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