C++ PeakMap::size方法代码示例

 vector<vector<Size> > PScore::calculateRankMap(const PeakMap& peak_map, double mz_window)
 {
   vector<std::vector<Size> > rank_map; // note: ranks are zero based
   rank_map.reserve(peak_map.size());
   for (Size i = 0; i != peak_map.size(); ++i)
   {
     const PeakSpectrum& spec = peak_map[i];
     vector<double> mz;
     vector<double> intensities;
     for (Size j = 0; j != spec.size(); ++j)
     {
       mz.push_back(spec[j].getMZ());
       intensities.push_back(spec[j].getIntensity());
     }
     rank_map.push_back(calculateIntensityRankInMZWindow(mz, intensities, mz_window));
   }
   return rank_map;
 }

  // version for label-free linkers
  void XQuestResultXMLFile::writeXQuestXMLSpec(String out_file, String base_name, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms, const PeakMap& spectra)
  {
    // String spec_xml_filename = base_name + "_matched.spec.xml";
    // XML Header
    std::ofstream spec_xml_file;
    std::cout << "Writing spec.xml to " << out_file << std::endl;
    spec_xml_file.open(out_file.c_str(), std::ios::trunc); // ios::app = append to file, ios::trunc = overwrites file
    // TODO write actual data
    spec_xml_file << "<?xml version=\"1.0\" encoding=\"UTF-8\"?><xquest_spectra compare_peaks_version=\"3.4\" date=\"Tue Nov 24 12:41:18 2015\" author=\"Thomas Walzthoeni,Oliver Rinner\" homepage=\"http://proteomics.ethz.ch\" resultdir=\"aleitner_M1012_004_matched\" deffile=\"xquest.def\" >" << std::endl;

    // collect indices of spectra, that need to be written out
    std::vector <Size> spectrum_indices;

    for (Size i = 0; i < all_top_csms.size(); ++i)
    {
      if (!all_top_csms[i].empty())
      {
        if (all_top_csms[i][0].scan_index_light < spectra.size())
        {
          spectrum_indices.push_back(all_top_csms[i][0].scan_index_light);
        }
      }
    }

    // loop over list of indices and write out spectra
    for (Size i = 0; i < spectrum_indices.size(); ++i)
    {
      String spectrum_light_name = base_name + ".light." + spectrum_indices[i];
      String spectrum_heavy_name = base_name + ".heavy." + spectrum_indices[i];

      String spectrum_name = spectrum_light_name + String("_") + spectrum_heavy_name;

      // 4 Spectra resulting from a light/heavy spectra pair.  Write for each spectrum, that is written to xquest.xml (should be all considered pairs, or better only those with at least one sensible Hit, meaning a score was computed)
      spec_xml_file << "<spectrum filename=\"" << spectrum_light_name << ".dta" << "\" type=\"light\">" << std::endl;
      spec_xml_file << getxQuestBase64EncodedSpectrum_(spectra[spectrum_indices[i]], String(""));
      spec_xml_file << "</spectrum>" << std::endl;

      spec_xml_file << "<spectrum filename=\"" << spectrum_heavy_name << ".dta" << "\" type=\"heavy\">" << std::endl;
      spec_xml_file << getxQuestBase64EncodedSpectrum_(spectra[spectrum_indices[i]], String(""));
      spec_xml_file << "</spectrum>" << std::endl;

      String spectrum_common_name = spectrum_name + String("_common.txt");
      spec_xml_file << "<spectrum filename=\"" << spectrum_common_name << "\" type=\"common\">" << std::endl;
      spec_xml_file << getxQuestBase64EncodedSpectrum_(spectra[spectrum_indices[i]], spectrum_light_name + ".dta," + spectrum_heavy_name + ".dta");
      spec_xml_file << "</spectrum>" << std::endl;

      String spectrum_xlink_name = spectrum_name + String("_xlinker.txt");
      spec_xml_file << "<spectrum filename=\"" << spectrum_xlink_name << "\" type=\"xlinker\">" << std::endl;
      spec_xml_file << getxQuestBase64EncodedSpectrum_(spectra[spectrum_indices[i]], spectrum_light_name + ".dta," + spectrum_heavy_name + ".dta");
      spec_xml_file << "</spectrum>" << std::endl;
    }

    spec_xml_file << "</xquest_spectra>" << std::endl;
    spec_xml_file.close();

