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DIAScoring.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H
36 #define OPENMS_ANALYSIS_OPENSWATH_DIASCORING_H
37 
38 #include <boost/math/special_functions/fpclassify.hpp> // for isnan
41 
46 
47 namespace OpenMS
48 {
82  class OPENMS_DLLAPI DIAScoring :
83  public DefaultParamHandler
84  {
86 
94 
95 public:
96 
98 
99  DIAScoring();
101 
103  virtual ~DIAScoring() {}
105 
107 
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);
112 
114  // DIA / SWATH scoring
115 
117 
118  void dia_isotope_scores(const std::vector<TransitionType>& transitions,
120  SpectrumPtrType spectrum, OpenSwath::IMRMFeature* mrmfeature, double& isotope_corr,
121  double& isotope_overlap);
122 
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);
127 
136  bool dia_ms1_massdiff_score(double precursor_mz, SpectrumPtrType spectrum,
137  double& ppm_score);
138 
140  void dia_ms1_isotope_scores(double precursor_mz, SpectrumPtrType spectrum, size_t charge_state,
141  double& isotope_corr, double& isotope_overlap);
142 
143 
145  void dia_by_ion_score(SpectrumPtrType spectrum, AASequence& sequence,
146  int charge, double& bseries_score, double& yseries_score);
147 
149  void score_with_isotopes(SpectrumPtrType spectrum, const std::vector<TransitionType>& transitions,
150  double& dotprod, double& manhattan);
152 
153 private:
154 
156  DIAScoring(const DIAScoring& rhs);
157 
159  DIAScoring& operator=(const DIAScoring& rhs);
160 
162  void updateMembers_();
163 
165  void diaIsotopeScoresSub_(const std::vector<TransitionType>& transitions,
166  SpectrumPtrType spectrum, std::map<std::string, double>& intensities,
167  double& isotope_corr, double& isotope_overlap);
168 
171  void getFirstIsotopeRelativeIntensities_(const std::vector<TransitionType>& transitions,
172  OpenSwath::IMRMFeature* mrmfeature,
173  std::map<std::string, double>& intensities //experimental intensities of transitions
174  );
175 
176 private:
177 
193  void largePeaksBeforeFirstIsotope_(SpectrumPtrType spectrum, double mono_mz, double mono_int, int& nr_occurences, double& max_ratio);
194 
203  double scoreIsotopePattern_(double product_mz, const std::vector<double>& isotopes_int, int putative_fragment_charge);
204 
205  // Parameters
213  };
214 }
215 
216 #endif
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

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:45 using doxygen 1.8.9.1