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SvmTheoreticalSpectrumGenerator.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Sandro Andreotti $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 #include <OpenMS/config.h>
39 #include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
40 #include <OpenMS/ANALYSIS/SVM/SVMWrapper.h>
41
42 #include <OpenMS/KERNEL/StandardDeclarations.h>
43 #include <OpenMS/KERNEL/StandardTypes.h>
44 #include <OpenMS/KERNEL/MSSpectrum.h>
45 #include <OpenMS/KERNEL/MSExperiment.h>
46
47 #include <boost/random/mersenne_twister.hpp>
48
49
50
51 namespace OpenMS
52 {
71 class OPENMS_DLLAPI SvmTheoreticalSpectrumGenerator :
72 public DefaultParamHandler
73 {
74 friend class SvmTheoreticalSpectrumGeneratorTrainer;
75 public:
76
81 struct IonType
83 {
84 Residue::ResidueType residue;
85 EmpiricalFormula loss;
86 Int charge;
87
90 //Default constructor
91 IonType() :
92 residue((Residue::ResidueType) 0),
93 loss(),
94 charge(0)
95 {
96 }
97
98 //Custom constructor
99 IonType(Residue::ResidueType local_residue, EmpiricalFormula local_loss = EmpiricalFormula(), Int local_charge = 1) :
100 residue(local_residue),
101 loss(local_loss),
102 charge(local_charge)
103 {
104 }
105
106 //Copy constructor
107 IonType(const IonType & rhs) :
108 residue(rhs.residue),
109 loss(rhs.loss),
110 charge(rhs.charge)
111 {
112 }
113
114 //Assignment operator
115 IonType & operator=(const IonType & rhs)
116 {
117 if (this != &rhs)
118 {
119 residue = rhs.residue;
120 loss = rhs.loss;
121 charge = rhs.charge;
122 }
123 return *this;
124 }
125
126 bool operator<(const IonType & rhs) const
127 {
128 if (residue != rhs.residue)
129 return residue < rhs.residue;
130 else if (loss.toString() != rhs.loss.toString())
131 return loss.toString() < rhs.loss.toString();
132 else
133 return charge < rhs.charge;
134 }
135
136 };
138
140 struct DescriptorSet
141 {
142 typedef std::vector<svm_node> DescriptorSetType;
143 DescriptorSetType descriptors;
144 };
145
146
148 struct SvmModelParameterSet
149 {
150 //pointers to the svm classification models (one per ion_type)
151 std::vector<boost::shared_ptr<SVMWrapper> > class_models;
152
153 //pointers to the svm regression models (one per ion_type)
154 std::vector<boost::shared_ptr<SVMWrapper> > reg_models;
155
156 //The intensity for each ion type for the SVC mode
157 std::map<Residue::ResidueType, double> static_intensities;
158
159 //The selected primary IonTypes
160 std::vector<IonType> ion_types;
161
162 //The selected secondary IonTypes
163 std::map<IonType, std::vector<IonType> > secondary_types;
164
165 //The number of intensity levels
166 Size number_intensity_levels;
167
168 //The number of regions for every spectrum
169 Size number_regions;
170
171 //upper limits (required for scaling)
172 std::vector<double> feature_max;
173
174 //lower limits (required for scaling)
175 std::vector<double> feature_min;
176
177 //lower bound for scaling
178 double scaling_lower;
179
180 //upper bound for scaling
181 double scaling_upper;
182
183 //border values for binning secondary types intensity
184 std::vector<double> intensity_bin_boarders;
185
186 //intensity values for binned secondary types intensity
187 std::vector<double> intensity_bin_values;
188
189 //conditional probabilities for secondary types
190 std::map<std::pair<IonType, Size>, std::vector<std::vector<double> > > conditional_prob;
191 };
192
193
194
198 SvmTheoreticalSpectrumGenerator();
200
202 SvmTheoreticalSpectrumGenerator(const SvmTheoreticalSpectrumGenerator & source);
203
205 SvmTheoreticalSpectrumGenerator & operator=(const SvmTheoreticalSpectrumGenerator & tsg);
206
207
209 ~SvmTheoreticalSpectrumGenerator() override;
211
212
214 void simulate(PeakSpectrum & spectrum, const AASequence & peptide, boost::random::mt19937_64& rng, Size precursor_charge);
215
217 void load();
218
220 const std::vector<IonType> & getIonTypes()
221 {
222 return mp_.ion_types;
223 }
224
225 protected:
226 typedef std::map<IonType, double> IntensityMap;
227
229 Size precursor_charge_;
230
232 SvmModelParameterSet mp_;
233
235 static std::map<String, Size> aa_to_index_;
236
238 static std::map<String, double> hydrophobicity_;
