MzDataHandler.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
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
#include <sstream>
 
namespace OpenMS
{
  namespace Internal
  {
  typedef PeakMap MapType;
  typedef MSSpectrum SpectrumType;
  typedef MSChromatogram ChromatogramType;
 
    class OPENMS_DLLAPI MzDataHandler :
      public XMLHandler
    {
public:
      MzDataHandler(MapType & exp, const String & filename, const String & version, ProgressLogger & logger);
 
      MzDataHandler(const MapType & exp, const String & filename, const String & version, const ProgressLogger & logger);
 
      ~MzDataHandler() 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;
      }
 
private:
      void init_();
 
protected:
 
      typedef MapType::PeakType PeakType;
      typedef MSSpectrum SpectrumType;
 
      MapType * exp_;
      const MapType * cexp_;
 
      PeakFileOptions options_;
 
      UInt peak_count_;
      SpectrumType spec_;
      std::vector<std::pair<String, MetaInfoDescription> > meta_id_descs_;
      std::vector<String> data_to_decode_;
      std::vector<float> data_to_encode_;
      std::vector<std::vector<float> > decoded_list_;
      std::vector<std::vector<double> > decoded_double_list_;
      std::vector<String> precisions_;
      std::vector<String> endians_;
 
      bool skip_spectrum_;
 
      const ProgressLogger & logger_;
 
      void fillData_();
 
 
 
      inline void writeCVS_(std::ostream & os, double value, const String & acc, const String & name, UInt indent = 4) const;
 
      inline void writeCVS_(std::ostream & os, const String & value, const String & acc, const String & name, UInt indent = 4) const;
 
      inline void writeCVS_(std::ostream & os, UInt value, UInt map, const String & acc, const String & name, UInt indent = 4);
 
      inline void writeUserParam_(std::ostream & os, const MetaInfoInterface & meta, UInt indent = 4);
 
      void cvParam_(const String & name, const String & value);
 
      inline void writeBinary_(std::ostream & os, Size size, const String & tag, const String & name = "", SignedSize id = -1);
 
      //Data processing auxiliary variable
      boost::shared_ptr< DataProcessing > data_processing_;
 
    };
 
    //--------------------------------------------------------------------------------
  }   // namespace Internal
 
} // namespace OpenMS