OpenMS
SiriusFragmentAnnotation.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2023.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Oliver Alka $
32 // $Authors: Oliver Alka $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41  class OPENMS_DLLAPI SiriusFragmentAnnotation
42  {
43  public:
44 
49  {
50  public:
51 
54 
56  SiriusTargetDecoySpectra(MSSpectrum target_spectrum, MSSpectrum decoy_spectrum) : target(std::move(target_spectrum)), decoy(std::move(decoy_spectrum)) {}
57  };
58 
71  static std::vector<SiriusTargetDecoySpectra> extractAndResolveSiriusAnnotations(const std::vector<String>& sirius_workspace_subdirs, double score_threshold,
72  bool use_exact_mass);
73  static std::vector<MSSpectrum> extractSiriusAnnotationsTgtOnly(const std::vector<String>& sirius_workspace_subdirs, double score_threshold, bool use_exact_mass, bool resolve);
74 
75 
107  static std::vector<MSSpectrum> extractAnnotationsFromSiriusFile(const String& path_to_sirius_workspace, Size max_rank = 1, bool decoy = false, bool use_exact_mass = false);
108 
109  protected:
118  static OpenMS::String extractConcatNativeIDsFromSiriusMS_(const OpenMS::String& path_to_sirius_workspace);
119 
130  static OpenMS::String extractConcatMIDsFromSiriusMS_(const String& path_to_sirius_workspace);
131 
140  static OpenMS::String extractFeatureIDFromSiriusMS_(const String& path_to_sirius_workspace);
141 
150  static std::map< Size, String > extractCompoundRankingAndFilename_(const String& path_to_sirius_workspace);
151 
160  static std::map< Size, double > extractCompoundRankingAndScore_(const String& path_to_sirius_workspace);
161 
162  };
163 } // namespace OpenMS
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
SiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from S...
Definition: SiriusFragmentAnnotation.h:49
SiriusTargetDecoySpectra(MSSpectrum target_spectrum, MSSpectrum decoy_spectrum)
Definition: SiriusFragmentAnnotation.h:56
MSSpectrum target
Definition: SiriusFragmentAnnotation.h:52
MSSpectrum decoy
Definition: SiriusFragmentAnnotation.h:53
Definition: SiriusFragmentAnnotation.h:42
static std::map< Size, double > extractCompoundRankingAndScore_(const String &path_to_sirius_workspace)
extractCompoundRankingAndFilename Extract compound ranking and score (./formula_candidates....
static std::vector< MSSpectrum > extractAnnotationsFromSiriusFile(const String &path_to_sirius_workspace, Size max_rank=1, bool decoy=false, bool use_exact_mass=false)
extractSiriusFragmentAnnotationMapping Extract concatenated native ids and concatenated m_ids (unique...
static OpenMS::String extractConcatMIDsFromSiriusMS_(const String &path_to_sirius_workspace)
extractConcatMIDsFromSiriusMS Extract m_ids from SIRIUS output (./spectrum.ms) and concatenates them....
static OpenMS::String extractFeatureIDFromSiriusMS_(const String &path_to_sirius_workspace)
extractConcatMIDsFromSiriusMS Extract fid (i.e. original OpenMS feature ID) from SIRIUS output (....
static OpenMS::String extractConcatNativeIDsFromSiriusMS_(const OpenMS::String &path_to_sirius_workspace)
extractConcatNativeIDsFromSiriusMS Extract concatenated native id from SIRIUS output (....
static std::map< Size, String > extractCompoundRankingAndFilename_(const String &path_to_sirius_workspace)
extractCompoundRankingAndFilename Extract compound ranking and filename (./formula_candidates....
static std::vector< SiriusTargetDecoySpectra > extractAndResolveSiriusAnnotations(const std::vector< String > &sirius_workspace_subdirs, double score_threshold, bool use_exact_mass)
extractAndResolveSiriusAnnotations Extract and resolves SIRIUS target and/or decoy annotation for map...
static std::vector< MSSpectrum > extractSiriusAnnotationsTgtOnly(const std::vector< String > &sirius_workspace_subdirs, double score_threshold, bool use_exact_mass, bool resolve)
A more convenient string class.
Definition: String.h:60
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48