MascotGenericFile.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.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 std::string& filename, const PeakMap& experiment,
               bool compact = false);
 
    void store(std::ostream& os, const std::string& filename,
               const PeakMap& experiment, bool compact = false);
 
    template <typename MapType>
    void load(const std::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; // (re-)initialized for every block by getNextSpectrum_()
      while (getNextSpectrum_(is, spectrum, line_number, spectrum_number))
      {
        exp.addSpectrum(spectrum);
        setProgress(is.tellg());
        ++spectrum_number;
      } // next spectrum
      exp.updateRanges();
      endProgress();
    }
 
    std::pair<std::string, std::string> getHTTPPeakListEnclosure(const std::string& filename) const;
 
    void writeSpectrum(std::ostream& os, const PeakSpectrum& spec, const std::string& filename, const std::string& native_id_type_accession);
 
protected:
 
    bool store_compact_;
 
    std::map<std::string, std::string> mod_group_map_;
 
    void writeParameterHeader_(const std::string& name, std::ostream& os);
 
    void writeModifications_(const std::vector<std::string>& mods, std::ostream& os,
                             bool variable_mods = false);
 
    void writeHeader_(std::ostream& os);
 
    void writeMSExperiment_(std::ostream& os, const std::string& filename, const PeakMap& experiment);
 
    template <typename SpectrumType>
    bool getNextSpectrum_(std::ifstream& is, SpectrumType& spectrum, Size& line_number, const Size& spectrum_number)
    {
      // Start every block from a pristine spectrum: clear(true) removes the peaks and data arrays,
      // all SpectrumSettings (precursors, native ID, meta values such as TITLE/SEQ/NAME, ...) and
      // resets RT, drift time and MS level. Every field below is only set when its line is present
      // (e.g. CHARGE is commonly omitted), so nothing from the previous block may survive here.
      spectrum.clear(true);
      spectrum.setMSLevel(2);
      spectrum.getPrecursors().resize(1);
      spectrum.setType(SpectrumSettings::SpectrumType::CENTROID); // MGF is always centroided, by definition
      spectrum.setNativeID(std::string("index=") + (spectrum_number));
 
      typename SpectrumType::PeakType p;
 
      std::string line;
      // seek to next peak list block
      while (getline(is, line, '\n'))
      {
        ++line_number;
 
        StringUtils::trim(line); // remove whitespaces, line-endings etc
 
        // found peak list block?
        if (line == "BEGIN IONS")
        {
          while (getline(is, line, '\n'))
          {
            ++line_number;
            StringUtils::trim(line); // remove whitespaces, line-endings etc
 
            if (line.empty()) continue;
 
            if (line == "END IONS")
            {
              // block without peak lines: return it as an empty spectrum instead of silently
              // merging it with the next block (or dropping it if it is the last one in the file)
              return true;
            }
 
            if (isdigit(line[0])) // actual data .. this comes first, since its the most common case
            {
              std::vector<std::string> split;
              do
              {
                if (line.empty())
                {
                  continue;
                }
 
