Exemple #1
0
    public void applyUncalled() {
        Progress progress = new Progress(uncalled.size(), 50);

        while (!uncalled.isEmpty()) {
            List<FunType> uncalledDup = new ArrayList<>(uncalled);

            for (FunType cl : uncalledDup) {
                progress.tick();
                Call.apply(cl, null, null, null, null, null, null);
            }
        }
    }
  private Map<String, Double> getExpressionPvals(
      Set<String> targets, boolean[] set1, boolean[] set2) {
    Map<String, Double> map = new HashMap<String, Double>();

    Histogram2D h = new Histogram2D(0.2);

    System.out.println("targets = " + targets.size());
    Progress prg = new Progress(targets.size());
    for (String sym : targets) {
      prg.tick();

      if (expMan.getNonZeroRatio(sym) == 0) continue;
      double pval = calcDiffPval(sym, set1, set2, true);

      if (Double.isNaN(pval)) continue;
      if (pval == 0) pval = 1E-11;

      double pPerm = calcDiffPval(sym, set1, set2, false);
      if (pPerm == 0) pPerm = 1E-5;

      h.count(-Math.log(pval), -Math.log(pPerm));

      // pval = 0 is not real and it is not compatible with fisher's combined probability.
      // below is a better approximation.
      //			if (pval == 0)
      //			{
      //				pval = 1E-11;
      //			}

      map.put(sym, pval);
    }

    Histogram2DPlot p = new Histogram2DPlot(h);
    p.setLines(Arrays.asList(new double[] {1, 0}));
    p.setVisible(true);

    return map;
  }
Exemple #3
0
    @Nullable
    private Type parseAndResolve(String file) {
        try {
            Node ast = getAstForFile(file);

            if (ast == null) {
                failedToParse.add(file);
                return null;
            } else {
                Type type = Node.transformExpr(ast, globaltable);
                if (!loadedFiles.contains(file)) {
                    loadedFiles.add(file);
                    loadingProgress.tick();
                }
                return type;
            }
        } catch (OutOfMemoryError e) {
            if (astCache != null) {
                astCache.clear();
            }
            System.gc();
            return null;
        }
    }