Example #1
0
  protected final void printCallInfo(
      final VariantContext vc,
      final double[] log10AlleleFrequencyPriors,
      final long runtimeNano,
      final AFCalcResult result) {
    printCallElement(vc, "type", "ignore", vc.getType());

    int allelei = 0;
    for (final Allele a : vc.getAlleles())
      printCallElement(vc, "allele", allelei++, a.getDisplayString());

    for (final Genotype g : vc.getGenotypes())
      printCallElement(vc, "PL", g.getSampleName(), g.getLikelihoodsString());

    for (int priorI = 0; priorI < log10AlleleFrequencyPriors.length; priorI++)
      printCallElement(vc, "priorI", priorI, log10AlleleFrequencyPriors[priorI]);

    printCallElement(vc, "runtime.nano", "ignore", runtimeNano);
    printCallElement(vc, "log10PosteriorOfAFEq0", "ignore", result.getLog10PosteriorOfAFEq0());
    printCallElement(vc, "log10PosteriorOfAFGt0", "ignore", result.getLog10PosteriorOfAFGT0());

    for (final Allele allele : result.getAllelesUsedInGenotyping()) {
      if (allele.isNonReference()) {
        printCallElement(vc, "MLE", allele, result.getAlleleCountAtMLE(allele));
        printCallElement(
            vc, "pNonRefByAllele", allele, result.getLog10PosteriorOfAFGt0ForAllele(allele));
      }
    }

    callReport.flush();
  }
Example #2
0
 /**
  * automatically generate non-existing help html files for existing commands in the CommandLoader
  *
  * @param cl the CommandLoader where you look for the existing commands
  */
 public void createHelpText(CommandLoader cl) {
   File dir = new File((getClass().getResource("..").getPath()));
   dir = new File(dir, language);
   if (!dir.exists() && !dir.mkdirs()) {
     System.out.println("Failed to create " + dir.getAbsolutePath());
     return;
   }
   for (String mnemo : cl.getMnemoList()) {
     if (!exists(mnemo)) {
       File file = new File(dir, mnemo + ".htm");
       try {
         file.createNewFile();
         BufferedOutputStream os = new BufferedOutputStream(new FileOutputStream(file));
         PrintStream ps = new PrintStream(os);
         ps.println("<html>\n<head>\n<title>" + mnemo + "\n</title>\n</head>\n<body>");
         ps.println("Command: " + mnemo.toUpperCase() + "<br>");
         ps.println("arguments: <br>");
         ps.println("effects: <br>");
         ps.println("flags to be set: <br>");
         ps.println("approx. clockcycles: <br>");
         ps.println("misc: <br>");
         ps.println("</body>\n</html>");
         ps.flush();
         ps.close();
       } catch (IOException e) {
         System.out.println("failed to create " + file.getAbsolutePath());
       }
     }
   }
 }
Example #3
0
  static void processFile(String fname, PrintStream out) throws IOException {
    System.err.println("Processing: " + fname);

    FileInputStream fio = new FileInputStream(new File(fname));
    InputStreamReader fread = new InputStreamReader(fio, JetTest.encoding);
    BufferedReader fp = new BufferedReader(fread);
    StringBuffer buf = new StringBuffer();

    int docno = 0, allsents = 0, processedsents = 0;
    while (true) {
      String line = fp.readLine();

      // EOF or an empty line: the end of a Document.
      if (line == null || line.equals("")) {
        if (0 < buf.length()) {
          SGMLProcessor.allTags = true;
          Document doc = SGMLProcessor.sgmlToDoc(buf.toString(), (String[]) null);
          doc.setSGMLwrapMargin(0);
          System.err.println(
              "Doc-" + docno + ": sents=" + allsents + ", processed=" + processedsents);
          processDoc1(doc, docno);
          writeDoc1(doc, out);
          out.flush();
          buf = new StringBuffer();
          docno++;
          allsents = 0;
          processedsents = 0;
        }
        if (line == null) {
          break;
        } else {
          continue;
        }
      }

      if (line.startsWith("#")) {
        // "#" indicates a comment line.
        buf.append(line + "\n");
      } else {
        allsents++;
        if (processedsents < MaxProcessSentences) {
          buf.append("<sentence>");
          String[] words = line.split(" ");
          for (int i = 0; i < words.length; i++) {
            if (0 != words[i].length()) {
              buf.append("<token>" + words[i] + " </token>");
            }
          }
          buf.append("</sentence>\n");
          processedsents++;
        }
      }
    }

