SpectrumLookup.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:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    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: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
 
#include <boost/regex.hpp>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SpectrumLookup
  {
  public:
 
    static const String& default_scan_regexp;
 
    std::vector<boost::regex> reference_formats;
 
    double rt_tolerance;
 
    SpectrumLookup();
 
    virtual ~SpectrumLookup();
 
    bool empty() const;
 
    template <typename SpectrumContainer>
    void readSpectra(const SpectrumContainer& spectra, 
                     const String& scan_regexp = default_scan_regexp)
    {
      rts_.clear();
      ids_.clear();
      scans_.clear();
      n_spectra_ = spectra.size();
      setScanRegExp_(scan_regexp);
      for (Size i = 0; i < n_spectra_; ++i)
      {
        const MSSpectrum& spectrum = spectra[i];
        const String& native_id = spectrum.getNativeID();
        Int scan_no = -1;
        if (!scan_regexp.empty())
        {
          scan_no = extractScanNumber(native_id, scan_regexp_, true);
          if (scan_no < 0)
          {
            OPENMS_LOG_WARN << "Warning: Could not extract scan number from spectrum native ID '" + native_id + "' using regular expression '" + scan_regexp + "'. Look-up by scan number may not work properly." << std::endl;
          }
        }
        addEntry_(i, spectrum.getRT(), scan_no, native_id);
      }
    }
 
    Size findByRT(double rt) const;
 
    Size findByNativeID(const String& native_id) const;
    
    Size findByIndex(Size index, bool count_from_one = false) const;
 
    Size findByScanNumber(Size scan_number) const;
 
    Size findByReference(const String& spectrum_ref) const;
 
    void addReferenceFormat(const String& regexp);
 
    static Int extractScanNumber(const String& native_id,
                                 const boost::regex& scan_regexp,
                                 bool no_error = false);
 
    static Int extractScanNumber(const String& native_id,
                                 const String& native_id_type_accession);
    static std::string getRegExFromNativeID(const String& id);
 
    static bool isNativeID(const String& id);
 
  protected:
 
    static const String& regexp_names_;
 
    Size n_spectra_; 
 
    boost::regex scan_regexp_; 
 
    std::vector<String> regexp_name_list_; 
 
    std::map<double, Size> rts_; 
    std::map<String, Size> ids_; 
    std::map<Size, Size> scans_; 
 
    void addEntry_(Size index, double rt, Int scan_number,
                   const String& native_id);
 
    Size findByRegExpMatch_(const String& spectrum_ref, const String& regexp, 
                            const boost::smatch& match) const;
 
    void setScanRegExp_(const String& scan_regexp);
 
  private:
 
    SpectrumLookup(const SpectrumLookup&);
 
    SpectrumLookup& operator=(const SpectrumLookup&);
 
  };
 
} //namespace OpenMS