MascotGenericFile.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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/SpectrumSettings.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/CONCEPT/Constants.h>
 
#include <vector>
#include <fstream>
 
#ifdef _OPENMP
#include <omp.h>
#endif
 
namespace OpenMS
{
  class OPENMS_DLLAPI MascotGenericFile :
    public ProgressLogger,
    public DefaultParamHandler
  {
public:
 
    MascotGenericFile();
 
    ~MascotGenericFile() override;
 
    void updateMembers_() override;
 
    void store(const String& filename, const PeakMap& experiment,
               bool compact = false);
 
    void store(std::ostream& os, const String& filename,
               const PeakMap& experiment, bool compact = false);
 
    template <typename MapType>
    void load(const String& filename, MapType& exp)
    {
      if (!File::exists(filename))
      {
        throw Exception::FileNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
      }
 
      exp.reset();
 
      std::ifstream is(filename.c_str());
      // get size of file
      is.seekg(0, std::ios::end);
      startProgress(0, is.tellg(), "loading MGF");
      is.seekg(0, std::ios::beg);
 
      UInt spectrum_number(0);
      Size line_number(0); // carry line number for error messages within getNextSpectrum()
 
      typename MapType::SpectrumType spectrum;
      spectrum.setMSLevel(2);
      spectrum.getPrecursors().resize(1);
      spectrum.setType(SpectrumSettings::SpectrumType::CENTROID); // MGF is always centroided, by definition
      while (getNextSpectrum_(is, spectrum, line_number, spectrum_number))
      {
        exp.addSpectrum(spectrum);
        setProgress(is.tellg());
        ++spectrum_number;
      } // next spectrum
 
      endProgress();
    }
 
    std::pair<String, String> getHTTPPeakListEnclosure(const String& filename) const;
 
    void writeSpectrum(std::ostream& os, const PeakSpectrum& spec, const String& filename, const String& native_id_type_accession);
 
protected:
 
    bool store_compact_;
 
    std::map<String, String> mod_group_map_;
 
    void writeParameterHeader_(const String& name, std::ostream& os);
 
    void writeModifications_(const std::vector<String>& mods, std::ostream& os,
                             bool variable_mods = false);
 
    void writeHeader_(std::ostream& os);
 
    void writeMSExperiment_(std::ostream& os, const String& filename, const PeakMap& experiment);
 
    template <typename SpectrumType>
    bool getNextSpectrum_(std::ifstream& is, SpectrumType& spectrum, Size& line_number, const Size& spectrum_number)
    {
      spectrum.resize(0);
      spectrum.setNativeID(String("index=") + (spectrum_number));
 
      if (spectrum.metaValueExists("TITLE"))
      {
        spectrum.removeMetaValue("TITLE");
      }
      typename SpectrumType::PeakType p;
 
      String line;
      // seek to next peak list block
      while (getline(is, line, '\n'))
      {
        ++line_number;
 
        line.trim(); // remove whitespaces, line-endings etc
 
        // found peak list block?
        if (line == "BEGIN IONS")
        {
          while (getline(is, line, '\n'))
          {
            ++line_number;
            line.trim(); // remove whitespaces, line-endings etc
 
            if (line.empty()) continue;
 
            if (isdigit(line[0])) // actual data .. this comes first, since its the most common case
            {
              std::vector<String> split;
              do
              {
                if (line.empty())
                {
                  continue;
                }
 
                line.simplify(); // merge double spaces (explicitly allowed by MGF), to prevent empty split() chunks and subsequent parse error
                line.substitute('\t', ' '); // also accept Tab (strictly, only space(s) are allowed)
                if (line.split(' ', split, false))
                {
                  try
                  {
                    p.setPosition(split[0].toDouble());
                    p.setIntensity(split[1].toDouble());
                  }
                  catch (Exception::ConversionError& /*e*/)
                  {
                    throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "The content '" + line + "' at line #" + String(line_number) + " could not be converted to a number! Expected two (m/z int) or three (m/z int charge) numbers separated by whitespace (space or tab).", "");
                  }
                  spectrum.push_back(p);
                }
                else
                {
                  throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "The content '" + line + "' at line #" + String(line_number) + " does not contain m/z and intensity values separated by whitespace (space or tab)!", "");
                }
              }
              while (getline(is, line, '\n') && ++line_number && line.trim() != "END IONS"); // line.trim() is important here!
 
