libopenms-dev 1.11.1-3 / usr / include / OpenMS / FORMAT / DTAFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// $Maintainer: Andreas Bertsch $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_DTAFILE_H
#define OPENMS_FORMAT_DTAFILE_H

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/METADATA/Precursor.h>
#include <OpenMS/SYSTEM/File.h>

#include <fstream>
#include <vector>

namespace OpenMS
{
  /**
      @brief File adapter for DTA files.

  The first line contains the singly protonated peptide mass (MH+) and the peptide charge state separated by a space.
  Subsequent lines contain space separated pairs of fragment ion m/z and intensity values.

  From precusor mass and charge state the mass-charge-ratio is calculated and stored in the spectrum as precursor mass.

  @ingroup FileIO
*/
  class OPENMS_DLLAPI DTAFile
  {
public:
    /// Default constructor
    DTAFile();
    /// Destructor
    virtual ~DTAFile();

    /**
              @brief Loads a DTA file to a spectrum.

              The content of the file is stored in @p spectrum.
              @p spectrum has to be a MSSpectrum or have the same interface.

              @exception Exception::FileNotFound is thrown if the file could not be opened
              @exception Exception::ParseError is thrown if an error occurs during parsing
    */
    template <typename SpectrumType>
    void load(const String & filename, SpectrumType & spectrum)
    {
      std::ifstream is(filename.c_str());
      if (!is)
      {
        throw Exception::FileNotFound(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);
      }

      //  Delete old spectrum
      spectrum.clear(true);

      //temporary variables
      String line;
      std::vector<String> strings(2);
      typename SpectrumType::PeakType p;
      char delimiter;

      // line number counter
      Size line_number = 1;

      //read first line and store precursor m/z and charge
      getline(is, line, '\n');
      line.trim();

      //test which delimiter is used in the line
      if (line.has('\t'))
      {
        delimiter = '\t';
      }
      else
      {
        delimiter = ' ';
      }

      line.split(delimiter, strings);
      if (strings.size() != 2)
      {
        throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, std::string("Bad data line (" + String(line_number) + "): \"") + line + "\" (got  " + String(strings.size()) + ", expected 2 entries)", filename);
      }
      Precursor precursor;
      DoubleReal mh_mass;
      Int charge;
      try
      {
        // by convention the first line holds: singly protonated peptide mass, charge state
        mh_mass = strings[0].toDouble();
        charge = strings[1].toInt();
      }
      catch (...)
      {
        throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, std::string("Bad data line (" + String(line_number) + "): \"") + line + "\": not a float number.", filename);
      }
      if (charge != 0)
      {
        precursor.setMZ((mh_mass - Constants::PROTON_MASS_U) / charge + Constants::PROTON_MASS_U);
      }
      else
      {
        precursor.setMZ(mh_mass);
      }
      precursor.setCharge(charge);
      spectrum.getPrecursors().push_back(precursor);

      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 = ' ';
        }

        line.split(delimiter, strings);
        if (strings.size() != 2)
        {
          throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, std::string("Bad data line (" + String(line_number) + "): \"") + line + "\" (got  " + String(strings.size()) + ", expected 2 entries)", filename);
        }
        try
        {
          //fill peak
          p.setPosition((typename SpectrumType::PeakType::PositionType)strings[0].toDouble());
          p.setIntensity((typename SpectrumType::PeakType::IntensityType)strings[1].toDouble());
        }
        catch (Exception::BaseException & /*e*/)
        {
          throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, std::string("Bad data line (" + String(line_number) + "): \"") + line + "\": not a float number.", filename);
        }
        spectrum.push_back(p);
      }

      spectrum.setName(File::basename(filename));
      is.close();
    }

    /**
      @brief Stores a spectrum in a DTA file.

      The content of @p spectrum is stored in a file.
      @p spectrum has to be a MSSpectrum or have the same interface.

              @exception Exception::UnableToCreateFile is thrown if the file could not be created
    */
    template <typename SpectrumType>
    void store(const String & filename, const SpectrumType & spectrum) const
    {
      std::ofstream os(filename.c_str());
      if (!os)
      {
        throw Exception::UnableToCreateFile(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);
      }
      os.precision(writtenDigits<DoubleReal>());

      //write precursor information
      Precursor precursor;
      if (spectrum.getPrecursors().size() > 0)
      {
        precursor = spectrum.getPrecursors()[0];
      }
      if (spectrum.getPrecursors().size() > 1)
      {
        std::cerr << "Warning: The spectrum written to the DTA file '" << filename << "' has more than one precursor. The first precursor is used!" << "\n";
      }
      //unknown charge
      if (precursor.getCharge() == 0)
      {
        os << precursor.getMZ();
      }
      //known charge
      else
      {
        os << ((precursor.getMZ() - 1.0) * precursor.getCharge() + 1.0);
      }
      //charge
      os << " " << precursor.getCharge() << "\n";

      // Iterate over all peaks of the spectrum and
      // write one line for each peak of the spectrum.
      typename SpectrumType::ConstIterator it(spectrum.begin());
      for (; it != spectrum.end(); ++it)
      {
        // Write m/z and intensity.
        os << it->getPosition() << " " << it->getIntensity() << "\n";
      }

      // Done.
      os.close();
    }

  };
} // namespace OpenMS

#endif // OPENMS_FORMAT_DTAFILE_H