private double calcMean(
HashMap<Integer, String> singleGeneCaseValueMap,
String groupType,
String profileStableId) { // group type: altered or unaltered
switch (groupType) {
case "altered":
int _index_altered = 0;
double[] alteredArray = new double[alteredSampleIds.size()];
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
alteredArray[_index_altered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
alteredArray[_index_altered] =
Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_altered += 1;
}
}
return StatUtils.mean(alteredArray);
case "unaltered":
int _index_unaltered = 0;
double[] unalteredArray = new double[unalteredSampleIds.size()];
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
unalteredArray[_index_unaltered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
unalteredArray[_index_unaltered] =
Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_unaltered += 1;
}
}
return StatUtils.mean(unalteredArray);
default:
return Double.NaN; // error
}
}
private double runTTest(HashMap<Integer, String> singleGeneCaseValueMap, String profileStableId)
throws IllegalArgumentException {
double[] unalteredArray = new double[unalteredSampleIds.size()];
double[] alteredArray = new double[alteredSampleIds.size()];
int _index_unaltered = 0, _index_altered = 0;
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
alteredArray[_index_altered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
alteredArray[_index_altered] =
Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_altered += 1;
}
}
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
unalteredArray[_index_unaltered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
unalteredArray[_index_unaltered] =
Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_unaltered += 1;
}
}
if (alteredArray.length < 2 || unalteredArray.length < 2) return Double.NaN;
else {
double pvalue = TestUtils.tTest(alteredArray, unalteredArray);
return pvalue;
}
}
private double calcSTDev(
HashMap<Integer, String> singleGeneCaseValueMap, String groupType, String profileStableId) {
switch (groupType) {
case "altered":
DescriptiveStatistics stats_altered = new DescriptiveStatistics();
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
stats_altered.addValue(
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)))
/ Math.log(2));
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
stats_altered.addValue(
Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
}
return stats_altered.getStandardDeviation();
case "unaltered":
DescriptiveStatistics stats_unaltered = new DescriptiveStatistics();
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
stats_unaltered.addValue(
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)))
/ Math.log(2));
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
stats_unaltered.addValue(
Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
}
return stats_unaltered.getStandardDeviation();
default:
return Double.NaN; // error
}
}
/**
* Get multiple bonuses
*
* @param ssn
* @param multiplier
* @return
*/
private MultipleBonus[] getBonuses(String[] ssn, String[] multiplierStr) {
// 2 input arrays do not have the same length
MultipleBonus[] multipleBonus = new MultipleBonus[multiplierStr.length];
for (int i = 0; i < multiplierStr.length; i++) {
MultipleBonus b = new MultipleBonus();
int iSsn = (int) i / 3;
log.info("(i, iSsn) = (" + i + ", " + iSsn + ")");
try {
Ssn _ssn = new Ssn();
_ssn.setSsn(ssn[iSsn]);
b.setSsn(new Ssn());
double m = Double.valueOf(multiplierStr[i]);
b.setBonus(m);
} catch (NumberFormatException e) {
log.error(e.getStackTrace());
b.setBonus(-1); // if multiplier is not filled correctly
} finally {
String msg = String.format("bonus[%d]=%s", i, b.toString());
log.info(msg);
multipleBonus[i] = b;
}
}
return multipleBonus;
}
/**
* Thrown to indicate that the application has attempted to convert a string to one of the numeric
* types, but that the string does not have the appropriate format.