    return;
  }

 void getPrecursors_(const PeakMap & exp, vector<Precursor> & precursors, vector<double> & precursors_rt)
 {
   for (Size i = 0; i != exp.size(); ++i)
   {
     vector<Precursor> pcs = exp[i].getPrecursors();
     if (pcs.empty())
     {
       continue;
     }
     vector<double> pcs_rt(pcs.size(), exp[i].getRT());
     copy(pcs.begin(), pcs.end(), back_inserter(precursors));
     copy(pcs_rt.begin(), pcs_rt.end(), back_inserter(precursors_rt));
   }
 }

  void FeatureFinder::run(const String& algorithm_name, PeakMap& input_map, FeatureMap& features, const Param& param, const FeatureMap& seeds)
  {
    // Nothing to do if there is no data
    if ((algorithm_name != "mrm" && input_map.empty()) || (algorithm_name == "mrm" && input_map.getChromatograms().empty()))
    {
      features.clear(true);
      return;
    }

    // check input
    {
      // We need updated ranges => check number of peaks
      if (algorithm_name != "mrm" && input_map.getSize() == 0)
      {
        throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "FeatureFinder needs updated ranges on input map. Aborting.");
      }

      // We need MS1 data only => check levels
      if (algorithm_name != "mrm" && (input_map.getMSLevels().size() != 1 || input_map.getMSLevels()[0] != 1))
      {
        throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "FeatureFinder can only operate on MS level 1 data. Please do not use MS/MS data. Aborting.");
      }

      //Check if the peaks are sorted according to m/z
      if (!input_map.isSorted(true))
      {
        LOG_WARN << "Input map is not sorted by RT and m/z! This is done now, before applying the algorithm!" << std::endl;
        input_map.sortSpectra(true);
        input_map.sortChromatograms(true);
      }
      for (Size s = 0; s < input_map.size(); ++s)
      {
        if (input_map[s].empty())
          continue;
        if (input_map[s][0].getMZ() < 0)
        {
          throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "FeatureFinder can only operate on spectra that contain peaks with positive m/z values. Filter the data accordingly beforehand! Aborting.");
        }
      }
    }

    // initialize
    if (algorithm_name != "mrm" && algorithm_name != "centroided")
    {
      // Resize peak flag vector
      flags_.resize(input_map.size());
      for (Size i = 0; i < input_map.size(); ++i)
      {
        flags_[i].assign(input_map[i].size(), UNUSED);
      }
    }

    // do the work
    if (algorithm_name != "none")
    {
      FeatureFinderAlgorithm* algorithm = Factory<FeatureFinderAlgorithm>::create(algorithm_name);
      algorithm->setParameters(param);
      algorithm->setData(input_map, features, *this);
      algorithm->setSeeds(seeds);
      algorithm->run();
      delete(algorithm);
    }

    if (algorithm_name != "mrm") // mrm  works on chromatograms; the next section is only for conventional data
    {
      //report RT apex spectrum index and native ID for each feature
      for (Size i = 0; i < features.size(); ++i)
      {
        //index
        Size spectrum_index = input_map.RTBegin(features[i].getRT()) - input_map.begin();
        features[i].setMetaValue("spectrum_index", spectrum_index);
        //native id
        if (spectrum_index < input_map.size())
        {
          String native_id = input_map[spectrum_index].getNativeID();
          features[i].setMetaValue("spectrum_native_id", native_id);
        }
        else
        {
          /// @todo that happens sometimes using IsotopeWaveletFeatureFinder (Rene, Marc, Andreas, Clemens)
          std::cerr << "FeatureFinderAlgorithm_impl, line=" << __LINE__ << "; FixMe this cannot be, but happens" << std::endl;
        }
      }
    }
  }

  ExitCodes main_(int, const char **)
  {
    //-------------------------------------------------------------
    // parsing parameters
    //-------------------------------------------------------------
    String in(getStringOption_("in"));
    String out(getStringOption_("out"));
    Size num_spots_per_row(getIntOption_("num_spots_per_row"));
    double RT_distance(getDoubleOption_("RT_distance"));

    //-------------------------------------------------------------
    // reading input
    //-------------------------------------------------------------

    PeakMap exp;
    MzMLFile f;
    f.setLogType(log_type_);
    f.load(in, exp);

