List of usage examples for java.io DataInputStream readLine
@Deprecated public final String readLine() throws IOException
readLine method of DataInput. From source file:org.apache.hadoop.hive.sql.QTestUtil.java
public void addFile(File qf) throws Exception { FileInputStream fis = new FileInputStream(qf); BufferedInputStream bis = new BufferedInputStream(fis); DataInputStream dis = new DataInputStream(bis); StringBuilder qsb = new StringBuilder(); // Look for a hint to not run a test on some Hadoop versions Pattern pattern = Pattern.compile("-- EXCLUDE_HADOOP_MAJOR_VERSIONS(.*)"); // Read the entire query boolean excludeQuery = false; String hadoopVer = ShimLoader.getMajorVersion(); while (dis.available() != 0) { String line = dis.readLine(); // While we are reading the lines, detect whether this query wants to be // excluded from running because the Hadoop version is incorrect Matcher matcher = pattern.matcher(line); if (matcher.find()) { String group = matcher.group(); int start = group.indexOf('('); int end = group.indexOf(')'); assert end > start; // versions might be something like '0.17, 0.19' String versions = group.substring(start + 1, end); Set<String> excludedVersionSet = new HashSet<String>(); for (String s : versions.split("\\,")) { s = s.trim();//from w w w .j a va 2 s . co m excludedVersionSet.add(s); } if (excludedVersionSet.contains(hadoopVer)) { excludeQuery = true; } } qsb.append(line + "\n"); } qMap.put(qf.getName(), qsb.toString()); if (excludeQuery) { System.out.println("Due to the Hadoop Version (" + hadoopVer + "), " + "adding query " + qf.getName() + " to the set of tests to skip"); qSkipSet.add(qf.getName()); } dis.close(); }
From source file:org.apache.hadoop.hive.ql.QTestUtil2.java
public void addFile(File qf) throws Exception { FileInputStream fis = new FileInputStream(qf); BufferedInputStream bis = new BufferedInputStream(fis); DataInputStream dis = new DataInputStream(bis); StringBuilder qsb = new StringBuilder(); // Look for a hint to not run a test on some Hadoop versions Pattern pattern = Pattern.compile("-- EXCLUDE_HADOOP_MAJOR_VERSIONS(.*)"); // Read the entire query boolean excludeQuery = false; String hadoopVer = ShimLoader.getMajorVersion(); while (dis.available() != 0) { String line = dis.readLine(); // While we are reading the lines, detect whether this query wants // to be/*from w ww . j av a2s . c o m*/ // excluded from running because the Hadoop version is incorrect Matcher matcher = pattern.matcher(line); if (matcher.find()) { String group = matcher.group(); int start = group.indexOf('('); int end = group.indexOf(')'); assert end > start; // versions might be something like '0.17, 0.19' String versions = group.substring(start + 1, end); Set<String> excludedVersionSet = new HashSet<String>(); for (String s : versions.split("\\,")) { s = s.trim(); excludedVersionSet.add(s); } if (excludedVersionSet.contains(hadoopVer)) { excludeQuery = true; } } qsb.append(line + "\n"); } qMap.put(qf.getName(), qsb.toString()); if (excludeQuery) { System.out.println("Due to the Hadoop Version (" + hadoopVer + "), " + "adding query " + qf.getName() + " to the set of tests to skip"); qSkipSet.add(qf.getName()); } dis.close(); }
From source file:com.polyvi.xface.extension.advancedfiletransfer.FileUploader.java
/** * ??????id?/*from ww w . j a va 2 s .co m*/ * * @return true:??false:? */ private boolean handleShake() { HttpURLConnection httpConnection = null; DataInputStream dataInputStream = null; String souceid = mFileTransferRecorder.getSourceId(mFilePath, "" + mUploadFileSize); try { httpConnection = getHttpConnection(mServer); // ? httpConnection.setRequestProperty("Charset", "UTF-8"); httpConnection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); httpConnection.setRequestProperty("ACTIONNAME", ACTION_NAME_HAND); httpConnection.setRequestProperty("RESOURCEID", souceid); httpConnection.setRequestProperty("FILENAME", getUploadFileName()); httpConnection.setRequestProperty("FILESIZE", "" + mUploadFileSize); if (HttpURLConnection.HTTP_OK == httpConnection.getResponseCode()) { // ????? RESOURCEID=?;BFFORE=? dataInputStream = new DataInputStream(httpConnection.getInputStream()); // ???response? handleResponse(dataInputStream.readLine()); // souceid? setSourceId(souceid); } else { onError(INVALID_URL_ERR); } } catch (Exception e) { onError(INVALID_URL_ERR); e.printStackTrace(); return false; } finally { if (null != httpConnection) { httpConnection.disconnect(); httpConnection = null; } // ?? try { if (null != dataInputStream) { dataInputStream.close(); } } catch (IOException e) { e.printStackTrace(); } } return true; }
