Пример #1
0
  ExitCodes main_(int, const char**)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    String in = getStringOption_("in");
    String out = getStringOption_("out");
    String trafo_in = getStringOption_("trafo_in");
    String trafo_out = getStringOption_("trafo_out");
    Param model_params = getParam_().copy("model:", true);
    String model_type = model_params.getValue("type");
    model_params = model_params.copy(model_type + ":", true);

    ProgressLogger progresslogger;
    progresslogger.setLogType(log_type_);

    //-------------------------------------------------------------
    // check for valid input
    //-------------------------------------------------------------
    if (out.empty() && trafo_out.empty())
    {
      writeLog_("Error: Either a data or a transformation output file has to be provided (parameters 'out'/'trafo_out')");
      return ILLEGAL_PARAMETERS;
    }
    if (in.empty() != out.empty())
    {
      writeLog_("Error: Data input and output parameters ('in'/'out') must be used together");
      return ILLEGAL_PARAMETERS;
    }

    //-------------------------------------------------------------
    // apply transformation
    //-------------------------------------------------------------
    TransformationXMLFile trafoxml;
    TransformationDescription trafo;
    trafoxml.load(trafo_in, trafo);
    if (model_type != "none")
    {
      trafo.fitModel(model_type, model_params);
    }
    if (getFlag_("invert"))
    {
      trafo.invert();
    }
    if (!trafo_out.empty())
    {
      trafoxml.store(trafo_out, trafo);
    }
    if (!in.empty()) // load input
    {
      FileTypes::Type in_type = FileHandler::getType(in);
      if (in_type == FileTypes::MZML)
      {
        MzMLFile file;
        MSExperiment<> map;
        applyTransformation_(in, out, trafo, file, map);
      }
      else if (in_type == FileTypes::FEATUREXML)
      {
        FeatureXMLFile file;
        FeatureMap map;
        applyTransformation_(in, out, trafo, file, map);
      }
      else if (in_type == FileTypes::CONSENSUSXML)
      {
        ConsensusXMLFile file;
        ConsensusMap map;
        applyTransformation_(in, out, trafo, file, map);
      }
      else if (in_type == FileTypes::IDXML)
      {
        IdXMLFile file;
        vector<ProteinIdentification> proteins;
        vector<PeptideIdentification> peptides;
        file.load(in, proteins, peptides);
        bool store_original_rt = getFlag_("store_original_rt");
        MapAlignmentTransformer::transformRetentionTimes(peptides, trafo,
                                                         store_original_rt);
        // no "data processing" section in idXML
        file.store(out, proteins, peptides);
      }
    }

    return EXECUTION_OK;
  }
  ExitCodes main_(int, const char **)
  {
    StringList file_list = getStringList_("in");
    String tr_file_str = getStringOption_("tr");
    String out = getStringOption_("out");
    bool is_swath = getFlag_("is_swath");
    bool ppm = getFlag_("ppm");
    bool extract_MS1 = getFlag_("extract_MS1");
    double min_upper_edge_dist = getDoubleOption_("min_upper_edge_dist");
    double mz_extraction_window = getDoubleOption_("mz_window");
    double rt_extraction_window = getDoubleOption_("rt_window");

    String extraction_function = getStringOption_("extraction_function");

    // If we have a transformation file, trafo will transform the RT in the
    // scoring according to the model. If we dont have one, it will apply the
    // null transformation.
    String trafo_in = getStringOption_("rt_norm");
    TransformationDescription trafo;
    if (trafo_in.size() > 0) 
    {
      TransformationXMLFile trafoxml;

      String model_type = getStringOption_("model:type");
      Param model_params = getParam_().copy("model:", true);
      trafoxml.load(trafo_in, trafo);
      trafo.fitModel(model_type, model_params);
    }
    TransformationDescription trafo_inverse = trafo;
    trafo_inverse.invert();

    const char * tr_file = tr_file_str.c_str();

    MapType out_exp;
    std::vector< OpenMS::MSChromatogram > chromatograms;
    TraMLFile traml;
    OpenMS::TargetedExperiment targeted_exp;

    std::cout << "Loading TraML file" << std::endl;
    traml.load(tr_file, targeted_exp);
    std::cout << "Loaded TraML file" << std::endl;