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------

    ProgressLogger pl;
    pl.setLogType(log_type_);
    pl.startProgress(0, exp.size(), "Assigning pseudo RTs.");
    Size num_ms1(0), num_ms1_base(0), row_counter(0);
    bool row_to_reverse(false);
    double actual_RT(0);
    for (Size i = 0; i != exp.size(); ++i)
    {
      pl.setProgress(i);
      if (row_to_reverse)
      {
        actual_RT = (double)(num_ms1_base + (num_spots_per_row - row_counter)) * RT_distance;
        writeDebug_("RT=" + String(actual_RT) + " (modified, row_counter=" + String(row_counter) + ")", 1);
      }
      else
      {
        actual_RT = (double)num_ms1 * RT_distance;
        writeDebug_("RT=" + String(actual_RT), 1);
      }

      exp[i].setRT(actual_RT);

      if (exp[i].getMSLevel() == 1)
      {
        if (++row_counter >= num_spots_per_row)
        {
          row_counter = 0;
          if (row_to_reverse)
          {
            row_to_reverse = false;
          }
          else
          {
            row_to_reverse = true;
          }
        }
        ++num_ms1;
        if (!row_to_reverse)
        {
          num_ms1_base = num_ms1;
        }
      }
    }
    pl.endProgress();

    // sort the spectra according to their new RT
    exp.sortSpectra();

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------


    f.store(out, exp);

    return EXECUTION_OK;
  }

  /**
  * @brief Applies the peak-picking algorithm to a map (MSExperiment). This
  * method picks peaks for each scan in the map consecutively. The resulting
  * picked peaks are written to the output map.
  *
  * @param input  input map in profile mode
  * @param output  output map with picked peaks
  * @param boundaries_spec  boundaries of the picked peaks in spectra
  * @param boundaries_chrom  boundaries of the picked peaks in chromatograms
  * @param check_spectrum_type  if set, checks spectrum type and throws an exception if a centroided spectrum is passed 
  */
  void PeakPickerHiRes::pickExperiment(const PeakMap& input, PeakMap& output, 
                                       std::vector<std::vector<PeakBoundary> >& boundaries_spec, 
                                       std::vector<std::vector<PeakBoundary> >& boundaries_chrom,
                                       const bool check_spectrum_type) const
  {
    // make sure that output is clear
    output.clear(true);

    // copy experimental settings
    static_cast<ExperimentalSettings &>(output) = input;

    // resize output with respect to input
    output.resize(input.size());

    Size progress = 0;
    startProgress(0, input.size() + input.getChromatograms().size(), "picking peaks");

    if (input.getNrSpectra() > 0)
    {
      for (Size scan_idx = 0; scan_idx != input.size(); ++scan_idx)
      {
        if (ms_levels_.empty()) // auto mode
        {
          SpectrumSettings::SpectrumType spectrum_type = input[scan_idx].getType();
          if (spectrum_type == SpectrumSettings::CENTROID)
          {
            output[scan_idx] = input[scan_idx];
          }
          else
          {
            std::vector<PeakBoundary> boundaries_s; // peak boundaries of a single spectrum

            pick(input[scan_idx], output[scan_idx], boundaries_s);
            boundaries_spec.push_back(boundaries_s);
          }
        }
        else if (!ListUtils::contains(ms_levels_, input[scan_idx].getMSLevel())) // manual mode
        {
          output[scan_idx] = input[scan_idx];
        }
        else
        {
          std::vector<PeakBoundary> boundaries_s; // peak boundaries of a single spectrum

                                                  // determine type of spectral data (profile or centroided)
          SpectrumSettings::SpectrumType spectrum_type = input[scan_idx].getType();

          if (spectrum_type == SpectrumSettings::CENTROID && check_spectrum_type)
          {
            throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, __FUNCTION__, "Error: Centroided data provided but profile spectra expected.");
          }

          pick(input[scan_idx], output[scan_idx], boundaries_s);
          boundaries_spec.push_back(boundaries_s);
        }
        setProgress(++progress);
      }
    }


    for (Size i = 0; i < input.getChromatograms().size(); ++i)
    {
      MSChromatogram chromatogram;
      std::vector<PeakBoundary> boundaries_c; // peak boundaries of a single chromatogram
      pick(input.getChromatograms()[i], chromatogram, boundaries_c);
      output.addChromatogram(chromatogram);
      boundaries_chrom.push_back(boundaries_c);
      setProgress(++progress);
    }
    endProgress();

    return;
  }

  ExitCodes main_(int, const char **) override
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    //input/output files
    String in(getStringOption_("in"));
    String out(getStringOption_("out"));

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------

    PeakMap exp;
    MzMLFile f;
    f.setLogType(log_type_);

    PeakFileOptions options;
    options.clearMSLevels();
    options.addMSLevel(2);
    f.getOptions() = options;
    f.load(in, exp);

    writeDebug_("Data set contains " + String(exp.size()) + " spectra", 1);

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------

    vector<PeptideIdentification> pep_ids;
    CompNovoIdentificationCID comp_novo_id;