*/
@ExceptionHandler(NumberFormatException.class)
public ResponseEntity<Map<String, Object>> handleNumberFormatException(
NumberFormatException error) {
Map<String, Object> errorMap = new HashMap<String, Object>();
errorMap.put("hasErrors", "true");
errorMap.put("developerMessage", error.getMessage());
errorMap.put("userMessage", "");
errorMap.put("moreInfo", error.getStackTrace()[0]);
errorMap.put("errorCode", HttpStatus.BAD_REQUEST);
error.printStackTrace();
return new ResponseEntity<Map<String, Object>>(errorMap, HttpStatus.INTERNAL_SERVER_ERROR);
}
/**
* Get multiple bonuses
*
* @param ssn
* @param multiplier
* @return
*/
private Bonus[] getBonuses(String[] ssn, String[] multiplierStr) throws NamingException {
// If there's any configuration problem, take a look at:
//
// EJB invocations from a remote client using JNDI
// https://docs.jboss.org/author/display/AS71/EJB+invocations+from+a+remote+client+using+JNDI
//
// Remote EJB invocations via JNDI - EJB client API or remote-naming project
// https://docs.jboss.org/author/display/AS71/Remote+EJB+invocations+via+JNDI+-+EJB+client+API+or+remote-naming+project
//
// javax.naming.NamingException: Failed instantiate InitialContextFactory
// org.jboss.naming.remote.client.InitialContextFactory from classloader
// http://stackoverflow.com/questions/13065025/javax-naming-namingexception-failed-instantiate-initialcontextfactory-org-jboss
//
// Cannot connect to Remote EJB deployed to 7.1 instance, from another 7.1 instance
// https://developer.jboss.org/thread/195516?tstart=0
Properties props = new Properties();
props.put(
Context.INITIAL_CONTEXT_FACTORY, "org.jboss.naming.remote.client.InitialContextFactory");
props.put(Context.URL_PKG_PREFIXES, "org.jboss.ejb.client.naming");
props.put(Context.PROVIDER_URL, "remote://192.168.1.13:4447");
props.put(Context.SECURITY_PRINCIPAL, "testuser");
props.put(Context.SECURITY_CREDENTIALS, "testpassword");
Context ctx = new InitialContext(props);
CalculatorRemote calculator = (CalculatorRemote) ctx.lookup(JNDI_BINDING);
// assume that 2 input arrays have the same length
Bonus[] bonus = new Bonus[ssn.length];
for (int i = 0; i < ssn.length; i++) {
Bonus b = new Bonus();
try {
b.setSsn(ssn[i]);
double m = Double.valueOf(multiplierStr[i]);
b.setMultiplier(m);
b.setBonus(Double.toString(calculator.bonus(m)));
} catch (NumberFormatException e) {
log.error(e.getStackTrace());
b.setBonus(null); // if multiplier is not filled correctly
} finally {
String msg = String.format("bonus[%d]=%s", i, b.toString());
log.debug(msg);
bonus[i] = b;
}
}
return bonus;
}
/**
* Check the correct validity of the parameter value
*
* @param replacement : the parameter
* @param parType : the parameter type
* @param attribute : the attribute
* @return
*/
private static String checkParType(String replacement, String parType, String attribute)
throws NumberFormatException {
logger.debug("IN");
String toReturn = replacement;
// check if numbers are number otherwise throw exception
try {
if (parType.equalsIgnoreCase("NUMBER")) {
toReturn = replacement.replaceAll("\'", "");
toReturn = replacement.replaceAll(";", ",");
if (toReturn.indexOf(",") >= 0) {
// multivalues management
String[] values = toReturn.split(",");
for (int i = 0; i < values.length; i++) {
Double double1 = Double.valueOf(values[i]);
}
} else {
Double double1 = Double.valueOf(toReturn);
}
}
} catch (NumberFormatException e) {
String me = e.getMessage();
me += " - attribute " + attribute + " should be of number type";
NumberFormatException numberFormatException = new NumberFormatException(attribute);
numberFormatException.setStackTrace(e.getStackTrace());
throw numberFormatException;
}
// check when type is RAW that there are not '' surrounding values (in case remove them)
// remotion done here in order to not modify SpagoBI Analytical driver of type string handling
try {
if (parType.equalsIgnoreCase("RAW")) {
logger.debug("Parmaeter is Raw type, check if there are '' and remove them");
