List of usage examples for java.io DataOutputStream writeBytes
public final void writeBytes(String s) throws IOException
From source file:net.maizegenetics.analysis.imputation.FILLINImputationAccuracy.java
private void accuracyMAFOut() { DecimalFormat df = new DecimalFormat("0.########"); if (this.MAF != null && this.MAFClass != null) try {//from w ww . j a v a 2 s. c o m String ext = FilenameUtils.getExtension(this.outFile); File outputFile = new File(this.outFile.replace(ext, "MAFAccuracy.txt")); DataOutputStream outStream = new DataOutputStream( new BufferedOutputStream(new FileOutputStream(outputFile))); outStream.writeBytes( "##\tMAFClass\tTotalSitesMasked\tTotalSitesCompared\tTotalPropUnimputed\tNumHets\tHetToMinor\tHetToMajor\tCorrectHet\tUnimpHet\tNumMinor\tMinorToMajor\tMinorToHet\tCorrectMinor\t" + "UnimpMinor\tNumMajor\tMajorToMinor\tMajorToHet\tCorrectMajor\tUnimputedMajor\tr2\n"); for (int i = 0; i < this.MAFClass.length; i++) { outStream .writeBytes("##TotalByImputed\t" + this.MAFClass[i] + "\t" + (this.mafAll[i][0][4] + this.mafAll[i][1][4] + this.mafAll[i][2][4]) + "\t" + (this.mafAll[i][0][4] + this.mafAll[i][1][4] + this.mafAll[i][2][4] - this.mafAll[i][0][3] - this.mafAll[i][1][3] - this.mafAll[i][2][3]) + "\t" + ((this.mafAll[i][0][3] + this.mafAll[i][1][3] + this.mafAll[i][2][3]) / (this.mafAll[i][0][4] + this.mafAll[i][1][4] + this.mafAll[i][2][4])) + "\t" + this.mafAll[i][0][4] + "\t" + this.mafAll[i][0][0] + "\t" + this.mafAll[i][0][1] + "\t" + this.mafAll[i][0][2] + "\t" + this.mafAll[i][0][3] + "\t" + this.mafAll[i][1][4] + "\t" + this.mafAll[i][1][0] + "\t" + this.mafAll[i][1][1] + "\t" + this.mafAll[i][1][2] + "\t" + this.mafAll[i][1][3] + "\t" + this.mafAll[i][2][4] + "\t" + this.mafAll[i][2][0] + "\t" + this.mafAll[i][2][1] + "\t" + this.mafAll[i][2][2] + "\t" + this.mafAll[i][2][3] + "\t" + pearsonR2(this.mafAll[i], false) + "\n"); } outStream.writeBytes( "#MAFClass,Minor=0,Het=1,Major=2;x is masked(known), y is predicted\nMAF\tx\ty\tN\tprop\n"); for (int i = 0; i < this.MAFClass.length; i++) { outStream.writeBytes(this.MAFClass[i] + "\t" + 0 + "\t" + 0 + "\t" + this.mafAll[i][0][0] + "\t" + df.format((this.mafAll[i][0][0]) / (this.mafAll[i][0][0] + this.mafAll[i][0][1] + this.mafAll[i][0][2])) + "\n" + this.MAFClass[i] + "\t" + 0 + "\t" + .5 + "\t" + this.mafAll[i][0][1] + "\t" + df.format((this.mafAll[i][0][1]) / (this.mafAll[i][0][0] + this.mafAll[i][0][1] + this.mafAll[i][0][2])) + "\n" + this.MAFClass[i] + "\t" + 0 + "\t" + 1 + "\t" + this.mafAll[i][0][2] + "\t" + df.format((this.mafAll[i][0][2]) / (this.mafAll[i][0][0] + this.mafAll[i][0][1] + this.mafAll[i][0][2])) + "\n" + this.MAFClass[i] + "\t" + .5 + "\t" + 0 + "\t" + this.mafAll[i][1][0] + "\t" + df.format((this.mafAll[i][1][0]) / (this.mafAll[i][1][0] + this.mafAll[i][1][1] + this.mafAll[i][1][2])) + "\n" + this.MAFClass[i] + "\t" + .5 + "\t" + .5 + "\t" + this.mafAll[i][1][1] + "\t" + df.format((this.mafAll[i][1][1]) / (this.mafAll[i][1][0] + this.mafAll[i][1][1] + this.mafAll[i][1][2])) + "\n" + this.MAFClass[i] + "\t" + .5 + "\t" + 1 + "\t" + this.mafAll[i][1][2] + "\t" + df.format((this.mafAll[i][1][2]) / (this.mafAll[i][1][0] + this.mafAll[i][1][1] + this.mafAll[i][1][2])) + "\n" + this.MAFClass[i] + "\t" + 1 + "\t" + 0 + "\t" + this.mafAll[i][2][0] + "\t" + df.format((this.mafAll[i][2][0]) / (this.mafAll[i][2][0] + this.mafAll[i][2][1] + this.mafAll[i][2][2])) + "\n" + this.MAFClass[i] + "\t" + 