MzIdentMLDOMHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// 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"
// 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
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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// --------------------------------------------------------------------------
// $Maintainer: Mathias Walzer $
// $Authors: Mathias Walzer$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
 
#include <OpenMS/FORMAT/ControlledVocabulary.h>
#include <OpenMS/METADATA/ProteinHit.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CONCEPT/UniqueIdGenerator.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/METADATA/CVTermList.h>
 
#include <xercesc/dom/DOM.hpp>
#include <xercesc/dom/DOMDocument.hpp>
#include <xercesc/dom/DOMDocumentType.hpp>
#include <xercesc/dom/DOMElement.hpp>
#include <xercesc/dom/DOMImplementation.hpp>
#include <xercesc/dom/DOMImplementationLS.hpp>
#include <xercesc/dom/DOMNodeIterator.hpp>
#include <xercesc/dom/DOMNodeList.hpp>
#include <xercesc/dom/DOMText.hpp>
#include <xercesc/util/OutOfMemoryException.hpp>
#include <xercesc/util/XMLString.hpp>
#include <xercesc/util/PlatformUtils.hpp>
#include <xercesc/framework/LocalFileFormatTarget.hpp>
 
#include <xercesc/parsers/XercesDOMParser.hpp>
#include <xercesc/util/XMLUni.hpp>
#include <xercesc//framework/psvi/XSValue.hpp>
 
#include <string>
#include <stdexcept>
#include <vector>
#include <map>
 
// Error codes
//enum {
//   ERROR_ARGS = 1,
//   ERROR_XERCES_INIT,
//   ERROR_PARSE,
//   ERROR_EMPTY_DOCUMENT
//};
 
namespace OpenMS
{
  class ProgressLogger;
 
  namespace Internal
  {
    class OPENMS_DLLAPI MzIdentMLDOMHandler
    {
public:
      MzIdentMLDOMHandler(const std::vector<ProteinIdentification>& pro_id, const std::vector<PeptideIdentification>& pep_id, const String& version, const ProgressLogger& logger);
 
      MzIdentMLDOMHandler(std::vector<ProteinIdentification>& pro_id, std::vector<PeptideIdentification>& pep_id, const String& version, const ProgressLogger& logger);
 
      virtual ~MzIdentMLDOMHandler();
 
      void readMzIdentMLFile(const std::string& mzid_file);
      void writeMzIdentMLFile(const std::string& mzid_file);
 
protected:
      const ProgressLogger& logger_;
 
      ControlledVocabulary cv_;
      ControlledVocabulary unimod_;
 
      std::vector<ProteinIdentification>* pro_id_;
      std::vector<PeptideIdentification>* pep_id_;
 
      const std::vector<ProteinIdentification>* cpro_id_;
      const std::vector<PeptideIdentification>* cpep_id_;
 
      const String schema_version_;
 
      ControlledVocabulary::CVTerm getChildWithName_(const String& parent_accession, const String& name) const;
 
      std::pair<CVTermList, std::map<String, DataValue> > parseParamGroup_(xercesc::DOMNodeList* paramGroup);
      CVTerm parseCvParam_(xercesc::DOMElement* param);
      std::pair<String, DataValue> parseUserParam_(xercesc::DOMElement* param);
      void parseAnalysisSoftwareList_(xercesc::DOMNodeList* analysisSoftwareElements);
      void parseDBSequenceElements_(xercesc::DOMNodeList* dbSequenceElements);
      void parsePeptideElements_(xercesc::DOMNodeList* peptideElements);
      //AASequence parsePeptideSiblings_(xercesc::DOMNodeList* peptideSiblings);
      AASequence parsePeptideSiblings_(xercesc::DOMElement* peptide);
      void parsePeptideEvidenceElements_(xercesc::DOMNodeList* peptideEvidenceElements);
      void parseSpectrumIdentificationElements_(xercesc::DOMNodeList* spectrumIdentificationElements);
      void parseSpectrumIdentificationProtocolElements_(xercesc::DOMNodeList* spectrumIdentificationProtocolElements);
      void parseInputElements_(xercesc::DOMNodeList* inputElements);
      void parseSpectrumIdentificationListElements_(xercesc::DOMNodeList* spectrumIdentificationListElements);
      void parseSpectrumIdentificationItemSetXLMS(std::set<String>::const_iterator set_it, std::multimap<String, int> xl_val_map, xercesc::DOMElement* element_res, String spectrumID);
      void parseSpectrumIdentificationItemElement_(xercesc::DOMElement* spectrumIdentificationItemElement, PeptideIdentification& spectrum_identification, String& spectrumIdentificationList_ref);
      void parseProteinDetectionHypothesisElement_(xercesc::DOMElement* proteinDetectionHypothesisElement, ProteinIdentification& protein_identification);
      void parseProteinAmbiguityGroupElement_(xercesc::DOMElement* proteinAmbiguityGroupElement, ProteinIdentification& protein_identification);
      void parseProteinDetectionListElements_(xercesc::DOMNodeList* proteinDetectionListElements);
      static ProteinIdentification::SearchParameters findSearchParameters_(std::pair<CVTermList, std::map<String, DataValue> > as_params);
 