    fp.close();
    fread.close();
    fio.close();
    return;
  }
 /**
  * Closes down connections to the underlying process. This method will be used only if the
  * supporting Java Native Interface library could be loaded.
  */
 private synchronized void native_close(PrintStream out) {
   try {
     in.close();
     out.flush();
     out.close();
   } catch (IOException ioe) {
   }
 }
 /**
  * Logs the event message to the output stream.
  *
  * @param out Stream to which the message is logged.
  * @param event Message to be logged.
  */
 private void log(PrintStream out, String event) {
   if (null == log) {
     out.println(event);
     out.flush();
   } else {
     log.log(event);
   }
 }
Example #6
0
  public static void main(String args[]) throws Exception {
    int testCases = Integer.parseInt(in.readLine());
    for (int i = 0; i < testCases; i++) {
      char[] path = in.readLine().toCharArray();
      output(path);
      out.println();
    }

    out.flush();
  }
  protected static void writeReferencePositions(String filePath, ArrayList<Position> positions)
      throws FileNotFoundException {
    PrintStream os = new PrintStream(new File(filePath));

    for (Position pos : positions) {
      os.format(
          "%.5f %.5f %.4f\n",
          pos.getLatitude().degrees, pos.getLongitude().degrees, pos.getElevation());
    }

    os.flush();
  }
  /**
   * Render status using a given printer.
   *
   * @param status the IRunStatus to render to String
   * @param printer the IRunStatusPrinter to use (defaults to AJC_PRINTER if null)
   * @return the String rendering of the status, or "((IRunStatus) null)" if null
   */
  public static String render(IRunStatus status, IRunStatusPrinter printer) {
    if (null == status) {
      return "((IRunStatus) null)";
    }
    if (null == printer) {
      printer = RunUtils.AJC_PRINTER;
    }
    ByteArrayOutputStream outStream = new ByteArrayOutputStream();
    PrintStream out = new PrintStream(outStream);
    printer.printRunStatus(out, status);
    out.flush();

    return outStream.toString();
  }
Example #9
0
  public static void main(String args[]) throws Exception {
    StringTokenizer tokenizer = new StringTokenizer(in.readLine());
    int n = Integer.parseInt(tokenizer.nextToken()), m = Integer.parseInt(tokenizer.nextToken());

    Graph graph = new Graph(n, m);
    for (long i = 0; i < m; i++) {
      tokenizer = new StringTokenizer(in.readLine());
      int from = Integer.parseInt(tokenizer.nextToken()),
          to = Integer.parseInt(tokenizer.nextToken());

      graph.connect(from, to);
    }

    output(graph, n);
    out.println();
    out.flush();
  }
Example #10
0
  // made synchronized for 0087
  // attempted to remove synchronized for 0136 to fix bug #775 (no luck tho)
  // http://dev.processing.org/bugs/show_bug.cgi?id=775
  public synchronized void message(String s) {
    //    System.out.println("M" + s.length() + ":" + s.trim()); // + "MMM" + s.length());

    // this eats the CRLFs on the lines.. oops.. do it later
    // if (s.trim().length() == 0) return;

    // this is PApplet sending a message (via System.out.println)
    // that signals that the applet has been quit.
    if (s.indexOf(PApplet.EXTERNAL_STOP) == 0) {
      // System.out.println("external: quit");
      if (editor != null) {
        //        editor.internalCloseRunner();  // [091124]
        //        editor.handleStop();  // prior to 0192
        editor.internalCloseRunner(); // 0192
      }
      return;
    }

    // this is the PApplet sending us a message that the applet
    // is being moved to a new window location
    if (s.indexOf(PApplet.EXTERNAL_MOVE) == 0) {
      String nums = s.substring(s.indexOf(' ') + 1).trim();
      int space = nums.indexOf(' ');
      int left = Integer.parseInt(nums.substring(0, space));
      int top = Integer.parseInt(nums.substring(space + 1));
      // this is only fired when connected to an editor
      editor.setSketchLocation(new Point(left, top));
      // System.out.println("external: move to " + left + " " + top);
      return;
    }

    // these are used for debugging, in case there are concerns
    // that some errors aren't coming through properly
    //    if (s.length() > 2) {
    //      System.err.println(newMessage);
    //      System.err.println("message " + s.length() + ":" + s);
    //    }

    // always shove out the message, since it might not fall under
    // the same setup as we're expecting
    sketchErr.print(s);
    // System.err.println("[" + s.length() + "] " + s);
    sketchErr.flush();
  }
Example #11
0
  public static void main(String args[]) throws Exception {
    int testCases = Integer.parseInt(in.readLine());
    for (int i = 0; i < testCases; i++) {
      StringTokenizer tokenizer = new StringTokenizer(in.readLine());
      int n = Integer.parseInt(tokenizer.nextToken());