1 + "\t" + .5 + "\t" + this.mafAll[i][2][1] + "\t" + df.format((this.mafAll[i][2][1]) / (this.mafAll[i][2][0] + this.mafAll[i][2][1] + this.mafAll[i][2][2])) + "\n" + this.MAFClass[i] + "\t" + 1 + "\t" + 1 + "\t" + this.mafAll[i][2][2] + "\t" + df.format((this.mafAll[i][2][2]) / (this.mafAll[i][2][0] + this.mafAll[i][2][1] + this.mafAll[i][2][2])) + "\n"); } outStream.writeBytes("#Proportion unimputed:\n#MAF\tminor\thet\tmajor\n"); for (int i = 0; i < this.MAFClass.length; i++) { outStream.writeBytes("#" + this.MAFClass[i] + "\t" + this.mafAll[i][0][3] / this.mafAll[i][0][4] + "\t" + this.mafAll[i][1][3] / this.mafAll[i][1][4] + "\t" + this.mafAll[i][2][3] / this.mafAll[i][2][4] + "\n"); } outStream.flush(); outStream.close(); } catch (Exception e) { if (this.verboseOutput) System.out.println(e); } }
From source file:net.maizegenetics.analysis.imputation.FILLINImputationAccuracy.java
private void accuracyOut(double time) { DecimalFormat df = new DecimalFormat("0.########"); double r2 = pearsonR2(this.all, this.verboseOutput); try {/*from w w w. j av a 2s . c om*/ String ext = FilenameUtils.getExtension(this.outFile); File outputFile = new File(this.outFile.replace(ext, "Accuracy.txt")); DataOutputStream outStream = new DataOutputStream( new BufferedOutputStream(new FileOutputStream(outputFile))); outStream.writeBytes( "##Taxon\tTotalSitesMasked\tTotalSitesCompared\tTotalPropUnimputed\tNumMinor\tCorrectMinor\tMinorToHet\tMinorToMajor\tUnimpMinor" + "\tNumHets\tHetToMinor\tCorrectHet\tHetToMajor\tUnimpHet\tNumMajor\tMajorToMinor\tMajorToHet\tCorrectMajor\tUnimpMajor\tR2\n"); outStream.writeBytes("##TotalByImputed\t" + (this.all[0][4] + this.all[1][4] + this.all[2][4]) + "\t" + (this.all[0][4] + this.all[1][4] + this.all[2][4] - this.all[0][3] - this.all[1][3] - this.all[2][3]) + "\t" + ((this.all[0][3] + this.all[1][3] + this.all[2][3]) / (this.all[0][4] + this.all[1][4] + this.all[2][4])) + "\t" + this.all[0][4] + "\t" + this.all[0][0] + "\t" + this.all[0][1] + "\t" + this.all[0][2] + "\t" + this.all[0][3] + "\t" + this.all[1][4] + "\t" + this.all[1][0] + "\t" + this.all[1][1] + "\t" + this.all[1][2] + "\t" + this.all[1][3] + "\t" + this.all[2][4] + "\t" + this.all[2][0] + "\t" + this.all[2][1] + "\t" + this.all[2][2] + "\t" + this.all[2][3] + "\t" + r2 + "\n"); outStream.writeBytes("#Minor=0,Het=1,Major=2;x is masked(known), y is predicted\nx\ty\tN\tprop\n" + 0 + "\t" + 0 + "\t" + this.all[0][0] + "\t" + df.format((this.all[0][0]) / (this.all[0][0] + this.all[0][1] + this.all[0][2])) + "\n" + 0 + "\t" + .5 + "\t" + this.all[0][1] + "\t" + df.format((this.all[0][1]) / (this.all[0][0] + this.all[0][1] + this.all[0][2])) + "\n" + 0 + "\t" + 1 + "\t" + this.all[0][2] + "\t" + df.format((this.all[0][2]) / (this.all[0][0] + this.all[0][1] + this.all[0][2])) + "\n" + .5 + "\t" + 0 + "\t" + this.all[1][0] + "\t" + df.format((this.all[1][0]) / (this.all[1][0] + this.all[1][1] + this.all[1][2])) + "\n" + .5 + "\t" + .5 + "\t" + this.all[1][1] + "\t" + df.format((this.all[1][1]) / (this.all[1][0] + this.all[1][1] + this.all[1][2])) + "\n" + .5 + "\t" + 1 + "\t" + this.all[1][2] + "\t" + df.format((this.all[1][2]) / (this.all[1][0] + this.all[1][1] + this.all[1][2])) + "\n" + 1 + "\t" + 0 + "\t" + this.all[2][0] + "\t" + df.format((this.all[2][0]) / (this.all[2][0] + this.all[2][1] + this.all[2][2])) + "\n" + 1 + "\t" + .5 + "\t" + this.all[2][1] + "\t" + df.format((this.all[2][1]) / (this.all[2][0] + this.all[2][1] + this.all[2][2])) + "\n" + 1 + "\t" + 1 + "\t" + this.all[2][2] + "\t" + df.format((this.all[2][2]) / (this.all[2][0] + this.all[2][1] + this.all[2][2])) + "\n"); outStream.writeBytes("#Proportion unimputed:\n#minor <- " + this.all[0][3] / this.all[0][4] + "\n#het<- " + this.all[1][3] / this.all[1][4] + "\n#major<- " + this.all[2][3] / this.all[2][4] + "\n"); outStream.writeBytes("#Time to impute and calculate accuracy: " + time + " seconds"); if (this.verboseOutput) System.out.println( "##Taxon\tTotalSitesMasked\tTotalSitesCompared\tTotalPropUnimputed\tNumMinor\tCorrectMinor\tMinorToHet\tMinorToMajor\tUnimpMinor" + "\tNumHets\tHetToMinor\tCorrectHet\tHetToMajor\tUnimpHet\tNumMajor\tMajorToMinor\tMajorToHet\tCorrectMajor\tUnimpMajor\tR2"); if (this.verboseOutput) System.out.println("TotalByImputed\t" + (this.all[0][4] + this.all[1][4] + this.all[2][4]) + "\t" + (this.all[0][4] + this.all[1][4] + this.all[2][4] - this.all[0][3] - this.all[1][3] - this.all[2][3]) + "\t" + ((this.all[0][3] + this.all[1][3] + this.all[2][3]) / (this.all[0][4] + this.all[1][4] + this.all[2][4])) + "\t" + this.all[0][4] + "\t" + this.all[0][0] + "\t" + this.all[0][1] + "\t" + this.all[0][2] + "\t" + this.all[0][3] + "\t" + this.all[1][4] + "\t" + this.all[1][0] + "\t" + this.all[1][1] + "\t" + this.all[1][2] + "\t" + this.all[1][3] + "\t" + this.all[2][4] + "\t" + this.all[2][0] + "\t" + this.all[2][1] + "\t" + this.all[2][2] + "\t" + this.all[2][3] + "\t" + r2); if (this.verboseOutput) System.out.println("Proportion unimputed:\nminor: " + this.all[0][3] / this.all[0][4] + "\nhet: " + this.all[1][3] / this.all[1][4] + "\nmajor: " + this.all[2][3] / this.all[2][4]); if (this.verboseOutput) System.out.println("#Minor=0,Het=1,Major=2;x is masked(known), y is predicted\nx\ty\tN\tprop\n" + 0 + "\t" + 0 + "\t" + this.all[0][0] + "\t" + (this.all[0][0]) / (this.all[0][0] + this.all[0][1] + this.all[0][2]) + "\n" + 0 + "\t" + .5 + "\t" + this.all[0][1] + "\t" + (this.all[0][1]) / (this.all[0][0] + this.all[0][1] + this.all[0][2]) + "\n" + 0 + "\t" + 1 + "\t" + this.all[0][2] + "\t" + (this.all[0][2]) / (this.all[0][0] + this.all[0][1] + this.all[0][2]) + "\n" + .5 + "\t" + 0 + "\t" + this.all[1][0] + "\t" + (this.all[1][0]) / (this.all[1][0] + this.all[1][1] + this.all[1][2]) + "\n" + .5 + "\t" + .5 + "\t" + this.all[1][1] + "\t" + (this.all[1][1]) / (this.all[1][0] + this.all[1][1] + this.all[1][2]) + "\n" + .5 + "\t" + 1 + "\t" + this.all[1][2] + "\t" + (this.all[1][2]) / (this.all[1][0] + this.all[1][1] + this.all[1][2]) + "\n" + 1 + "\t" + 0 + "\t" + this.all[2][0] + "\t" + (this.all[2][0]) / (this.all[2][0] + this.all[2][1] + this.all[2][2]) + "\n" + 1 + "\t" + .5 + "\t" + this.all[2][1] + "\t" + (this.all[2][1]) / (this.all[2][0] + this.all[2][1] + this.all[2][2]) + "\n" + 1 + "\t" + 1 + "\t" + this.all[2][2] + "\t" + (this.all[2][2]) / (this.all[2][0] + this.all[2][1] + this.all[2][2]) + "\n"); outStream.close(); } catch (Exception e) { if (this.verboseOutput) System.out.println(e); } }
From source file:copter.ServerConnection.java
