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PSLPFormulation.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/KERNEL/FeatureMap.h>
39 #include <OpenMS/KERNEL/MSExperiment.h>
40
41 #include <OpenMS/DATASTRUCTURES/LPWrapper.h>
42 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
43
44 //#define DEBUG_OPS
45 namespace OpenMS
46 {
47 class PrecursorIonSelectionPreprocessing;
48 class PSProteinInference;
49
55 class OPENMS_DLLAPI PSLPFormulation :
56 public DefaultParamHandler
57 {
58
59
60
61 public:
62
63 PSLPFormulation();
64
65 ~PSLPFormulation() override;
66
70 struct IndexTriple
71 {
72 Size feature;
73 Int scan;
74 Size variable;
75 double rt_probability;
76 double signal_weight;
77 String prot_acc;
78 };
79
80
92 void createAndSolveILPForKnownLCMSMapFeatureBased(const FeatureMap& features,
93 const PeakMap& experiment,
94 std::vector<IndexTriple>& variable_indices,
95 std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
96 std::set<Int>& charges_set, UInt ms2_spectra_per_rt_bin,
97 std::vector<int>& solution_indices);
98
103 void createAndSolveILPForInclusionListCreation(PrecursorIonSelectionPreprocessing& preprocessing,
104 UInt ms2_spectra_per_rt_bin, UInt max_list_size,
105 FeatureMap& precursors,
106 bool solve_ILP = true);
107
108 void createAndSolveCombinedLPForKnownLCMSMapFeatureBased(const FeatureMap& features,
109 const PeakMap& experiment,
110 std::vector<IndexTriple>& variable_indices,
111 std::vector<int>& solution_indices,
112 std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
113 std::set<Int>& charges_set, UInt ms2_spectra_per_rt_bin,
114 Size step_size = 0, bool sequential_order = false);
115
116 void updateStepSizeConstraint(Size iteration, UInt step_size);
117 void updateFeatureILPVariables(FeatureMap& new_features, std::vector<IndexTriple>& variable_indices, std::map<Size, std::vector<String> >& feature_constraints_map);
118 void updateRTConstraintsForSequentialILP(Size& rt_index, UInt ms2_spectra_per_rt_bin, Size max_rt_index);
119 void updateCombinedILP(FeatureMap& features, PrecursorIonSelectionPreprocessing& preprocessed_db, std::vector<IndexTriple>& variable_indices,
120 std::vector<String>& new_protein_accs, std::vector<String>& protein_accs, PSProteinInference& prot_inference, Size& variable_counter,
121 std::map<String, std::vector<Size> >& protein_feature_map, Feature& new_feature, std::map<String, Size>& protein_variable_index_map,
122 std::map<String, std::set<String> >& prot_id_counter);
123
124
128 void solveILP(std::vector<int>& solution_indices);
129
130 void setLPSolver(LPWrapper::SOLVER solver)
131 {
132 solver_ = solver;
133 }
134
135 LPWrapper::SOLVER getLPSolver()
136 {
137 return solver_;
138 }
139
140 struct IndexLess :
141 std::binary_function<IndexTriple, IndexTriple, bool>
142 {
143 inline bool operator()(IndexTriple const& left,
144 IndexTriple const& right) const
145 {
146 return left.feature < right.feature;
147 }
148
149 };
150
151
152 struct ScanLess :
153 std::binary_function<IndexTriple, IndexTriple, bool>
154 {
155 inline bool operator()(IndexTriple const& left,
156 IndexTriple const& right) const
157 {
158 return left.scan < right.scan;
159 }
160
161 };
162
163 struct VariableIndexLess :
164 std::binary_function<IndexTriple, IndexTriple, bool>
165 {
166 inline bool operator()(IndexTriple const& left,
167 IndexTriple const& right) const
168 {
169 return left.variable < right.variable;
170 }
171
172 };
173
174 protected:
175
176 void getXIC_(const std::vector<std::pair<Size, Size> >& end_points,
177 std::vector<double>& weights,
178 const PeakMap& experiment,
179 const bool normalize);
180
184 void calculateXICs_(std::vector<std::vector<double> >& xics,
185 const FeatureMap& features,
186 const PeakMap& experiment,
187 const std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
188 const bool normalize);
189
193 void createAndSolveILP_(const FeatureMap& features, std::vector<std::vector<double> >& intensity_weights,
194 std::set<Int>& charges_set, std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
195 std::vector<IndexTriple>& variable_indices, std::vector<int>& solution_indices,
196 UInt ms2_spectra_per_rt_bin, Size number_of_scans);
197
198 void createAndSolveCombinedLPFeatureBased_(const FeatureMap& features, std::vector<std::vector<double> >& intensity_weights,
199 std::set<Int>& charges_set, std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
200 std::vector<IndexTriple>& variable_indices, std::vector<Int>& solution_indices,
201 UInt ms2_spectra_per_rt_bin, Size number_of_scans, Size step_size = 0, bool sequential_order = false);
202
203 void addProteinToILP_(PrecursorIonSelectionPreprocessing& preprocessing,
204 std::map<String, std::vector<double> >::const_iterator map_iter,