    // set the options
    Param algorithm_param = getParam_().copy("algorithm:", true);
    comp_novo_id.setParameters(algorithm_param);
    comp_novo_id.getIdentifications(pep_ids, exp);
    algorithm_param = comp_novo_id.getParameters();

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------

    DateTime now = DateTime::now();
    String date_string = now.get();
    String identifier("CompNovoCID_" + date_string);

    for (vector<PeptideIdentification>::iterator it = pep_ids.begin(); it != pep_ids.end(); ++it)
    {
      it->assignRanks();
      it->setIdentifier(identifier);
    }

    vector<ProteinIdentification> prot_ids;
    ProteinIdentification prot_id;
    prot_id.setIdentifier(identifier);
    prot_id.setDateTime(now);
    StringList ms_runs;
    exp.getPrimaryMSRunPath(ms_runs);
    prot_id.setPrimaryMSRunPath(ms_runs);

    ProteinIdentification::SearchParameters search_parameters;
    search_parameters.charges = "+2-+3";
    if (algorithm_param.getValue("tryptic_only").toBool())
    {
      search_parameters.digestion_enzyme = *(ProteaseDB::getInstance()->getEnzyme("Trypsin"));
    }
    else
    {
      search_parameters.digestion_enzyme = *(ProteaseDB::getInstance()->getEnzyme("no cleavage"));
    }
    search_parameters.mass_type = ProteinIdentification::MONOISOTOPIC;
    search_parameters.fixed_modifications = algorithm_param.getValue("fixed_modifications");
    search_parameters.variable_modifications = algorithm_param.getValue("variable_modifications");

    search_parameters.missed_cleavages = (UInt)algorithm_param.getValue("missed_cleavages");
    search_parameters.fragment_mass_tolerance = (double)algorithm_param.getValue("fragment_mass_tolerance");
    search_parameters.precursor_mass_tolerance = (double)algorithm_param.getValue("precursor_mass_tolerance");
    search_parameters.fragment_mass_tolerance_ppm = false;
    search_parameters.precursor_mass_tolerance_ppm = false;
    prot_id.setSearchParameters(search_parameters);
    prot_id.setSearchEngineVersion("0.9beta");
    prot_id.setSearchEngine("CompNovo");
    prot_ids.push_back(prot_id);

    IdXMLFile().store(out, prot_ids, pep_ids);

    return EXECUTION_OK;
  }

    // Wrong assignment of the mono-isotopic mass for precursors are assumed:
    // - if precursor_mz matches the mz of a non-monoisotopic feature mass trace
    // - and in the case that believe_charge is true: if feature_charge matches the precursor_charge
    // In the case of wrong mono-isotopic assignment several options for correction are available:
    // keep_original will create a copy of the precursor and tandem spectrum for the new mono-isotopic mass trace and retain the original one
    // all_matching_features does this not for only the closest feature but all features in a question
    set<Size> correctToNearestFeature(const FeatureMap& features, PeakMap & exp, double rt_tolerance_s = 0.0, double mz_tolerance = 0.0, bool ppm = true, bool believe_charge = false, bool keep_original = false, bool all_matching_features = false, int max_trace = 2)
    {
      set<Size> corrected_precursors;
      // for each precursor/MS2 find all features that are in the given tolerance window (bounding box + rt tolerances)
      // if believe_charge is set, only add features that match the precursor charge
      map<Size, set<Size> > scan_idx_to_feature_idx;

      for (Size scan = 0; scan != exp.size(); ++scan)
      {
        // skip non-tandem mass spectra
        if (exp[scan].getMSLevel() != 2 || exp[scan].getPrecursors().empty()) continue;

        // extract precusor / MS2 information
        const double pc_mz = exp[scan].getPrecursors()[0].getMZ();
        const double rt = exp[scan].getRT();
        const int pc_charge = exp[scan].getPrecursors()[0].getCharge();

        for (Size f = 0; f != features.size(); ++f)
        {
          // feature  is incompatible if believe_charge is set and charges don't match
          if (believe_charge && features[f].getCharge() != pc_charge) continue;

          // check if precursor/MS2 position overlap with feature
          if (overlaps_(features[f], rt, pc_mz, rt_tolerance_s))
          {
            scan_idx_to_feature_idx[scan].insert(f);
          }
        }
      }

      // filter sets to retain compatible features:
      // if precursor_mz = feature_mz + n * feature_charge (+/- mz_tolerance) a feature is compatible, others are removed from the set
      for (map<Size, set<Size> >::iterator it = scan_idx_to_feature_idx.begin(); it != scan_idx_to_feature_idx.end(); ++it)
      {
        const Size scan = it->first;
        const double pc_mz = exp[scan].getPrecursors()[0].getMZ();
        const double mz_tolerance_da = ppm ? pc_mz * mz_tolerance * 1e-6  : mz_tolerance;