private String postToServer(String postUrl, Map<String, String> parameters) { String serverHost = Config.getInstance().getString("main", "server_host"); URL url;//from w ww. j a va2 s .c o m try { url = new URL("http://" + serverHost + postUrl); HttpURLConnection con = (HttpURLConnection) url.openConnection(); //add reuqest header con.setRequestMethod("POST"); //con.setRequestProperty("User-Agent", USER_AGENT); con.setRequestProperty("Accept-Language", "en-US,en;q=0.5"); // Send post request con.setDoOutput(true); DataOutputStream wr = new DataOutputStream(con.getOutputStream()); String urlParameters = ""; for (Map.Entry<String, String> entry : parameters.entrySet()) { String paramName = entry.getKey(); String paramValue = entry.getValue(); String encodedParamValue = URLEncoder.encode(paramValue, "UTF-8"); urlParameters += paramName + "=" + encodedParamValue + "&"; } if (urlParameters.endsWith("&")) { urlParameters = urlParameters.substring(0, urlParameters.length() - 1); } wr.writeBytes(urlParameters); wr.flush(); wr.close(); int responseCode = con.getResponseCode(); //logger.log("\nSending 'POST' request to URL : " + url); //logger.log("Post parameters : " + urlParameters); //logger.log("Response Code : " + responseCode); BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream())); String inputLine; StringBuilder response = new StringBuilder(); while ((inputLine = in.readLine()) != null) { response.append(inputLine); } in.close(); String serverResponse = response.toString(); return serverResponse; } catch (Exception ex) { logger.log(ex.getMessage()); return null; } }
From source file:com.qcloud.PicCloud.java
/** * Download /*from ww w. j a v a2 s.c om*/ * @param url * @param fileName ? * @return ?0? */ public int download(String url, String fileName) { JSONObject rspData = null; try { String rsp = mClient.get(url, null, null); File file = new File(fileName); DataOutputStream ops = new DataOutputStream(new FileOutputStream(file)); ops.writeBytes(rsp); ops.close(); } catch (Exception e) { return setError(-1, "url exception, e=" + e.toString()); } return setError(0, "success"); }
From source file:edu.ku.brc.specify.tools.StrLocaleFile.java
/** * Save as Ascii./*w w w . j av a 2 s. c o m*/ */ public boolean save() { FileOutputStream fos = null; DataOutputStream dos = null; try { fos = new FileOutputStream(dstPath); dos = new DataOutputStream(fos);//, "UTF-8"); for (StrLocaleEntry entry : items) { String str = ""; if (entry.getKey() == null) { } else if (entry.getKey().equals("#")) { str = entry.getSrcStr(); } else { str = entry.getKey() + "=" + (entry.getDstStr() == null ? "" : entry.getDstStr()); } str += '\n'; dos.writeBytes(str); } dos.flush(); dos.close(); return true; } catch (Exception e) { System.out.println("e: " + e); } return false; }
From source file:net.larry1123.elec.util.logger.EELogger.java
/** * Will Log a StackTrace and Post it on to http://paste.larry1123.net/ * Will return true if it was able to post and false if it was not able to post * Throws with the Level given// www .j av a 2 s . c o m * * @param lvl The Level to be thrown with * @param message Message to be Logged * @param thrown Throwable Error To be logged * * @return {@code true} if paste was made of stackTrace; {@code falase} if it failed for any reason */ public boolean logStackTraceToPasteBin(Level lvl, String message, Throwable thrown) { if (getConfig().isPastingAllowed()) { EELogger eeLogger = FactoryManager.getFactoryManager().getEELoggerFactory().getSubLogger("EEUtil", "PasteBinLog"); try { URL url = new URL("https://paste.larry1123.net/api/xml/create"); HttpURLConnection con = (HttpURLConnection) url.openConnection(); con.setRequestMethod("POST"); con.setRequestProperty("User-Agent", "Mozilla/5.0"); con.setRequestProperty("Accept-Language", "en-US,en;q=0.5"); String urlParameters = "data=" + "[" + lvl.getName() + "] " + message + "\n" + org.apache.commons.lang3.exception.ExceptionUtils.getStackTrace(thrown); urlParameters += "&"; String title = "[" + lvl.getName() + "] " + message; urlParameters += "title=" + (title.length() > 30 ? title.substring(0, 30) : title); urlParameters += "&"; urlParameters += "language=Java"; // Send post request con.setDoOutput(true); DataOutputStream wr = new DataOutputStream(con.getOutputStream()); wr.writeBytes(urlParameters); wr.flush(); wr.close(); if (con.getResponseCode() == 200) { DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder dBuilder = dbFactory.newDocumentBuilder(); Document document = dBuilder.parse(con.getInputStream()); document.getDocumentElement().normalize(); NodeList nodeList = document.getElementsByTagName("id"); Node node = nodeList.item(0); String id = node.getTextContent(); eeLogger.info("Logger " + getName() + ": https://paste.larry1123.net/" + id); return true; } return false; } catch (MalformedURLException e) { eeLogger.error("Failed to send: Malformed", e); return false; } catch (IOException e) { eeLogger.error("Failed to send: IOException", e); return false; } catch (ParserConfigurationException e) { eeLogger.error("Failed to send: ParserConfigurationException", e); return false; } catch (SAXException e) { eeLogger.error("Failed to send: SAXException", e); return false; } } else { return false; } }
From source file:com.tandong.sa.aq.AbstractAjaxCallback.java
private static void writeData(DataOutputStream dos, String name, String filename, InputStream is) throws IOException { dos.writeBytes(twoHyphens + boundary + lineEnd); dos.writeBytes("Content-Disposition: form-data; name=\"" + name + "\";" + " filename=\"" + filename + "\"" + lineEnd);/* ww w . j av a 2 s . c o m*/ dos.writeBytes(lineEnd); AQUtility.copy(is, dos); dos.writeBytes(lineEnd); }
From source file:com.retroteam.studio.retrostudio.EditorLandscape.java
/** * Write the 8bit PCM audio to the wav file format to the public music dir. * http://www-mmsp.ece.mcgill.ca/Documents/AudioFormats/WAVE/WAVE.html * @param proj/*from w w w . j a va 2s. c om*/ * @param filename */ private void exportAsWav(Project proj, String filename) { try { File file = new File(Environment.getExternalStoragePublicDirectory(Environment.DIRECTORY_MUSIC), filename + ".wav"); DataOutputStream os = new DataOutputStream(new FileOutputStream(file)); // get project length int pLength = proj.export().getBytes().length; os.writeBytes("RIFF"); // Chunk ID 'RIFF' os.write(intToByteArray(36 + pLength), 0, 4); //file size os.writeBytes("WAVE"); // Wave ID os.writeBytes("fmt "); // Chunk ID 'fmt ' os.write(intToByteArray(16), 0, 4); // chunk size os.write(intToByteArray(1), 0, 2); // pcm audio os.write(intToByteArray(1), 0, 2); // mono os.write(intToByteArray(8000), 0, 4); // samples/sec os.write(intToByteArray(pLength), 0, 4); // bytes/sec os.write(intToByteArray(1), 0, 2); // 1 byte/sample os.write(intToByteArray(8), 0, 2); // 8 bits/sample os.writeBytes("data"); // Chunk ID 'data' os.write(intToByteArray(pLength), 0, 4); // size of data chunk os.write(proj.export().getBytes()); // write the data os.close(); Toast.makeText(this, "Saved file to: " + file.getPath(), Toast.LENGTH_SHORT).show(); } catch (IOException e) { Toast.makeText(this, "IOException while saving project.", Toast.LENGTH_SHORT).show(); } }
