ItraqQuantifier.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 2002-2012.
//
// 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: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H
#define OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H

#include <vector>

#include <OpenMS/ANALYSIS/QUANTITATION/ItraqConstants.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>


namespace OpenMS
{

  class OPENMS_DLLAPI ItraqQuantifier :
    public DefaultParamHandler,
    public ItraqConstants
  {

public:

    typedef ItraqConstants::ChannelInfo ChannelInfo;
    typedef ItraqConstants::ChannelMapType ChannelMapType;
    typedef ItraqConstants::IsotopeMatrices IsotopeMatrices;

    ItraqQuantifier();

    explicit ItraqQuantifier(Int itraq_type);

    ItraqQuantifier(Int itraq_type, const Param & param);

    ItraqQuantifier(const ItraqQuantifier & cp);

    ItraqQuantifier & operator=(const ItraqQuantifier & rhs);

    void run(const ConsensusMap & consensus_map_in,
             ConsensusMap & consensus_map_out
             );

    struct ItraqQuantifierStats
    {
      ItraqQuantifierStats() :
        channel_count(0),
        iso_number_ms2_negative(0),
        iso_number_reporter_negative(0),
        iso_number_reporter_different(0),
        iso_solution_different_intensity(0),
        iso_total_intensity_negative(0),
        number_ms2_total(0),
        number_ms2_empty(0),
        empty_channels()
      {
      }

      Size channel_count;  //< 4plex, 6plex, or 8 plex?!
      Size iso_number_ms2_negative; //< number of MS2 spectra where one or more channels had negative solution
      Size iso_number_reporter_negative;  //< number of channels where naive solution was negative
      Size iso_number_reporter_different; //< number of channels >0 where naive solution was different; happens when naive solution is negative in other channels
      DoubleReal iso_solution_different_intensity; //< absolute intensity difference between both solutions (for channels > 0)
      DoubleReal iso_total_intensity_negative; //< only for spectra where naive solution is negative
      Size number_ms2_total; //< total number of MS2 spectra
      Size number_ms2_empty; //< number of empty MS2 (no reporters at all)
      std::map<Size, Size> empty_channels; //< Channel_ID -> Missing; indicating the number of empty channels from all MS2 scans, i.e., numbers are between number_ms2_empty and number_ms2_total
    };

    ItraqQuantifierStats getStats() const;

protected:

    void setDefaultParams_();

    void updateMembers_();

private:

    void initIsotopeCorrections_();

    void reconstructChannelInfo_(const ConsensusMap & consensus_map);

    bool isIdentityCorrectionMatrix_(const Matrix<double>& channel_frequency) const;
    
    Int itraq_type_;

    ChannelMapType channel_map_;

    IsotopeMatrices isotope_corrections_;

    ItraqQuantifierStats stats_;

  };   // !class

  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const ItraqQuantifier::ItraqQuantifierStats & stats);

} // !namespace

#endif // OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H