PSProteinInference.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Alexandra Zerck $
// --------------------------------------------------------------------------
//
 
#pragma once
 
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/DATASTRUCTURES/LPWrapper.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI PSProteinInference
  {
public:
 
    PSProteinInference();
 
    virtual ~PSProteinInference();
 
 
    Size findMinimalProteinList(const std::vector<PeptideIdentification> & peptide_ids);
 
    void calculateProteinProbabilities(const std::vector<PeptideIdentification> & ids);
 
//     double getProteinProbability(const String& acc,const std::vector<String>& accessions, const std::vector<double>& probabilities);
 
    double getProteinProbability(const String & acc);
 
    bool isProteinInMinimalList(const String & acc);
    Int getNumberOfProtIds(double protein_id_threshold);
    Int getNumberOfProtIdsPeptideRule(Int min_peptides, std::map<String, std::set<String> > & prot_id_counter);
 
    LPWrapper::SOLVER getSolver()
    {
      return solver_;
    }
 
private:
    std::vector<String> minimal_protein_list_accessions_;
    std::vector<String> accessions_;
    std::vector<double> probabilities_;
    LPWrapper::SOLVER solver_;
  };
 
}