ExitCodes main_(int, const char **)
  {

    String in = getStringOption_("in");
    String out = getStringOption_("out");
    String tr_file = getStringOption_("tr");
    bool force = getFlag_("force");

    boost::shared_ptr<PeakMap > exp ( new PeakMap );
    MzMLFile mzmlfile;
    mzmlfile.setLogType(log_type_);
    mzmlfile.load(in, *exp);

    TargetedExpType transition_exp;
    TraMLFile().load(tr_file, transition_exp);

    FeatureMap output;
    OpenSwath::SpectrumAccessPtr input = SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr(exp);
    run_(input, output, transition_exp, force);

    output.ensureUniqueId();
    StringList ms_runs;
    exp->getPrimaryMSRunPath(ms_runs);
    output.setPrimaryMSRunPath(ms_runs);
    FeatureXMLFile().store(out, output);

    return EXECUTION_OK;
  }
Example #2
0
  ExitCodes main_(int, const char **)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    String in = getStringOption_("in");
    String out = getStringOption_("out");

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------
    MzMLFile mzMLFile;
    mzMLFile.setLogType(log_type_);
    MSExperiment<Peak1D> input;
    mzMLFile.getOptions().addMSLevel(1);
    mzMLFile.load(in, input);

    if (input.empty())
    {
      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 if spectra are sorted
    for (Size i = 0; i < input.size(); ++i)
    {
      if (!input[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;
      }
    }

    //-------------------------------------------------------------
    // pick
    //-------------------------------------------------------------
    FeatureMap<> output;

    FeatureFinder ff;
    Param param = getParam_().copy("algorithm:", true);

    FFSH ffsh;
    ffsh.setParameters(param);
    ffsh.setData(input, output, ff);
    ffsh.run();

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------
    //annotate output with data processing info
    addDataProcessing_(output, getProcessingInfo_(DataProcessing::PEAK_PICKING));
    addDataProcessing_(output, getProcessingInfo_(DataProcessing::QUANTITATION));
    output.ensureUniqueId();
    for (Size i = 0; i < output.size(); i++)
    {
      output[i].ensureUniqueId();
    }
    FeatureXMLFile().store(out, output);

    return EXECUTION_OK;
  }