "Move");
action.put("actionNumber", gameInfo.getCount());
action.put("location", coords);
action.put("pointsAdded", addPoints);
action.put("points", gameInfo.getPoints());
jObj.put("action", action);
jObj.put("user", gameInfo.getUser());
} catch (JSONException e) {
System.out.println("could not put");
}
return jObj;
}
private JSONObject endGame(int gameCount) {
Random randomNum = new Random();
GameInfo gameInfo;
JSONObject jObj = new JSONObject();
JSONObject action = new JSONObject();
int game;
String status;
game = getRandomGame(gameCount);
gameInfo = gameRecord.get(game);
gameInfo.incrementCount();
if (gameInfo.getCount() < 9) {
return moveUser(gameCount);
}
if (gameInfo.getPoints() > 40 || gameInfo.getPoints() < -40) {
status = "WIN";
} else {
status = "LOSS";
}
try {
jObj.put("game", game);
action.put("actionType", "gameEnd");
action.put("gameStatus", status);
action.put("actionNumber", gameInfo.getCount());
action.put("points", gameInfo.getPoints());
jObj.put("action", action);
jObj.put("user", gameInfo.getUser());
userIds[gameInfo.getId()] = false;
gameRecord.remove(game);
} catch (JSONException e) {
System.out.println("could not put");
}
return jObj;
}
/**
* Sends login command.
*
* @param username the username.
* @return is command successful.
*/
@SuppressWarnings("unchecked")
private boolean login(String username) {
if (connection == null || username == null) return false;
JSONObject obj = new JSONObject();
try {
obj.put("class", "login_id");
obj.put("company", "Jitsi");
String os = "x11";
if (OSUtils.IS_WINDOWS) os = "win";
else if (OSUtils.IS_MAC) os = "mac";
obj.put("ident", username + "@" + os);
obj.put("userid", username);
obj.put("version", "9999");
obj.put("xivoversion", "1.1");
return send(obj);
} catch (Exception e) {
logger.error("Error login", e);
return false;
}
}
/**
* 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";
}
}
private JSONObject specialMove(int gameCount) {
Random randomNum = new Random();
GameInfo gameInfo;
JSONObject jObj = new JSONObject();
JSONObject action = new JSONObject();
int game;
int addPoints;
int special;
// Gets random number to denote which game to use action on
game = getRandomGame(gameCount);
gameInfo = gameRecord.get(game);
// Checks if all specials are used
if (gameInfo.checkSpecial()) {
return moveUser(gameCount);
}
// Gets random number to denote which special move to use
special = randomNum.nextInt(4);
while (gameInfo.checkSpecialMove(special)) {
special = randomNum.nextInt(4);
}
gameInfo.useSpecialMove(special);
addPoints = randomNum.nextInt(41) - 20;
gameInfo.addPoints(addPoints);
gameInfo.incrementCount();
try {
jObj.put("game", game);
action.put("actionType", "specialMove");
action.put("actionNumber", gameInfo.getCount());
action.put("pointsAdded", addPoints);
if (special == SHUFFLE) {
action.put("move", "Shuffle");
} else if (special == CLEAR) {
action.put("move", "Clear");
} else if (special == INVERT) {
action.put("move", "Invert");
} else {
action.put("move", "Rotate");
}
action.put("points", gameInfo.getPoints());
jObj.put("action", action);
jObj.put("user", gameInfo.getUser());
} catch (JSONException e) {
System.out.println("could not put");
}
return jObj;
}
/** @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response) */
@SuppressWarnings("unchecked")
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
response.setContentType("application/json");
response.setHeader("Cache-Control", "nocache");
response.setCharacterEncoding("utf-8");
PrintWriter out = response.getWriter();
StringWriter result = new StringWriter();
// get received JSON data from request
BufferedReader br = new BufferedReader(new InputStreamReader(request.getInputStream()));
String postData = "";
if (br != null) {
postData = br.readLine();
}
try {
JSONObject json = (JSONObject) new JSONParser().parse(postData);
JSONObject resultObj = new JSONObject();