                StringUtils::simplify(line); // merge double spaces (explicitly allowed by MGF), to prevent empty split() chunks and subsequent parse error
                StringUtils::substitute(line, '\t', ' '); // also accept Tab (strictly, only space(s) are allowed)
                if (StringUtils::split(line, ' ', split, false))
                {
                  try
                  {
                    p.setPosition(StringUtils::toDouble(split[0]));
                    p.setIntensity(StringUtils::toDouble(split[1]));
                  }
                  catch (Exception::ConversionError& /*e*/)
                  {
                    throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "The content '" + line + "' at line #" + StringUtils::toStr(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 #" + StringUtils::toStr(line_number) + " does not contain m/z and intensity values separated by whitespace (space or tab)!", "");
                }
              }
              while (getline(is, line, '\n') && ++line_number && StringUtils::trim(line) != "END IONS"); // StringUtils::trim(line) 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 (StringUtils::hasPrefix(line, "PEPMASS")) // parse precursor position
            {
              std::string tmp = StringUtils::substr(line, 8); // copy since we might need the original line for error reporting later
              StringUtils::substitute(tmp, '\t', ' ');
              std::vector<std::string> split;
              StringUtils::split(tmp, ' ', split);
              if (split.size() == 1)
              {
                spectrum.getPrecursors()[0].setMZ(StringUtils::toDouble(StringUtils::trim(split[0])));
              }
              else if (split.size() == 2)
              {
                spectrum.getPrecursors()[0].setMZ(StringUtils::toDouble(StringUtils::trim(split[0])));
                spectrum.getPrecursors()[0].setIntensity(StringUtils::toDouble(StringUtils::trim(split[1])));
              }
              else
              {
                throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Cannot parse PEPMASS in '" + line + "' at line #" + StringUtils::toStr(line_number) + " (expected 1 or 2 entries, but " + StringUtils::toStr(split.size()) + " were present)!", "");
              }
            }
            else if (StringUtils::hasPrefix(line, "CHARGE"))
            {
              std::string tmp = StringUtils::substr(line, 7);
              StringUtils::remove(tmp, '+');
              spectrum.getPrecursors()[0].setCharge(StringUtils::toInt32(tmp));
            }
            else if (StringUtils::hasPrefix(line, "RTINSECONDS"))
            {
              std::string tmp = StringUtils::substr(line, 12);
              spectrum.setRT(StringUtils::toDouble(tmp));
            }
            else if (StringUtils::hasPrefix(line, "TITLE"))
            {
              // test if we have a line like "TITLE= Cmpd 1, +MSn(595.3), 10.9 min"
              if (StringUtils::hasSubstring(line, "min"))
              {
                try
                {
                  std::vector<std::string> split;
                  StringUtils::split(line, ',', split);
                  if (!split.empty())
                  {
                    for (Size i = 0; i != split.size(); ++i)
                    {
                      if (StringUtils::hasSubstring(split[i], "min"))
                      {
                        std::vector<std::string> split2;
                        StringUtils::trim(split[i]);
                        StringUtils::split(split[i], ' ', split2);
                        if (!split2.empty())
                        {
                          StringUtils::trim(split2[0]);
                          spectrum.setRT(StringUtils::toDouble(split2[0]) * 60.0);
                        }
                      }
                    }
                  }
                }
                catch (Exception::BaseException& /*e*/)
                {
                  // just do nothing and write the whole title to spec
                  std::vector<std::string> split;
                  if (StringUtils::split(line, '=', 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 (StringUtils::hasSubstring(StringUtils::toStr(spectrum.getMetaValue("TITLE")), spectrum.getNativeID()))
                  {
                    spectrum.setMetaValue("TITLE", StringUtils::substr(line, firstEqual + 1));
                  }
                  else
                  {
                    spectrum.setMetaValue("TITLE", StringUtils::substr(line, firstEqual + 1) + "_" + spectrum.getNativeID());
                  }
                }
              }
            }
            else if (StringUtils::hasPrefix(line, "NAME"))
            {
              std::string tmp = StringUtils::substr(line, 5);
              spectrum.setMetaValue(Constants::UserParam::MSM_METABOLITE_NAME, tmp);
            }
            else if (StringUtils::hasPrefix(line, "COMPOUND_NAME"))
            {
              std::string tmp = StringUtils::substr(line, 14);
              spectrum.setMetaValue(Constants::UserParam::MSM_METABOLITE_NAME, tmp);
            }
            else if (StringUtils::hasPrefix(line, "INCHI="))
            {
              std::string tmp = StringUtils::substr(line, 6);
              spectrum.setMetaValue(Constants::UserParam::MSM_INCHI_STRING, tmp);
            }
            else if (StringUtils::hasPrefix(line, "SMILES"))
            {
              std::string tmp = StringUtils::substr(line, 7);
              spectrum.setMetaValue(Constants::UserParam::MSM_SMILES_STRING, tmp);
            }
            else if (StringUtils::hasPrefix(line, "IONMODE"))
            {
              std::string tmp = StringUtils::substr(line, 8);
              spectrum.setMetaValue("IONMODE", tmp);
            }
            else if (StringUtils::hasPrefix(line, "MSLEVEL")) 
            {
             std::string tmp = StringUtils::substr(line, 8);
            try 
            {
            int ms_level = std::stoi(tmp); 
            spectrum.setMSLevel(ms_level);
            }
            catch (const std::invalid_argument& /*e*/)
            {
            // Default to MS2 if parsing fails
            spectrum.setMSLevel(2);
            spectrum.setMetaValue("MSLEVEL", "2");
            }
            catch (const std::out_of_range& /*e*/)
            {
                spectrum.setMSLevel(2);
            }
            }               
            else if (StringUtils::hasPrefix(line, "SOURCE_INSTRUMENT"))
            {
              std::string tmp = StringUtils::substr(line, 18);
              spectrum.setMetaValue("SOURCE_INSTRUMENT", tmp);
            }
            else if (StringUtils::hasPrefix(line, "ORGANISM"))
            {
              std::string tmp = StringUtils::substr(line, 9);
              spectrum.setMetaValue("ORGANISM", tmp);
            }
            else if (StringUtils::hasPrefix(line, "PI"))
            {
              std::string tmp = StringUtils::substr(line, 3);
              spectrum.setMetaValue("PI", tmp);
            }
            else if (StringUtils::hasPrefix(line, "DATACOLLECTOR"))
            {
              std::string tmp = StringUtils::substr(line, 14);
              spectrum.setMetaValue("DATACOLLECTOR", tmp);
            }
            else if (StringUtils::hasPrefix(line, "LIBRARYQUALITY"))
            {
              std::string tmp = StringUtils::substr(line, 15);
              spectrum.setMetaValue("LIBRARYQUALITY", tmp);
            }
            else if (StringUtils::hasPrefix(line, "SPECTRUMID"))
            {
              std::string tmp = StringUtils::substr(line, 11);
              spectrum.setMetaValue("GNPS_Spectrum_ID", tmp);
            }
            else if (StringUtils::hasPrefix(line, "SCANS="))
            {
              std::string tmp = StringUtils::substr(line, 6);
              spectrum.setMetaValue("Scan_ID", tmp);
            }
            else if (StringUtils::hasPrefix(line, "SEQ="))
            {
              // Mascot sequence-query field: peptide sequence in one-letter code.
              // Per spec, SEQ may appear multiple times per query (each entry is
              // an independent sequence filter). Always stored as a StringList
              // under the "SEQ" key for a stable interface regardless of how
              // many SEQ lines were present.
              std::string sequence = StringUtils::substr(line, 4);
              StringList sequences;
              if (spectrum.metaValueExists("SEQ"))
              {
                sequences = spectrum.getMetaValue("SEQ").toStringList();
              }
              sequences.push_back(sequence);
              spectrum.setMetaValue("SEQ", sequences);
            }
          }
        }
      }
 
      return false; // found end of file
    }
 
  };
} // namespace OpenMS