        // Note: This is the "delete while iterating" pattern so mind the pre- and postincrement
        for (set<Size>::iterator sit = it->second.begin(); sit != it->second.end(); )
        {
          if (!compatible_(features[*sit], pc_mz, mz_tolerance_da, max_trace))
          {
            it->second.erase(sit++);
          }
          else
          {
            ++sit;
          }
        }
      }

      // remove entries with no compatible features (empty sets).
      // Note: This is the "delete while iterating" pattern so mind the pre- and postincrement
      for (map<Size, set<Size> >::iterator it = scan_idx_to_feature_idx.begin(); it != scan_idx_to_feature_idx.end(); )
      {
        if (it->second.empty())
        {
          scan_idx_to_feature_idx.erase(it++);
        }
        else
        {
          ++it;
        }
      }

      if (debug_level_ > 0)
      {
        LOG_INFO << "Number of precursors with compatible features: " << scan_idx_to_feature_idx.size() << endl;
      }

      if (!all_matching_features)
      {
        // keep only nearest features in set
        for (map<Size, set<Size> >::iterator it = scan_idx_to_feature_idx.begin(); it != scan_idx_to_feature_idx.end(); ++it)
        {
          const Size scan = it->first;
          const double pc_rt = exp[scan].getRT();

          double min_distance = 1e16;
          set<Size>::iterator best_feature = it->second.begin();

          // determine nearest/best feature
          for (set<Size>::iterator sit = it->second.begin(); sit != it->second.end(); ++sit)
          {
            const double current_distance = fabs(pc_rt - features[*sit].getRT());
            if (current_distance < min_distance)
            {
              min_distance = current_distance;
              best_feature = sit;
            }
          }

          // delete all except the nearest/best feature
//.........这里部分代码省略.........

  ExitCodes main_(int argc, const char** argv)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    //input/output files
    String in(getStringOption_("in")), out(getStringOption_("out"));
    FileHandler fh;
    FileTypes::Type in_type = fh.getType(in);

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------

    PeakMap exp;
    // keep only MS2 spectra
    fh.getOptions().addMSLevel(2);
    fh.loadExperiment(in, exp, in_type, log_type_);
    writeDebug_(String("Spectra loaded: ") + exp.size(), 2);

    if (exp.getSpectra().empty())
    {
      throw OpenMS::Exception::FileEmpty(__FILE__, __LINE__, __FUNCTION__, "Error: No MS2 spectra in input file.");
    }

    // determine type of spectral data (profile or centroided)
    SpectrumSettings::SpectrumType spectrum_type = exp[0].getType();

    if (spectrum_type == SpectrumSettings::RAWDATA)
    {
      if (!getFlag_("force"))
      {
        throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, __FUNCTION__, "Error: Profile data provided but centroided MS2 spectra expected. To enforce processing of the data set the -force flag.");
      }
    }

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------

    Param mascot_param = getParam_().copy("Mascot_parameters:", true);
    MascotGenericFile mgf_file;
    Param p;
    // TODO: switch this to mzML (much smaller)
    p.setValue("internal:format", "Mascot generic", "Sets the format type of the peak list, this should not be changed unless you write the header only.", ListUtils::create<String>("advanced"));
    p.setValue("internal:HTTP_format", "true", "Write header with MIME boundaries instead of simple key-value pairs. For HTTP submission only.", ListUtils::create<String>("advanced"));
    p.setValue("internal:content", "all", "Use parameter header + the peak lists with BEGIN IONS... or only one of them.", ListUtils::create<String>("advanced"));
    mgf_file.setParameters(mascot_param);

    // get the spectra into string stream
    writeDebug_("Writing MGF file to stream", 1);
    stringstream ss;
    mgf_file.store(ss, in, exp, true); // write in compact format

    // Usage of a QCoreApplication is overkill here (and ugly too), but we just use the
    // QEventLoop to process the signals and slots and grab the results afterwards from
    // the MascotRemotQuery instance
    char** argv2 = const_cast<char**>(argv);
    QCoreApplication event_loop(argc, argv2);
    MascotRemoteQuery* mascot_query = new MascotRemoteQuery(&event_loop);
    Param mascot_query_param = getParam_().copy("Mascot_server:", true);
    writeDebug_("Setting parameters for Mascot query", 1);
    mascot_query->setParameters(mascot_query_param);
    writeDebug_("Setting spectra for Mascot query", 1);
    mascot_query->setQuerySpectra(ss.str());

    // remove unnecessary spectra
    ss.clear();

