MQExporterHelper.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
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// $Maintainer: Chris Bielow$
// $Authors: Virginia Rossow, Lenny Kovac, Hendrik Beschorner$
// --------------------------------------------------------------------------

#pragma once

#include <fstream>
#include <OpenMS/KERNEL/ConsensusFeature.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>

class OPENMS_DLLAPI MQExporterHelper
{
public:

  struct MQCommonOutputs
  {
    std::stringstream modifications;
    char acetyl;
    std::stringstream oxidation;
    std::stringstream gene_names;
    std::stringstream protein_names;
    std::stringstream msms_mz;
    std::stringstream mass_error_ppm;
    std::stringstream mass_error_da;
    std::stringstream uncalibrated_mass_error_ppm;
    std::stringstream uncalibrated_mass_error_da;
    std::stringstream uncalibrated_calibrated_mz_ppm;
    std::stringstream uncalibrated_calibrated_mz_mda;
    std::stringstream base_peak_fraction;

    // common columns in msms and evividence exporter
    //file_ << "Sequence" << "\t"; maybe, relativ trivial
    //file_ << "Length" << "\t";
    //file_ << "Modifications" << "\t"; implementieren
    // file_ << "Modified sequence" << "\t"; implementieren
    //file_ << "Acetyl (Protein N-term)" << "\t"; implementieren
    //file_ << "Oxidation (M)" << "\t"; implementieren
    //file_ << "Missed cleavages" << "\t"; trivial
    //file_ << "Proteins" << "\t"; trivial
    //file_ << "Gene Names" << "\t"; // in progress, aber implementieren
    //file_ << "Protein Names" << "\t"; // in progress, aber implementieren
    //file_ << "Type" << "\t"; TODO different type
    //file_ << "Raw file" << "\t"; trivial
    //file_ << "MS/MS m/z" << "\t"; implementieren TODO is m/z in MSMS MS/MS m/z
    //file_ << "Charge" << "\t"; trivial
    //file_ << "m/z" << "\t"; trivial TODO
    //file_ << "Mass" << "\t"; trivial
    //file_ << "Mass Error [ppm]" << "\t"; vielleicht, beim einen halt noch calibrated dabei
    //file_ << "Mass Error [Da]" << "\t"; vielleicht, beim einen halt noch calibrated dabei
    //file_ << "Retention time" << "\t"; trivial
    //file_ << "Fraction of total spectrum" << "\t"; trivial
    //file_ << "Base peak fraction" << "\t"; trvial
    //file_ << "PEP" << "\t"; trivial
    //file_ << "MS/MS Scan Number" << "\t"; trivial
    //file_ << "Score" << "\t"; trivial
    //file_ << "Delta score" << "\t"; trivial
    //file_ << "Reverse" << "\t";
    //file_ << "id" << "\t"; ?
    //file_ << "Protein group IDs" << "\n"; trivial

    explicit MQCommonOutputs(
      const OpenMS::Feature& f,
      const OpenMS::ConsensusMap& cmap,
      const OpenMS::Size c_feature_number,
      const std::multimap<OpenMS::String, std::pair<OpenMS::Size, OpenMS::Size>>& UIDs,
      const OpenMS::ProteinIdentification::Mapping& mp_f,
      const OpenMS::MSExperiment& exp,
      const std::map<OpenMS::String,OpenMS::String>& prot_mapper);
  };

static OpenMS::String extractGeneName(const OpenMS::String& prot_description);

 static OpenMS::Size proteinGroupID_(std::map<OpenMS::String, OpenMS::Size>& database,
                                     const OpenMS::String& protein_accession);

  static std::map<OpenMS::Size, OpenMS::Size> makeFeatureUIDtoConsensusMapIndex_(const OpenMS::ConsensusMap& cmap);

  static 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);

  static bool hasPeptideIdentifications_(const OpenMS::ConsensusFeature& cf);


  static bool isValid(const std::string& filename_);
};