37 #include <boost/math/special_functions/fpclassify.hpp> 48 class TheoreticalSpectrumGenerator;
110 void dia_isotope_scores(
const std::vector<TransitionType>& transitions,
114 double& isotope_corr,
115 double& isotope_overlap);
118 void dia_massdiff_score(
const std::vector<TransitionType>& transitions,
120 const std::vector<double>& normalized_library_intensity,
121 double& ppm_score,
double& ppm_score_weighted);
131 bool dia_ms1_massdiff_score(
double precursor_mz,
SpectrumPtrType spectrum,
135 void dia_ms1_isotope_scores(
double precursor_mz,
SpectrumPtrType spectrum,
size_t charge_state,
136 double& isotope_corr,
double& isotope_overlap,
const std::string& sum_formula =
"");
140 int charge,
double& bseries_score,
double& yseries_score);
144 const std::vector<TransitionType>& transitions,
158 void updateMembers_()
override;
161 void diaIsotopeScoresSub_(
const std::vector<TransitionType>& transitions,
163 std::map<std::string, double>& intensities,
164 double& isotope_corr,
165 double& isotope_overlap);
169 void getFirstIsotopeRelativeIntensities_(
const std::vector<TransitionType>& transitions,
171 std::map<std::string, double>& intensities
191 void largePeaksBeforeFirstIsotope_(
SpectrumPtrType spectrum,
double mono_mz,
double mono_int,
int& nr_occurrences,
double& max_ratio);
201 double scoreIsotopePattern_(
double product_mz,
202 const std::vector<double>& isotopes_int,
203 int putative_fragment_charge,
204 const std::string& sum_formula =
"");
double dia_extract_window_
Definition: DIAScoring.h:207
double peak_before_mono_max_ppm_diff_
Definition: DIAScoring.h:213
double dia_nr_isotopes_
Definition: DIAScoring.h:211
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:270
Generates theoretical spectra with various options.
Definition: TheoreticalSpectrumGenerator.h:63
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
OpenSwath::SpectrumPtr SpectrumPtrType
Type definitions.
Definition: DIAScoring.h:89
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
double dia_byseries_ppm_diff_
Definition: DIAScoring.h:210
double dia_byseries_intensity_min_
Definition: DIAScoring.h:209
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:83
bool dia_extraction_ppm_
Definition: DIAScoring.h:214
double dia_centroided_
Definition: DIAScoring.h:208
double dia_nr_charges_
Definition: DIAScoring.h:212
OpenSwath::LightTransition TransitionType
Transition interface (Transition, Peptide, Protein)
Definition: DIAScoring.h:91
Definition: TransitionExperiment.h:46
Definition: ITransition.h:55
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
TheoreticalSpectrumGenerator * generator
Definition: DIAScoring.h:216