PeptideProteinResolution.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.
//
// This software is released under a three-clause BSD license:
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/LogStream.h>
#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;
    
    // Default constructor
    ConnectedComponent();

    friend std::ostream& operator << (std::ostream& os, const ConnectedComponent& conn_comp);
  };

  class OPENMS_DLLAPI PeptideProteinResolution
  {
  
  private:
    // to build bipartite graph as two maps (adjacency "lists"):
    // ProtGroups-Indices <-> PepID-Indices
    // so we get bidirectional connectivity
    // We always take first PepHit from PepID, because those were used for
    // inference in Fido
    typedef std::map<Size, std::set<Size> > IndexMap_;

    // 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);
    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