ClassFDR.h

Go to the documentation of this file.

// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
 
#include <functional>
#include <string>
#include <vector>
 
namespace OpenMS
{
  class PeptideHit;
 
  class OPENMS_DLLAPI ClassFDR
  {
  public:
    enum class Method
    {
      POOLED_NULL, 
      CLASS_TDC    
    };
 
    struct OPENMS_DLLAPI ClassSummary
    {
      std::string name;
      Size targets = 0;
      Size decoys = 0;
      Method method = Method::POOLED_NULL;
      double pi0 = 1.0;
    };
 
    static const std::string CLASS_Q_VALUE;
 
    static std::vector<ClassSummary> annotateClassQValues(PeptideIdentificationList& ids,
                                                          const std::function<std::string(const PeptideHit&)>& class_of,
                                                          bool use_all_hits = false);
 
    static Size raiseToClassQValues(PeptideIdentificationList& ids);
 
    static std::string classFromMetaValue(const PeptideHit& hit, const std::string& name);
 
    static std::string classFromModifications(const PeptideHit& hit, const std::vector<std::string>& ignore);
 
    static std::vector<double> storeyQValues(const std::vector<double>& p, double& pi0);
  };
} // namespace OpenMS