Package gem.util

Examples of gem.util.Progress.tick()

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//      int[][][] c = CaseCounter.countComplete(t);
//      t.dcmi = MINDy.calcDMI(c);
//      t.pvalDcmi = MINDy.calcPval(c);

      p.tick();
    }
  }

  public static List<Triplet> assignBestCountsConsiderAbsent(Collection<Triplet> trips, Set<Gene> absent)
  {
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    Progress p = new Progress(mods.size());

    for (String u1 : mods)
    {
      p.tick();

      Gene U1 = id2gene.get(u1);
      if (U1 == null) continue;

      for (String u2 : mods)
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      if (!adjusted.contains(t.M)) { t.M.rankAdjustStatus(tailRatio); adjusted.add(t.M);}
      if (!adjusted.contains(t.F)) { t.F.rankAdjustStatus(tailRatio); adjusted.add(t.F);}
      if (!adjusted.contains(t.T)) { t.T.rankAdjustStatus(tailRatio); adjusted.add(t.T);}

      count(t);
      p.tick();
    }
  }

  public static void count(Collection<Triplet> trips, double tailRatio, boolean[] ignore)
  {
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      if (!adjusted.contains(t.M)) { t.M.rankAdjustStatus(tailRatio, 1-tailRatio, ignore, tc); adjusted.add(t.M);}
      if (!adjusted.contains(t.F)) { t.F.rankAdjustStatus(tailRatio, 1-tailRatio, ignore, tc); adjusted.add(t.F);}
      if (!adjusted.contains(t.T)) { t.T.rankAdjustStatus(tailRatio, 1-tailRatio, ignore, tc); adjusted.add(t.T);}

      count(t);
      p.tick();
    }
  }

  public static void count(Triplet t)
  {
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      BufferedWriter writer = new BufferedWriter(new FileWriter(filename));

      for (Gene gene : set)
      {
        writer.write(gene + "\n");
        p.tick();
      }

      writer.close();
    }
    catch (IOException e)
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    Progress p = new Progress(modMap.size());

    for (Mod mod : modMap.values())
    {
      p.tick();
      for (Triplet t : trips)
      {
        mod.count(t);
      }
    }
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