    // Do parallelization over the different input files
    // Only in OpenMP 3.0 are unsigned loop variables allowed
#ifdef _OPENMP
#pragma omp parallel for
#endif
    for (SignedSize i = 0; i < boost::numeric_cast<SignedSize>(file_list.size()); ++i)
    {
      boost::shared_ptr<PeakMap > exp(new PeakMap);
      MzMLFile f;
      // Logging and output to the console
      // IF_MASTERTHREAD f.setLogType(log_type_); 

      // Find the transitions to extract and extract them
      MapType tmp_out;
      OpenMS::TargetedExperiment transition_exp_used;
      f.load(file_list[i], *exp);
      if (exp->empty() ) { continue; } // if empty, go on
      OpenSwath::SpectrumAccessPtr expptr = SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr(exp);
      bool do_continue = true;
      if (is_swath)
      {
        do_continue = OpenSwathHelper::checkSwathMapAndSelectTransitions(*exp, targeted_exp, transition_exp_used, min_upper_edge_dist);  
      }
      else
      {
        transition_exp_used = targeted_exp;
      }

#ifdef _OPENMP
#pragma omp critical (OpenSwathChromatogramExtractor_metadata)
#endif
      // after loading the first file, copy the meta data from that experiment
      // this may happen *after* chromatograms were already added to the
      // output, thus we do NOT fill the experiment here but rather store all
      // the chromatograms in the "chromatograms" array and store them in
      // out_exp afterwards.
      if (i == 0) 
      {
        out_exp = *exp;
        out_exp.clear(false);
      }

      std::cout << "Extracting " << transition_exp_used.getTransitions().size() << " transitions" << std::endl;
      std::vector< OpenSwath::ChromatogramPtr > chromatogram_ptrs;
      std::vector< ChromatogramExtractor::ExtractionCoordinates > coordinates;

      // continue if the map is not empty
      if (do_continue)
      {

        // Prepare the coordinates (with or without rt extraction) and then extract the chromatograms
        ChromatogramExtractor extractor;
        if (rt_extraction_window < 0)
        {
          extractor.prepare_coordinates(chromatogram_ptrs, coordinates, transition_exp_used, rt_extraction_window, extract_MS1);
        }
        else
        {
          // Use an rt extraction window of 0.0 which will just write the retention time in start / end positions
          extractor.prepare_coordinates(chromatogram_ptrs, coordinates, transition_exp_used, 0.0, extract_MS1);
          for (std::vector< ChromatogramExtractor::ExtractionCoordinates >::iterator it = coordinates.begin(); it != coordinates.end(); ++it)
          {
            it->rt_start = trafo_inverse.apply(it->rt_start) - rt_extraction_window / 2.0;
            it->rt_end = trafo_inverse.apply(it->rt_end) + rt_extraction_window / 2.0;
          }
        }
        extractor.extractChromatograms(expptr, chromatogram_ptrs, coordinates, 
            mz_extraction_window, ppm, extraction_function);

#ifdef _OPENMP
#pragma omp critical (OpenSwathChromatogramExtractor_insertMS1)
#endif
        {
          // Remove potential meta value indicating cached data
          SpectrumSettings exp_settings = (*exp)[0];
          for (Size j = 0; j < exp_settings.getDataProcessing().size(); j++)
          {
            if (exp_settings.getDataProcessing()[j]->metaValueExists("cached_data"))
            { exp_settings.getDataProcessing()[j]->removeMetaValue("cached_data"); }
          }
          extractor.return_chromatogram(chromatogram_ptrs, coordinates, transition_exp_used, exp_settings, chromatograms, extract_MS1);
        }

      } // end of do_continue
    } // end of loop over all files / end of OpenMP

    // TODO check that no chromatogram IDs occur multiple times !
    
    // store the output
    out_exp.setChromatograms(chromatograms);
    MzMLFile mzf;
    mzf.setLogType(log_type_); 
    addDataProcessing_(out_exp, getProcessingInfo_(DataProcessing::SMOOTHING));
    mzf.store(out, out_exp);

    return EXECUTION_OK;
  }