From source file:android.core.SSLSocketTest.java
/** * Does a number of HTTPS requests on some host and consumes the response. * We don't use the HttpsUrlConnection class, but do this on our own * with the SSLSocket class. This gives us a chance to test the basic * behavior of SSL./*from w ww .j a va 2 s . co m*/ * * @param host The host name the request is being sent to. * @param port The port the request is being sent to. * @param path The path being requested (e.g. "/index.html"). * @param outerLoop The number of times we reconnect and do the request. * @param innerLoop The number of times we do the request for each * connection (using HTTP keep-alive). * @param delay The delay after each request (in seconds). * @throws IOException When a problem occurs. */ private void fetch(SSLSocketFactory socketFactory, String host, int port, boolean secure, String path, int outerLoop, int innerLoop, int delay, int timeout) throws IOException { InetSocketAddress address = new InetSocketAddress(host, port); for (int i = 0; i < outerLoop; i++) { // Connect to the remote host Socket socket = secure ? socketFactory.createSocket() : new Socket(); if (timeout >= 0) { socket.setKeepAlive(true); socket.setSoTimeout(timeout * 1000); } socket.connect(address); // Get the streams OutputStream output = socket.getOutputStream(); PrintWriter writer = new PrintWriter(output); try { DataInputStream input = new DataInputStream(socket.getInputStream()); try { for (int j = 0; j < innerLoop; j++) { android.util.Log.d("SSLSocketTest", "GET https://" + host + path + " HTTP/1.1"); // Send a request writer.println("GET https://" + host + path + " HTTP/1.1\r"); writer.println("Host: " + host + "\r"); writer.println("Connection: " + (j == innerLoop - 1 ? "Close" : "Keep-Alive") + "\r"); writer.println("\r"); writer.flush(); int length = -1; boolean chunked = false; String line = input.readLine(); if (line == null) { throw new IOException("No response from server"); // android.util.Log.d("SSLSocketTest", "No response from server"); } // Consume the headers, check content length and encoding type while (line != null && line.length() != 0) { // System.out.println(line); int dot = line.indexOf(':'); if (dot != -1) { String key = line.substring(0, dot).trim(); String value = line.substring(dot + 1).trim(); if ("Content-Length".equalsIgnoreCase(key)) { length = Integer.valueOf(value); } else if ("Transfer-Encoding".equalsIgnoreCase(key)) { chunked = "Chunked".equalsIgnoreCase(value); } } line = input.readLine(); } assertTrue("Need either content length or chunked encoding", length != -1 || chunked); // Consume the content itself if (chunked) { length = Integer.parseInt(input.readLine(), 16); while (length != 0) { byte[] buffer = new byte[length]; input.readFully(buffer); input.readLine(); length = Integer.parseInt(input.readLine(), 16); } input.readLine(); } else { byte[] buffer = new byte[length]; input.readFully(buffer); } // Sleep for the given number of seconds try { Thread.sleep(delay * 1000); } catch (InterruptedException ex) { // Shut up! } } } finally { input.close(); } } finally { writer.close(); } // Close the connection socket.close(); } }
From source file:com.curso.listadapter.net.RESTClient.java
/** * upload multipart/*from w w w. j a va 2 s . c om*/ * this method receive the file to be uploaded * */ @SuppressWarnings("deprecation") public String uploadMultiPart(Map<String, File> files) throws Exception { disableSSLCertificateChecking(); Thread.currentThread().setPriority(Thread.MAX_PRIORITY); HttpURLConnection conn = null; DataOutputStream dos = null; DataInputStream inStream = null; try { URL endpoint = new URL(url); conn = (HttpURLConnection) endpoint.openConnection(); conn.setDoInput(true); conn.setDoOutput(true); conn.setUseCaches(false); conn.setRequestMethod("POST"); conn.setRequestProperty("Connection", "Keep-Alive"); conn.setRequestProperty("Content-Type", "multipart/form-data;boundary=" + boundary); dos = new DataOutputStream(conn.getOutputStream()); String post = ""; //WRITE ALL THE PARAMS for (NameValuePair p : params) post += writeMultipartParam(p); dos.flush(); //END WRITE ALL THE PARAMS //BEGIN THE UPLOAD ArrayList<FileInputStream> inputStreams = new ArrayList<FileInputStream>(); for (Entry<String, File> entry : files.entrySet()) { post += lineEnd; post += twoHyphens + boundary + lineEnd; String NameParamImage = entry.getKey(); File file = entry.getValue(); int bytesRead, bytesAvailable, bufferSize; byte[] buffer; int maxBufferSize = 1 * 1024 * 1024; FileInputStream fileInputStream = new FileInputStream(file); post += "Content-Disposition: attachment; name=\"" + NameParamImage + "\"; filename=\"" + file.getName() + "\"" + lineEnd; String mimetype = getMimeType(file.getName()); post += "Content-Type: " + mimetype + lineEnd; post += "Content-Transfer-Encoding: binary" + lineEnd + lineEnd; dos.write(post.toString().getBytes("UTF-8")); bytesAvailable = fileInputStream.available(); bufferSize = Math.min(bytesAvailable, maxBufferSize); buffer = new byte[bufferSize]; bytesRead = fileInputStream.read(buffer, 0, bufferSize); while (bytesRead > 0) { dos.write(buffer, 0, bufferSize); bytesAvailable = fileInputStream.available(); bufferSize = Math.min(bytesAvailable, maxBufferSize); bytesRead = fileInputStream.read(buffer, 0, bufferSize); inputStreams.add(fileInputStream); } Log.d("Test", post); dos.flush(); post = ""; } //END THE UPLOAD dos.writeBytes(lineEnd); dos.writeBytes(twoHyphens + boundary + twoHyphens); // for(FileInputStream inputStream: inputStreams){ // inputStream.close(); // } dos.flush(); dos.close(); conn.connect(); Log.d("upload", "finish flush:" + conn.getResponseCode()); } catch (MalformedURLException ex) { Log.e("Debug", "error: " + ex.getMessage(), ex); } catch (IOException ioe) { Log.e("Debug", "error: " + ioe.getMessage(), ioe); } try { String response_data = ""; inStream = new DataInputStream(conn.getInputStream()); String str; while ((str = inStream.readLine()) != null) { response_data += str; } inStream.close(); return response_data; } catch (IOException ioex) { Log.e("Debug", "error: " + ioex.getMessage(), ioex); } return null; }
From source file:MiGA.StatsSelection.java
public void getImPerfectCompoundSSRs(String[] organisms, int length, boolean flag, int gap) throws SQLException, ClassNotFoundException, FileNotFoundException, IOException { String statsfile = ""; for (int i = 0; i < organisms.length; i++) { boolean found = false; String buffer = new String(); int seekstart = 0; int seekend = 0; List<String> ssrs = new ArrayList<String>(); // 18/11/2013 added starting here String filetype = ""; String filepro = ""; if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else//from w w w.java2 s .c om indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //List<String> files = getFiles(organisms[i], minlen, flag); // 18/11/2013 added ending here PrintWriter out; PrintWriter stats; PrintWriter html; DataOutputStream lt = null; if (filetype.contains("organism")) { File f = new File("organisms/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter( new FileWriter("organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); lt = new DataOutputStream(new BufferedOutputStream(new FileOutputStream("organisms/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compim"))); html = new PrintWriter(new FileWriter("organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("organisms/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } String toopen = "organisms/" + organisms[i] + "/results/allCompImPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; statsfile = toopen; out = new PrintWriter(toopen); out.println("Results for organism: " + organisms[i] + "\t Search Parameters --> Maximum Inter-repeat Region for Imperfect Compound SSRs(bp) : " + gap + " - minimum SSR length(bp): " + length); } else { File f = new File("local/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); lt = new DataOutputStream(new BufferedOutputStream(new FileOutputStream("local/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compim"))); html = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("local/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } Calendar calendar = Calendar.getInstance(); Date now = calendar.getTime(); String toopen = "local/" + organisms[i] + "/results/allCompImPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; statsfile = toopen; out = new PrintWriter(toopen); out.println("Results for project: " + organisms[i] + "\t Search Parameters --> Maximum Inter-repeat Region for Imperfect Compound SSRs(bp) : " + gap + " - minimum SSR length(bp): " + length); } int countpc = 0; int bpcount = 0, Aperc = 0, Tperc = 0, Gperc = 0, Cperc = 0; while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream(new BufferedInputStream(new FileInputStream(files))); //PrintWriter out = new PrintWriter(files + "-minlentgh_" + length + "_ImPerfect.stats"); boolean eof = false; while (!eof) { try { SSR = new ArrayList<String>(); repeats = new ArrayList<Integer>(); EndOfSsr = new ArrayList<Integer>(); start = new ArrayList<Integer>(); int len = in.readInt(); int line = in.readInt(); for (int k = 0; k < len; k++) { //THIS String temp = in.readUTF(); if (!temp.contains("N")) { SSR.add(temp); EndOfSsr.add(in.readInt()); repeats.add(in.readInt()); start.add(EndOfSsr.get(k) - (SSR.get(k).length() * repeats.get(k))); } else { int junk = in.readInt(); junk = in.readInt(); } } List<String> SSRlen = new ArrayList<String>(); List<Integer> Endlen = new ArrayList<Integer>(); List<Integer> repslen = new ArrayList<Integer>(); List<Integer> startlen = new ArrayList<Integer>(); for (int k = 0; k < SSR.size(); k++) { if (SSR.get(k).length() * repeats.get(k) >= length) { SSRlen.add(SSR.get(k)); Endlen.add(EndOfSsr.get(k)); repslen.add(repeats.get(k)); startlen.add(start.get(k)); } } List<Integer> sortedstart = new ArrayList<Integer>(); List<Integer> sortedend = new ArrayList<Integer>(); for (int t = 0; t < startlen.size(); t++) { sortedstart.add(startlen.get(t)); sortedend.add(Endlen.get(t)); } Collections.sort(sortedstart); Collections.sort(sortedend); //List<String> tofile = new ArrayList<String>(); for (int k = 0; k < sortedstart.size() - 2; k++) { found = false; ssrs.clear(); ssrs = new ArrayList<String>(); if (sortedstart.get(k + 1) - sortedend.get(k) <= gap && sortedstart.get(k + 1) - sortedend.get(k) >= 0) { seekstart = sortedstart.get(k); while (k < sortedstart.size() - 1 && sortedstart.get(k + 1) - sortedend.get(k) <= gap && sortedstart.get(k + 1) - sortedend.get(k) >= 0) { for (int c = 0; c < startlen.size(); c++) { if (sortedstart.get(k) == startlen.get(c)) { ssrs.add(SSRlen.get(c)); } if (sortedstart.get(k + 1) == startlen.get(c)) { ssrs.add(SSRlen.get(c)); seekend = Endlen.get(c); found = true; } } k++; } k--; } boolean check = checkallsame(ssrs); boolean check2 = checkalldiff(ssrs); if (found && !check && !check2) { BufferedReader stdin = null; if (flag) { String[] temp = files.split("/"); boolean type = CheckForKaryotype(organisms[i]); String newdir = ""; if (type) { newdir = temp[0] + "/" + temp[1] + "/chrom-" + temp[3].substring(0, temp[3].lastIndexOf('.')) + "-slices.txt"; } else { newdir = temp[0] + "/" + temp[1] + "/slice-" + temp[3].substring(0, temp[3].lastIndexOf('.')) + ".txt"; } stdin = new BufferedReader(new FileReader(newdir)); } else { String[] temp = files.split("data/"); String newdir = temp[0] + "/" + temp[1].substring(0, temp[1].lastIndexOf('.')) + ".txt"; stdin = new BufferedReader(new FileReader(newdir)); } buffer = ""; for (int c = 0; c < line; c++) { buffer = stdin.readLine(); } //System.out.println(buffer.length() + "\t" + seekstart + "\t" + seekend); int real_end = (line - 1) * 20000 + seekend; int real_start = (line - 1) * 20000 + seekstart; //tofile.add("SSR: "+buffer.substring(seekstart, seekend) + "start-end: "+ real_start + "-" +real_end ); countpc++; if (seekstart < 0) seekstart++; String tmp = buffer.substring(seekstart, seekend); bpcount += tmp.length(); if (tmp.contains("A")) { Aperc += StringUtils.countMatches(tmp, "A"); } if (tmp.contains("T")) { Tperc += StringUtils.countMatches(tmp, "T"); } if (tmp.contains("G")) { Gperc += StringUtils.countMatches(tmp, "G"); } if (tmp.contains("C")) { Cperc += StringUtils.countMatches(tmp, "C"); } out.println("SSR: " + tmp + " start-end: " + real_start + "-" + real_end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); stdin.close(); } } } catch (EOFException e) { eof = true; } } in.close(); } out.close(); Runtime.getRuntime().exec("notepad " + statsfile); try { Class.forName("com.mysql.jdbc.Driver"); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Connection con = null; try { con = DriverManager.getConnection("jdbc:mysql://localhost:3306", "biouser", "thesis2012"); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Statement st = null; try { st = con.createStatement(); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } st.executeUpdate("use lobid"); int seqcount = 0; if (filetype.contains("organisms")) { ResultSet rs = st.executeQuery( "SELECT end FROM slices INNER JOIN organism WHERE slices.org_id=organism.org_id AND organism.name='" + organisms[i] + "'"); while (rs.next()) { seqcount += Long.parseLong(rs.getString(1)); } } else if (filetype.contains("local")) { BufferedReader in = new BufferedReader(new FileReader("local/" + organisms[i] + "/index.txt")); int count = countlines("local/" + organisms[i] + "/index.txt"); for (int c = 0; c < count; c++) { String temp = in.readLine(); BufferedReader tmp = new BufferedReader( new FileReader("local/" + organisms[i] + "/" + temp + ".txt")); boolean eof = false; while (!eof) { String s = tmp.readLine(); if (s != null) { seqcount += s.length(); } else { eof = true; } } tmp.close(); } } DecimalFormat round = new DecimalFormat("#.###"); html.println("<html><h1>******* Compound Imperfect SSRs *******</h1>"); html.println("<h4>Results for project: " + organisms[i] + "</h4><h4>Search Parameters --> Maximum Inter-repeat Region for Imperfect Compound SSRs (bp) : " + gap + "</h4><h4>minimum SSR length (bp): " + length + "</h4>"); html.println( "<table border=\"1\"><tr><td> </td><td><b>count</b></td><td><b>bp</b></td><td><b>A%</b></td><td><b>T%</b></td><td><b>C%</b></td><td><b>G%</b></td><td><b>Relative Frequency</b></td><td><b>Abundance</b></td><td><b>Relative Abundance</b></td></tr>"); html.println("<tr><td><b>Compound Imperf.</b></td><td>" + countpc + "</td><td>" + bpcount + "</td><td>" + round.format((float) Aperc * 100 / bpcount) + "</td><td>" + round.format((float) Tperc * 100 / bpcount) + "</td><td>" + round.format((float) Cperc * 100 / bpcount) + "</td><td>" + round.format((float) Gperc * 100 / bpcount) + "</td><td>" + round.format((float) countpc / countpc) + "</td><td>" + round.format((float) bpcount / seqcount) + "</td><td>" + round.format((float) bpcount / bpcount) + "</td></tr>"); html.println("<tr><td><b>TOTAL</b></td><td>" + countpc + "</td><td>" + bpcount + "</td><td>" + round.format((float) Aperc * 100 / bpcount) + "</td><td>" + round.format((float) Tperc * 100 / bpcount) + "</td><td>" + round.format((float) Cperc * 100 / bpcount) + "</td><td>" + round.format((float) Gperc * 100 / bpcount) + "</td><td>" + round.format((float) countpc / countpc) + "</td><td>" + round.format((float) bpcount / seqcount) + "</td><td>" + round.format((float) bpcount / bpcount) + "</td></tr></table></html>"); html.close(); stats.println("******* Compound Imperfect SSRs *******"); stats.println("Results for project: " + organisms[i] + "\nSearch Parameters --> Maximum Inter-repeat Region for Imperfect Compound SSRs(bp) : " + gap + "\nminimum SSR length(bp): " + length); stats.println( " ____________________________________________________________________________________________________________________ "); stats.println( "| | | | | | | | Relative | | Relative |"); stats.println( "| | count | bp | A% | T% | C% | G% | Frequency | Abundance | Abundance |"); stats.println( "|===============|=======|============|=======|=======|=======|=======|===============|===============|===============|"); stats.printf( "|Compound Imper.