      Party party = new Party();
      for (int j = 0; j < n; j++) {
        Person person = new Person(j);
        tokenizer = new StringTokenizer(in.readLine());
        while (tokenizer.hasMoreTokens()) person.add(Integer.parseInt(tokenizer.nextToken()));

        party.invite(person);
      }

      output(party);
      out.println();
    }

    out.flush();
  }
 /**
  * Closes down connections to the underlying process. This method will be used only if the
  * supporting Java Native Interface library could not be loaded.
  */
 private synchronized void pure_close(PrintStream out) {
   /*
    * Try to close this process for at least 30 seconds.
    */
   for (int i = 0; i < 30; i++) {
     try {
       in.close();
       err.close();
       out.flush();
       out.close();
     } catch (IOException ioe) {
     }
     try {
       exit_code = p.waitFor();
       p.destroy();
       break;
     } catch (InterruptedException ie) {
     }
     try {
       Thread.sleep(1000);
     } catch (InterruptedException ie) {
     }
   }
 }
  public HTTPResponse post(String host, int port, boolean isKeepAlive) {
    HTTPResponse httpRes = new HTTPResponse();

    setConnection((isKeepAlive == true) ? HTTP.KEEP_ALIVE : HTTP.CLOSE);

    boolean isHeaderRequest = isHeadRequest();

    OutputStream out = null;
    InputStream in = null;

    try {
      if (postSocket == null) postSocket = new Socket(host, port);

      out = postSocket.getOutputStream();
      PrintStream pout = new PrintStream(out);
      pout.print(getHeader());
      pout.print(HTTP.CRLF);

      boolean isChunkedRequest = isChunked();

      String content = getContentString();
      int contentLength = 0;
      if (content != null) contentLength = content.length();

      if (0 < contentLength) {
        if (isChunkedRequest == true) {
          String chunSizeBuf = Long.toString(contentLength);
          pout.print(chunSizeBuf);
          pout.print(HTTP.CRLF);
        }
        pout.print(content);
        if (isChunkedRequest == true) pout.print(HTTP.CRLF);
      }

      if (isChunkedRequest == true) {
        pout.print("0");
        pout.print(HTTP.CRLF);
      }

      pout.flush();

      in = postSocket.getInputStream();
      httpRes.set(in, isHeaderRequest);
    } catch (Exception e) {
      httpRes.setStatusCode(HTTPStatus.INTERNAL_SERVER_ERROR);
    } finally {
      if (isKeepAlive == false) {
        try {
          in.close();
        } catch (Exception e) {
        }
        ;
        if (in != null)
          try {
            out.close();
          } catch (Exception e) {
          }
        ;
        if (out != null)
          try {
            postSocket.close();
          } catch (Exception e) {
          }
        ;
        postSocket = null;
      }
    }

    return httpRes;
  }
Example #14
0
 /**
  * ** Encodes the specified DBRecordKyes into XML and writes it to ** a specified PrintStream
  * ** @param out The PrintStream ** @param dbrk The list of DBRecordKeys
  */
 public static void printXML(PrintStream out, DBRecordKey... dbrk) {
   if (out != null) {
     DBRecordKey.printXML(new PrintWriter(out), dbrk);
     out.flush();
   }
 }
 /** Finalizes output file. */
 public void finished() {
   m_printstream.flush();
 }
Example #16
0
  /** Starts main program with the specified arguments. */
  public synchronized boolean run(String args[]) {
    ok = true;
    if (!parseArgs(args)) {
      return false;
    }
    try {
      if (cflag || uflag) {
        if (fname != null) {
          // The name of the zip file as it would appear as its own
          // zip file entry. We use this to make sure that we don't
          // add the zip file to itself.
          zname = fname.replace(File.separatorChar, '/');
          if (zname.startsWith("./")) {
            zname = zname.substring(2);
          }
        }
      }
      if (cflag) {
        Manifest manifest = null;
        InputStream in = null;