205 Size& counter, Size& pep_counter, Size& feature_counter,
206 std::vector<IndexTriple>& variable_indices,
207 std::map<String, Size>& protein_penalty_index_map, FeatureMap& precursors);
208
209 void addPrecursorAcquisitionNumberConstraint_(std::vector<IndexTriple>& variable_indices, Size number_of_features, UInt number_of_msms_per_precursor);
210
211 void addMaxInclusionListSizeConstraints_(std::vector<IndexTriple>& variable_indices, /*Size number_of_features,*/ UInt max_list_size);
212
213 void addRTBinCapacityConstraint_(std::vector<IndexTriple>& variable_indices,
214 Size max_rt_index, UInt ms2_spectra_per_rt_bin, bool sequential_order = false);
215
216 void addProteinCoverageConstraint_(std::vector<IndexTriple>& variable_indices,
217 PrecursorIonSelectionPreprocessing& preprocessing,
218 std::map<String, Size> protein_variable_index_map);
219
220 void addStepSizeConstraint_(std::vector<IndexTriple>& variable_indices, UInt step_size);
221
222
223 void assembleInclusionListForProteinBasedLP_(std::vector<IndexTriple>& variable_indices, FeatureMap& precursors, std::vector<int>& solution_indices, PrecursorIonSelectionPreprocessing& preprocessing);
224
225 void updateObjFunction_(String acc, FeatureMap& features, PrecursorIonSelectionPreprocessing& preprocessed_db, std::vector<IndexTriple>& variable_indices);
226
227
228 Int getNumberOfPrecsInSpectrum_(Int constr_idx);
229
230 LPWrapper* model_;
231 LPWrapper::SOLVER solver_;
232 };
233
234 inline OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const PSLPFormulation::IndexTriple& triple)
235 {
236 os << "feature: " << triple.feature << " scan: " << triple.scan << " variable: " << triple.variable << " prot_acc: " << triple.prot_acc;
237 return os;
238 }
239
240 } // namespace
241
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::PSLPFormulation
Implements ILP formulation of precursor selection problems.
Definition: PSLPFormulation.h:55
OpenMS::PSLPFormulation::IndexLess::operator()
bool operator()(IndexTriple const &left, IndexTriple const &right) const
Definition: PSLPFormulation.h:143
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::PSProteinInference
This class implements protein inference for the precursor ion selection strategies.
Definition: PSProteinInference.h:52
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::PSLPFormulation::model_
LPWrapper * model_
Definition: PSLPFormulation.h:230
OpenMS::PSLPFormulation::IndexTriple::feature
Size feature
Definition: PSLPFormulation.h:72
OpenMS::PSLPFormulation::IndexTriple::rt_probability
double rt_probability
Definition: PSLPFormulation.h:75
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::PSLPFormulation::IndexTriple::prot_acc
String prot_acc
Definition: PSLPFormulation.h:77
OpenMS::LPWrapper
Definition: LPWrapper.h:67
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
StandardTypes.h
OpenMS::PSLPFormulation::IndexLess
Definition: PSLPFormulation.h:140
OpenMS::PrecursorIonSelectionPreprocessing
This class implements the database preprocessing needing for precursor ion selection.
Definition: PrecursorIonSelectionPreprocessing.h:55
OpenMS::PSLPFormulation::ScanLess::operator()
bool operator()(IndexTriple const &left, IndexTriple const &right) const
Definition: PSLPFormulation.h:155
OpenMS::PSLPFormulation::VariableIndexLess
Definition: PSLPFormulation.h:163
OpenMS::PSLPFormulation::solver_
LPWrapper::SOLVER solver_
Definition: PSLPFormulation.h:231
FeatureMap.h
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
LPWrapper.h
OpenMS::PSLPFormulation::getLPSolver
LPWrapper::SOLVER getLPSolver()
Definition: PSLPFormulation.h:135
OpenMS::PSLPFormulation::ScanLess
Definition: PSLPFormulation.h:152
MSExperiment.h
OpenSwath::normalize
OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
Normalize intensities in vector by normalization_factor.
OpenMS::PSLPFormulation::IndexTriple::variable
Size variable
Definition: PSLPFormulation.h:74
DefaultParamHandler.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
int
OpenMS::PSLPFormulation::setLPSolver
void setLPSolver(LPWrapper::SOLVER solver)
Definition: PSLPFormulation.h:130
OpenMS::PSLPFormulation::IndexTriple::scan
Int scan
Definition: PSLPFormulation.h:73
OpenMS::PSLPFormulation::IndexTriple::signal_weight
double signal_weight
Definition: PSLPFormulation.h:76
OpenMS::PSLPFormulation::IndexTriple
Struct that holds the indices of the precursors in the feature map and the ilp formulation.
Definition: PSLPFormulation.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::LPWrapper::SOLVER
SOLVER
Definition: LPWrapper.h:130
OpenMS::PSLPFormulation::VariableIndexLess::operator()
bool operator()(IndexTriple const &left, IndexTriple const &right) const
Definition: PSLPFormulation.h:166