|" + cell(Integer.toString(countpc), 7) + "|" + cell(Integer.toString(bpcount), 12) + "|%s|%s|%s|%s|" + cell((float) countpc / countpc, 15) + "|" + cell((float) bpcount / seqcount, 15) + "|" + cell((float) bpcount / bpcount, 15) + "|\n", cell((float) Aperc * 100 / bpcount, 7), cell((float) Tperc * 100 / bpcount, 7), cell((float) Cperc * 100 / bpcount, 7), cell((float) Gperc * 100 / bpcount, 7)); stats.println( "|---------------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); lt.writeLong(seqcount); lt.writeInt(countpc); lt.writeInt(bpcount); lt.writeInt(Aperc); lt.writeInt(Tperc); lt.writeInt(Gperc); lt.writeInt(Cperc); stats.println("|TOTAL |" + cell(Integer.toString(countpc), 7) + "|" + cell(Long.toString(bpcount), 12) + "|" + cell((float) Aperc * 100 / bpcount, 7) + "|" + cell((float) Tperc * 100 / bpcount, 7) + "|" + cell((float) Cperc * 100 / bpcount, 7) + "|" + cell((float) Gperc * 100 / bpcount, 7) + "|" + cell((float) countpc / countpc, 15) + "|" + cell((float) bpcount / seqcount, 15) + "|" + cell((float) bpcount / bpcount, 15) + "|"); stats.println( "|_______________|_______|____________|_______|_______|_______|_______|_______________|_______________|_______________|"); stats.println("Genome length (bp): " + seqcount); stats.println("Relative Frequency: Count of each motif type / total SSR count"); stats.println("Abundance: bp of each motif type / total sequence bp"); stats.println("Relative Abundance: bp of each motif type / total microsatellites bp"); stats.println(); stats.println(); stats.close(); lt.close(); } }
From source file:MiGA.StatsSelection.java
public void getCompoundPerfectSSRs(String[] organisms, int length, boolean flag, int gap) throws SQLException, ClassNotFoundException, FileNotFoundException, IOException { String statsfile = ""; for (int i = 0; i < organisms.length; i++) { boolean found = false; String buffer = new String(); int seekstart = 0; int seekend = 0; List<String> ssrs = new ArrayList<String>(); // 18/11/2013 added starting here String filetype = ""; String filepro = ""; if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else/*from w w w . j av a2 s. co m*/ indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //List<String> files = getFiles(organisms[i], minlen, flag); // 18/11/2013 added ending here PrintWriter stats = null; PrintWriter html = null; PrintWriter out; DataOutputStream lt = null; if (filetype.contains("organism")) { File f = new File("organisms/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter( new FileWriter("organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); lt = new DataOutputStream(new BufferedOutputStream(new FileOutputStream("organisms/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compp"))); html = new PrintWriter(new FileWriter("organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("organisms/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } String toopen = "organisms/" + organisms[i] + "/results/allCompPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; statsfile = toopen; out = new PrintWriter(toopen); out.println("Results for organism: " + organisms[i] + "\t Search Parameters --> Maximum Inter-repeat Region for Perfect Compound SSRs (bp) : " + gap + " - minimum SSR length (bp): " + length); } else { File f = new File("local/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); lt = new DataOutputStream(new BufferedOutputStream(new FileOutputStream("local/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compp"))); html = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("local/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } String toopen = "local/" + organisms[i] + "/results/allCompPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; statsfile = toopen; out = new PrintWriter(toopen); out.println("Results for project: " + organisms[i] + "\t Search Parameters --> Maximum Inter-repeat Region for Perfect Compound SSRs (bp) : " + gap + " - minimum SSR length (bp): " + length); } int countpc = 0; int bpcount = 0, Aperc = 0, Tperc = 0, Gperc = 0, Cperc = 0; while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream(new BufferedInputStream(new FileInputStream(files))); boolean eof = false; while (!eof) { try { SSR = new ArrayList<String>(); repeats = new ArrayList<Integer>(); EndOfSsr = new ArrayList<Integer>(); start = new ArrayList<Integer>(); int len = in.readInt(); int line = in.readInt(); for (int k = 0; k < len; k++) { String temp = in.readUTF(); if (!temp.contains("N")) { SSR.add(temp); EndOfSsr.add(in.readInt()); repeats.add(in.readInt()); int st = EndOfSsr.get(k) - (SSR.get(k).length() * repeats.get(k)); if (st >= 0) start.add(st); else start.add(0); } else { int junk = in.readInt(); junk = in.readInt(); } /* int real_end = end+(line-1)*20000; int