JSONArray list = new JSONArray();
List<Tracking> trackingList = new ArrayList<Tracking>();
// get the website list
if (json.get("type").equals("websiteslist")) {
trackingList = trackingDao.websiteList(pool);
for (Tracking item : trackingList) {
list.add(item.getWebsite());
}
}
// render report
else if (json.get("type").equals("submit")) {
if (json.get("criteria").equals("date")) {
// render repoty by date
trackingList = trackingDao.getListByDate(pool, json.get("date").toString());
} else if (json.get("criteria").equals("daterange")) {
// render repoty by date range
trackingList =
trackingDao.getListByDateRange(
pool, json.get("fromdate").toString(), json.get("todate").toString());
} else if (json.get("criteria").equals("website")) {
// render repoty by website
String website = (json.get("website") == null ? "" : json.get("website").toString());
trackingList = trackingDao.getListByWebsite(pool, website);
}
for (Tracking item : trackingList) {
JSONObject trackingObj = new JSONObject();
trackingObj.put("date", item.getDate());
trackingObj.put("website", item.getWebsite());
trackingObj.put("visit", item.getVisit());
list.add(trackingObj);
}
}
resultObj.put("result", list);
resultObj.writeJSONString(result);
// finally output the json string
out.print(result.toString());
} catch (ParseException | SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
/** @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse response) */
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
// TODO Auto-generated method stub
PrintWriter out = response.getWriter();
String id = request.getParameter("hashID");
JSONObject result = new JSONObject();
if (id != null && id.trim().isEmpty()) {
response.setContentType("text/plain");
response.setStatus(400);
out.println("Empty hash ID");
return;
}
Connection conn = null;
Statement st = null;
ResultSet rs = null;
String password;
try {
// Read the SQL password from a file
BufferedReader reader = null;
try {
InputStream inputStream = getClass().getClassLoader().getResourceAsStream("SQLpw.txt");
reader = new BufferedReader(new InputStreamReader(inputStream));
password = reader.readLine();
} catch (NullPointerException e) {
e.getStackTrace();
password = "";
}
// create a mysql database connection
String myDriver = "com.mysql.jdbc.Driver";
String myUrl = "jdbc:mysql://localhost/lodstories";
Class.forName(myDriver);
conn = DriverManager.getConnection(myUrl, "root", password);
st = conn.createStatement();
rs = st.executeQuery("SELECT hash,title,author FROM hash_objects where id='" + id + "'");
if (!rs.next()) {
response.setContentType("text/plain");
response.setStatus(400);
out.println("Error retrieving hash object");
return;
}
result.put("hash", rs.getString("hash"));
result.put("title", rs.getString("title"));
result.put("author", rs.getString("author"));
// result.put("path", rs.getString("path"));
// result.put("rating", rs.getInt("rating"));
// Update the lastAccessed field
st.executeUpdate(
"UPDATE hash_objects SET lastAccessed=CURRENT_TIMESTAMP() WHERE id='" + id + "'");
response.setContentType("application/json");
response.setCharacterEncoding("UTF-8");
out.println(result);
} catch (ClassNotFoundException e) {
System.err.println("Could not connect to driver!");
System.err.println(e.getMessage());
} catch (SQLException ex) {
System.err.println(
"SQLException: "
+ ex.getMessage()
+ ", SQLState: "
+ ex.getSQLState()
+ "VendorError: "
+ ex.getErrorCode());
} catch (JSONException ex) {
ex.printStackTrace();
} finally {
if (conn != null) {
try {
conn.close();
} catch (SQLException ex) {
ex.printStackTrace();
}
}
if (st != null) {
try {
st.close();
} catch (SQLException ex) {
ex.printStackTrace();
}
}
if (rs != null) {
try {
rs.close();
} catch (SQLException ex) {
ex.printStackTrace();
}
}
}
}
/**
* 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;
}