IdentificationSummary.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Axel Walter $
// $Authors: Axel Walter $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/QC/QCBase.h>
#include <vector>
namespace OpenMS
{
  class OPENMS_DLLAPI IdentificationSummary : public QCBase
  {
  public:
    IdentificationSummary() = default;
 
    virtual ~IdentificationSummary() = default;
 
    // small struct for unique peptide / protein identifications (considering sequence only)
    // count: number of unique identifications, fdr_threshold: significance threshold if score type is FDR, else -1
    struct OPENMS_DLLAPI UniqueID {
      UInt count = 0;
      float fdr_threshold = -1.0;
    };
 
    // stores identification summary values calculated by compute function
    struct OPENMS_DLLAPI Result {
      UInt peptide_spectrum_matches = 0;
      UniqueID unique_peptides;
      UniqueID unique_proteins;
      float missed_cleavages_mean = 0;
      double protein_hit_scores_mean = 0;
      double peptide_length_mean = 0;
 
      bool operator==(const Result& rhs) const;
    };
 
    Result compute(std::vector<ProteinIdentification>& prot_ids, PeptideIdentificationList& pep_ids);
 
    const String& getName() const override;
 
    QCBase::Status requirements() const override;
 
  private:
    const String name_ = "Summary of detected Proteins and Peptides from idXML file";
  };
} // namespace OpenMS