      void buildCvList_(xercesc::DOMElement* cvElements);
      void buildAnalysisSoftwareList_(xercesc::DOMElement* analysisSoftwareElements);
      void buildSequenceCollection_(xercesc::DOMElement* sequenceCollectionElements);
      void buildAnalysisCollection_(xercesc::DOMElement* analysisCollectionElements);
      void buildAnalysisProtocolCollection_(xercesc::DOMElement* protocolElements);
      void buildInputDataCollection_(xercesc::DOMElement* inputElements);
      void buildEnclosedCV_(xercesc::DOMElement* parentElement, String encel, String acc, String name, String cvref);
      void buildAnalysisDataCollection_(xercesc::DOMElement* analysisElements);
 
 
private:
      MzIdentMLDOMHandler();
      MzIdentMLDOMHandler(const MzIdentMLDOMHandler& rhs);
      MzIdentMLDOMHandler& operator=(const MzIdentMLDOMHandler& rhs);
 
      struct AnalysisSoftware
      {
        String name;
        String version;
      };
      struct PeptideEvidence
      {
        int start;
        int stop;
        char pre;
        char post;
        bool idec;
      };
      struct DBSequence
      {
        String sequence;
        String database_ref;
        String accession;
        CVTermList cvs;
      };
      struct SpectrumIdentification
      {
        String spectra_data_ref;
        String search_database_ref;
        String spectrum_identification_protocol_ref;
        String spectrum_identification_list_ref;
      };
      struct ModificationParam
      {
        String fixed_mod;
        long double mass_delta;
        String residues;
        CVTermList modification_param_cvs;
        CVTermList specificities;
      };
      struct SpectrumIdentificationProtocol
      {
        CVTerm searchtype;
        String enzyme;
        CVTermList parameter_cvs;
        std::map<String, DataValue> parameter_ups;
//        std::vector<ModificationParam> modification_parameter;
        CVTermList modification_parameter;
        long double precursor_tolerance;
        long double fragment_tolerance;
        CVTermList threshold_cvs;
        std::map<String, DataValue> threshold_ups;
      };
      struct DatabaseInput
      {
        String name;
        String location;
        String version;
        DateTime date;
      };
 
      XMLCh* xml_root_tag_ptr_;
      XMLCh* xml_cvparam_tag_ptr_;
      XMLCh* xml_name_attr_ptr_;
 
      xercesc::XercesDOMParser mzid_parser_;
 
      //from AnalysisSoftware
      String search_engine_;
      String search_engine_version_;
      //mapping from AnalysisSoftware
      std::map<String, AnalysisSoftware> as_map_; 
 
      //mapping from DataCollection Inputs
      std::map<String, String> sr_map_; 
      std::map<String, String> sd_map_; 
      std::map<String, DatabaseInput> db_map_; 
 
      //mapping from SpectrumIdentification - SpectrumIdentification will be the new IdentificationRuns
      std::map<String, SpectrumIdentification> si_map_; 
      std::map<String, size_t> si_pro_map_; 
 
      //mapping from SpectrumIdentificationProtocol
      std::map<String, SpectrumIdentificationProtocol> sp_map_; 
 
      //mapping from SequenceCollection
      std::map<String, AASequence> pep_map_; 
      std::map<String, PeptideEvidence> pe_ev_map_; 
      std::map<String, String> pv_db_map_; 
      std::multimap<String, String> p_pv_map_; 
      std::map<String, DBSequence> db_sq_map_; 
 
      std::list<std::list<String> > hit_pev_; 
 
      bool xl_ms_search_; 
      std::map<String, String> xl_id_donor_map_; 
      //std::map<String, String> xl_id_acceptor_map_; ///< mapping Peptide id -> cross-link acceptor value
      std::map<String, String> xl_id_acceptor_map_; 
      std::map<String, SignedSize> xl_donor_pos_map_; 
      std::map<String, SignedSize> xl_acceptor_pos_map_; 
      std::map<String, double> xl_mass_map_; 
      std::map<String, String> xl_mod_map_; 
 
    };
  } // namespace Internal
} // namespace OpenMS