| check_defaults_ | DefaultParamHandler | protected |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| dia_by_ion_score(SpectrumPtrType spectrum, AASequence &sequence, int charge, double &bseries_score, double &yseries_score) | DIAScoring | |
| dia_byseries_intensity_min_ | DIAScoring | private |
| dia_byseries_ppm_diff_ | DIAScoring | private |
| dia_centroided_ | DIAScoring | private |
| dia_extract_window_ | DIAScoring | private |
| dia_isotope_scores(const std::vector< TransitionType > &transitions, SpectrumPtrType spectrum, OpenSwath::IMRMFeature *mrmfeature, double &isotope_corr, double &isotope_overlap) | DIAScoring | |
| dia_massdiff_score(const std::vector< TransitionType > &transitions, SpectrumPtrType spectrum, const std::vector< double > &normalized_library_intensity, double &ppm_score, double &ppm_score_weighted) | DIAScoring | |
| dia_ms1_isotope_scores(double precursor_mz, SpectrumPtrType spectrum, size_t charge_state, double &isotope_corr, double &isotope_overlap, std::string sum_formula="") | DIAScoring | |
| dia_ms1_massdiff_score(double precursor_mz, SpectrumPtrType spectrum, double &ppm_score) | DIAScoring | |
| dia_nr_charges_ | DIAScoring | private |
| dia_nr_isotopes_ | DIAScoring | private |
| diaIsotopeScoresSub_(const std::vector< TransitionType > &transitions, SpectrumPtrType spectrum, std::map< std::string, double > &intensities, double &isotope_corr, double &isotope_overlap) | DIAScoring | private |
| DIAScoring() | DIAScoring | |
| DIAScoring(const DIAScoring &rhs) | DIAScoring | private |
| error_name_ | DefaultParamHandler | protected |
| getDefaults() const | DefaultParamHandler | |
| getFirstIsotopeRelativeIntensities_(const std::vector< TransitionType > &transitions, OpenSwath::IMRMFeature *mrmfeature, std::map< std::string, double > &intensities) | DIAScoring | private |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| largePeaksBeforeFirstIsotope_(SpectrumPtrType spectrum, double mono_mz, double mono_int, int &nr_occurences, double &max_ratio) | DIAScoring | private |
| operator=(const DIAScoring &rhs) | DIAScoring | private |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| peak_before_mono_max_ppm_diff_ | DIAScoring | private |
| score_with_isotopes(SpectrumPtrType spectrum, const std::vector< TransitionType > &transitions, double &dotprod, double &manhattan) | DIAScoring | |
| scoreIsotopePattern_(double product_mz, const std::vector< double > &isotopes_int, int putative_fragment_charge, std::string sum_formula="") | DIAScoring | private |
| set_dia_parameters(double dia_extract_window, double dia_centroided, double dia_byseries_intensity_min, double dia_byseries_ppm_diff, double dia_nr_isotopes, double dia_nr_charges) | DIAScoring | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| SpectrumPtrType typedef | DIAScoring | private |
| subsections_ | DefaultParamHandler | protected |
| TransitionType typedef | DIAScoring | private |
| updateMembers_() | DIAScoring | privatevirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~DIAScoring() | DIAScoring | inlinevirtual |