C++ PeakMap::empty方法代码示例

  ExitCodes main_(int, const char **)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    in = getStringOption_("in");
    out = getStringOption_("out");
    String process_option = getStringOption_("processOption");

    Param filter_param = getParam_().copy("algorithm:", true);
    writeDebug_("Parameters passed to filter", filter_param, 3);

    SavitzkyGolayFilter sgolay;
    sgolay.setLogType(log_type_);
    sgolay.setParameters(filter_param);

    if (process_option == "lowmemory")
    {
      return doLowMemAlgorithm(sgolay);
    }

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------
    MzMLFile mz_data_file;
    mz_data_file.setLogType(log_type_);
    PeakMap exp;
    mz_data_file.load(in, exp);

    if (exp.empty() && exp.getChromatograms().size() == 0)
    {
      LOG_WARN << "The given file does not contain any conventional peak data, but might"
                  " contain chromatograms. This tool currently cannot handle them, sorry.";
      return INCOMPATIBLE_INPUT_DATA;
    }
    //check for peak type (profile data required)
    if (!exp.empty() && PeakTypeEstimator().estimateType(exp[0].begin(), exp[0].end()) == SpectrumSettings::PEAKS)
    {
      writeLog_("Warning: OpenMS peak type estimation indicates that this is not profile data!");
    }

    //check if spectra are sorted
    for (Size i = 0; i < exp.size(); ++i)
    {
      if (!exp[i].isSorted())
      {
        writeLog_("Error: Not all spectra are sorted according to peak m/z positions. Use FileFilter to sort the input!");
        return INCOMPATIBLE_INPUT_DATA;
      }
    }

    //check if chromatograms are sorted
    for (Size i = 0; i < exp.getChromatograms().size(); ++i)
    {
      if (!exp.getChromatogram(i).isSorted())
      {
        writeLog_("Error: Not all chromatograms are sorted according to peak m/z positions. Use FileFilter to sort the input!");
        return INCOMPATIBLE_INPUT_DATA;
      }
    }

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------
    sgolay.filterExperiment(exp);

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

    //annotate output with data processing info
    addDataProcessing_(exp, getProcessingInfo_(DataProcessing::SMOOTHING));

    mz_data_file.store(out, exp);

    return EXECUTION_OK;
  }

  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;
        }
      }
    }
  }