35 #ifndef OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H
36 #define OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H
38 #include <boost/math/special_functions/fpclassify.hpp>
102 void set_dia_parameters(
double dia_extract_window,
double dia_centroided,
104 double dia_byseries_intensity_min,
double dia_byseries_ppm_diff,
double dia_nr_isotopes,
double dia_nr_charges);
112 void dia_isotope_scores(
const std::vector<TransitionType>& transitions,
115 double& isotope_overlap);
118 void dia_massdiff_score(
const std::vector<TransitionType>& transitions,
119 SpectrumType spectrum,
const std::vector<double>& normalized_library_intensity,
120 double& ppm_score,
double& ppm_score_weighted);
123 void dia_by_ion_score(SpectrumType spectrum,
AASequence& sequence,
124 int charge,
double& bseries_score,
double& yseries_score);
127 void score_with_isotopes(SpectrumType spectrum,
const std::vector<TransitionType>& transitions,
128 double& dotprod,
double& manhattan);
140 void updateMembers_();
143 void diaIsotopeScoresSub_(
const std::vector<TransitionType>& transitions,
144 SpectrumType spectrum, std::map<std::string, double>& intensities,
145 double& isotope_corr,
double& isotope_overlap);
149 void getFirstIsotopeRelativeIntensities_(
const std::vector<TransitionType>& transitions,
151 std::map<std::string, double>& intensities
163 DoubleReal largePeaksBeforeFirstIsotope_(
double product_mz,
164 SpectrumType& spectrum,
double max_ppm_diff,
double main_peak);
172 DoubleReal scoreIsotopePattern_(
double product_mz,
173 const std::vector<double>& isotopes_int,
int putative_fragment_charge);
double dia_extract_window_
Definition: DIAScoring.h:176
OpenSwath::LightProtein ProteinType
Definition: DIAScoring.h:86
double dia_nr_isotopes_
Definition: DIAScoring.h:180
OpenSwath::LightPeptide PeptideType
Definition: DIAScoring.h:85
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
Definition: TransitionExperiment.h:99
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< Spectrum > SpectrumPtr
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:227
double dia_byseries_ppm_diff_
Definition: DIAScoring.h:179
double dia_byseries_intensity_min_
Definition: DIAScoring.h:178
virtual ~DIAScoring()
Destructor.
Definition: DIAScoring.h:97
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:76
double dia_centroided_
Definition: DIAScoring.h:177
double dia_nr_charges_
Definition: DIAScoring.h:181
OpenSwath::LightTransition TransitionType
Transition interface (Transition, Peptide, Protein)
Definition: DIAScoring.h:84
Definition: TransitionExperiment.h:46
Definition: ITransition.h:56
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
Definition: TransitionExperiment.h:114
OpenSwath::SpectrumPtr SpectrumType
Type definitions.
Definition: DIAScoring.h:82