MsInspectFile.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.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/FORMAT/TextFile.h>
 
#include <fstream>
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI MsInspectFile
  {
public:
    MsInspectFile();
    virtual ~MsInspectFile();
 
    template <typename FeatureMapType>
    void load(const String& filename, FeatureMapType& feature_map)
    {
      // load input
      TextFile input(filename);
 
      // reset map
      FeatureMapType fmap;
      feature_map = fmap;
 
      bool first_line = true;
      for (TextFile::ConstIterator it = input.begin(); it != input.end(); ++it)
      {
        String line = *it;
 
        //ignore comment lines
        if (line.empty() || line[0] == '#') continue;
 
        //skip leader line
        if (first_line)
        {
          first_line = false;
          continue;
        }
 
        //split lines: scan\ttime\tmz\taccurateMZ\tmass\tintensity\tcharge\tchargeStates\tkl\tbackground\tmedian\tpeaks\tscanFirst\tscanLast\tscanCount\ttotalIntensity\tsumSquaresDist\tdescription
        std::vector<String> parts;
        line.split('\t', parts);
 
        if (parts.size() < 18)
        {
          throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "", String("Failed to convert line ")  + String((it - input.begin()) + 1) + ". Not enough columns (expected 18 or more, got " + String(parts.size()) + ")");
        }
 
        //create feature
        Feature f;
        Size column_to_convert = 0;
        try
        {
          column_to_convert = 1;
          f.setRT(parts[1].toDouble());
          column_to_convert = 2;
          f.setMZ(parts[2].toDouble());
          column_to_convert = 5;
          f.setIntensity(parts[5].toDouble());
          column_to_convert = 6;
          f.setCharge(parts[6].toInt());
          column_to_convert = 8;
          f.setOverallQuality(parts[8].toDouble());
 
          column_to_convert = 3;
          f.setMetaValue("accurateMZ", parts[3]);
          column_to_convert = 4;
          f.setMetaValue("mass", parts[4].toDouble());
          column_to_convert = 7;
          f.setMetaValue("chargeStates", parts[7].toInt());
          column_to_convert = 9;
          f.setMetaValue("background", parts[9].toDouble());
          column_to_convert = 10;
          f.setMetaValue("median", parts[10].toDouble());
          column_to_convert = 11;
          f.setMetaValue("peaks", parts[11].toInt());
          column_to_convert = 12;
          f.setMetaValue("scanFirst", parts[12].toInt());
          column_to_convert = 13;
          f.setMetaValue("scanLast", parts[13].toInt());
          column_to_convert = 14;
          f.setMetaValue("scanCount", parts[14].toInt());
          column_to_convert = 15;
          f.setMetaValue("totalIntensity", parts[15].toDouble());
          column_to_convert = 16;
          f.setMetaValue("sumSquaresDist", parts[16].toDouble());
        }
        catch ( Exception::BaseException& )
        {
          throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "", String("Failed to convert value in column ") + String(column_to_convert + 1) + " into a number (line '" + String((it - input.begin()) + 1) + ")");
        }
        f.setMetaValue("description", parts[17]);
        feature_map.push_back(f);
      }
 
    }
 
    template <typename SpectrumType>
    void store(const String& filename, const SpectrumType& spectrum) const
    {
      std::cerr << "Store() for MsInspectFile not implemented. Filename was: " << filename << ", spec of size " << spectrum.size() << "\n";
      throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
 
  };
} // namespace OpenMS