SiriusFragmentAnnotation.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 2002-2021.
//
// 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: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MSSpectrum.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SiriusFragmentAnnotation
      {
      public:
 
          class SiriusTargetDecoySpectra
          {
          public:
 
            MSSpectrum target;
            MSSpectrum decoy;
 
            SiriusTargetDecoySpectra() = default;
            SiriusTargetDecoySpectra(MSSpectrum target_spectrum, MSSpectrum decoy_spectrum) : target(target_spectrum), decoy(decoy_spectrum) {}
          };
 
          static std::vector<SiriusTargetDecoySpectra> extractAndResolveSiriusAnnotations(const std::vector<String>& sirius_workspace_subdirs, const double& score_threshold, bool use_exact_mass);
 
          static void extractSiriusFragmentAnnotationMapping(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill, bool use_exact_mass = false);
 
          static void extractSiriusDecoyAnnotationMapping(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill);
      protected:
          static OpenMS::String extractConcatNativeIDsFromSiriusMS_(const OpenMS::String& path_to_sirius_workspace);
 
          static OpenMS::String extractConcatMIDsFromSiriusMS_(const String& path_to_sirius_workspace);
 
          static void extractAnnotationFromSiriusFile_(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill, bool use_exact_mass = false);
 
          static std::map< Size, String > extractCompoundRankingAndFilename_(const String& path_to_sirius_workspace);
 
          static std::map< Size, double > extractCompoundRankingAndScore_(const String& path_to_sirius_workspace);
 
          static void extractAnnotationFromDecoyFile_(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill);
  };
} // namespace OpenMS