MS2File.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// 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: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/DocumentIdentifier.h>
 
#include <vector>
#include <fstream>
 
namespace OpenMS
{
  class OPENMS_DLLAPI MS2File :
    public ProgressLogger
  {
public:
 
    MS2File();
 
    ~MS2File() override;
 
    template <typename MapType>
    void load(const String & filename, MapType & exp)
    {
      //startProgress(0,0,"loading DTA2D file");
 
      if (!File::exists(filename))
      {
        throw Exception::FileNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
      }
      if (!File::readable(filename))
      {
        throw Exception::FileNotReadable(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
      }
 
      exp.reset();
 
      //set DocumentIdentifier
      exp.setLoadedFileType(filename);
      exp.setLoadedFilePath(filename);
 
      std::ifstream in(filename.c_str());
 
      UInt spectrum_number = 0;
      typename MapType::SpectrumType spec;
      typename MapType::SpectrumType::PeakType p;
 
      String line;
      bool first_spec(true);
 
      // line number counter
      Size line_number = 0;
 
      while (getline(in, line, '\n'))
      {
        ++line_number;
 
        line.trim();
        if (line.empty()) continue;
 
        // header
        if (line[0] == 'H')
        {
          continue;
        }
 
        // scan
        if (line[0] == 'S')
        {
          if (!first_spec)
          {
            spec.setMSLevel(2);
            spec.setNativeID(String("index=") + (spectrum_number++));
            exp.addSpectrum(spec);
          }
          else
          {
            first_spec = false;
          }
          spec.clear(true);
          line.simplify();
          std::vector<String> split;
          line.split(' ', split);
          if (split.size() != 4)
          {
            throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "line (" + String(line_number) + ") '" + line  + "' should contain four values, got " + String(split.size()) + "!", "");
          }
          spec.getPrecursors().resize(1);
          spec.getPrecursors()[0].setMZ(split[3].toDouble());
          continue;
        }
 
        // charge-independent analysis
        if (line[0] == 'I')
        {
          continue;
        }
 
        // charge specification
        if (line[0] == 'Z')
        {
          continue;
        }
 
        // charge-dependent analysis
        if (line[0] == 'D')
        {
          continue;
        }
 
        // yet another peak, hopefully
        line.simplify();
        std::vector<String> split;
        line.split(' ', split);
        if (split.size() != 2)
        {
          throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "line (" + String(line_number) + ") '" + line  + "' should contain two values, got " + String(split.size()) + "!", "");
        }
 
        try
        {
          p.setPosition(split[0].toDouble());
          p.setIntensity(split[1].toFloat());
        }
        catch ( Exception::ConversionError& )
        {
          throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "ConversionError: line (" + String(line_number) + ") '" + line  + "' does not contain two numbers!", "");
        }
        spec.push_back(p);
      }
 
      if (!first_spec)
      {
        spec.setMSLevel(2);
        spec.setNativeID(String("index=") + (spectrum_number++));
        exp.addSpectrum(spec);
      }
    }
 
    /*
    template <typename MapType> void store(const String& filename, MapType& map)
    {
 
    }
    */
 
protected:
 
  };
 
} // namespace OpenMS