Exemplo n.º 1
0
  public PeptideTerminalAAResult calculateForAnalysis(int analysisId) {

    DAOFactory daoFactory = DAOFactory.instance();

    MsRunSearchAnalysisDAO rsaDao = daoFactory.getMsRunSearchAnalysisDAO();
    List<Integer> runSearchAnalysisIds = rsaDao.getRunSearchAnalysisIdsForAnalysis(analysisId);

    PeptideTerminalAAResult result =
        calculateForRunSearchAnalysisIds(analysisId, runSearchAnalysisIds);
    result.setEnzyme(enzyme);
    return result;
  }
  private PsmRetTimeDistribution getPercolatorResults() {

    List<PercolatorFilteredPsmResult> filteredResults = null;
    if (scoreCutoff == 0.01) {
      // Look in the database first for pre-calculated results
      PercolatorFilteredPsmResultDAO dao =
          DAOFactory.instance().getPrecolatorFilteredPsmResultDAO();
      filteredResults = dao.loadForAnalysis(analysisId);
    }

    if (filteredResults == null || filteredResults.size() == 0) {

      // Results were not found in the database; calculate now
      PercolatorFilteredPsmDistributionCalculator calc =
          new PercolatorFilteredPsmDistributionCalculator(analysisId, scoreCutoff);
      calc.calculate();
      filteredResults = calc.getFilteredResults();
    }

    if (filteredResults == null || filteredResults.size() == 0) {
      log.error("No results for searchAnalysisID: " + analysisId);
      return null;
    }

    PercolatorFilteredPsmResultDAO statsDao =
        DAOFactory.instance().getPrecolatorFilteredPsmResultDAO();
    double populationMax = RoundingUtils.getInstance().roundOne(statsDao.getPopulationMax());
    double populationMin = RoundingUtils.getInstance().roundOne(statsDao.getPopulationMin());
    double populationMean =
        RoundingUtils.getInstance().roundOne(statsDao.getPopulationAvgFilteredPercent());
    double populationStddev =
        RoundingUtils.getInstance().roundOne(statsDao.getPopulationStdDevFilteredPercent());

    int[] allPsmCounts = null;
    int[] filteredPsmCounts = null;

    int maxPsmCount = 0;
    double maxRt = 0;

    List<FileStats> fileStats = new ArrayList<FileStats>(filteredResults.size());
    MsRunSearchAnalysisDAO rsaDao = DAOFactory.instance().getMsRunSearchAnalysisDAO();

    maxRt = getMaxRtForPercolatorResults(filteredResults.get(0).getBinnedResults());
    int binIncr = getBinIncrement(maxRt);
    int numBins = (int) Math.ceil(maxRt / binIncr);

    for (PercolatorFilteredPsmResult res : filteredResults) {

      int runSearchAnalysisId = res.getRunSearchAnalysisId();
      String filename = rsaDao.loadFilenameForRunSearchAnalysis(runSearchAnalysisId);
      FileStats stats = new FileStats(res.getRunSearchAnalysisId(), filename);
      stats.setGoodCount(res.getFiltered());
      stats.setTotalCount(res.getTotal());
      if (scoreCutoff == 0.01) {
        stats.setPopulationMean(populationMean);
        stats.setPopulationStandardDeviation(populationStddev);
        stats.setPopulationMin(populationMin);
        stats.setPopulationMax(populationMax);
      }

      fileStats.add(stats);

      List<PercolatorBinnedPsmResult> binnedResults = res.getBinnedResults();
      Collections.sort(
          binnedResults,
          new Comparator<PercolatorBinnedPsmResult>() {
            @Override
            public int compare(PercolatorBinnedPsmResult o1, PercolatorBinnedPsmResult o2) {
              return Double.valueOf(o1.getBinStart()).compareTo(o2.getBinStart());
            }
          });

      if (allPsmCounts == null) allPsmCounts = new int[numBins];
      if (filteredPsmCounts == null) filteredPsmCounts = new int[numBins];

      maxRt = Math.max(maxRt, binnedResults.get(binnedResults.size() - 1).getBinEnd());

      int idx = 0;
      for (int j = 0; j < binnedResults.size(); j++) {
        PercolatorBinnedPsmResult binned = binnedResults.get(j);
        allPsmCounts[idx] += binned.getTotal();
        filteredPsmCounts[idx] += binned.getFiltered();
        maxPsmCount = Math.max(allPsmCounts[idx], maxPsmCount);
        if (j > 0 && j % binIncr == 0) idx++;
      }
    }

    PsmRetTimeDistribution distribution = new PsmRetTimeDistribution(Program.PERCOLATOR);
    distribution.setScoreCutoff(this.scoreCutoff);
    distribution.setNumBins(allPsmCounts.length);
    distribution.setMaxRT(maxRt);
    distribution.setMaxPsmCount(maxPsmCount);
    distribution.setFilteredPsmCounts(filteredPsmCounts);
    distribution.setAllPsmCounts(allPsmCounts);
    distribution.setBinSize(binIncr);
    distribution.setFileStatsList(fileStats);

    return distribution;
  }
  private PsmRetTimeDistribution getPeptideProphetResults() {