start = real_end - (ssr.length()*reps); //SSR.add(ssr); repeats.add(in.readInt()); EndOfSsr.add(real_end); this.start.add(start); * */ } List<String> SSRlen = new ArrayList<String>(); List<Integer> Endlen = new ArrayList<Integer>(); List<Integer> repslen = new ArrayList<Integer>(); List<Integer> startlen = new ArrayList<Integer>(); for (int k = 0; k < SSR.size(); k++) { if (SSR.get(k).length() * repeats.get(k) >= length) { SSRlen.add(SSR.get(k)); Endlen.add(EndOfSsr.get(k)); repslen.add(repeats.get(k)); startlen.add(start.get(k)); } } List<Integer> sortedstart = new ArrayList<Integer>(); List<Integer> sortedend = new ArrayList<Integer>(); for (int t = 0; t < startlen.size(); t++) { sortedstart.add(startlen.get(t)); sortedend.add(Endlen.get(t)); } Collections.sort(sortedstart); Collections.sort(sortedend); for (int k = 0; k < sortedstart.size() - 2; k++) { found = false; ssrs = new ArrayList<String>(); if (sortedstart.get(k + 1) - sortedend.get(k) <= gap && sortedstart.get(k + 1) - sortedend.get(k) >= 0) { seekstart = sortedstart.get(k); while (k < sortedstart.size() - 1 && sortedstart.get(k + 1) - sortedend.get(k) <= gap && sortedstart.get(k + 1) - sortedend.get(k) >= 0) { for (int c = 0; c < startlen.size(); c++) { if (sortedstart.get(k) == startlen.get(c)) { ssrs.add(SSRlen.get(c)); } if (sortedstart.get(k + 1) == startlen.get(c)) { ssrs.add(SSRlen.get(c)); seekend = Endlen.get(c); found = true; } } k++; } k--; } boolean check = checkalldiff(ssrs); if (found && check) { BufferedReader stdin = null; String newdir = ""; if (flag) { String[] temp = files.split("/"); boolean type = CheckForKaryotype(organisms[i]); newdir = ""; if (type) { newdir = temp[0] + "/" + temp[1] + "/chrom-" + temp[3].substring(0, temp[3].lastIndexOf('.')) + "-slices.txt"; } else { newdir = temp[0] + "/" + temp[1] + "/slice-" + temp[3].substring(0, temp[3].lastIndexOf('.')) + ".txt"; } stdin = new BufferedReader(new FileReader(newdir)); } else { String[] temp = files.split("data/"); newdir = temp[0] + "/" + temp[1].substring(0, temp[1].lastIndexOf('.')) + ".txt"; stdin = new BufferedReader(new FileReader(newdir)); } buffer = ""; String prebuf = ""; for (int c = 0; c < line; c++) { buffer = stdin.readLine(); } stdin.close(); //System.out.println(buffer.length() + "\t" + seekstart + "\t" + seekend); int real_end = (line - 1) * 20000 + seekend; int real_start = (line - 1) * 20000 + seekstart; //tofile.add("SSR: "+buffer.substring(seekstart, seekend) + "start-end: "+ real_start + "-" +real_end ); countpc++; String tmp = ""; if (seekstart < 0) { stdin = new BufferedReader(new FileReader(newdir)); for (int c = 0; c < line - 1; c++) { prebuf = stdin.readLine(); } stdin.close(); tmp += prebuf.substring(prebuf.length() + seekstart); tmp += buffer.substring(0, seekend); } else tmp = buffer.substring(seekstart, seekend); bpcount += tmp.length(); if (tmp.contains("A")) { Aperc += StringUtils.countMatches(tmp, "A"); } if (tmp.contains("T")) { Tperc += StringUtils.countMatches(tmp, "T"); } if (tmp.contains("G")) { Gperc += StringUtils.countMatches(tmp, "G"); } if (tmp.contains("C")) { Cperc += StringUtils.countMatches(tmp, "C"); } out.println("SSR: " + tmp + " start-end: " + real_start + "-" + real_end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); } } } catch (EOFException e) { eof = true; } } in.close(); } out.close(); Runtime.getRuntime().exec("notepad " + statsfile); try { Class.forName("com.mysql.jdbc.Driver"); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Connection con = null; try { con = DriverManager.getConnection("jdbc:mysql://localhost:3306", "biouser", "thesis2012"); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Statement st = null; try { st = con.createStatement(); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } st.executeUpdate("use lobid"); int seqcount = 0; if (filetype.contains("organisms")) { ResultSet rs = st.executeQuery( "SELECT end FROM slices INNER JOIN organism WHERE slices.org_id=organism.org_id AND organism.name='" + organisms[i] + "'"); while (rs.next()) { seqcount += Long.parseLong(rs.getString(1)); } } else if (filetype.contains("local")) { BufferedReader in = new BufferedReader(new FileReader("local/" + organisms[i] + "/index.txt")); int count = countlines("local/" + organisms[i] + "/index.txt"); for (int c = 0; c < count; c++) { String temp = in.readLine(); BufferedReader tmp = new BufferedReader( new FileReader("local/" + organisms[i] + "/" + temp + ".txt")); boolean eof = false; while (!eof) { String s = tmp.readLine(); if (s != null) { seqcount += s.length(); } else { eof = true; } } tmp.close(); } } DecimalFormat round = new DecimalFormat("#.