コード例 #1
0
ファイル: NexusExporter.java プロジェクト: 4ment/beast-mcmc
  /**
   * name suitable for printing - quotes if necessary
   *
   * @param taxon
   * @param builder
   * @return
   */
  private StringBuilder appendTaxonName(Taxon taxon, StringBuilder builder) {

    String name = taxon.getId();
    if (!name.matches(SPECIAL_CHARACTERS_REGEX)) {
      // JEBL way of quoting the quote character
      name = name.replace("\'", "\'\'");
      builder.append("\'").append(name).append("\'");
      return builder;
    }
    return builder.append(name);
  }
コード例 #2
0
 public String asText(int indentlen) {
   StringBuilder s = new StringBuilder();
   Formatter formatter = new Formatter(s, Locale.US);
   if (lft < 0) {
     formatter.format("%s ", taxon.getId());
   } else {
     formatter.format("%s ", "+");
   }
   while (s.length() < 20 - indentlen) {
     formatter.format("%s", " ");
   }
   formatter.format("%s ", AlloppMisc.nonnegIn8Chars(height));
   formatter.format("%20s ", AlloppMisc.FixedBitSetasText(union));
   formatter.format("%3d  ", nlineages);
   for (int c = 0; c < coalheights.size(); c++) {
     formatter.format(AlloppMisc.nonnegIn8Chars(coalheights.get(c)) + ",");
   }
   return s.toString();
 }
コード例 #3
0
  public static void main(String[] arg) throws IOException {

    // READ DEMOGRAPHIC FUNCTION

    String filename = arg[0];
    BufferedReader reader = new BufferedReader(new FileReader(filename));

    double popSizeScale = 1.0;
    double generationTime = 1.0;
    if (arg.length > 2) {
      popSizeScale = Double.parseDouble(arg[2]);
    }
    if (arg.length > 3) {
      generationTime = Double.parseDouble(arg[3]);
    }

    PrintWriter populationFuncLogger = null;
    if (arg.length > 5) {
      String logFileName = arg[5];
      if (logFileName.equals("-")) {
        populationFuncLogger = new PrintWriter(System.out);
      } else {
        populationFuncLogger = new PrintWriter(new FileWriter(logFileName));
      }
    }

    List<Double> times = new ArrayList<Double>();

    String line = reader.readLine();
    String[] tokens = line.trim().split("[\t ]+");
    if (tokens.length < 2) throw new RuntimeException();

    ArrayList<ArrayList> popSizes = new ArrayList<ArrayList>();
    while (line != null) {
      double time = Double.parseDouble(tokens[0]) / generationTime;
      times.add(time);

      for (int i = 1; i < tokens.length; i++) {
        popSizes.add(new ArrayList<Double>());
        popSizes.get(i - 1).add(Double.parseDouble(tokens[i]));
      }
      line = reader.readLine();
      if (line != null) {
        tokens = line.trim().split("[\t ]+");
        if (tokens.length != popSizes.size() + 1) throw new RuntimeException();
      }
    }

    reader.close();

    // READ SAMPLE TIMES

    String samplesFilename = arg[1];

    reader = new BufferedReader(new FileReader(samplesFilename));

    line = reader.readLine();
    Taxa taxa = new Taxa();
    int id = 0;
    while (line != null) {

      if (!line.startsWith("#")) {

        tokens = line.split("[\t ]+");

        if (tokens.length == 4) {

          double t0 = Double.parseDouble(tokens[0]);
          double t1 = Double.parseDouble(tokens[1]);
          double dt = Double.parseDouble(tokens[2]);
          int k = Integer.parseInt(tokens[3]);
          for (double time = t0; time <= t1; time += dt) {

            double sampleTime = time / generationTime;
            for (int i = 0; i < k; i++) {
              Taxon taxon = new Taxon("t" + id);
              taxon.setAttribute(
                  dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
              taxa.addTaxon(taxon);
              id += 1;
            }
          }

        } else {

          // sample times are in the same units as simulation
          double sampleTime = Double.parseDouble(tokens[0]) / generationTime;
          int count = Integer.parseInt(tokens[1]);

          for (int i = 0; i < count; i++) {
            Taxon taxon = new Taxon(id + "");
            taxon.setAttribute(
                dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
            taxa.addTaxon(taxon);
            id += 1;
          }
        }
      }
      line = reader.readLine();
    }

    double minTheta = Double.MAX_VALUE;
    double maxTheta = 0.0;

    PrintWriter out;
    if (arg.length > 4) {
      out = new PrintWriter(new FileWriter(arg[4]));
    } else {
      out = new PrintWriter(System.out);
    }

    int pp = 0;
    for (List<Double> popSize : popSizes) {
      double[] thetas = new double[popSize.size()];
      double[] intervals = new double[times.size() - 1];

      if (populationFuncLogger != null) {
        populationFuncLogger.println("# " + pp);
        ++pp;
      }

      // must reverse the direction of the model
      for (int j = intervals.length; j > 0; j--) {
        intervals[intervals.length - j] = times.get(j) - times.get(j - 1);

        final double theta = popSize.get(j) * popSizeScale;
        thetas[intervals.length - j] = theta;
        if (theta < minTheta) {
          minTheta = theta;
        }
        if (theta > maxTheta) {
          maxTheta = theta;
        }

        final double t = times.get(intervals.length) - times.get(j);
        if (populationFuncLogger != null) {
          populationFuncLogger.println(t + "\t" + theta);
        }
      }

      if (debug != null) {
        debug.println("min theta = " + minTheta);
        debug.println("max theta = " + maxTheta);
      }

      PiecewiseLinearPopulation demo =
          new PiecewiseLinearPopulation(intervals, thetas, Units.Type.GENERATIONS);

      CoalescentSimulator simulator = new CoalescentSimulator();
      Tree tree = simulator.simulateTree(taxa, demo);

      out.println(Tree.Utils.newick(tree));
      if (debug != null) {
        debug.println(Tree.Utils.newick(tree));
      }
    }

    if (populationFuncLogger != null) {
      populationFuncLogger.flush();
      populationFuncLogger.close();
    }

    out.flush();
    out.close();
  }