if (toReturn.length() > 2) {
if (toReturn.startsWith("'")) {
logger.debug("first character is ', remove");
toReturn = toReturn.substring(1);
}
if (toReturn.endsWith("'")) {
logger.debug("last character is ', remove");
toReturn = toReturn.substring(0, replacement.length() - 1);
}
}
}
} catch (Exception e) {
logger.error("Error in removing the '' in value " + toReturn + " do not substitute them");
}
logger.debug("OUT");
return toReturn;
}
public Bitmap readMjpegFrame() throws IOException {
mark(FRAME_MAX_LENGTH);
int headerLen = getStartOfSequence(this, SOI_MARKER);
reset();
byte[] header = new byte[headerLen];
readFully(header);
try {
mContentLength = parseContentLength(header);
} catch (NumberFormatException nfe) {
nfe.getStackTrace();
Log.d(TAG, "catch NumberFormatException hit", nfe);
mContentLength = getEndOfSeqeunce(this, EOF_MARKER);
}
reset();
byte[] frameData = new byte[mContentLength];
skipBytes(headerLen);
readFully(frameData);
return BitmapFactory.decodeStream(new ByteArrayInputStream(frameData));
}
private void handleGetDistance(String[] params) {
if (params.length < 4) {
return;
}
try {
double lat1 = Double.valueOf(params[0]);
double lon1 = Double.valueOf(params[1]);
double lat2 = Double.valueOf(params[2]);
double lon2 = Double.valueOf(params[3]);
double distance = -1;
LatLng p1 = new LatLng(lat1, lon1);
LatLng p2 = new LatLng(lat2, lon2);
distance = DistanceUtil.getDistance(p1, p2);
// // 判断，如果是小距离
// if ((Math.abs(lat1 - lat2) < MyDistanceUtils.SMALL_DISTANCE_FLAG)
// && (Math.abs(lon1 - lon2) < MyDistanceUtils.SMALL_DISTANCE_FLAG))
// {
// distance = MyDistanceUtils.getShortDistance(lon1, lat1, lon2,
// lat2);
// }
// // 大距离
// else {
// distance = MyDistanceUtils.getLongDistance(lon1, lat1, lon2,
// lat2);
// }
jsCallback(EBaiduMapUtils.MAP_FUN_CB_GET_DISTANCE, 0, EUExCallback.F_C_TEXT, "" + distance);
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
@Override
public SampleResult sample(Entry entry) {
ServiceSocket socket = null;
SampleResult sampleResult = new SampleResult();
sampleResult.setSampleLabel(getName());
sampleResult.setDataEncoding(getContentEncoding());
StringBuilder errorList = new StringBuilder();
errorList.append("\n\n[Problems]\n");
boolean isOK = false;
String payloadMessage = getRequestPayload();
sampleResult.setSamplerData(payloadMessage);
sampleResult.sampleStart();
try {
socket = getConnectionSocket();
if (socket == null) {
sampleResult.setResponseCode("500");
sampleResult.setSuccessful(false);
sampleResult.sampleEnd();
sampleResult.setResponseMessage(errorList.toString());
errorList.append(" - Connection couldn't be opened").append("\n");
return sampleResult;
}
if (!payloadMessage.isEmpty()) {
socket.sendMessage(payloadMessage);
}
int responseTimeout = Integer.parseInt(getResponseTimeout());
socket.awaitClose(responseTimeout, TimeUnit.MILLISECONDS);
if (socket.getResponseMessage() == null || socket.getResponseMessage().isEmpty()) {
sampleResult.setResponseCode("204");
}
if (socket.getError() != 0) {
isOK = false;
sampleResult.setResponseCode(socket.getError().toString());
} else {
sampleResult.setResponseCodeOK();
isOK = true;
}
sampleResult.setResponseData(socket.getResponseMessage(), getContentEncoding());
} catch (URISyntaxException e) {
errorList
.append(" - Invalid URI syntax: ")
.append(e.getMessage())
.append("\n")
.append(StringUtils.join(e.getStackTrace(), "\n"))
.append("\n");
} catch (IOException e) {
errorList
.append(" - IO Exception: ")
.append(e.getMessage())
.append("\n")
.append(StringUtils.join(e.getStackTrace(), "\n"))
.append("\n");
} catch (NumberFormatException e) {
errorList
.append(" - Cannot parse number: ")
.append(e.getMessage())
.append("\n")
.append(StringUtils.join(e.getStackTrace(), "\n"))
.append("\n");
} catch (InterruptedException e) {
errorList
.append(" - Execution interrupted: ")
.append(e.getMessage())
.append("\n")
.append(StringUtils.join(e.getStackTrace(), "\n"))
.append("\n");
} catch (Exception e) {
