MQEvidenceExporter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// 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
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow$
// $Authors: Valentin Noske, Vincent Musch$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <fstream>
#include <OpenMS/KERNEL/ConsensusFeature.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/KERNEL/FeatureMap.h>
 
class OPENMS_DLLAPI MQEvidence
{
private:
    std::fstream file_; 
    OpenMS::Size id_ = 0; 
    std::map<OpenMS::String, OpenMS::Size> protein_id_; 
    OpenMS::String filename_; 
 
    void exportHeader_();
 
    OpenMS::Size proteinGroupID_(const OpenMS::String& protein_accession);
 
    std::map<OpenMS::Size, OpenMS::Size> makeFeatureUIDtoConsensusMapIndex_(const OpenMS::ConsensusMap& cmap);
 
    bool hasValidPepID_(
            const OpenMS::Feature& f,
            const OpenMS::Size c_feature_number,
            const std::multimap<OpenMS::String, std::pair<OpenMS::Size, OpenMS::Size>>& UIDs,
            const OpenMS::ProteinIdentification::Mapping& mp_f);
 
    bool hasPeptideIdentifications_(const OpenMS::ConsensusFeature& cf);
 
    void exportRowFromFeature_(
            const OpenMS::Feature& f,
            const OpenMS::ConsensusMap& cmap,
            const OpenMS::Size c_feature_number,
            const OpenMS::String& raw_file,
            const std::multimap<OpenMS::String, std::pair<OpenMS::Size, OpenMS::Size>>& UIDs,
            const OpenMS::ProteinIdentification::Mapping& mp_f);
 
public:
    explicit MQEvidence(const OpenMS::String& path);
 
    ~MQEvidence();
 
    bool isValid();
 
    void exportFeatureMap(
            const OpenMS::FeatureMap& feature_map,
            const OpenMS::ConsensusMap& cmap);
};