35 #ifndef OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H 36 #define OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H 38 #include <boost/math/special_functions/fpclassify.hpp> 106 void set_dia_parameters(
double dia_extract_window,
double dia_centroided,
108 double dia_byseries_intensity_min,
double dia_byseries_ppm_diff,
double dia_nr_isotopes,
double dia_nr_charges);
116 void dia_isotope_scores(
const std::vector<TransitionType>& transitions,
119 double& isotope_overlap);
122 void dia_massdiff_score(
const std::vector<TransitionType>& transitions,
123 SpectrumPtrType spectrum,
const std::vector<double>& normalized_library_intensity,
124 double& ppm_score,
double& ppm_score_weighted);
134 bool dia_ms1_massdiff_score(
double precursor_mz, SpectrumPtrType spectrum,
138 void dia_ms1_isotope_scores(
double precursor_mz, SpectrumPtrType spectrum,
size_t charge_state,
139 double& isotope_corr,
double& isotope_overlap, std::string sum_formula =
"");
142 void dia_by_ion_score(SpectrumPtrType spectrum,
AASequence& sequence,
143 int charge,
double& bseries_score,
double& yseries_score);
146 void score_with_isotopes(SpectrumPtrType spectrum,
const std::vector<TransitionType>& transitions,
147 double& dotprod,
double& manhattan);
159 void updateMembers_();
162 void diaIsotopeScoresSub_(
const std::vector<TransitionType>& transitions,
163 SpectrumPtrType spectrum, std::map<std::string, double>& intensities,
164 double& isotope_corr,
double& isotope_overlap);
168 void getFirstIsotopeRelativeIntensities_(
const std::vector<TransitionType>& transitions,
170 std::map<std::string, double>& intensities
190 void largePeaksBeforeFirstIsotope_(SpectrumPtrType spectrum,
double mono_mz,
double mono_int,
int& nr_occurences,
double& max_ratio);
200 double scoreIsotopePattern_(
double product_mz,
const std::vector<double>& isotopes_int,
201 int putative_fragment_charge, std::string sum_formula =
"");
214 #endif // OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H double dia_extract_window_
Definition: DIAScoring.h:204
double peak_before_mono_max_ppm_diff_
Definition: DIAScoring.h:210
double dia_nr_isotopes_
Definition: DIAScoring.h:208
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:244
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
OpenSwath::SpectrumPtr SpectrumPtrType
Type definitions.
Definition: DIAScoring.h:88
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
double dia_byseries_ppm_diff_
Definition: DIAScoring.h:207
double dia_byseries_intensity_min_
Definition: DIAScoring.h:206
virtual ~DIAScoring()
Destructor.
Definition: DIAScoring.h:101
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:82
double dia_centroided_
Definition: DIAScoring.h:205
double dia_nr_charges_
Definition: DIAScoring.h:209
OpenSwath::LightTransition TransitionType
Transition interface (Transition, Peptide, Protein)
Definition: DIAScoring.h:90
Definition: TransitionExperiment.h:47
Definition: ITransition.h:56
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92