// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry               
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathHelper.h>

#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/FORMAT/TraMLFile.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

using namespace std;

#ifdef _OPENMP
  #define IF_MASTERTHREAD if (omp_get_thread_num() ==0)  
#else
  #define IF_MASTERTHREAD 
#endif    

using namespace OpenMS;

//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------

/**
  @page TOPP_OpenSwathChromatogramExtractor OpenSwathChromatogramExtractor

  @brief Extracts chromatograms (XICs) from a file containing spectra.

  <CENTER>
      <table>
          <tr>
              <td ALIGN = "center" BGCOLOR="#EBEBEB"> potential predecessor tools </td>
              <td VALIGN="middle" ROWSPAN=2> \f$ \longrightarrow \f$ OpenSwathChromatogramExtractor \f$ \longrightarrow \f$</td>
              <td ALIGN = "center" BGCOLOR="#EBEBEB"> potential successor tools </td>
          </tr>
          <tr>
              <td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_FileFilter </td>
              <td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_OpenSwathAnalyzer </td>
          </tr>
      </table>
  </CENTER>

  This module extracts ion traces (extracted ion chromatograms or XICs) from a
  file containing spectra.  The masses at which the chromatograms should be
  extracted are stored in a TraML file and the result is stored in a mzML file
  holding chromatograms. This tool is designed to extract chromatogams from
  SWATH (data independent acquisition) data (see ref[1]), thus it will extract
  the masses found in the product ion section of the TraML transitions,
  returning as many chromatograms as input transitions were provided.

  For SWATH data, the "is_swath" flag which will check the precursor
  isolation window of the first scan and assume all scans in that file were
  recorded with this precursor window (thus making it necessary to provide one
  input file per SWATH window). The module will then only extract transitions
  whose precursors fall into the corresponding isolation window.

  For the extraction method, two convolution functions are available: top-hat
  and bartlett. While top-hat will just sum up the signal within a quadratic
  window, bartlett will weigh the signal in the center of the window more than
  the signal on the edge.

  [1] Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R. \n
  <a href="http://dx.doi.org/10.1074/mcp.O111.016717"> Targeted data extraction of the MS/MS spectra generated by data-independent
  acquisition: a new concept for consistent and accurate proteome analysis. </a> \n
  Mol Cell Proteomics. 2012 Jun;11(6):O111.016717. 

  <B>The command line parameters of this tool are:</B>
  @verbinclude TOPP_OpenSwathChromatogramExtractor.cli
 
  <B>The algorithm parameters for the Analyzer filter are:</B>
  @htmlinclude TOPP_OpenSwathChromatogramExtractor.html

*/

// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPOpenSwathChromatogramExtractor 
  : public TOPPBase
{
public:

  TOPPOpenSwathChromatogramExtractor() 
    : TOPPBase("OpenSwathChromatogramExtractor", "Extract chromatograms (XIC) from a MS2 map file.", true)
  {
  }

protected:

  void registerOptionsAndFlags_()
  {
    registerInputFileList_("in", "<files>", StringList(), "Input files separated by blank");
    setValidFormats_("in", StringList::create("mzML"));

    registerInputFile_("tr", "<file>", "", "transition file ('TraML' or 'csv')");
    setValidFormats_("tr", StringList::create("csv,traML"));
    
    registerInputFile_("rt_norm", "<file>", "", "RT normalization file (how to map the RTs of this run to the ones stored in the library)", false);
    setValidFormats_("rt_norm", StringList::create("trafoXML"));

    registerOutputFile_("out", "<file>", "", "output file");
    setValidFormats_("out", StringList::create("mzML"));

    registerDoubleOption_("min_upper_edge_dist", "<double>", 0.0, "Minimal distance to the edge to still consider a precursor, in Thomson", false);
    registerDoubleOption_("extraction_window", "<double>", 0.05, "Extraction window used (in Thomson, to use ppm see -ppm flag)", false);
    registerDoubleOption_("rt_extraction_window", "<double>", -1, "Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution).", false);
    setMinFloat_("extraction_window", 0.0);

    registerFlag_("is_swath", "Set this flag if the data is SWATH data");
    registerFlag_("ppm", "extraction_window is in ppm");

    registerStringOption_("extraction_function", "<name>", "tophat", "Function used to extract the signal", false);
    StringList model_types;
    model_types.push_back("tophat");
    model_types.push_back("bartlett"); // bartlett if we use zeros at the end
    setValidStrings_("extraction_function", model_types);

    registerModelOptions_("linear");
  }

  void registerModelOptions_(const String & default_model)
  {
    registerTOPPSubsection_("model", "Options to control the modeling of retention time transformations from data");
    registerStringOption_("model:type", "<name>", default_model, "Type of model", false);
    StringList model_types;
    TransformationDescription::getModelTypes(model_types);
    if (!model_types.contains(default_model)) {
      model_types.insert(model_types.begin(), default_model);
    }
    setValidStrings_("model:type", model_types);
    registerFlag_("model:symmetric_regression", "Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.");
    registerIntOption_("model:num_breakpoints", "<number>", 5,
        "Only for 'b_spline' model: Number of breakpoints of the cubic spline in the smoothing step. The breakpoints are spaced uniformly on the retention time interval. More breakpoints mean less smoothing. Reduce this number if the transformation has an unexpected shape.",
        false);
    setMinInt_("model:num_breakpoints", 2);
    registerStringOption_("model:interpolation_type", "<name>", "cspline", "Only for 'interpolated' model: Type of interpolation to apply.", false);
  }

  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");
    DoubleReal min_upper_edge_dist = getDoubleOption_("min_upper_edge_dist");
    DoubleReal extraction_window = getDoubleOption_("extraction_window");
    DoubleReal rt_extraction_window = getDoubleOption_("rt_extraction_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);
    }

    const char * tr_file = tr_file_str.c_str();

    typedef MSExperiment<Peak1D> MapType;

    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)
    {
      MapType exp;
      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);
      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.
      if (i == 0) 
      {
        out_exp = exp;
        out_exp.clear(false);
      }

      // continue if the map is not empty
      if (do_continue)
      {
        std::cout << "Extracting " << transition_exp_used.getTransitions().size() << " transitions" << std::endl;
        ChromatogramExtractor extractor;
        IF_MASTERTHREAD extractor.setLogType(log_type_); // no progress log on the console in parallel
        extractor.extractChromatograms(exp, tmp_out, transition_exp_used, extraction_window, ppm, trafo, rt_extraction_window, extraction_function);

        // adding the chromatogram to the output needs to be atomic
#ifdef _OPENMP
#pragma omp critical (OpenSwathChromatogramExtractor_insert)
#endif
        {
          chromatograms.reserve(chromatograms.size() + distance(tmp_out.getChromatograms().begin(),tmp_out.getChromatograms().end()));
          chromatograms.insert(chromatograms.end(), tmp_out.getChromatograms().begin(), tmp_out.getChromatograms().end());
        }

      } // 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;
  }

};


int main(int argc, const char ** argv)
{
  TOPPOpenSwathChromatogramExtractor tool;
  return tool.main(argc, argv);
}

/// @endcond