OpenMS  2.8.0
PrecursorCorrection.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 2002-2021.
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: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg, Oliver Alka $
33 // --------------------------------------------------------------------------
34 //
35 
36 #pragma once
37 
41 
44 
46 
47 #include <string>
48 #include <vector>
49 #include <set>
50 
51 namespace OpenMS
52 {
63 class OPENMS_DLLAPI PrecursorCorrection
64 {
65  public:
66 
67  static const std::string csv_header;
68 
77  static void getPrecursors(const MSExperiment & exp,
78  std::vector<Precursor> & precursors,
79  std::vector<double> & precursors_rt,
80  std::vector<Size> & precursor_scan_index);
81 
82 
97  static void writeHist(const String& out_csv,
98  const std::vector<double> & delta_mzs,
99  const std::vector<double> & mzs,
100  const std::vector<double> & rts);
115  static std::set<Size> correctToNearestMS1Peak(MSExperiment & exp,
116  double mz_tolerance,
117  bool ppm,
118  std::vector<double> & delta_mzs,
119  std::vector<double> & mzs,
120  std::vector<double> & rts);
121 
136  static std::set<Size> correctToHighestIntensityMS1Peak(MSExperiment & exp,
137  double mz_tolerance,
138  bool ppm,
139  std::vector<double> & delta_mzs,
140  std::vector<double> & mzs,
141  std::vector<double> & rts);
142 
143 
167  static std::set<Size> correctToNearestFeature(const FeatureMap& features,
168  MSExperiment & exp,
169  double rt_tolerance_s = 0.0,
170  double mz_tolerance = 0.0,
171  bool ppm = true,
172  bool believe_charge = false,
173  bool keep_original = false,
174  bool all_matching_features = false,
175  int max_trace = 2,
176  int debug_level = 0);
177 
178  protected:
179 
191  static bool overlaps_(const Feature& feature,
192  const double rt,
193  const double pc_mz,
194  const double rt_tolerance);
195 
208  static bool compatible_(const Feature& feature,
209  double pc_mz,
210  double mz_tolerance,
211  Size max_trace_number = 2,
212  int debug_level = 0);
213 
214 };
215 }
A container for features.
Definition: FeatureMap.h:106
An LC-MS feature.
Definition: Feature.h:72
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
This class provides methods for precursor correction.
Definition: PrecursorCorrection.h:64
static const std::string csv_header
Definition: PrecursorCorrection.h:67
static void writeHist(const String &out_csv, const std::vector< double > &delta_mzs, const std::vector< double > &mzs, const std::vector< double > &rts)
Writer can be used in association with correctToNearestMS1Peak or correctToHighestIntensityMS1Peak.
static std::set< Size > correctToNearestFeature(const FeatureMap &features, MSExperiment &exp, double rt_tolerance_s=0.0, double mz_tolerance=0.0, bool ppm=true, bool believe_charge=false, bool keep_original=false, bool all_matching_features=false, int max_trace=2, int debug_level=0)
Reassigns a precursor to the nearest feature in a given rt and mass range. Wrong assignment of the mo...
static bool overlaps_(const Feature &feature, const double rt, const double pc_mz, const double rt_tolerance)
Check if precursor is located in the bounding box of a features convex hull. Here the bounding box of...
static void getPrecursors(const MSExperiment &exp, std::vector< Precursor > &precursors, std::vector< double > &precursors_rt, std::vector< Size > &precursor_scan_index)
Extract precursors and associated information (precursor retention time and precursor scan index).
static std::set< Size > correctToNearestMS1Peak(MSExperiment &exp, double mz_tolerance, bool ppm, std::vector< double > &delta_mzs, std::vector< double > &mzs, std::vector< double > &rts)
Selection of the peak in closest proximity as corrected precursor mass in a given mass range (e....
static std::set< Size > correctToHighestIntensityMS1Peak(MSExperiment &exp, double mz_tolerance, bool ppm, std::vector< double > &delta_mzs, std::vector< double > &mzs, std::vector< double > &rts)
Selection of the peak with the highest intensity as corrected precursor mass in a given mass range (e...
static bool compatible_(const Feature &feature, double pc_mz, double mz_tolerance, Size max_trace_number=2, int debug_level=0)
Check precursor and feature compatibility If the precursor mz is in one of the masstraces the feature...
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:47