    List<ProphetFilteredPsmResult> filteredResults = null;
    if (scoreCutoff == QCStatsGetter.PEPPROPHET_ERR_RATE_DEFAULT) {
      // Look in the database first for pre-calculated results
      ProphetFilteredPsmResultDAO dao = DAOFactory.instance().getProphetFilteredPsmResultDAO();
      filteredResults = dao.loadForAnalysis(analysisId);
    }

    if (filteredResults == null || filteredResults.size() == 0) {

      // Results were not found in the database; calculate now

      PeptideProphetRocDAO rocDao = DAOFactory.instance().getPeptideProphetRocDAO();
      PeptideProphetROC roc = rocDao.loadRoc(analysisId);
      double probability = roc.getMinProbabilityForError(scoreCutoff);
      log.info("Probability for error rate of " + scoreCutoff + " is: " + probability);

      ProphetFilteredPsmDistributionCalculator calc =
          new ProphetFilteredPsmDistributionCalculator(analysisId, probability);
      calc.calculate();
      filteredResults = calc.getFilteredResults();
    }

    if (filteredResults == null || filteredResults.size() == 0) {
      log.error("No results for searchAnalysisID: " + analysisId);
      return null;
    }

    ProphetFilteredPsmResultDAO statsDao = DAOFactory.instance().getProphetFilteredPsmResultDAO();
    double populationMax = RoundingUtils.getInstance().roundOne(statsDao.getPopulationMax());
    double populationMin = RoundingUtils.getInstance().roundOne(statsDao.getPopulationMin());
    double populationMean =
        RoundingUtils.getInstance().roundOne(statsDao.getPopulationAvgFilteredPercent());
    double populationStddev =
        RoundingUtils.getInstance().roundOne(statsDao.getPopulationStdDevFilteredPercent());

    int[] allPsmCounts = null;
    int[] filteredPsmCounts = null;

    int maxPsmCount = 0;
    double maxRt = 0;

    List<FileStats> fileStats = new ArrayList<FileStats>(filteredResults.size());
    MsRunSearchAnalysisDAO rsaDao = DAOFactory.instance().getMsRunSearchAnalysisDAO();

    maxRt = getMaxRtForProphetResults(filteredResults.get(0).getBinnedResults());
    int binIncr = getBinIncrement(maxRt);
    int numBins = (int) Math.ceil(maxRt / binIncr);

    double actualScoreCutoff =
        -1.0; // actual probability cutoff used (that corresponds to the given error rate)

    for (ProphetFilteredPsmResult res : filteredResults) {

      actualScoreCutoff = res.getProbability();

      int runSearchAnalysisId = res.getRunSearchAnalysisId();
      String filename = rsaDao.loadFilenameForRunSearchAnalysis(runSearchAnalysisId);
      FileStats stats = new FileStats(res.getRunSearchAnalysisId(), filename);
      stats.setGoodCount(res.getFiltered());
      stats.setTotalCount(res.getTotal());
      if (scoreCutoff == 0.01) {
        stats.setPopulationMean(populationMean);
        stats.setPopulationStandardDeviation(populationStddev);
        stats.setPopulationMin(populationMin);
        stats.setPopulationMax(populationMax);
      }

      fileStats.add(stats);

      List<ProphetBinnedPsmResult> binnedResults = res.getBinnedResults();
      Collections.sort(
          binnedResults,
          new Comparator<ProphetBinnedPsmResult>() {
            @Override
            public int compare(ProphetBinnedPsmResult o1, ProphetBinnedPsmResult o2) {
              return Double.valueOf(o1.getBinStart()).compareTo(o2.getBinStart());
            }
          });

      if (allPsmCounts == null) allPsmCounts = new int[numBins];
      if (filteredPsmCounts == null) filteredPsmCounts = new int[numBins];

      maxRt = Math.max(maxRt, binnedResults.get(binnedResults.size() - 1).getBinEnd());

      int idx = 0;
      for (int j = 0; j < binnedResults.size(); j++) {
        ProphetBinnedPsmResult binned = binnedResults.get(j);
        allPsmCounts[idx] += binned.getTotal();
        filteredPsmCounts[idx] += binned.getFiltered();
        maxPsmCount = Math.max(allPsmCounts[idx], maxPsmCount);
        if (j > 0 && j % binIncr == 0) idx++;
      }
    }

    PsmRetTimeDistribution distribution = new PsmRetTimeDistribution(Program.PEPTIDE_PROPHET);
    distribution.setScoreCutoff(actualScoreCutoff);
    distribution.setNumBins(allPsmCounts.length);
    distribution.setMaxRT(maxRt);
    distribution.setMaxPsmCount(maxPsmCount);
    distribution.setFilteredPsmCounts(filteredPsmCounts);
    distribution.setAllPsmCounts(allPsmCounts);
    distribution.setBinSize(binIncr);
    distribution.setFileStatsList(fileStats);

    return distribution;
  }