DTA2DFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/CONCEPT/PrecisionWrapper.h>
 
#include <fstream>
#include <iostream>
 
namespace OpenMS
{
  class OPENMS_DLLAPI DTA2DFile :
    public ProgressLogger
  {
private:
    PeakFileOptions options_;
 
public:
 
    DTA2DFile();
    ~DTA2DFile() override;
 
    PeakFileOptions& getOptions();
 
    const PeakFileOptions& getOptions() const;
 
    template <typename MapType>
    void load(const String& filename, MapType& map)
    {
      startProgress(0, 0, "loading DTA2D file");
 
      //try to open file
      std::ifstream is(filename.c_str());
      if (!is)
      {
        throw Exception::FileNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
      }
 
      map.reset();
 
      //set DocumentIdentifier
      map.setLoadedFileType(filename);
      map.setLoadedFilePath(filename);
 
      // temporary variables to store the data in
      std::vector<String> strings(3);
      typename MapType::SpectrumType spec;
      spec.setRT(-1.0); //to make sure the first RT is different from the the initialized value
      typename MapType::SpectrumType::PeakType p;
      double rt(0.0);
      char delimiter;
 
      // default dimension of the data
      Size rt_dim = 0;
      Size mz_dim = 1;
      Size int_dim = 2;
 
      //RT unit (default is seconds)
      bool time_in_minutes = false;
 
      // string to store the current line in
      String line;
 
      // native ID (numbers from 0)
      UInt native_id = 0;
 
      // line number counter
      Size line_number = 0;
 
      while (getline(is, line, '\n'))
      {
        ++line_number;
        line.trim();
 
        if (line.empty()) continue;
 
        //test which delimiter is used in the line
        if (line.has('\t'))
        {
          delimiter = '\t';
        }
        else
        {
          delimiter = ' ';
        }
 
        //is header line
        if (line.hasPrefix("#"))
        {
          line = line.substr(1).trim().toUpper();
          line.split(delimiter, strings);
 
          // flags to check if dimension is set correctly
          bool rt_set = false;
          bool mz_set = false;
          bool int_set = false;
 
          //assign new order
          for (Size i = 0; i < 3; ++i)
          {
            if (strings[i] == "RT" || strings[i] == "RETENTION_TIME" || strings[i] == "MASS-TO-CHARGE" || strings[i] == "IT" || strings[i] == "INTENSITY")
            {
              std::cerr << "Warning: This file contains the deprecated keyword '" << strings[i] << "'." << "\n";
              std::cerr << "         Please use only the new keywords SEC/MIN, MZ, INT." << "\n";
            }
            if ((strings[i] == "SEC" || strings[i] == "RT" || strings[i] == "RETENTION_TIME") && rt_set == false)
            {
              rt_dim = i;
              rt_set = true;
            }
            else if ((strings[i] == "MIN") && rt_set == false)
            {
              rt_dim = i;
              rt_set = true;
              time_in_minutes = true;
            }
            else if ((strings[i] == "MZ" || strings[i] == "MASS-TO-CHARGE") && mz_set == false)
            {
              mz_dim = i;
              mz_set = true;
            }
            else if ((strings[i] == "INT" || strings[i] == "IT" || strings[i] == "INTENSITY") && int_set == false)
            {
              int_dim = i;
              int_set = true;
            }
            else
            {
              throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Misformatted header line!", filename);
            }
          }
          continue;
        }
 
        try
        {
          line.split(delimiter, strings);
          if (strings.size() != 3)
          {
            throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, std::string("Bad data line (" + String(line_number) + "): \"") + line + "\" (got  " + String(strings.size()) + ", expected 3 entries)", filename);
          }
          p.setIntensity(strings[int_dim].toFloat());
          p.setMZ(strings[mz_dim].toDouble());
          rt = (strings[rt_dim].toDouble()) * (time_in_minutes ? 60.0 : 1.0);
        }
        // conversion to double or something else could have gone wrong
        catch (Exception::BaseException& /*e*/)
        {
          throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, std::string("Bad data line (" + String(line_number) + "): \"") + line + "\"", filename);
        }
 
        // Retention time changed -> new Spectrum
        if (fabs(rt - spec.getRT()) > 0.0001)
        {
          if (spec.size() != 0
             &&
              (!options_.hasRTRange() || options_.getRTRange().encloses(DPosition<1>(spec.getRT())))) // RT restriction fulfilled
          {
            map.addSpectrum(spec);
          }
          setProgress(0);
          spec.clear(true);
          spec.setRT(rt);
          spec.setNativeID(String("index=") + native_id);
          ++native_id;
        }
 
        //Skip peaks with invalid m/z or intensity value
        if (
          (!options_.hasMZRange() || options_.getMZRange().encloses(DPosition<1>(p.getMZ())))
           &&
          (!options_.hasIntensityRange() || options_.getIntensityRange().encloses(DPosition<1>(p.getIntensity())))
          )
        {
          spec.push_back(p);
        }
      }
 
      // add last Spectrum
      if (
        spec.size() != 0
         &&
        (!options_.hasRTRange() || options_.getRTRange().encloses(DPosition<1>(spec.getRT()))) // RT restriction fulfilled
        )
      {
        map.addSpectrum(spec);
      }
 
      is.close();
      endProgress();
    }
 
    template <typename MapType>
    void store(const String& filename, const MapType& map) const
    {
      startProgress(0, map.size(), "storing DTA2D file");
 
      std::ofstream os(filename.c_str());
      if (!os)
      {
        throw Exception::UnableToCreateFile(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
      }
 
      // write header
      os << "#SEC\tMZ\tINT\n";
 
      // Iterate over all peaks of each spectrum and
      // write one line for each peak of the spectrum.
      UInt count = 0;
      for (typename MapType::const_iterator spec = map.begin(); spec != map.end(); ++spec)
      {
        setProgress(count++);
        for (typename MapType::SpectrumType::ConstIterator it = spec->begin(); it != spec->end(); ++it)
        {
          // Write rt, m/z and intensity.
          os << precisionWrapper(spec->getRT()) << "\t" << precisionWrapper(it->getPos()) << "\t" << precisionWrapper(it->getIntensity()) << "\n";
        }
 
      }
      os.close();
      endProgress();
    }
 
    template <typename MapType>
    void storeTIC(const String& filename, const MapType& map) const
    {
      startProgress(0, map.size(), "storing DTA2D file");
 
      std::ofstream os(filename.c_str());
      if (!os)
      {
        throw Exception::UnableToCreateFile(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
      }
 
      // write header (Always MZ=0 for chromatograms in DTA2D.)
      os << "#SEC\tMZ\tINT\n";
 
      typename MapType::ChromatogramType TIC = map.calculateTIC();
      for (typename MapType::ChromatogramType::ConstIterator it = TIC.begin(); it != TIC.end(); ++it)
      {
        // write rt, (mz=0) and intensity.
        os << precisionWrapper(it->getRT()) << "\t0\t" << precisionWrapper(it->getIntensity()) << "\n";
      }
 
      os.close();
      endProgress();
    }
 
  };
 
} // namespace OpenMS