61 static float preScore(
Size matched_alpha,
Size ions_alpha,
Size matched_beta,
Size ions_beta);
68 static float preScore(
Size matched_alpha,
Size ions_alpha);
79 static double matchOddsScore(
const PeakSpectrum& theoretical_spec,
const Size matched_size,
double fragment_mass_tolerance,
bool fragment_mass_tolerance_unit_ppm,
bool is_xlink_spectrum =
false,
Size n_charges = 1);
81 static double matchOddsScoreSimpleSpec(
const std::vector< SimpleTSGXLMS::SimplePeak >& theoretical_spec,
const Size matched_size,
double fragment_mass_tolerance,
bool fragment_mass_tolerance_unit_ppm,
bool is_xlink_spectrum =
false,
Size n_charges = 1);
91 static double logOccupancyProb(
const PeakSpectrum& theoretical_spec,
const Size matched_size,
double fragment_mass_tolerance,
bool fragment_mass_tolerance_unit_ppm);
103 static double weightedTICScoreXQuest(
Size alpha_size,
Size beta_size,
double intsum_alpha,
double intsum_beta,
double total_current,
bool type_is_cross_link);
115 static double weightedTICScore(
Size alpha_size,
Size beta_size,
double intsum_alpha,
double intsum_beta,
double total_current,
bool type_is_cross_link);
124 static double matchedCurrentChain(
const std::vector< std::pair< Size, Size > >& matched_spec_linear,
const std::vector< std::pair< Size, Size > >& matched_spec_xlinks,
const PeakSpectrum& spectrum_linear_peaks,
const PeakSpectrum& spectrum_xlink_peaks);
135 static double totalMatchedCurrent(
const std::vector< std::pair< Size, Size > >& matched_spec_linear_alpha,
const std::vector< std::pair< Size, Size > >& matched_spec_linear_beta,
const std::vector< std::pair< Size, Size > >& matched_spec_xlinks_alpha,
const std::vector< std::pair< Size, Size > >& matched_spec_xlinks_beta,
const PeakSpectrum& spectrum_linear_peaks,
const PeakSpectrum& spectrum_xlink_peaks);