XQuestResultXMLHandler.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   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.
// --------------------------------------------------------------------------
// 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
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Eugen Netz $
// $Authors: Lukas Zimmermann $
// --------------------------------------------------------------------------
#pragma once
 
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideHit.h>
#include <OpenMS/CHEMISTRY/ProteaseDB.h>
 
namespace OpenMS
{
  namespace Internal
  {
    class OPENMS_DLLAPI XQuestResultXMLHandler :
      public XMLHandler
    {
    public:
 
      static std::map< Size, String > enzymes;
 
      static std::map<String, UInt> months;
 
      XQuestResultXMLHandler(const String & filename,
                             std::vector< PeptideIdentification > & pep_ids,
                             std::vector< ProteinIdentification > & prot_ids
                             );
 
      XQuestResultXMLHandler(const std::vector<ProteinIdentification>& pro_id,
                             const std::vector<PeptideIdentification>& pep_id,
                             const String& filename,
                             const String& version
                           );
 
      ~XQuestResultXMLHandler() override;
 
      // Docu in base class
      void endElement(const XMLCh * const uri, const XMLCh * const local_name, const XMLCh * const qname) override;
 
      // Docu in base class
      void startElement(const XMLCh * const uri, const XMLCh * const local_name, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
 
      double getMinScore() const;
 
      double getMaxScore() const;
 
      UInt getNumberOfHits() const;
 
      //Docu in base class
      virtual void writeTo(std::ostream& os) override;
 
      // TODO move these to StringUtils?
      static StringList splitByNth(const String& input, const char separator, const Size n);
 
      static StringList splitByMiddle(const String& input, const char separator);
 
    private:
 
 
      // Decoy string used by xQuest, initialize to a default value
      String decoy_string_ = "decoy_";
      int spectrum_index_light_;
      int spectrum_index_heavy_;
      String cross_linker_name_;
 
      // Main data structures that are populated during loading the file
      std::vector< PeptideIdentification >* pep_ids_;
      std::vector< ProteinIdentification >* prot_ids_;
 
      // internal ID items for writing files
      const std::vector<ProteinIdentification>* cpro_id_;
      const std::vector<PeptideIdentification>* cpep_id_;
 
      UInt n_hits_; 
 
      // Keeps track of the minscore and maxscore encountered
      double min_score_;
      double max_score_;
 
      bool is_openpepxl_;
 
      std::set< String > accessions_;
 
      ProteaseDB* enzymes_db_;
 
      std::set< UInt > charges_;
      UInt min_precursor_charge_;
      UInt max_precursor_charge_;
 
      // Current Retention time of spectrum pair
      double rt_light_;
      double rt_heavy_;
 
      // Current experimental m/z of spectrum pair
      double mz_light_;
      double mz_heavy_;
 
      // primary MS run path
      StringList ms_run_path_;
      String spectrum_input_file_;
 
      std::vector< PeptideIdentification > current_spectrum_search_;
 
      std::map<String, DataValue> peptide_id_meta_values_;
 
      inline void extractDateTime_(const String & xquest_datetime_string, DateTime & date_time);
 
      void addMetaValues_(MetaInfoInterface & meta_info_interface);
 
      void getLinkPosition_(const xercesc::Attributes & attributes, std::pair<SignedSize, SignedSize> & pair);
 
      void setPeptideEvidence_(const String & prot_string, PeptideHit & pep_hit);
 
    };
  } // namespace Internal
} // namespace OpenMS