From source file:org.openecomp.sdc.ci.tests.datatypes.http.HttpRequest.java
public RestResponse httpSendPostWithAuth(String url, String body, Map<String, String> headers, String username, String password) throws IOException { String userPassword = username + ":" + password; String encoding = Base64.encodeBase64String(userPassword.getBytes()); RestResponse restResponse = new RestResponse(); URL obj = new URL(url); HttpURLConnection con = (HttpURLConnection) obj.openConnection(); // add request method con.setRequestMethod("POST"); con.setRequestProperty("Authorization", "Basic " + encoding); // add request headers if (headers != null) { for (Entry<String, String> header : headers.entrySet()) { String key = header.getKey(); String value = header.getValue(); con.setRequestProperty(key, value); }/* w w w. j ava2s.co m*/ } // Send post request con.setDoOutput(true); DataOutputStream wr = new DataOutputStream(con.getOutputStream()); wr.writeBytes(body); wr.flush(); wr.close(); // con.connect(); int responseCode = con.getResponseCode(); logger.debug("Send POST http request, url: {}", url); logger.debug("Response Code: {}", responseCode); StringBuffer response = new StringBuffer(); try { BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream())); String inputLine; while ((inputLine = in.readLine()) != null) { response.append(inputLine); } in.close(); } catch (Exception e) { response = null; } logger.debug("Response body: {}", response); // print result restResponse.setErrorCode(responseCode); if (response == null) { restResponse.setResponse(null); } else { restResponse.setResponse(response.toString()); } Map<String, List<String>> headerFields = con.getHeaderFields(); restResponse.setHeaderFields(headerFields); String responseMessage = con.getResponseMessage(); restResponse.setResponseMessage(responseMessage); con.disconnect(); return restResponse; }
From source file:TimestreamsTests.java
/** * Performs HTTP post for a given URL/*from ww w.j a va2 s.c o m*/ * * @param url * is the URL to get * @param params * is a URL encoded string in the form x=y&a=b... * @return a String with the contents of the get */ private Map<String, List<String>> doPost(URL url, String params) { HttpURLConnection connection; try { connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("POST"); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); connection.setRequestProperty("Content-Length", "" + Integer.toString(params.getBytes().length)); connection.setDoInput(true); connection.setDoOutput(true); DataOutputStream wr = new DataOutputStream(connection.getOutputStream()); wr.writeBytes(params); wr.flush(); wr.close(); Map<String, List<String>> responseHeaderFields = connection.getHeaderFields(); System.out.println(responseHeaderFields); if (responseHeaderFields.get(null).get(0).equals("HTTP/1.1 200 OK")) { InputStream is = connection.getInputStream(); BufferedReader rd = new BufferedReader(new InputStreamReader(is)); String line; StringBuffer response = new StringBuffer(); while ((line = rd.readLine()) != null) { response.append(line); response.append('\r'); } rd.close(); System.out.println(response); } return responseHeaderFields; } catch (IOException e1) { fail("Post " + url + " failed: " + e1.getLocalizedMessage()); } return null; }