MzXMLHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// 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.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/FORMAT/Base64.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/INTERFACES/IMSDataConsumer.h>

#include <stack>

namespace OpenMS
{
  class MetaInfoInterface;

  namespace Internal
  {

    typedef PeakMap MapType;
    typedef MSSpectrum SpectrumType;

    class OPENMS_DLLAPI MzXMLHandler :
      public XMLHandler
    {
public:
      MzXMLHandler(MapType& exp, const String& filename, const String& version, ProgressLogger& logger);

      MzXMLHandler(const MapType& exp, const String& filename, const String& version, const ProgressLogger& logger);

      ~MzXMLHandler() 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;

      // Docu in base class
      void characters(const XMLCh* const chars, const XMLSize_t length) override;

      void writeTo(std::ostream& os) override;

      void setOptions(const PeakFileOptions& options)
      {
        options_ = options;
      }

      UInt getScanCount()
      {
        return scan_count_;
      }

      void setMSDataConsumer(Interfaces::IMSDataConsumer * consumer)
      {
        consumer_ = consumer;
      }

protected:

      typedef MapType::PeakType PeakType;
      typedef MSSpectrum SpectrumType;

      MapType* exp_;
      const MapType* cexp_;

      PeakFileOptions options_;

      Base64 decoder_;
      Int nesting_level_;

      struct SpectrumData
      {
        UInt peak_count_;
        String precision_;
        String compressionType_;
        String char_rest_;
        SpectrumType spectrum;
        bool skip_data;
      };

      std::vector< SpectrumData > spectrum_data_;

      bool skip_spectrum_;

      UInt spec_write_counter_;

      Interfaces::IMSDataConsumer* consumer_;

      UInt scan_count_;

      const ProgressLogger& logger_;


      inline std::ostream& writeAttributeIfExists_(std::ostream& os, const MetaInfoInterface& meta, const String& metakey, const String& attname);

      inline void writeUserParam_(std::ostream& os, const MetaInfoInterface& meta, int indent = 4, String tag = "nameValue");

      void doPopulateSpectraWithData_(SpectrumData & spectrum_data);

      void populateSpectraWithData_();

      std::vector< boost::shared_ptr< DataProcessing> > data_processing_;


private:
      MzXMLHandler();
      
      void init_();

      // init all the static members, which is necessary because otherwise the undefined order will cause problems
      void initStaticMembers_();

      static const XMLCh* s_value_;
      static const XMLCh* s_count_;
      static const XMLCh* s_type_;
      static const XMLCh* s_name_;
      static const XMLCh* s_version_;
      static const XMLCh* s_filename_;
      static const XMLCh* s_filetype_;
      static const XMLCh* s_filesha1_;
      static const XMLCh* s_completiontime_;
      static const XMLCh* s_precision_;
      static const XMLCh* s_byteorder_;
      static const XMLCh* s_contentType_;
      static const XMLCh* s_compressionType_;
      static const XMLCh* s_precursorintensity_;
      static const XMLCh* s_precursorcharge_;
      static const XMLCh* s_windowwideness_;
      static const XMLCh* s_mslevel_;
      static const XMLCh* s_peakscount_;
      static const XMLCh* s_polarity_;
      static const XMLCh* s_scantype_;
      static const XMLCh* s_filterline_;
      static const XMLCh* s_retentiontime_;
      static const XMLCh* s_startmz_;
      static const XMLCh* s_endmz_;
      static const XMLCh* s_first_;
      static const XMLCh* s_last_;
      static const XMLCh* s_phone_;
      static const XMLCh* s_email_;
      static const XMLCh* s_uri_;
      static const XMLCh* s_num_;
      static const XMLCh* s_intensitycutoff_;
      static const XMLCh* s_centroided_;
      static const XMLCh* s_deisotoped_;
      static const XMLCh* s_chargedeconvoluted_;
    };

  } // namespace Internal

} // namespace OpenMS