DBSuitability.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 2002-2020.
//
// 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: Tom Waschischeck $
// $Authors: Tom Waschischeck $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
#include <cfloat>
#include <map>
#include <vector>
 
namespace OpenMS
{
  class PeptideIdentification;
  class PeptideHit;
 
  class OPENMS_DLLAPI DBSuitability:
    public DefaultParamHandler
  {
  public:
    struct SuitabilityData
    {
      Size num_top_novo = 0;
 
      Size num_top_db = 0;
      
      Size num_interest = 0;
 
      Size num_re_ranked = 0;
 
      double cut_off = DBL_MAX;
 
      double suitability = 0;
    };
 
    DBSuitability();
 
    ~DBSuitability() = default;
 
    void compute(std::vector<PeptideIdentification> pep_ids);
 
    const std::vector<SuitabilityData>& getResults() const;
 
  private:
    std::vector<SuitabilityData> results_;
 
    double getDecoyDiff_(const PeptideIdentification& pep_id);
 
    double getDecoyCutOff_(const std::vector<PeptideIdentification>& pep_ids, double reranking_cutoff_percentile);
 
    bool isNovoHit_(const PeptideHit& hit);
 
    bool passesFDR_(const PeptideHit& hit, double FDR);
  };
}