35 #ifndef OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H
36 #define OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H
38 #include <boost/math/special_functions/fpclassify.hpp>
108 void set_dia_parameters(
double dia_extract_window,
double dia_centroided,
110 double dia_byseries_intensity_min,
double dia_byseries_ppm_diff,
double dia_nr_isotopes,
double dia_nr_charges);
118 void dia_isotope_scores(
const std::vector<TransitionType>& transitions,
121 double& isotope_overlap);
124 void dia_massdiff_score(
const std::vector<TransitionType>& transitions,
125 SpectrumPtrType spectrum,
const std::vector<double>& normalized_library_intensity,
126 double& ppm_score,
double& ppm_score_weighted);
136 bool dia_ms1_massdiff_score(
double precursor_mz, SpectrumPtrType spectrum,
140 void dia_ms1_isotope_scores(
double precursor_mz, SpectrumPtrType spectrum,
size_t charge_state,
141 double& isotope_corr,
double& isotope_overlap);
145 void dia_by_ion_score(SpectrumPtrType spectrum,
AASequence& sequence,
146 int charge,
double& bseries_score,
double& yseries_score);
149 void score_with_isotopes(SpectrumPtrType spectrum,
const std::vector<TransitionType>& transitions,
150 double& dotprod,
double& manhattan);
162 void updateMembers_();
165 void diaIsotopeScoresSub_(
const std::vector<TransitionType>& transitions,
166 SpectrumPtrType spectrum, std::map<std::string, double>& intensities,
167 double& isotope_corr,
double& isotope_overlap);
171 void getFirstIsotopeRelativeIntensities_(
const std::vector<TransitionType>& transitions,
173 std::map<std::string, double>& intensities
193 void largePeaksBeforeFirstIsotope_(SpectrumPtrType spectrum,
double mono_mz,
double mono_int,
int& nr_occurences,
double& max_ratio);
203 double scoreIsotopePattern_(
double product_mz,
const std::vector<double>& isotopes_int,
int putative_fragment_charge);
double dia_extract_window_
Definition: DIAScoring.h:206
OpenSwath::LightProtein ProteinType
Definition: DIAScoring.h:92
double peak_before_mono_max_ppm_diff_
Definition: DIAScoring.h:212
double dia_nr_isotopes_
Definition: DIAScoring.h:210
OpenSwath::LightPeptide PeptideType
Definition: DIAScoring.h:91
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:232
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
OpenSwath::SpectrumPtr SpectrumPtrType
Type definitions.
Definition: DIAScoring.h:88
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Definition: TransitionExperiment.h:155
double dia_byseries_ppm_diff_
Definition: DIAScoring.h:209
double dia_byseries_intensity_min_
Definition: DIAScoring.h:208
virtual ~DIAScoring()
Destructor.
Definition: DIAScoring.h:103
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:82
double dia_centroided_
Definition: DIAScoring.h:207
double dia_nr_charges_
Definition: DIAScoring.h:211
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
Definition: TransitionExperiment.h:173