FalseDiscoveryRate.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Chris Bielow $
// $Authors: Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>

#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI FalseDiscoveryRate :
    public DefaultParamHandler
  {
public:
    FalseDiscoveryRate();

    void apply(std::vector<PeptideIdentification> & fwd_ids, std::vector<PeptideIdentification> & rev_ids) const;

    void apply(std::vector<PeptideIdentification> & id) const;

    void apply(std::vector<ProteinIdentification> & fwd_ids, std::vector<ProteinIdentification> & rev_ids) const;

    void apply(std::vector<ProteinIdentification> & ids) const;

private:
    FalseDiscoveryRate(const FalseDiscoveryRate &);

    FalseDiscoveryRate & operator=(const FalseDiscoveryRate &);

    void calculateFDRs_(Map<double, double> & score_to_fdr, std::vector<double> & target_scores, std::vector<double> & decoy_scores, bool q_value, bool higher_score_better) const;

  };

} // namespace OpenMS