FalseDiscoveryRate.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Chris Bielow $
// $Authors: Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_ID_FALSEDISCOVERYRATE_H
#define OPENMS_ANALYSIS_ID_FALSEDISCOVERYRATE_H

#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);

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

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

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

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);

  };

} // namespace OpenMS

#endif // OPENMS_ANALYSIS_ID_FALSEDISCOVERYRATE_H