        if (!Mflag) {
          if (mname != null) {
            in = new FileInputStream(mname);
            manifest = new Manifest(new BufferedInputStream(in));
          } else {
            manifest = new Manifest();
          }
          addVersion(manifest);
          addCreatedBy(manifest);
          if (isAmbiguousMainClass(manifest)) {
            if (in != null) {
              in.close();
            }
            return false;
          }
          if (ename != null) {
            addMainClass(manifest, ename);
          }
          if (pname != null) {
            if (!addProfileName(manifest, pname)) {
              if (in != null) {
                in.close();
              }
              return false;
            }
          }
        }
        OutputStream out;
        if (fname != null) {
          out = new FileOutputStream(fname);
        } else {
          out = new FileOutputStream(FileDescriptor.out);
          if (vflag) {
            // Disable verbose output so that it does not appear
            // on stdout along with file data
            // error("Warning: -v option ignored");
            vflag = false;
          }
        }
        expand(null, files, false);
        create(new BufferedOutputStream(out, 4096), manifest);
        if (in != null) {
          in.close();
        }
        out.close();
      } else if (uflag) {
        File inputFile = null, tmpFile = null;
        FileInputStream in;
        FileOutputStream out;
        if (fname != null) {
          inputFile = new File(fname);
          tmpFile = createTempFileInSameDirectoryAs(inputFile);
          in = new FileInputStream(inputFile);
          out = new FileOutputStream(tmpFile);
        } else {
          in = new FileInputStream(FileDescriptor.in);
          out = new FileOutputStream(FileDescriptor.out);
          vflag = false;
        }
        InputStream manifest = (!Mflag && (mname != null)) ? (new FileInputStream(mname)) : null;
        expand(null, files, true);
        boolean updateOk = update(in, new BufferedOutputStream(out), manifest, null);
        if (ok) {
          ok = updateOk;
        }
        in.close();
        out.close();
        if (manifest != null) {
          manifest.close();
        }
        if (ok && fname != null) {
          // on Win32, we need this delete
          inputFile.delete();
          if (!tmpFile.renameTo(inputFile)) {
            tmpFile.delete();
            throw new IOException(getMsg("error.write.file"));
          }
          tmpFile.delete();
        }
      } else if (tflag) {
        replaceFSC(files);
        if (fname != null) {
          list(fname, files);
        } else {
          InputStream in = new FileInputStream(FileDescriptor.in);
          try {
            list(new BufferedInputStream(in), files);
          } finally {
            in.close();
          }
        }
      } else if (xflag) {
        replaceFSC(files);
        if (fname != null && files != null) {
          extract(fname, files);
        } else {
          InputStream in =
              (fname == null) ? new FileInputStream(FileDescriptor.in) : new FileInputStream(fname);
          try {
            extract(new BufferedInputStream(in), files);
          } finally {
            in.close();
          }
        }
      } else if (iflag) {
        genIndex(rootjar, files);
      }
    } catch (IOException e) {
      fatalError(e);
      ok = false;
    } catch (Error ee) {
      ee.printStackTrace();
      ok = false;
    } catch (Throwable t) {
      t.printStackTrace();
      ok = false;
    }
    out.flush();
    err.flush();
    return ok;
  }
Example #17
0
 static void writeDocRaw(Document doc, PrintStream out) throws IOException {
   out.println(doc.writeSGML(null).toString());
   out.flush();
   return;
 }
Example #18
0
File: Log.java Project: EEAT/EEAT
 public static final void print(Object msg) {
   out.print(msg);
   out.flush();
 }
Example #19
0
  public static void main(String argv[]) {
    try {
      BufferedReader buf1 = new BufferedReader(new FileReader("./index/pIndex"));
      FileOutputStream out = new FileOutputStream("finalindex");
      PrintStream p = new PrintStream(out);
      String nline1, nline2, term1, term2, term3, term, t1, t2;
      StringBuffer sbuff = new StringBuffer();
      StringBuffer sbuff1;
      long df, postings = 0, line = 0;
      String[] id;
      int flag = 0;
      while (true) {
        nline1 = buf1.readLine();
        // System.out.println(nline1);
        if (nline1 == null) break;
        line++;
        String[] words = nline1.split(" ");
        String search_word = words[0];
        char ch = search_word.charAt(0);
        // System.out.println("c"+ch);
        id = words[1].split(",");
        df = id.length;
        flag = 0;
        sbuff1 = new StringBuffer(); // System.out.println(df);
        if (df > 30000 && ((ch == 't') || ch == 'o' || ch == 'c')) {
          int count = 0;
          postings = 0;
          System.out.println("before df" + df + ";line" + line); // System.out.println("here\n");
          while (count < df) {
            String temp1 = id[count];
            String temp[] = temp1.split(":");
            int t = Integer.parseInt(temp[1]);
            // System.out.println("t:"+t);
            if (t != 1) {
              if (flag == 0) {
                // System.out.println("here\n");
                sbuff1.append(search_word);
                sbuff1.append(" ");
                sbuff1.append(temp1);
                flag = 1;
              } else {
                sbuff1.append(",");
                sbuff1.append(temp1);
                postings++;
              }
            }
            count++;
          }
          // System.out.println(sbuff1);
          System.out.println("postings size after:" + postings + ";line" + line);
          p.println(sbuff1.toString());
          p.flush();
        } else {

          p.println(nline1);
          p.flush();
        }
      }

    } catch (IOException E) {
    }
  }
Example #20
0
 public String sendKommando(String kommando) throws IOException {
   System.out.println("send: " + kommando);
   ud.println(kommando);
   ud.flush(); // sørg for at data sendes til værten før vi læser svar
   return læsSvar();
 }