239
241 static std::map<String, double> helicity_;
242
244 static std::map<String, double> basicity_;
245
247 std::map<IonType, bool> hide_type_;
248
250 inline void scaleSingleFeature_(double & value, double feature_min, double feature_max, double lower = -1.0, double upper = 1.0);
251
253 void scaleDescriptorSet_(DescriptorSet & desc, double lower, double upper);
254
256 Size generateDescriptorSet_(AASequence peptide, Size position, IonType type, Size precursor_charge, DescriptorSet & desc_set);
257
259 String ResidueTypeToString_(Residue::ResidueType type);
260
262 static void initializeMaps_();
263
265 static bool initializedMaps_;
266
267 void updateMembers_() override;
268 };
269
270 void inline SvmTheoreticalSpectrumGenerator::scaleSingleFeature_(double & value, double lower, double upper, double feature_min, double feature_max)
271 {
272 double prev = value;
273 if (feature_max == feature_min)
274 {
275 return;
276 }
277
278 if (value <= feature_min)
279 {
280 value = lower;
281 }
282 else if (value >= feature_max)
283 {
284 value = upper;
285 }
286 else
287 {
288 value = lower + (upper - lower) *
289 (value - feature_min) /
290 (feature_max - feature_min);
291 }
292
293 if (value < 0)
294 {
295 std::cerr << "negative value!! " << value << " l: " << lower << " u: " << upper << " fm: " << feature_min << " fma: " << feature_max << " prev: " << prev << std::endl;
296 }
297 }
298
299 } // namespace OpenMS
300
OpenMS::SvmTheoreticalSpectrumGenerator::IonType::IonType
IonType(Residue::ResidueType local_residue, EmpiricalFormula local_loss=EmpiricalFormula(), Int local_charge=1)
Definition: SvmTheoreticalSpectrumGenerator.h:99
OpenMS::SvmTheoreticalSpectrumGenerator::IonType::operator<
bool operator<(const IonType &rhs) const
Definition: SvmTheoreticalSpectrumGenerator.h:126
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::class_models
std::vector< boost::shared_ptr< SVMWrapper > > class_models
Definition: SvmTheoreticalSpectrumGenerator.h:151
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::scaling_upper
double scaling_upper
Definition: SvmTheoreticalSpectrumGenerator.h:181
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
seqan::position
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
StandardDeclarations.h
OpenMS::Residue
Representation of a residue.
Definition: Residue.h:61
OpenMS::SvmTheoreticalSpectrumGenerator::basicity_
static std::map< String, double > basicity_
basicity values for each AA
Definition: SvmTheoreticalSpectrumGenerator.h:244
OpenMS::SvmTheoreticalSpectrumGenerator::IonType
nested class
Definition: SvmTheoreticalSpectrumGenerator.h:82
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::static_intensities
std::map< Residue::ResidueType, double > static_intensities
Definition: SvmTheoreticalSpectrumGenerator.h:157
OpenMS::SvmTheoreticalSpectrumGenerator::hide_type_
std::map< IonType, bool > hide_type_
whether ion types are hidden or not
Definition: SvmTheoreticalSpectrumGenerator.h:247
StandardTypes.h
OpenMS::SvmTheoreticalSpectrumGenerator::IonType::residue
Residue::ResidueType residue
Definition: SvmTheoreticalSpectrumGenerator.h:84
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::reg_models
std::vector< boost::shared_ptr< SVMWrapper > > reg_models
Definition: SvmTheoreticalSpectrumGenerator.h:154
OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet::descriptors
DescriptorSetType descriptors
Definition: SvmTheoreticalSpectrumGenerator.h:143
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::number_regions
Size number_regions
Definition: SvmTheoreticalSpectrumGenerator.h:169
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::ion_types
std::vector< IonType > ion_types
Definition: SvmTheoreticalSpectrumGenerator.h:160
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::intensity_bin_boarders
std::vector< double > intensity_bin_boarders
Definition: SvmTheoreticalSpectrumGenerator.h:184
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::scaling_lower
double scaling_lower
Definition: SvmTheoreticalSpectrumGenerator.h:178
SVMWrapper.h
OpenMS::SvmTheoreticalSpectrumGenerator
Simulates MS2 spectra with support vector machines.
