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 2002-2023.
//
// 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.
// --------------------------------------------------------------------------
// 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
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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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/CHEMISTRY/ResidueDB.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, double rt_tolerance = 0.01);
 
    void keepNativeSpectrumName(bool keep)
    {
      keep_native_name_ = keep;
    }
 
    void setPreferredFixedModifications(const std::vector<const ResidueModification*>& mods);
 
    void setPreferredVariableModifications(const std::vector<const ResidueModification*>& mods);
 
    void setParseUnknownScores(bool parse_unknown_scores);
 
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);
 
    struct AminoAcidModification
    {
      private:
 
      String aminoacid_;
      double massdiff_;
      double mass_;
      bool is_variable_;
      String description_;
      String terminus_;
      bool is_protein_terminus_; // "true" if protein terminus, "false" if peptide terminus
      ResidueModification::TermSpecificity term_spec_;
      std::vector<String> errors_;
      const ResidueModification* registered_mod_;
 
      const ResidueModification* lookupModInPreferredMods_(const std::vector<const ResidueModification*>& preferred_fixed_mods,
                                                           const String& aminoacid,
                                                           double massdiff,
                                                           const String& description,
                                                           const ResidueModification::TermSpecificity term_spec,
                                                           double tolerance);
 
      public:
      AminoAcidModification() = delete;
 
      AminoAcidModification(
          const String& aminoacid, const String& massdiff, const String& mass,
          String variable, const String& description, String terminus, const String& protein_terminus,
          const std::vector<const ResidueModification*>& preferred_fixed_mods,
          const std::vector<const ResidueModification*>& preferred_var_mods,
          double tolerance);
 
      AminoAcidModification(const AminoAcidModification& rhs) = default;
 
      virtual ~AminoAcidModification() = default;
 
      AminoAcidModification& operator=(const AminoAcidModification& rhs) = default;
 
      String toUnimodLikeString() const;
 
      const String& getDescription() const;
 
      bool isVariable() const;
 
      const ResidueModification* getRegisteredMod() const;
 
      double getMassDiff() const;
 
      double getMass() const;
 
      const String& getTerminus() const;
 
      const String& getAminoAcid() const;
 
      const std::vector<String>& getErrors() const;
    };
 
    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_{};
 
    bool has_decoys_{};
 
    bool parse_unknown_scores_{};
 
    String decoy_prefix_;
 
    String current_base_name_;
 
    std::vector<std::vector<ProteinIdentification>::iterator> current_proteins_;
 
    ProteinIdentification::SearchParameters params_;
 
    String enzyme_;
    String enzyme_cuttingsite_;
 
    PeptideIdentification current_peptide_;
 
    PeptideHit::PepXMLAnalysisResult current_analysis_result_;
 
    PeptideHit peptide_hit_;
 
    String current_sequence_;
 
    double rt_{}, mz_{};
 
    Size scannr_{};
 
    Int charge_{};
 
    UInt search_id_{};
 
    String prot_id_;
 
    DateTime date_;
 
    double hydrogen_mass_{};
 
    std::vector<std::pair<const ResidueModification*, Size> > current_modifications_;
 
    std::vector<AminoAcidModification> fixed_modifications_;
 
    std::vector<AminoAcidModification> variable_modifications_;
 
    std::vector<const ResidueModification*> preferred_fixed_modifications_;
 
    std::vector<const ResidueModification*> preferred_variable_modifications_;
 
 
    static const double mod_tol_;
    static const double xtandem_artificial_mod_tol_;
 
    bool lookupAddFromHeader_(double modification_mass,
                              Size modification_position,
                              std::vector<AminoAcidModification> const& header_mods);
 
    //static std::vector<int> getIsotopeErrorsFromIntSetting_(int intSetting);
  };
} // namespace OpenMS