PepXMLFile.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
//    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"
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// $Maintainer: Chris Bielow, Hendrik Weisser $
// $Authors: Chris Bielow, Hendrik Weisser $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/Element.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/SpectrumMetaDataLookup.h>

#include <vector>
#include <map>
#include <set>


namespace OpenMS
{
  class OPENMS_DLLAPI PepXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile
  {
public:

    PepXMLFile();

    ~PepXMLFile() override;

    void load(const String& filename,
              std::vector<ProteinIdentification>& proteins,
              std::vector<PeptideIdentification>& peptides,
              const String& experiment_name,
              const SpectrumMetaDataLookup& lookup);

    void load(const String& filename,
              std::vector<ProteinIdentification>& proteins,
              std::vector<PeptideIdentification>& peptides,
              const String& experiment_name = "");

    void store(const String& filename, std::vector<ProteinIdentification>& protein_ids, 
               std::vector<PeptideIdentification>& peptide_ids, const String& mz_file = "",
               const String& mz_name = "", bool peptideprophet_analyzed = false);

    void keepNativeSpectrumName(bool keep) 
    {
      keep_native_name_ = keep;
    }

protected:

    void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;

    void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;

private:

    void makeScanMap_();

    void readRTMZCharge_(const xercesc::Attributes& attributes);

    void matchModification_(const double mass, const String& origin, String& modification_description);

    struct AminoAcidModification
    {
      String aminoacid;
      String massdiff;
      double mass;
      bool variable;
      String description;
      String terminus;

      AminoAcidModification() :
        mass(0),
        variable(false)
      {
      }

      AminoAcidModification(const AminoAcidModification& rhs) :
        aminoacid(rhs.aminoacid),
        massdiff(rhs.massdiff),
        mass(rhs.mass),
        variable(rhs.variable),
        description(rhs.description),
        terminus(rhs.terminus)
      {
      }

      virtual ~AminoAcidModification()
      {
      }

      AminoAcidModification& operator=(const AminoAcidModification& rhs)
      {
        if (this != &rhs)
        {
          aminoacid = rhs.aminoacid;
          massdiff = rhs.massdiff;
          mass = rhs.mass;
          variable = rhs.variable;
          description = rhs.description;
          terminus = rhs.terminus;
        }
        return *this;
      }

    };

    std::vector<ProteinIdentification>* proteins_;

    std::vector<PeptideIdentification>* peptides_;

    const SpectrumMetaDataLookup* lookup_;

    String exp_name_;

    String search_engine_;

    String native_spectrum_name_;
    String experiment_label_;
    String swath_assay_;
    String status_;

    bool use_precursor_data_;

    std::map<Size, Size> scan_map_;

    Element hydrogen_;

    bool analysis_summary_;

    bool keep_native_name_;

    bool search_score_summary_;

    bool search_summary_;

    bool wrong_experiment_;

    bool seen_experiment_;

    bool checked_base_name_;

    String current_base_name_;

    std::vector<std::vector<ProteinIdentification>::iterator> current_proteins_;

    ProteinIdentification::SearchParameters params_;

    String enzyme_;

    PeptideIdentification current_peptide_;

    PeptideHit::PepXMLAnalysisResult current_analysis_result_;

    PeptideHit peptide_hit_;

    String current_sequence_;

    double rt_, mz_;

    Int charge_;

    UInt search_id_;

    String prot_id_;

    DateTime date_;

    double hydrogen_mass_;

    std::vector<std::pair<String, Size> > current_modifications_;

    std::vector<AminoAcidModification> fixed_modifications_;

    std::vector<AminoAcidModification> variable_modifications_;


    static const double mod_tol_;
    static const double xtandem_artificial_mod_tol_;
  };

} // namespace OpenMS