Definition: SvmTheoreticalSpectrumGenerator.h:71
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SvmTheoreticalSpectrumGenerator::IonType::operator=
IonType & operator=(const IonType &rhs)
Definition: SvmTheoreticalSpectrumGenerator.h:115
OpenMS::SvmTheoreticalSpectrumGenerator::IonType::IonType
IonType()
Definition: SvmTheoreticalSpectrumGenerator.h:91
OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet
A set of descriptors for a single training row.
Definition: SvmTheoreticalSpectrumGenerator.h:140
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
Simple container storing the model parameters required for simulation.
Definition: SvmTheoreticalSpectrumGenerator.h:148
MSExperiment.h
OpenMS::SvmTheoreticalSpectrumGenerator::mp_
SvmModelParameterSet mp_
set of model parameters read from model file
Definition: SvmTheoreticalSpectrumGenerator.h:232
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::secondary_types
std::map< IonType, std::vector< IonType > > secondary_types
Definition: SvmTheoreticalSpectrumGenerator.h:163
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::conditional_prob
std::map< std::pair< IonType, Size >, std::vector< std::vector< double > > > conditional_prob
Definition: SvmTheoreticalSpectrumGenerator.h:190
OpenMS::SvmTheoreticalSpectrumGeneratorTrainer
Train SVM models that are used by SvmTheoreticalSpectrumGenerator.
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:65
OpenMS::SvmTheoreticalSpectrumGenerator::precursor_charge_
Size precursor_charge_
charge of the precursors used for training
Definition: SvmTheoreticalSpectrumGenerator.h:229
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
MSSpectrum.h
OpenMS::SvmTheoreticalSpectrumGenerator::IntensityMap
std::map< IonType, double > IntensityMap
Definition: SvmTheoreticalSpectrumGenerator.h:226
OpenMS::SvmTheoreticalSpectrumGenerator::IonType::IonType
IonType(const IonType &rhs)
Definition: SvmTheoreticalSpectrumGenerator.h:107
int
OpenMS::SvmTheoreticalSpectrumGenerator::IonType::loss
EmpiricalFormula loss
Definition: SvmTheoreticalSpectrumGenerator.h:85
OpenMS::SvmTheoreticalSpectrumGenerator::scaleSingleFeature_
void scaleSingleFeature_(double &value, double feature_min, double feature_max, double lower=-1.0, double upper=1.0)
scale value to the interval [lower,max] given the maximal and minimal entries for a feature ...
Definition: SvmTheoreticalSpectrumGenerator.h:270
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::intensity_bin_values
std::vector< double > intensity_bin_values
Definition: SvmTheoreticalSpectrumGenerator.h:187
OpenMS::SvmTheoreticalSpectrumGenerator::aa_to_index_
static std::map< String, Size > aa_to_index_
map AA to integers
Definition: SvmTheoreticalSpectrumGenerator.h:235
TheoreticalSpectrumGenerator.h
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::number_intensity_levels
Size number_intensity_levels
Definition: SvmTheoreticalSpectrumGenerator.h:166
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::feature_min
std::vector< double > feature_min
Definition: SvmTheoreticalSpectrumGenerator.h:175
OpenMS::EmpiricalFormula::toString
String toString() const
returns the formula as a string (charges are not included)
OpenMS::Residue::ResidueType
ResidueType
Definition: Residue.h:150
OpenMS::SvmTheoreticalSpectrumGenerator::helicity_
static std::map< String, double > helicity_
helicity values for each AA
Definition: SvmTheoreticalSpectrumGenerator.h:241
OpenMS::SvmTheoreticalSpectrumGenerator::initializedMaps_
static bool initializedMaps_
flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized ...
Definition: SvmTheoreticalSpectrumGenerator.h:265
OpenMS::SvmTheoreticalSpectrumGenerator::getIonTypes
const std::vector< IonType > & getIonTypes()
return the set of ion types that are modeled by the loaded SVMs
Definition: SvmTheoreticalSpectrumGenerator.h:220
OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::feature_max
std::vector< double > feature_max
Definition: SvmTheoreticalSpectrumGenerator.h:172
OpenMS::SvmTheoreticalSpectrumGenerator::IonType::charge
Int charge
Definition: SvmTheoreticalSpectrumGenerator.h:86
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet::DescriptorSetType
std::vector< svm_node > DescriptorSetType
Definition: SvmTheoreticalSpectrumGenerator.h:142
OpenMS::SvmTheoreticalSpectrumGenerator::hydrophobicity_
static std::map< String, double > hydrophobicity_
hydrophobicity values for each AA
Definition: SvmTheoreticalSpectrumGenerator.h:238