per-thread buffers (no heap allocations per candidate) and memoized match odds More...

#include <OpenNuXL/include/NuXLSearchIndex.h>

Classes
struct	FirstPassEntry

Public Member Functions
void	resetCandidate ()

template<class F >
double	matchOdds (size_t N, size_t matches, double p, F f)

Public Attributes
std::vector< double >	intensity_sum

std::vector< double >	b

std::vector< double >	y

std::vector< double >	a

std::vector< double >	intensity_xl

std::vector< double >	b_xl

std::vector< double >	y_xl

std::vector< double >	a_xl

std::vector< uint8_t >	peak_matched

std::vector< uint8_t >	peak_matched_xl

std::vector< FirstPassEntry >	fa_entries
	first pass of the shifted ion scoring, per fragment adduct mass

std::vector< int32_t >	fa_idx
	matched peak index (or -1) per [entry][ion type][charge][ion]

std::vector< std::tuple< size_t, size_t, const NuXLFragmentAdductDefinition *, int > >	matches_z_fa

std::vector< std::vector< double > >	match_odds
	[N][matches], NaN = not yet computed

Static Public Attributes
static constexpr int	N_ION_TYPES = 6
	shifted b, a, y (pre-selection) and b-H2O, y-H2O, y-NH3 (neutral loss peaks)

Detailed Description

per-thread buffers (no heap allocations per candidate) and memoized match odds

Class Documentation

◆ OpenMS::NuXLScoringScratch::FirstPassEntry

struct OpenMS::NuXLScoringScratch::FirstPassEntry

Class Members
uint32_t	cnt[3][2]
double	mass
size_t	off

Member Function Documentation

◆ matchOdds()

template<class F >

double matchOdds	(	size_t	N,
		size_t	matches,
		double	p,
		F	f
	)

inline

References NuXLScoringScratch::match_odds.

◆ resetCandidate()

void resetCandidate ( )

inline

References NuXLScoringScratch::fa_entries, and NuXLScoringScratch::fa_idx.

Member Data Documentation

◆ a

std::vector<double> a

◆ a_xl

std::vector<double> a_xl

◆ b

std::vector<double> b

◆ b_xl

std::vector<double> b_xl

◆ fa_entries

std::vector<FirstPassEntry> fa_entries

first pass of the shifted ion scoring, per fragment adduct mass

Referenced by NuXLScoringScratch::resetCandidate().

◆ fa_idx

std::vector<int32_t> fa_idx

matched peak index (or -1) per [entry][ion type][charge][ion]

Referenced by NuXLScoringScratch::resetCandidate().

◆ intensity_sum

std::vector<double> intensity_sum

◆ intensity_xl

std::vector<double> intensity_xl

◆ match_odds

std::vector<std::vector<double> > match_odds

[N][matches], NaN = not yet computed

Referenced by NuXLScoringScratch::matchOdds().

◆ matches_z_fa

std::vector<std::tuple<size_t, size_t, const NuXLFragmentAdductDefinition*, int> > matches_z_fa

◆ N_ION_TYPES

constexpr int N_ION_TYPES = 6

staticconstexpr

shifted b, a, y (pre-selection) and b-H2O, y-H2O, y-NH3 (neutral loss peaks)

◆ peak_matched

std::vector<uint8_t> peak_matched

◆ peak_matched_xl

std::vector<uint8_t> peak_matched_xl

◆ y

std::vector<double> y

◆ y_xl

std::vector<double> y_xl

Classes

Public Member Functions

Public Attributes

Static Public Attributes