errorList
.append(" - Unexpected error: ")
.append(e.getMessage())
.append("\n")
.append(StringUtils.join(e.getStackTrace(), "\n"))
.append("\n");
}
sampleResult.sampleEnd();
sampleResult.setSuccessful(isOK);
String logMessage = (socket != null) ? socket.getLogMessage() : "";
sampleResult.setResponseMessage(logMessage + errorList);
return sampleResult;
}
private double runFisherExactTest(
HashMap<Integer, String> singleGeneCaseValueMap, String profileType) {
int a = 0, // non altered
b = 0, // x non altered, y altered
c = 0, // x altered, y non altered
d = 0; // both alered
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION.toString())) {
try {
Double value = Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId));
if (copyNumType.equals("del")) {
if (value == -2.0) {
d += 1;
} else {
c += 1;
}
} else if (copyNumType.equals("amp")) {
if (value == 2.0) {
d += 1;
} else {
c += 1;
}
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else if (profileType.equals(GeneticAlterationType.MUTATION_EXTENDED.toString())) {
String value = singleGeneCaseValueMap.get(alteredSampleId);
if (value.equals("Non")) {
c += 1;
} else {
d += 1;
}
}
}
}
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION.toString())) {
try {
Double value = Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId));
if (copyNumType.equals("del")) {
if (value == -2.0) {
b += 1;
} else {
a += 1;
}
} else if (copyNumType.equals("amp")) {
if (value == 2.0) {
b += 1;
} else {
a += 1;
}
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else if (profileType.equals(GeneticAlterationType.MUTATION_EXTENDED.toString())) {
String value = singleGeneCaseValueMap.get(unalteredSampleId);
if (value.equals("Non")) {
a += 1;
} else {
b += 1;
}
}
}
}
FisherExact fisher = new FisherExact(a + b + c + d);
return fisher.getCumlativeP(a, b, c, d);
}
private double calcPct(
HashMap<Integer, String> singleGeneCaseValueMap,
String profileType,
String groupType) { // group type: altered or unaltered
double _result_pct = 0, _count = 0; // altered samples count
if (profileType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION.toString())
&& copyNumType.equals("del")) {
switch (groupType) {
case "altered":
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
try {
if (Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)) == -2.0) {
_count += 1;
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
_result_pct = _count / alteredSampleIds.size();
break;
case "unaltered":
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
try {
if (Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)) == -2.0) {
_count += 1;
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
_result_pct = _count / unalteredSampleIds.size();
break;
}
} else if (profileType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION.toString())
&& copyNumType.equals("amp")) {
switch (groupType) {
case "altered":
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
try {
if (Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)) == 2.0) {
_count += 1;
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
_result_pct = _count / alteredSampleIds.size();
break;
case "unaltered":
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
try {
if (Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)) == 2.0) {
_count += 1;
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
_result_pct = _count / unalteredSampleIds.size();
break;
}
} else if (profileType.equals(GeneticAlterationType.MUTATION_EXTENDED.toString())) {
switch (groupType) {
case "altered":
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (!singleGeneCaseValueMap.get(alteredSampleId).equals("Non")) {
_count += 1;
}
}
}
_result_pct = _count / alteredSampleIds.size();
break;
case "unaltered":
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (!singleGeneCaseValueMap.get(unalteredSampleId).equals("Non")) {
_count += 1;
}
}
}
_result_pct = _count / unalteredSampleIds.size();
break;
}
}
return _result_pct;
}