23 class TheoreticalSpectrumGenerator;
85 void dia_isotope_scores(
const std::vector<TransitionType>& transitions,
91 double& isotope_overlap)
const;
96 const std::vector<double>& normalized_library_intensity,
99 double& ppm_score_weighted,
100 std::vector<double>& diff_ppm)
const;
112 double& ppm_score)
const;
116 double& isotope_corr,
double& isotope_overlap)
const;
118 double& isotope_corr,
double& isotope_overlap,
const EmpiricalFormula& sum_formula)
const;
122 int charge,
const RangeMobility& im_range,
double& bseries_score,
double& yseries_score)
const;
126 const std::vector<TransitionType>& transitions,
129 double& manhattan)
const;
146 std::map<std::string, double>& intensities,
148 double& isotope_corr,
149 double& isotope_overlap)
const;
155 std::map<std::string, double>& intensities
187 int putative_fragment_charge)
const;
212 std::vector<double>& isotopes_int)
const;
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:60
void dia_ms1_isotope_scores(double precursor_mz, const std::vector< SpectrumPtrType > &spectrum, RangeMobility &im_range, double &isotope_corr, double &isotope_overlap, const EmpiricalFormula &sum_formula) const
TheoreticalSpectrumGenerator * generator
Definition: DIAScoring.h:224
bool dia_ms1_massdiff_score(double precursor_mz, const SpectrumSequence &spectrum, const RangeMobility &im_range, double &ppm_score) const
double scoreIsotopePattern_(const std::vector< double > &isotopes_int, const IsotopeDistribution &isotope_dist) const
Compare an experimental isotope pattern to a theoretical one.
void getFirstIsotopeRelativeIntensities_(const std::vector< TransitionType > &transitions, OpenSwath::IMRMFeature *mrmfeature, std::map< std::string, double > &intensities) const
double dia_byseries_intensity_min_
Definition: DIAScoring.h:216
void diaIsotopeScoresSub_(const std::vector< TransitionType > &transitions, const SpectrumSequence &spectrum, std::map< std::string, double > &intensities, const RangeMobility &im_range, double &isotope_corr, double &isotope_overlap) const
Subfunction of dia_isotope_scores.
double scoreIsotopePattern_(const std::vector< double > &isotopes_int, double product_mz, int putative_fragment_charge) const
Compare an experimental isotope pattern to a theoretical one.
void largePeaksBeforeFirstIsotope_(const SpectrumSequence &spectrum, double mono_mz, double mono_int, int &nr_occurrences, double &max_ratio, const RangeMobility &im_range) const
Determine whether the current m/z value is a monoisotopic peak.
bool dia_extraction_ppm_
Definition: DIAScoring.h:221
void dia_by_ion_score(const SpectrumSequence &spectrum, AASequence &sequence, int charge, const RangeMobility &im_range, double &bseries_score, double &yseries_score) const
b/y ion scores
DIAScoring(const DIAScoring &rhs)
Copy constructor (algorithm class)
OpenSwath::LightTransition TransitionType
Transition interface (Transition, Peptide, Protein)
Definition: DIAScoring.h:66
void dia_massdiff_score(const std::vector< TransitionType > &transitions, const SpectrumSequence &spectrum, const std::vector< double > &normalized_library_intensity, const RangeMobility &im_range, double &ppm_score, double &ppm_score_weighted, std::vector< double > &diff_ppm) const
Massdiff scores, see class description.
OpenSwath::SpectrumPtr SpectrumPtrType
Type definitions.
Definition: DIAScoring.h:64
double dia_extract_window_
Definition: DIAScoring.h:215
void getIsotopeIntysFromExpSpec_(double precursor_mz, const SpectrumSequence &spectrum, int charge_state, const RangeMobility &im_range, std::vector< double > &isotopes_int) const
double peak_before_mono_max_ppm_diff_
Definition: DIAScoring.h:220
void updateMembers_() override
Synchronize members with param class.
double dia_nr_charges_
Definition: DIAScoring.h:219
void dia_ms1_isotope_scores_averagine(double precursor_mz, const SpectrumSequence &spectrum, int charge_state, RangeMobility &im_range, double &isotope_corr, double &isotope_overlap) const
Precursor isotope scores for precursors (peptides and metabolites)
double scoreIsotopePattern_(const std::vector< double > &isotopes_int, const EmpiricalFormula &sum_formula) const
Compare an experimental isotope pattern to a theoretical one.
double dia_byseries_ppm_diff_
Definition: DIAScoring.h:217
~DIAScoring() override
Destructor.
double dia_nr_isotopes_
Definition: DIAScoring.h:218
void score_with_isotopes(SpectrumSequence &spectrum, const std::vector< TransitionType > &transitions, const RangeMobility &im_range, double &dotprod, double &manhattan) const
Dotproduct / Manhattan score with theoretical spectrum.
DIAScoring & operator=(const DIAScoring &rhs)
Assignment operator (algorithm class)
bool dia_centroided_
Definition: DIAScoring.h:222
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
Definition: IsotopeDistribution.h:39
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:44
Definition: ITransition.h:31
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
std::vector< OpenSwath::SpectrumPtr > SpectrumSequence
a vector of spectrum pointers that DIA scores can operate on, allows for clever integration of only t...
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:20
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:276
Definition: RangeManager.h:463
Definition: TransitionExperiment.h:20