OSWFile.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 2002-2022.
//
// 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: George Rosenberger $
// $Authors: George Rosenberger, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/OSWData.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/FORMAT/SqliteConnector.h>
#include <OpenMS/KERNEL/StandardTypes.h>

#include <array>
#include <map>

namespace OpenMS
{
  class OPENMS_DLLAPI OSWFile
  {
  public:
    
    static constexpr Size ALL_PROTEINS = -1;

    OSWFile(const String& filename);
    OSWFile(const OSWFile& rhs) = default;
    OSWFile& operator=(const OSWFile& rhs) = default;

    void read(OSWData& swath_result);

    void readMinimal(OSWData& swath_result);

    void readProtein(OSWData& swath_result, const Size index);

    enum class OSWLevel
    {
      MS1,
      MS2,
      TRANSITION,
      SIZE_OF_OSWLEVEL
    };
    static const std::array<std::string, (Size)OSWLevel::SIZE_OF_OSWLEVEL> names_of_oswlevel;

    struct PercolatorFeature
    {
      PercolatorFeature(double score, double qvalue, double pep)
       : score(score), qvalue(qvalue), posterior_error_prob(pep)
       {}
      PercolatorFeature(const PercolatorFeature& rhs) = default;
      
      double score;
      double qvalue;
      double posterior_error_prob;
    };

    static void readToPIN(const std::string& filename, const OSWFile::OSWLevel osw_level, std::ostream& pin_output,
                          const double ipf_max_peakgroup_pep, const double ipf_max_transition_isotope_overlap, const double ipf_min_transition_sn);

    static void writeFromPercolator(const std::string& osw_filename, const OSWFile::OSWLevel osw_level, const std::map< std::string, PercolatorFeature >& features);

    UInt64 getRunID() const;

  protected:
    void readTransitions_(OSWData& swath_result);

    void getFullProteins_(OSWData& swath_result, Size prot_index = ALL_PROTEINS);

    void readMeta_(OSWData& data);

  private:
    String filename_;       
    SqliteConnector conn_;  
    bool has_SCOREMS2_;     
  };

} // namespace OpenMS