    QObject::connect(mascot_query, SIGNAL(done()), &event_loop, SLOT(quit()));
    QTimer::singleShot(1000, mascot_query, SLOT(run()));
    writeDebug_("Fire off Mascot query", 1);
    event_loop.exec();
    writeDebug_("Mascot query finished", 1);

    if (mascot_query->hasError())
    {
      writeLog_("An error occurred during the query: " + mascot_query->getErrorMessage());
      delete mascot_query;
      return EXTERNAL_PROGRAM_ERROR;
    }

    // write Mascot response to file
    String mascot_tmp_file_name(File::getTempDirectory() + "/" + File::getUniqueName() + "_Mascot_response");
    QFile mascot_tmp_file(mascot_tmp_file_name.c_str());
    mascot_tmp_file.open(QIODevice::WriteOnly);
    mascot_tmp_file.write(mascot_query->getMascotXMLResponse());
    mascot_tmp_file.close();

    // clean up
    delete mascot_query;

    vector<PeptideIdentification> pep_ids;
    ProteinIdentification prot_id;

    // set up mapping between scan numbers and retention times:
    MascotXMLFile::RTMapping rt_mapping;
    MascotXMLFile::generateRTMapping(exp.begin(), exp.end(), rt_mapping);

//.........这里部分代码省略.........

  ExitCodes
  main_(int, const char**)
  {
    //-------------------------------------------------------------
    // general variables and data
    //-------------------------------------------------------------
    FileHandler fh;
    vector<PeptideIdentification> peptide_identifications;
    vector<ProteinIdentification> protein_identifications;

    //-------------------------------------------------------------
    // reading input
    //-------------------------------------------------------------
    const String in = getStringOption_("in");

    ProgressLogger logger;
    logger.setLogType(ProgressLogger::CMD);
    logger.startProgress(0, 1, "Loading...");

    if (File::isDirectory(in))
    {
      const String in_directory = File::absolutePath(in).ensureLastChar('/');
      const String mz_file = getStringOption_("mz_file");
      const bool ignore_proteins_per_peptide = getFlag_("ignore_proteins_per_peptide");

      UInt i = 0;
      FileHandler fh;
      FileTypes::Type type;
      MSExperiment<Peak1D> msexperiment;
      // Note: we had issues with leading zeroes, so let us represent scan numbers as Int (next line used to be map<String, float> num_and_rt;)  However, now String::toInt() might throw.
      map<Int, float> num_and_rt;
      vector<String> NativeID;

      // The mz-File (if given)
      if (!mz_file.empty())
      {
        type = fh.getTypeByFileName(mz_file);
        fh.loadExperiment(mz_file, msexperiment, type);

        for (MSExperiment<Peak1D>::Iterator spectra_it = msexperiment.begin(); spectra_it != msexperiment.end(); ++spectra_it)
        {
          String(spectra_it->getNativeID()).split('=', NativeID);
          try
          {
            num_and_rt[NativeID[1].toInt()] = spectra_it->getRT();
            // cout << "num_and_rt: " << NativeID[1] << " = " << NativeID[1].toInt() << " : " << num_and_rt[NativeID[1].toInt()] << endl; // CG debuggging 2009-07-01
          }
          catch (Exception::ConversionError& e)
          {
            writeLog_(String("Error: Cannot read scan number as integer. '") + e.getMessage());
          }
        }
      }

      // Get list of the actual Sequest .out-Files
      StringList in_files;
      if (!File::fileList(in_directory, String("*.out"), in_files))
      {
        writeLog_(String("Error: No .out files found in '") + in_directory + "'. Aborting!");
      }

      // Now get to work ...
      for (vector<String>::const_iterator in_files_it = in_files.begin(); in_files_it != in_files.end(); ++in_files_it)
      {
        vector<PeptideIdentification> peptide_ids_seq;
        ProteinIdentification protein_id_seq;
        vector<double> pvalues_seq;
        vector<String> in_file_vec;

        SequestOutfile sequest_outfile;

        writeDebug_(String("Reading file ") + *in_files_it, 3);

        try
        {
          sequest_outfile.load((String) (in_directory + *in_files_it), peptide_ids_seq, protein_id_seq, 1.0, pvalues_seq, "Sequest", ignore_proteins_per_peptide);

          in_files_it->split('.', in_file_vec);

          for (Size j = 0; j < peptide_ids_seq.size(); ++j)
          {

            // We have to explicitly set the identifiers, because the normal set ones are composed of search engine name and date, which is the same for a bunch of sequest out-files.
            peptide_ids_seq[j].setIdentifier(*in_files_it + "_" + i);

            Int scan_number = 0;
            if (!mz_file.empty())
            {
              try
              {
                scan_number = in_file_vec[2].toInt();
                peptide_ids_seq[j].setRT(num_and_rt[scan_number]);
              }
              catch (Exception::ConversionError& e)
              {
                writeLog_(String("Error: Cannot read scan number as integer. '") + e.getMessage());
              }
              catch (exception& e)
              {
                writeLog_(String("Error: Cannot read scan number as integer. '") + e.what());
//.........这里部分代码省略.........

