NuXLSpectrumIndex Struct Reference

Search-time lookup structures for the OpenNuXL database search. More...

#include <OpenNuXL/include/NuXLSearchIndex.h>

Public Member Functions
void	build (const MSSpectrum &s)
size_t	lowerBound (double x) const
	same result as std::lower_bound on the peak m/z
size_t	nearest (double x) const
	same result as MSSpectrum::findNearest(x)

Public Attributes
const MSSpectrum *	spec = nullptr
std::vector< double >	mz
	peak m/z (copy, contiguous)
std::vector< float >	intensity
	peak intensities (copy, contiguous)
std::vector< int >	charge
	peak charges (IntegerDataArray NuXLConstants::IA_CHARGE_INDEX)
std::vector< uint16_t >	lb
	lb[k] = index of the first peak with m/z >= k * BIN
float	marker_ions_sub_score = 0
	MorpheusScore of the spectrum against all marker ions (independent of the candidate)
std::vector< uint8_t >	has_tag_for_fa_id
	fragment adduct name (by registry id) is listed in StringDataArray 0 (nucleotide tags)

Static Public Attributes
static constexpr double	BIN = 2.0
static constexpr double	INV_BIN = 1.0 / BIN

Detailed Description

Search-time lookup structures for the OpenNuXL database search.

Everything in here only changes how values are looked up, never what is computed: the lookups return the same results as MSSpectrum::findNearest or std::lower_bound / std::upper_bound on the full containers. Per-spectrum data that is computed once after preprocessing and reused for every candidate peptide.

Member Function Documentation

build()

void build ( const MSSpectrum &  s )

inline

References NuXLSpectrumIndex::BIN, NuXLSpectrumIndex::charge, MSSpectrum::clear(), MSSpectrum::getIntegerDataArrays(), NuXLConstants::IA_CHARGE_INDEX, NuXLSpectrumIndex::intensity, NuXLSpectrumIndex::INV_BIN, NuXLSpectrumIndex::lb, NuXLSpectrumIndex::mz, and NuXLSpectrumIndex::spec.

lowerBound()

size_t lowerBound ( double  x ) const

inline

same result as std::lower_bound on the peak m/z

References NuXLSpectrumIndex::INV_BIN, NuXLSpectrumIndex::lb, and NuXLSpectrumIndex::mz.

Referenced by NuXLSpectrumIndex::nearest().

nearest()

size_t nearest ( double  x ) const

inline

same result as MSSpectrum::findNearest(x)

References NuXLSpectrumIndex::lowerBound(), and NuXLSpectrumIndex::mz.

Member Data Documentation

BIN

constexpr double BIN = 2.0

staticconstexpr

Referenced by NuXLSpectrumIndex::build().

charge

std::vector<int> charge

peak charges (IntegerDataArray NuXLConstants::IA_CHARGE_INDEX)

Referenced by NuXLSpectrumIndex::build().

has_tag_for_fa_id

std::vector<uint8_t> has_tag_for_fa_id

fragment adduct name (by registry id) is listed in StringDataArray 0 (nucleotide tags)

Referenced by NuXLFragmentAdductRegistry::annotateSpectrum().

intensity

std::vector<float> intensity

peak intensities (copy, contiguous)

Referenced by NuXLSpectrumIndex::build().

INV_BIN

constexpr double INV_BIN = 1.0 / BIN

staticconstexpr

Referenced by NuXLSpectrumIndex::build(), and NuXLSpectrumIndex::lowerBound().

lb

std::vector<uint16_t> lb

lb[k] = index of the first peak with m/z >= k * BIN

Referenced by NuXLSpectrumIndex::build(), and NuXLSpectrumIndex::lowerBound().

marker_ions_sub_score

float marker_ions_sub_score = 0

MorpheusScore of the spectrum against all marker ions (independent of the candidate)

mz

std::vector<double> mz

peak m/z (copy, contiguous)

Referenced by NuXLSpectrumIndex::build(), NuXLSpectrumIndex::lowerBound(), and NuXLSpectrumIndex::nearest().

spec

const MSSpectrum* spec = nullptr

Referenced by NuXLFragmentAdductRegistry::annotateSpectrum(), and NuXLSpectrumIndex::build().