OpenMS
OfflinePrecursorIonSelection.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: Timo Sachsenberg $
32 // $Authors: Alexandra Zerck $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 
44 
45 namespace OpenMS
46 {
47  class PeptideIdentification;
48  class ProteinIdentification;
49  class String;
50 
51 
61  class OPENMS_DLLAPI OfflinePrecursorIonSelection :
62  public DefaultParamHandler
63  {
64 public:
66 
69 
80  const PeakMap& experiment,
81  PeakMap& ms2,
82  std::set<Int>& charges_set,
83  bool feature_based);
84 
92  void getMassRanges(const FeatureMap& features,
93  const PeakMap& experiment,
94  std::vector<std::vector<std::pair<Size, Size> > >& indices);
95 
96  void createProteinSequenceBasedLPInclusionList(String include, String rt_model_file, String pt_model_file, FeatureMap& precursors);
97 
99  {
100  solver_ = solver;
101  std::cout << " LPSolver set to " << solver_ << std::endl;
102  }
103 
105  {
106  return solver_;
107  }
108 
109 private:
110 
111  template <typename PairType>
113  {
114  bool operator()(const PairType & left, const PairType & right) const
115  {
116  return left.second < right.second;
117  }
118 
119  };
120 
121  typedef std::map<std::pair<double, double>, int, PairComparatorSecondElement<std::pair<double, double> > > ExclusionListType_;
122 
126  void calculateXICs_(const FeatureMap& features,
127  const std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
128  const PeakMap& experiment,
129  const std::set<Int>& charges_set,
130  std::vector<std::vector<std::pair<Size, double> > >& xics);
131 
135  void checkMassRanges_(std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
136  const PeakMap& experiment);
137 
139  void updateExclusionList_(ExclusionListType_& exclusion_list) const;
140 
142  };
143 
144 }
145 
146 
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
A container for features.
Definition: FeatureMap.h:106
SOLVER
Definition: LPWrapper.h:134
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
Implements different algorithms for precursor ion selection.
Definition: OfflinePrecursorIonSelection.h:63
std::map< std::pair< double, double >, int, PairComparatorSecondElement< std::pair< double, double > > > ExclusionListType_
Definition: OfflinePrecursorIonSelection.h:121
void setLPSolver(LPWrapper::SOLVER solver)
Definition: OfflinePrecursorIonSelection.h:98
void makePrecursorSelectionForKnownLCMSMap(const FeatureMap &features, const PeakMap &experiment, PeakMap &ms2, std::set< Int > &charges_set, bool feature_based)
Makes the precursor selection for a given feature map, either feature or scan based.
void calculateXICs_(const FeatureMap &features, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const PeakMap &experiment, const std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, double > > > &xics)
Calculate the sum of intensities of relevant features for each scan separately.
void checkMassRanges_(std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const PeakMap &experiment)
Eliminates overlapping peaks.
LPWrapper::SOLVER getLPSolver()
Definition: OfflinePrecursorIonSelection.h:104
void updateExclusionList_(ExclusionListType_ &exclusion_list) const
reduce scan count for each entry, and remove every entry which has reached 0 counts
void getMassRanges(const FeatureMap &features, const PeakMap &experiment, std::vector< std::vector< std::pair< Size, Size > > > &indices)
Calculates the mass ranges for each feature and stores them as indices of the raw data.
LPWrapper::SOLVER solver_
Definition: OfflinePrecursorIonSelection.h:141
void createProteinSequenceBasedLPInclusionList(String include, String rt_model_file, String pt_model_file, FeatureMap &precursors)
PSLPFormulation::IndexTriple IndexTriple
Definition: OfflinePrecursorIonSelection.h:65
Struct that holds the indices of the precursors in the feature map and the ilp formulation.
Definition: PSLPFormulation.h:71
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Definition: OfflinePrecursorIonSelection.h:113
bool operator()(const PairType &left, const PairType &right) const
Definition: OfflinePrecursorIonSelection.h:114