  TOLERANCE_ABSOLUTE(0.01)

  MzDataFile file;
  PeakMap e;

  // real test
  file.load(OPENMS_GET_TEST_DATA_PATH("MzDataFile_1.mzData"), e);

  //test DocumentIdentifier addition
  TEST_STRING_EQUAL(e.getLoadedFilePath(), OPENMS_GET_TEST_DATA_PATH("MzDataFile_1.mzData"));
  TEST_STRING_EQUAL(FileTypes::typeToName(e.getLoadedFileType()), "mzData");

  //---------------------------------------------------------------------------
  // ms-level, RT, native ID
  //---------------------------------------------------------------------------
  TEST_EQUAL(e.size(), 3)
  TEST_EQUAL(e[0].getMSLevel(), 1)
  TEST_EQUAL(e[1].getMSLevel(), 2)
  TEST_EQUAL(e[2].getMSLevel(), 1)
  TEST_REAL_SIMILAR(e[0].getRT(), 60)
  TEST_REAL_SIMILAR(e[1].getRT(), 120)
  TEST_REAL_SIMILAR(e[2].getRT(), 180)
  TEST_STRING_EQUAL(e[0].getNativeID(), "spectrum=10")
  TEST_STRING_EQUAL(e[1].getNativeID(), "spectrum=11")
  TEST_STRING_EQUAL(e[2].getNativeID(), "spectrum=12")
  TEST_EQUAL(e[0].getType(), SpectrumSettings::UNKNOWN)

  //---------------------------------------------------------------------------
  //meta data array meta data
  //---------------------------------------------------------------------------
  TEST_EQUAL(e[0].getFloatDataArrays()[0].getMetaValue("URL"), "www.open-ms.de")

  TOLERANCE_ABSOLUTE(0.01)

  PeakMap e;
  DTA2DFile file;

  //test exception
  TEST_EXCEPTION( Exception::FileNotFound , file.load("dummy/dummy.dta2d",e) )

  // real test
  file.load(OPENMS_GET_TEST_DATA_PATH("DTA2DFile_test_1.dta2d"),e);

  //test DocumentIdentifier addition
  TEST_STRING_EQUAL(e.getLoadedFilePath(), OPENMS_GET_TEST_DATA_PATH("DTA2DFile_test_1.dta2d"));
  TEST_STRING_EQUAL(FileTypes::typeToName(e.getLoadedFileType()),"dta2d");

  TEST_EQUAL(e.size(), 9);
  ABORT_IF(e.size() != 9)

  TEST_STRING_EQUAL(e[0].getNativeID(),"index=0")
  TEST_STRING_EQUAL(e[1].getNativeID(),"index=1")
  TEST_STRING_EQUAL(e[2].getNativeID(),"index=2")
  TEST_STRING_EQUAL(e[3].getNativeID(),"index=3")
  TEST_STRING_EQUAL(e[4].getNativeID(),"index=4")
  TEST_STRING_EQUAL(e[5].getNativeID(),"index=5")
  TEST_STRING_EQUAL(e[6].getNativeID(),"index=6")
  TEST_STRING_EQUAL(e[7].getNativeID(),"index=7")
  TEST_STRING_EQUAL(e[8].getNativeID(),"index=8")

  PeakMap::const_iterator it(e.begin());
  TEST_REAL_SIMILAR((*it)[0].getPosition()[0], 230.02)
  TEST_REAL_SIMILAR(it->getRT(), 4711.1)

	chrom2.setChromatogramType(ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM);
	ChromatogramPeak peak1, peak2, peak3;
	peak1.setRT(0.1);
	peak2.setRT(0.2);
	peak3.setRT(0.3);
	chrom1.push_back(peak1);
	chrom1.push_back(peak2);

	chrom2.push_back(peak2);
	chrom2.push_back(peak2);

	exp.addChromatogram(chrom1);
	exp.addChromatogram(chrom2);

