36 #ifndef OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATOR_H
37 #define OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATOR_H
39 #include <OpenMS/config.h>
43 #include <boost/smart_ptr.hpp>
90 residue((
Residue::ResidueType) 0),
106 residue(rhs.residue),
131 return charge < rhs.
charge;
188 std::map<std::pair<IonType, Size>, std::vector<std::vector<DoubleReal> > >
conditional_prob;
220 return mp_.ion_types;
248 inline void scaleSingleFeature_(
double & value,
double feature_min,
double feature_max,
double lower = -1.0,
double upper = 1.0);
251 void scaleDescriptorSet_(
DescriptorSet & desc,
double lower,
double upper);
260 static void initializeMaps_();
265 void updateMembers_();
271 if (feature_max == feature_min)
276 if (value <= feature_min)
280 else if (value >= feature_max)
286 value = lower + (upper - lower) *
287 (value - feature_min) /
288 (feature_max - feature_min);
293 std::cerr <<
"negative value!! " << value <<
" l: " << lower <<
" u: " << upper <<
" fm: " << feature_min <<
" fma: " << feature_max <<
" prev: " << prev << std::endl;
299 #endif // #ifdef OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATORTRAINER_H
nested class
Definition: SvmTheoreticalSpectrumGenerator.h:80
static std::map< String, Size > aa_to_index_
map AA to integers
Definition: SvmTheoreticalSpectrumGenerator.h:233
static std::map< String, DoubleReal > basicity_
basicity values for each AA
Definition: SvmTheoreticalSpectrumGenerator.h:242
A more convenient string class.
Definition: String.h:56
std::map< IonType, std::vector< IonType > > secondary_types
Definition: SvmTheoreticalSpectrumGenerator.h:161
Size number_regions
Definition: SvmTheoreticalSpectrumGenerator.h:167
double scaling_upper
Definition: SvmTheoreticalSpectrumGenerator.h:179
std::vector< DoubleReal > feature_min
Definition: SvmTheoreticalSpectrumGenerator.h:173
IonType()
Definition: SvmTheoreticalSpectrumGenerator.h:89
std::map< IonType, DoubleReal > IntensityMap
Definition: SvmTheoreticalSpectrumGenerator.h:224
Residue::ResidueType residue
Definition: SvmTheoreticalSpectrumGenerator.h:82
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
std::vector< svm_node > DescriptorSetType
Definition: SvmTheoreticalSpectrumGenerator.h:140
Representation of a residue.
Definition: Residue.h:64
std::map< Residue::ResidueType, DoubleReal > static_intensities
Definition: SvmTheoreticalSpectrumGenerator.h:155
Simulates ms2 spectra with support vector machines.
Definition: SvmTheoreticalSpectrumGenerator.h:69
EmpiricalFormula loss
Definition: SvmTheoreticalSpectrumGenerator.h:83
Simple container storing the model parameters required for simulation.
Definition: SvmTheoreticalSpectrumGenerator.h:146
std::vector< DoubleReal > intensity_bin_boarders
Definition: SvmTheoreticalSpectrumGenerator.h:182
Train SVM models that are used by SvmTheoreticalSpectrumGenerator.
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:62
A set of descriptors for a single training row.
Definition: SvmTheoreticalSpectrumGenerator.h:138
static bool initializedMaps_
flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized ...
Definition: SvmTheoreticalSpectrumGenerator.h:263
IonType(const IonType &rhs)
Definition: SvmTheoreticalSpectrumGenerator.h:105
std::vector< boost::shared_ptr< SVMWrapper > > reg_models
Definition: SvmTheoreticalSpectrumGenerator.h:152
void scaleSingleFeature_(double &value, double feature_min, double feature_max, double lower=-1.0, double upper=1.0)
scale value to the intervall [lower,max] given the maximal and minimal entries for a feature ...
Definition: SvmTheoreticalSpectrumGenerator.h:268
const std::vector< IonType > & getIonTypes()
return the set of ion types that are modeled by the loaded SVMs
Definition: SvmTheoreticalSpectrumGenerator.h:218
std::vector< DoubleReal > feature_max
Definition: SvmTheoreticalSpectrumGenerator.h:170
ResidueType
Definition: Residue.h:361
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
std::vector< boost::shared_ptr< SVMWrapper > > class_models
Definition: SvmTheoreticalSpectrumGenerator.h:149
Size precursor_charge_
charge of the precursors used for training
Definition: SvmTheoreticalSpectrumGenerator.h:227
DescriptorSetType descriptors
Definition: SvmTheoreticalSpectrumGenerator.h:141
SvmModelParameterSet mp_
set of model parameters read from model file
Definition: SvmTheoreticalSpectrumGenerator.h:230
std::vector< DoubleReal > intensity_bin_values
Definition: SvmTheoreticalSpectrumGenerator.h:185
std::map< IonType, bool > hide_type_
whether ion types are hidden or not
Definition: SvmTheoreticalSpectrumGenerator.h:245
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
Size number_intensity_levels
Definition: SvmTheoreticalSpectrumGenerator.h:164
Int charge
Definition: SvmTheoreticalSpectrumGenerator.h:84
IonType & operator=(const IonType &rhs)
Definition: SvmTheoreticalSpectrumGenerator.h:113
int Int
Signed integer type.
Definition: Types.h:100
std::map< std::pair< IonType, Size >, std::vector< std::vector< DoubleReal > > > conditional_prob
Definition: SvmTheoreticalSpectrumGenerator.h:188
IonType(Residue::ResidueType residue, EmpiricalFormula loss=EmpiricalFormula(), Int charge=1)
Definition: SvmTheoreticalSpectrumGenerator.h:97
bool operator<(const IonType &rhs) const
Definition: SvmTheoreticalSpectrumGenerator.h:124
static std::map< String, DoubleReal > hydrophobicity_
hydrophobicity values for each AA
Definition: SvmTheoreticalSpectrumGenerator.h:236
static std::map< String, DoubleReal > helicity_
helicity values for each AA
Definition: SvmTheoreticalSpectrumGenerator.h:239
std::vector< IonType > ion_types
Definition: SvmTheoreticalSpectrumGenerator.h:158
double scaling_lower
Definition: SvmTheoreticalSpectrumGenerator.h:176