IndexedMzMLHandler.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.
// --------------------------------------------------------------------------
// 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;
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// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/INTERFACES/DataStructures.h>
#include <OpenMS/INTERFACES/ISpectrumAccess.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
 
#include <string>
#include <fstream>
#include <unordered_map>
 
namespace OpenMS
{
 
namespace Internal
{
 
  class OPENMS_DLLAPI IndexedMzMLHandler
  {
    String filename_;
    std::vector< std::streampos > spectra_offsets_;
    std::unordered_map< std::string, Size > spectra_native_ids_;
    std::vector< std::streampos > chromatograms_offsets_;
    std::unordered_map< std::string, Size > chromatograms_native_ids_;
    std::streampos index_offset_;
    bool spectra_before_chroms_;
    std::ifstream filestream_;
    bool parsing_success_;
    bool skip_xml_checks_;
 
    void parseFooter_(String filename);
 
    std::string getChromatogramById_helper_(int id);
 
    std::string getSpectrumById_helper_(int id);
 
    public:
 
    IndexedMzMLHandler();
 
    explicit IndexedMzMLHandler(const String& filename);
 
    IndexedMzMLHandler(const IndexedMzMLHandler& source);
 
    ~IndexedMzMLHandler();
 
    void openFile(String filename);
 
    bool getParsingSuccess() const;
 
    size_t getNrSpectra() const;
 
    size_t getNrChromatograms() const;
 
    OpenMS::Interfaces::SpectrumPtr getSpectrumById(int id);
 
    const OpenMS::MSSpectrum getMSSpectrumById(int id);
 
    void getMSSpectrumByNativeId(std::string id, OpenMS::MSSpectrum& s);
 
    void getMSSpectrumById(int id, OpenMS::MSSpectrum& s);
 
    OpenMS::Interfaces::ChromatogramPtr getChromatogramById(int id);
 
    const OpenMS::MSChromatogram getMSChromatogramById(int id);
 
    void getMSChromatogramByNativeId(std::string id, OpenMS::MSChromatogram& c);
 
    void getMSChromatogramById(int id, OpenMS::MSChromatogram& c);
 
    void setSkipXMLChecks(bool skip)
    {
      skip_xml_checks_ = skip;
    }
 
  };
}
}