ConsensusMapMergerAlgorithm.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 2002-2023.
//
// 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: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/METADATA/ExperimentalDesign.h>
 
#include <unordered_set>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ConsensusMapMergerAlgorithm:
    public DefaultParamHandler,
    public ProgressLogger
  {
  public:
    ConsensusMapMergerAlgorithm ();
 
    void mergeProteinsAcrossFractionsAndReplicates(ConsensusMap& cmap, const ExperimentalDesign& exp_design) const;
 
    void mergeAllIDRuns(ConsensusMap& cmap) const;
 
    void mergeProteinIDRuns(ConsensusMap &cmap,
                            const std::map<unsigned, unsigned>& mapIdx_to_new_protIDRun) const;
 
  private:
 
    bool checkOldRunConsistency_(const std::vector<ProteinIdentification>& protRuns, const String& experiment_type) const;
    bool checkOldRunConsistency_(const std::vector<ProteinIdentification>& protRuns, const ProteinIdentification& ref, const String& experiment_type) const;
 
 
    static size_t accessionHash_(const ProteinHit& p)
    {
      return std::hash<String>()(p.getAccession());
    }
    static bool accessionEqual_(const ProteinHit& p1, const ProteinHit& p2)
    {
      return p1.getAccession() == p2.getAccession();
    }
    using hash_type = std::size_t (*)(const ProteinHit&);
    using equal_type = bool (*)(const ProteinHit&, const ProteinHit&);
 
  };
} // namespace OpenMS