SpectrumMetaDataLookup.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// 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: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/METADATA/SpectrumLookup.h>

#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/KERNEL/MSExperiment.h>

#include <limits> // for "quiet_NaN"

namespace OpenMS
{

  class OPENMS_DLLAPI SpectrumMetaDataLookup: public SpectrumLookup
  {
  public:

    typedef unsigned char MetaDataFlags;

    static const MetaDataFlags MDF_RT = 1;
    static const MetaDataFlags MDF_PRECURSORRT = 2;
    static const MetaDataFlags MDF_PRECURSORMZ = 4;
    static const MetaDataFlags MDF_PRECURSORCHARGE = 8;
    static const MetaDataFlags MDF_MSLEVEL = 16;
    static const MetaDataFlags MDF_SCANNUMBER = 32;
    static const MetaDataFlags MDF_NATIVEID = 64;
    static const MetaDataFlags MDF_ALL = 127;


    struct SpectrumMetaData
    {
      double rt; 
      double precursor_rt; 
      double precursor_mz; 
      Int precursor_charge; 
      Size ms_level; 
      Int scan_number; 
      String native_id; 

      SpectrumMetaData():
        rt(std::numeric_limits<double>::quiet_NaN()), 
        precursor_rt(std::numeric_limits<double>::quiet_NaN()), 
        precursor_mz(std::numeric_limits<double>::quiet_NaN()),
        precursor_charge(0), ms_level(0), scan_number(-1), native_id("")
      {
      }

      SpectrumMetaData(const SpectrumMetaData &) = default;
      SpectrumMetaData(SpectrumMetaData&&) = default;
      ~SpectrumMetaData() = default;

      SpectrumMetaData & operator=(const SpectrumMetaData &) = default;
      SpectrumMetaData& operator=(SpectrumMetaData&&) & = default;
    };

    SpectrumMetaDataLookup(): SpectrumLookup()
    {}

    ~SpectrumMetaDataLookup() override {}

    template <typename SpectrumContainer>
    void readSpectra(const SpectrumContainer& spectra, 
                     const String& scan_regexp = default_scan_regexp,
                     bool get_precursor_rt = false)
    {
      // If class SpectrumContainer is e.g. OnDiscMSExperiment, reading each
      // spectrum is expensive. Thus, to avoid iterating over all spectra twice,
      // we do not call "SpectrumLookup::readSpectra" here:
      n_spectra_ = spectra.size();
      metadata_.reserve(n_spectra_);
      setScanRegExp_(scan_regexp);
      // mapping: MS level -> RT of previous spectrum of that level
      std::map<Size, double> precursor_rts;
      for (Size i = 0; i < n_spectra_; ++i)
      {
        const MSSpectrum& spectrum = spectra[i];
        SpectrumMetaData meta;
        getSpectrumMetaData(spectrum, meta, scan_regexp_, precursor_rts);
        if (get_precursor_rt) precursor_rts[meta.ms_level] = meta.rt;
        addEntry_(i, meta.rt, meta.scan_number, meta.native_id);
        metadata_.push_back(meta);
      }
    }


    void setSpectraDataRef(const String& spectra_data)
    {
      this->spectra_data_ref = spectra_data;
    }


    void getSpectrumMetaData(Size index, SpectrumMetaData& meta) const;

    static void getSpectrumMetaData(
      const MSSpectrum& spectrum, SpectrumMetaData& meta,
      const boost::regex& scan_regexp = boost::regex(),
      const std::map<Size, double>& precursor_rts = (std::map<Size, double>()));

    void getSpectrumMetaData(const String& spectrum_ref, SpectrumMetaData& meta,
                             MetaDataFlags flags = MDF_ALL) const;

    static bool addMissingRTsToPeptideIDs(std::vector<PeptideIdentification>& peptides, const String &filename,
      bool stop_on_error = false);

    static bool addMissingSpectrumReferences(std::vector<PeptideIdentification>& peptides, 
      const String& filename,
      bool stop_on_error = false, 
      bool override_spectra_data = false, 
      bool override_spectra_references = false, 
      std::vector<ProteinIdentification> proteins = std::vector<ProteinIdentification>());

  protected:

    std::vector<SpectrumMetaData> metadata_; 
    String spectra_data_ref;

  private:

    SpectrumMetaDataLookup(const SpectrumMetaDataLookup&);

    SpectrumMetaDataLookup& operator=(const SpectrumMetaDataLookup&);

  };

} //namespace OpenMS