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 2002-2012.
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// $Maintainer: Chris Bielow, Hendrik Weisser $
// $Authors: Chris Bielow, Hendrik Weisser $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_PEPXMLFILE_H
#define OPENMS_FORMAT_PEPXMLFILE_H

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

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


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

    PepXMLFile();

    virtual ~PepXMLFile();

    void load(const String & filename, std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides, const String & experiment_name, const MSExperiment<> & experiment, bool use_precursor_data = false);

    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);

protected:

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

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

private:

    void makeScanMap_();

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

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

    struct AminoAcidModification
    {
      String aminoacid;
      String massdiff;
      DoubleReal 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 MSExperiment<> * experiment_;

    String exp_name_;

    String search_engine_;

    bool use_precursor_data_;

    std::map<Size, Size> scan_map_;

    DoubleReal rt_tol_, mz_tol_;

    Element hydrogen_;

    bool wrong_experiment_;

    bool seen_experiment_;

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

    ProteinIdentification::SearchParameters params_;

    ProteinIdentification::DigestionEnzyme enzyme_;

    PeptideIdentification current_peptide_;

    PeptideHit peptide_hit_;

    String current_sequence_;

    DoubleReal rt_, mz_;

    Int charge_;

    UInt search_id_;

    String prot_id_;

    DateTime date_;

    DoubleReal hydrogen_mass_;

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

    std::vector<AminoAcidModification> fixed_modifications_;

    std::vector<AminoAcidModification> variable_modifications_;


  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_PEPXMLFILE_H