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 2002-2018.
//
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//    may be used to endorse or promote products derived from this software
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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];
        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)
          {
            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);

  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