Package gem.util

Examples of gem.util.Kronometre

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    return rftSet.size();
  }

  public static void main(String[] args) throws Throwable
  {
    Kronometre kron = new Kronometre();
    GEM m = new GEM();
    m.run();
    kron.stop();
    kron.print();
  }
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{
  private static Map<String, Set<String>> tar2fac;

  public static void main(String[] args) throws Throwable
  {
    Kronometre k = new Kronometre();

//    writeTripsRecursive("result/temp/");
    createSeriesForTargetAndFactor();
//    writeTargetMachineryInGraphML("result/Result_fdr0.05_var1.0.xls");

    k.stop();
    k.print();
  }
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  //public static Font upFont;
  //public static Font downFont;

  public static void main(String[] args) throws Throwable
  {
    Kronometre kron = new Kronometre();
    String file = "result/Result_fdr0.05_var1.0_AR_expo_prostate";

    comtype = "33";
    String plat = "GPL8300";
    List<Triplet> trips = Triplet.readTripsAndAssociate(file + ".xls",
      "resource/expop/expop_1.txt", "resource/expop/expop_2.txt", "resource/expop/expop_3.txt");
//    List<Triplet> trips = Triplet.readTrips(file + ".xls");
    Iterator<Triplet> iter = trips.iterator();
    while (iter.hasNext())
    {
      Triplet t =  iter.next();
      if (t.fac_id.startsWith("M")) iter.remove();
    }
    System.out.println("trips.size() = " + trips.size());
//    CrossPlatformMapper.associateAndClean(trips, "resource/expop/nikidata.txt");
//    CrossPlatformMapper.associateWithGSE6919(trips, plat);

//    trips = Triplet.selectModulator(trips, "SPDEF");

    posCancer = CellTypeMatcher.getCancerProstateInExpop(comtype);
//    posNormal = CellTypeMatcher.getCancerProstateInExpop(comtype + "_primary");
    posNormal = CellTypeMatcher.getBenignProstateInExpop(comtype);
//    posCancer = CrossPlatformMapper.getPosInGSE6919(plat, false);
//    posNormal = CrossPlatformMapper.getPosInGSE6919(plat, true);

//    CellTypeMatcher.randomizeInside(posCancer, posNormal);

    boolean[] pos = CellTypeMatcher.takeOR(posNormal, posCancer);
    CellTypeMatcher.replaceValsToRanks(trips, pos);

    fillChangeMaps(trips);
    keepMostChangedTargetIsoforms(trips);
    fillMappingsAfter(trips);

    generateSVG(trips, file + "_in" + comtype);
//    generatePNG(trips, file);
//    printScores(trips);
    kron.stop();
    kron.print();
  }
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    return 1;
  }

  public static void main(String[] args) throws Throwable
  {
    Kronometre kron = new Kronometre();
    GEMAllPairs m = new GEMAllPairs();
    m.run();
    kron.stop();
    kron.print();
  }
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  public Progress(int totalTicks, int length)
  {
    this.length = length;
    this.totalTicks = totalTicks;
    this.total = totalTicks;
    this.kron = new Kronometre();
    kron.start();

    System.out.print("\n|");
    for (int i = 0; i < length; i++) System.out.print(" ");
    System.out.print("|\n ");
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Related Classes of gem.util.Kronometre

  • gem.GEM
  • gem.GEMAllPairs
  • gem.PlotForTissue2
  • gem.TripletGraphMLWriter
  • gem.util.Progress
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