PercolatorFeatureSetHelper.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: Mathias Walzer $
// $Authors: Mathias Walzer, Matthew The $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <vector>
#include <cmath>
#include <string>
#include <map>
// #include <algorithm>
#include <limits>
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/DataValue.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
 
namespace OpenMS
{
    class OPENMS_DLLAPI PercolatorFeatureSetHelper
    {
 
    public:
        static void mergeMULTISEProteinIds(std::vector<ProteinIdentification>& all_protein_ids, std::vector<ProteinIdentification>& new_protein_ids);
 
 
        static void addMSGFFeatures(PeptideIdentificationList& peptide_ids, StringList& feature_set);
 
        static void addXTANDEMFeatures(PeptideIdentificationList& peptide_ids, StringList& feature_set);
 
        static void addCOMETFeatures(PeptideIdentificationList& peptide_ids, StringList& feature_set);
 
        static void addANDESFeatures(PeptideIdentificationList& peptide_ids, StringList& feature_set);
 
        static void addMASCOTFeatures(PeptideIdentificationList& peptide_ids, StringList& feature_set);
 
        static void checkExtraFeatures(const std::vector<PeptideHit> &psms, StringList& extra_features);
 
        static void addMSFRAGGERFeatures(StringList& extra_features);
        
 
    protected:
        static double rescaleFragmentFeature_(double featureValue, int NumMatchedMainIons);
 
        static void assignDeltaScore_(std::vector<PeptideHit>& hits, const std::string& score_ref, const std::string& output_ref);
 
        struct lq_ProteinHit
        {
          inline bool operator() (const ProteinHit& h1, const ProteinHit& h2)
          {
            return (h1.getAccession() < h2.getAccession());
          }
        };
 
    };
 
} //namespace OpenMS