              if (line == "END IONS")
              {
                return true; // found end of spectrum
              }
              else
              {
                throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, R"(Reached end of file. Found "BEGIN IONS" but not the corresponding "END IONS"!)", "");
              }
            }
            else if (line.hasPrefix("PEPMASS")) // parse precursor position
            {
              String tmp = line.substr(8); // copy since we might need the original line for error reporting later
              tmp.substitute('\t', ' ');
              std::vector<String> split;
              tmp.split(' ', split);
              if (split.size() == 1)
              {
                spectrum.getPrecursors()[0].setMZ(split[0].trim().toDouble());
              }
              else if (split.size() == 2)
              {
                spectrum.getPrecursors()[0].setMZ(split[0].trim().toDouble());
                spectrum.getPrecursors()[0].setIntensity(split[1].trim().toDouble());
              }
              else
              {
                throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Cannot parse PEPMASS in '" + line + "' at line #" + String(line_number) + " (expected 1 or 2 entries, but " + String(split.size()) + " were present)!", "");
              }
            }
            else if (line.hasPrefix("CHARGE"))
            {
              String tmp = line.substr(7);
              tmp.remove('+');
              spectrum.getPrecursors()[0].setCharge(tmp.toInt());
            }
            else if (line.hasPrefix("RTINSECONDS"))
            {
              String tmp = line.substr(12);
              spectrum.setRT(tmp.toDouble());
            }
            else if (line.hasPrefix("TITLE"))
            {
              // test if we have a line like "TITLE= Cmpd 1, +MSn(595.3), 10.9 min"
              if (line.hasSubstring("min"))
              {
                try
                {
                  std::vector<String> split;
                  line.split(',', split);
                  if (!split.empty())
                  {
                    for (Size i = 0; i != split.size(); ++i)
                    {
                      if (split[i].hasSubstring("min"))
                      {
                        std::vector<String> split2;
                        split[i].trim().split(' ', split2);
                        if (!split2.empty())
                        {
                          spectrum.setRT(split2[0].trim().toDouble() * 60.0);
                        }
                      }
                    }
                  }
                }
                catch (Exception::BaseException& /*e*/)
                {
                  // just do nothing and write the whole title to spec
                  std::vector<String> split;
                  if (line.split('=', split))
                  {
                    if (!split[1].empty()) spectrum.setMetaValue("TITLE", split[1]);
                  }
                }
              }
              else // just write the title as metainfo to the spectrum and add native ID to make the titles unique
              {
                Size firstEqual = line.find('=', 4);
                if (firstEqual != std::string::npos)
                {
                  if (String(spectrum.getMetaValue("TITLE")).hasSubstring(spectrum.getNativeID()))
                  {
                    spectrum.setMetaValue("TITLE", line.substr(firstEqual + 1));
                  }
                  else
                  {
                    spectrum.setMetaValue("TITLE", line.substr(firstEqual + 1) + "_" + spectrum.getNativeID());
                  }
                }
              }
            }
            else if (line.hasPrefix("NAME"))
            {
              String tmp = line.substr(5);
              spectrum.setMetaValue(Constants::UserParam::MSM_METABOLITE_NAME, tmp);
            }
            else if (line.hasPrefix("INCHI="))
            {
              String tmp = line.substr(6);
              spectrum.setMetaValue(Constants::UserParam::MSM_INCHI_STRING, tmp);
            }
            else if (line.hasPrefix("SMILES"))
            {
              String tmp = line.substr(7);
              spectrum.setMetaValue(Constants::UserParam::MSM_SMILES_STRING, tmp);
            }
            else if (line.hasPrefix("SPECTRUMID"))
            {
              String tmp = line.substr(11);
              spectrum.setMetaValue("GNPS_Spectrum_ID", tmp);
            }
            else if (line.hasPrefix("SCANS="))
            {
              String tmp = line.substr(6);
              spectrum.setMetaValue("Scan_ID", tmp);
            }
          }
        }
      }
 
      return false; // found end of file
    }
 
  };
 
} // namespace OpenMS