Ms2IdentificationRate.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// 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.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow$
// $Authors: Patricia Scheil, Swenja Wagner$
// --------------------------------------------------------------------------
 
#pragma once
 
#include "OpenMS/QC/QCBase.h"
 
#include <OpenMS/CONCEPT/Types.h>
#include <string>
#include <vector>
 
namespace OpenMS
{
  class FeatureMap;
  class MSExperiment;
  class MzTabMetaData;
  class PeptideIdentification;
 
  class OPENMS_DLLAPI Ms2IdentificationRate : public QCBase
  {
  public:
    struct IdentificationRateData {
      Size num_peptide_identification = 0;
      Size num_ms2_spectra = 0;
      double identification_rate = 0.;
    };
 
  private:
    const String name_ = "Ms2IdentificationRate";
 
    std::vector<IdentificationRateData> rate_result_;
 
    Size getMS2Count_(const MSExperiment& exp);
 
    /*
     * @brief Checks pepID for target/decoy
     *
     * Only checks the first (!) hit, all other hits are ignored
     * Is static so that it can be used with MapUtilities::applyFunctionOnPeptideIDs() without creating a new object for each ID
     *
     * @param id             pepID to be checked
     * @param all_targets    always returns true (if the hits aren't empty)
     * @return               true/false
     * @throws               MissingInformation if target/decoy annotation is missing
     */
    static bool isTargetPeptide_(const PeptideIdentification& id, bool all_targets);
 
    /*
     * @brief Calculates id-rate and writes the result into a IdentificationRateData object which is appended to rate_result_
     *
     * @param ms2_spectra_count  number of found ms2 spectra
     * @param pep_ids_count      number of found (target) peptide identifications
     */
    void writeResults_(Size pep_ids_count, Size ms2_spectra_count);
 
  public:
    Ms2IdentificationRate() = default;
 
    virtual ~Ms2IdentificationRate() = default;
 
    void compute(const FeatureMap& feature_map, const MSExperiment& exp, bool assume_all_target = false);
 
    void compute(const std::vector<PeptideIdentification>& pep_ids, const MSExperiment& exp, bool assume_all_target = false);
 
    const String& getName() const override;
 
    const std::vector<IdentificationRateData>& getResults() const;
 
    QCBase::Status requirements() const override;
 
    void addMetaDataMetricsToMzTab(MzTabMetaData& meta) const;
  };
 
} // namespace OpenMS