OpenMS
DIAScoring.h
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32 // $Authors: Hannes Roest, Witold Wolski $
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34 
35 #pragma once
36 
39 
44 
45 namespace OpenMS
46 {
47  class TheoreticalSpectrumGenerator;
48 
82  class OPENMS_DLLAPI DIAScoring :
83  public DefaultParamHandler
84  {
86 
92 
93 public:
94 
96 
97  DIAScoring();
99 
101  ~DIAScoring() override;
103 
105  // DIA / SWATH scoring
106 
108 
109  void dia_isotope_scores(const std::vector<TransitionType>& transitions,
111  SpectrumPtrType spectrum,
112  OpenSwath::IMRMFeature* mrmfeature,
113  double& isotope_corr,
114  double& isotope_overlap) const;
115 
117  void dia_massdiff_score(const std::vector<TransitionType>& transitions,
118  const SpectrumPtrType& spectrum,
119  const std::vector<double>& normalized_library_intensity,
120  double& ppm_score,
121  double& ppm_score_weighted,
122  std::vector<double>& diff_ppm) const;
123 
132  bool dia_ms1_massdiff_score(double precursor_mz, SpectrumPtrType spectrum,
133  double& ppm_score) const;
134 
136  void dia_ms1_isotope_scores_averagine(double precursor_mz, const SpectrumPtrType& spectrum,
137  double& isotope_corr, double& isotope_overlap, int charge_state) const;
138  void dia_ms1_isotope_scores(double precursor_mz, const SpectrumPtrType& spectrum,
139  double& isotope_corr, double& isotope_overlap, const EmpiricalFormula& sum_formula) const;
140 
141 
143  void dia_by_ion_score(const SpectrumPtrType& spectrum, AASequence& sequence,
144  int charge, double& bseries_score, double& yseries_score) const;
145 
148  const std::vector<TransitionType>& transitions,
149  double& dotprod,
150  double& manhattan) const;
152 
153 private:
154 
156  DIAScoring(const DIAScoring& rhs);
157 
160 
162  void updateMembers_() override;
163 
165  void diaIsotopeScoresSub_(const std::vector<TransitionType>& transitions,
166  const SpectrumPtrType& spectrum,
167  std::map<std::string, double>& intensities,
168  double& isotope_corr,
169  double& isotope_overlap) const;
170 
173  void getFirstIsotopeRelativeIntensities_(const std::vector<TransitionType>& transitions,
174  OpenSwath::IMRMFeature* mrmfeature,
175  std::map<std::string, double>& intensities //experimental intensities of transitions
176  ) const;
177 
178 private:
179 
195  void largePeaksBeforeFirstIsotope_(const SpectrumPtrType& spectrum, double mono_mz, double mono_int, int& nr_occurrences, double& max_ratio) const;
196 
205  double scoreIsotopePattern_(const std::vector<double>& isotopes_int,
206  double product_mz,
207  int putative_fragment_charge) const;
208 
216  double scoreIsotopePattern_(const std::vector<double>& isotopes_int,
217  const EmpiricalFormula& sum_formula) const;
218 
226  double scoreIsotopePattern_(const std::vector<double>& isotopes_int,
227  const IsotopeDistribution& isotope_dist) const;
228 
231  void getIsotopeIntysFromExpSpec_(double precursor_mz, const SpectrumPtrType& spectrum,
232  std::vector<double>& isotopes_int,
233  int charge_state) const;
234 
235  // Parameters
244 
246  };
247 }
248 
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:84
TheoreticalSpectrumGenerator * generator
Definition: DIAScoring.h:245
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
void dia_ms1_isotope_scores_averagine(double precursor_mz, const SpectrumPtrType &spectrum, double &isotope_corr, double &isotope_overlap, int charge_state) const
Precursor isotope scores for precursors (peptides and metabolites)
double dia_byseries_intensity_min_
Definition: DIAScoring.h:237
void score_with_isotopes(SpectrumPtrType spectrum, const std::vector< TransitionType > &transitions, double &dotprod, double &manhattan) const
Dotproduct / Manhattan score with theoretical spectrum.
bool dia_ms1_massdiff_score(double precursor_mz, SpectrumPtrType spectrum, double &ppm_score) const
void dia_ms1_isotope_scores(double precursor_mz, const SpectrumPtrType &spectrum, double &isotope_corr, double &isotope_overlap, const EmpiricalFormula &sum_formula) const
void getIsotopeIntysFromExpSpec_(double precursor_mz, const SpectrumPtrType &spectrum, std::vector< double > &isotopes_int, int charge_state) const
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.
bool dia_extraction_ppm_
Definition: DIAScoring.h:242
DIAScoring(const DIAScoring &rhs)
Copy constructor (algorithm class)
OpenSwath::LightTransition TransitionType
Transition interface (Transition, Peptide, Protein)
Definition: DIAScoring.h:90
void dia_massdiff_score(const std::vector< TransitionType > &transitions, const SpectrumPtrType &spectrum, const std::vector< double > &normalized_library_intensity, 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:88
void dia_by_ion_score(const SpectrumPtrType &spectrum, AASequence &sequence, int charge, double &bseries_score, double &yseries_score) const
b/y ion scores
void diaIsotopeScoresSub_(const std::vector< TransitionType > &transitions, const SpectrumPtrType &spectrum, std::map< std::string, double > &intensities, double &isotope_corr, double &isotope_overlap) const
Subfunction of dia_isotope_scores.
void largePeaksBeforeFirstIsotope_(const SpectrumPtrType &spectrum, double mono_mz, double mono_int, int &nr_occurrences, double &max_ratio) const
Determine whether the current m/z value is a monoisotopic peak.
double dia_extract_window_
Definition: DIAScoring.h:236
double peak_before_mono_max_ppm_diff_
Definition: DIAScoring.h:241
void updateMembers_() override
Synchronize members with param class.
double dia_nr_charges_
Definition: DIAScoring.h:240
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:238
~DIAScoring() override
Destructor.
double dia_nr_isotopes_
Definition: DIAScoring.h:239
DIAScoring & operator=(const DIAScoring &rhs)
Assignment operator (algorithm class)
bool dia_centroided_
Definition: DIAScoring.h:243
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Representation of an empirical formula.
Definition: EmpiricalFormula.h:85
Definition: IsotopeDistribution.h:65
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:70
Definition: ITransition.h:57
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:296
Definition: TransitionExperiment.h:46