###"); html.println("<html><h1>******* Compound Perfect SSRs *******</h1>"); html.println("<h4>Results for project: " + organisms[i] + "</h4><h4>Search Parameters --> Maximum Inter-repeat Region for Perfect Compound SSRs (bp) : " + gap + "</h4><h4>minimum SSR length (bp): " + length + "</h4>"); html.println( "<table border=\"1\"><tr><td> </td><td><b>count</b></td><td><b>bp</b></td><td><b>A%</b></td><td><b>T%</b></td><td><b>C%</b></td><td><b>G%</b></td><td><b>Relative Frequency</b></td><td><b>Abundance</b></td><td><b>Relative Abundance</b></td></tr>"); html.println("<tr><td><b>Compound Perf.</b></td><td>" + countpc + "</td><td>" + bpcount + "</td><td>" + round.format((float) Aperc * 100 / bpcount) + "</td><td>" + round.format((float) Tperc * 100 / bpcount) + "</td><td>" + round.format((float) Cperc * 100 / bpcount) + "</td><td>" + round.format((float) Gperc * 100 / bpcount) + "</td><td>" + round.format((float) countpc / countpc) + "</td><td>" + round.format((float) bpcount / seqcount) + "</td><td>" + round.format((float) bpcount / bpcount) + "</td></tr>"); html.println("<tr><td><b>TOTAL</b></td><td>" + countpc + "</td><td>" + bpcount + "</td><td>" + round.format((float) Aperc * 100 / bpcount) + "</td><td>" + round.format((float) Tperc * 100 / bpcount) + "</td><td>" + round.format((float) Cperc * 100 / bpcount) + "</td><td>" + round.format((float) Gperc * 100 / bpcount) + "</td><td>" + round.format((float) countpc / countpc) + "</td><td>" + round.format((float) bpcount / seqcount) + "</td><td>" + round.format((float) bpcount / bpcount) + "</td></tr></table></html>"); html.close(); stats.println("******* Compound Perfect SSRs *******"); stats.println("Results for project: " + organisms[i] + "\nSearch Parameters --> Maximum Inter-repeat Region for Perfect Compound SSRs (bp) : " + gap + "\nminimum SSR length (bp): " + length); stats.println( " ___________________________________________________________________________________________________________________ "); stats.println( "| | | | | | | | Relative | | Relative |"); stats.println( "| | count | bp | A% | T% | C% | G% | Frequency | Abundance | Abundance |"); stats.println( "|==============|=======|============|=======|=======|=======|=======|===============|===============|===============|"); stats.printf( "|Compound Perf.|" + cell(Integer.toString(countpc), 7) + "|" + cell(Integer.toString(bpcount), 12) + "|%s|%s|%s|%s|" + cell((float) countpc / countpc, 15) + "|" + cell((float) bpcount / seqcount, 15) + "|" + cell((float) bpcount / bpcount, 15) + "|\n", cell((float) Aperc * 100 / bpcount, 7), cell((float) Tperc * 100 / bpcount, 7), cell((float) Cperc * 100 / bpcount, 7), cell((float) Gperc * 100 / bpcount, 7)); stats.println( "|--------------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); lt.writeLong(seqcount); lt.writeInt(countpc); lt.writeInt(bpcount); lt.writeInt(Aperc); lt.writeInt(Tperc); lt.writeInt(Gperc); lt.writeInt(Cperc); stats.println("|TOTAL |" + cell(Integer.toString(countpc), 7) + "|" + cell(Long.toString(bpcount), 12) + "|" + cell((float) Aperc * 100 / bpcount, 7) + "|" + cell((float) Tperc * 100 / bpcount, 7) + "|" + cell((float) Cperc * 100 / bpcount, 7) + "|" + cell((float) Gperc * 100 / bpcount, 7) + "|" + cell((float) countpc / countpc, 15) + "|" + cell((float) bpcount / seqcount, 15) + "|" + cell((float) bpcount / bpcount, 15) + "|"); stats.println( "|______________|_______|____________|_______|_______|_______|_______|_______________|_______________|_______________|"); stats.println("Genome length (bp): " + seqcount); stats.println("Relative Frequency: Count of each motif type / total SSR count"); stats.println("Abundance: bp of each motif type / total sequence bp"); stats.println("Relative Abundance: bp of each motif type / total microsatellites bp"); stats.println(); stats.println(); stats.close(); lt.close(); } }