PeptideProteinResolution.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 2002-2021.
//
// 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/CONCEPT/Types.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <vector>
#include <set>
 
namespace OpenMS
{
  struct OPENMS_DLLAPI ConnectedComponent
  {
    std::set<Size> prot_grp_indices;
    std::set<Size> pep_indices;
    friend std::ostream& operator<<(std::ostream& os, const ConnectedComponent& conn_comp);
  };
 
  class OPENMS_DLLAPI PeptideProteinResolution
  {
  
  private:
    typedef std::map<Size, std::set<Size> > IndexMap_;
 
    // TODO WIP for better tie resolution
    // std::vector<std::pair<bool,bool>> indist_prot_grp_td_;
    IndexMap_ indist_prot_grp_to_pep_;
    IndexMap_ pep_to_indist_prot_grp_;
    
    std::map<String, Size> prot_acc_to_indist_prot_grp_;
    
    bool statistics_;
    
  public:
    PeptideProteinResolution(bool statistics = false);
 
 
    static void resolve(ProteinIdentification& protein,
                        std::vector<PeptideIdentification>& peptides,
                        bool resolve_ties,
                        bool targets_first);
 
    static void run(std::vector<ProteinIdentification>& inferred_protein_id, 
                    std::vector<PeptideIdentification>& inferred_peptide_ids);
 
    void buildGraph(ProteinIdentification& protein,
                    const std::vector<PeptideIdentification>& peptides,
                    bool skip_sort = false);
      
    void resolveGraph(ProteinIdentification& protein,
                      std::vector<PeptideIdentification>& peptides);
    
    ConnectedComponent findConnectedComponent(Size& root_prot_grp);
    
 
    void resolveConnectedComponent(ConnectedComponent& conn_comp,
                                    ProteinIdentification& protein,
                                    std::vector<PeptideIdentification>& peptides);
};
  
} //namespace OpenMS