	TEST_EQUAL(exp.size(), 0)
	TEST_EQUAL(exp.getChromatograms().size(), 2)
	ChromatogramTools().convertChromatogramsToSpectra(exp);
	TEST_EQUAL(exp.size(), 4)
	TEST_EQUAL(exp.getChromatograms().size(), 0)
	TEST_REAL_SIMILAR(exp[0][0].getMZ(), 200.1)

	TEST_EQUAL(exp[0].getPrecursors().size(), 1)
	TEST_REAL_SIMILAR(exp[0].getPrecursors().begin()->getMZ(), 100.1)


}
END_SECTION

START_SECTION(template <typename ExperimentType> void convertSpectraToChromatograms(ExperimentType& exp, bool remove_spectra = false))
{

//.........这里部分代码省略.........
    infile.write(input_filename);

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------

    int status = QProcess::execute(xtandem_executable.toQString(), QStringList(input_filename.toQString())); // does automatic escaping etc...
    if (status != 0)
    {
      writeLog_("XTandem problem. Aborting! Calling command was: '" + xtandem_executable + " \"" + input_filename + "\"'.\nDoes the !XTandem executable exist?");
      // clean temporary files
      if (this->debug_level_ < 2)
      {
        File::removeDirRecursively(temp_directory);
        LOG_WARN << "Set debug level to >=2 to keep the temporary files at '" << temp_directory << "'" << std::endl;
      }
      else
      {
        LOG_WARN << "Keeping the temporary files at '" << temp_directory << "'. Set debug level to <2 to remove them." << std::endl;
      }
      return EXTERNAL_PROGRAM_ERROR;
    }

    vector<ProteinIdentification> protein_ids;
    ProteinIdentification protein_id;
    vector<PeptideIdentification> peptide_ids;

    // read the output of X!Tandem and write it to idXML
    XTandemXMLFile tandem_output;
    tandem_output.setModificationDefinitionsSet(ModificationDefinitionsSet(getStringList_("fixed_modifications"), getStringList_("variable_modifications")));
    // find the file, because XTandem extends the filename with a timestamp we do not know (exactly)
    StringList files;
    File::fileList(temp_directory, "_tandem_output_file*.xml", files);
    if (files.size() != 1)
    {
      throw Exception::FileNotFound(__FILE__, __LINE__, __PRETTY_FUNCTION__, tandem_output_filename);
    }
    tandem_output.load(temp_directory + files[0], protein_id, peptide_ids);

    // now put the RTs into the peptide_ids from the spectrum ids
    for (vector<PeptideIdentification>::iterator it = peptide_ids.begin(); it != peptide_ids.end(); ++it)
    {
      UInt id = (Int)it->getMetaValue("spectrum_id");
      --id; // native IDs were written 1-based
      if (id < exp.size())
      {
        it->setRT(exp[id].getRT());
        double pre_mz(0.0);
        if (!exp[id].getPrecursors().empty()) pre_mz = exp[id].getPrecursors()[0].getMZ();
        it->setMZ(pre_mz);
        //it->removeMetaValue("spectrum_id");
      }
      else
      {
        LOG_ERROR << "XTandemAdapter: Error: id '" << id << "' not found in peak map!" << endl;
      }
    }

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------

    // handle the search parameters
    ProteinIdentification::SearchParameters search_parameters;
    search_parameters.db = getStringOption_("database");
    search_parameters.charges = "+" + String(getIntOption_("min_precursor_charge")) + "-+" + String(getIntOption_("max_precursor_charge"));

START_SECTION((SpectraMerger(const SpectraMerger& source)))
	SpectraMerger copy(*e_ptr);
	TEST_EQUAL(copy.getParameters(), e_ptr->getParameters())
END_SECTION

START_SECTION((SpectraMerger& operator=(const SpectraMerger& source)))
	SpectraMerger copy;
	copy = *e_ptr;
	TEST_EQUAL(copy.getParameters(), e_ptr->getParameters())
END_SECTION

START_SECTION((template < typename MapType > void mergeSpectraBlockWise(MapType &exp)))
	PeakMap exp, exp2;
	MzMLFile().load(OPENMS_GET_TEST_DATA_PATH("SpectraMerger_input_2.mzML"), exp);
	TEST_EQUAL(exp.size(), 144)

  exp2 = exp;

	SpectraMerger merger;
  Param p;
  p.setValue("block_method:rt_block_size", 5);
  p.setValue("block_method:ms_levels", IntList::create(StringList::create("1")));
  merger.setParameters(p);
  merger.mergeSpectraBlockWise(exp);
  TEST_EQUAL(exp.size(), 130);
  exp=exp2;

  p.setValue("block_method:rt_block_size", 4);
  p.setValue("block_method:ms_levels", IntList::create(StringList::create("2")));
  merger.setParameters(p);