PercolatorFeatureSetHelper.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
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//  * Redistributions in binary form must reproduce the above copyright
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//    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"
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// --------------------------------------------------------------------------
// $Maintainer: Mathias Walzer $
// $Authors: Mathias Walzer, Matthew The $
// --------------------------------------------------------------------------

#pragma once

#include <vector>
#include <iostream>
#include <cmath>
#include <string>
#include <map>
#include <algorithm>
#include <limits>

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/DATASTRUCTURES/DataValue.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/CONCEPT/LogStream.h>

#include <boost/lexical_cast.hpp>

namespace OpenMS
{
    class OPENMS_DLLAPI PercolatorFeatureSetHelper
    {

    public:
        static void concatMULTISEPeptideIds(std::vector<PeptideIdentification>& all_peptide_ids, std::vector<PeptideIdentification>& new_peptide_ids, String search_engine);

        static void mergeMULTISEPeptideIds(std::vector<PeptideIdentification>& all_peptide_ids, std::vector<PeptideIdentification>& new_peptide_ids, String search_engine);

        static void mergeMULTISEProteinIds(std::vector<ProteinIdentification>& all_protein_ids, std::vector<ProteinIdentification>& new_protein_ids);
        

        static void addMSGFFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);

        static void addXTANDEMFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);

        static void addCOMETFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);

        static void addMASCOTFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);

        static void addMULTISEFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& search_engines_used, StringList& feature_set, bool complete_only = true, bool limits_imputation = false);

        static void addCONCATSEFeatures(std::vector<PeptideIdentification>& peptide_id_list, StringList& search_engines_used, StringList& feature_set);

        static void checkExtraFeatures(const std::vector<PeptideHit> &psms, StringList& extra_features);
        

    protected:
        static double rescaleFragmentFeature_(double featureValue, int NumMatchedMainIons);

        static void assignDeltaScore_(std::vector<PeptideHit>& hits, String score_ref, String output_ref);

        static String getScanMergeKey_(std::vector<PeptideIdentification>::iterator it, std::vector<PeptideIdentification>::iterator start);

        struct lq_ProteinHit
        {
          inline bool operator() (const ProteinHit& h1, const ProteinHit& h2)
          {
            return (h1.getAccession() < h2.getAccession());
          }
        };

        struct lq_PeptideEvidence
        {
          inline bool operator() (const PeptideEvidence& h1, const PeptideEvidence& h2)
          {
            return (h1.getProteinAccession() < h2.getProteinAccession());
          }
        };

    };

} //namespace OpenMS