OPXLDataStructs::CrossLinkSpectrumMatch Struct Reference

The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum in OpenPepXL. More...

#include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>

Public Member Functions
bool	operator< (const CrossLinkSpectrumMatch &other) const
bool	operator== (const CrossLinkSpectrumMatch &other) const

Public Attributes
ProteinProteinCrossLink	cross_link
	structure of the cross-link More...
Size	scan_index_light
	reference to pair of spectra More...
Size	scan_index_heavy
double	score
	final score More...
Size	rank
	rank among the matches to the same spectrum More...
double	pre_score
	counts, scores and other data for xQuest-like output More...
double	percTIC
double	wTIC
double	int_sum
double	match_odds
std::vector< double >	xcorrx
double	xcorrx_max
std::vector< double >	xcorrc
double	xcorrc_max
Size	matched_common_alpha
Size	matched_common_beta
Size	matched_xlink_alpha
Size	matched_xlink_beta
double	HyperCommon
double	HyperXlink
double	HyperAlpha
double	HyperBeta
double	HyperBoth
double	PScoreCommon
double	PScoreXlink
double	PScoreAlpha
double	PScoreBeta
double	PScoreBoth
std::vector< PeptideHit::PeakAnnotation >	frag_annotations
Size	peptide_id_index

Detailed Description

The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum in OpenPepXL.

This struct contains a ProteinProteinCrossLink and indices to one or two spectra. It also contains the results of a match between the ProteinProteinCrossLink and these spectra as scores and peak annotations. Used as a temporary container to collect results efficiently, since only a few top matches will be kept for each experimental spectrum for output.

Member Function Documentation

operator<()

bool operator< ( const CrossLinkSpectrumMatch &  other ) const

inline

References OPXLDataStructs::CrossLinkSpectrumMatch::score.

operator==()

bool operator== ( const CrossLinkSpectrumMatch &  other ) const

inline

References OPXLDataStructs::CrossLinkSpectrumMatch::cross_link, OPXLDataStructs::CrossLinkSpectrumMatch::HyperAlpha, OPXLDataStructs::CrossLinkSpectrumMatch::HyperBeta, OPXLDataStructs::CrossLinkSpectrumMatch::HyperBoth, OPXLDataStructs::CrossLinkSpectrumMatch::HyperCommon, OPXLDataStructs::CrossLinkSpectrumMatch::HyperXlink, OPXLDataStructs::CrossLinkSpectrumMatch::int_sum, OPXLDataStructs::CrossLinkSpectrumMatch::match_odds, OPXLDataStructs::CrossLinkSpectrumMatch::matched_common_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::matched_common_beta, OPXLDataStructs::CrossLinkSpectrumMatch::matched_xlink_alpha, OPXLDataStructs::CrossLinkSpectrumMatch::matched_xlink_beta, OPXLDataStructs::CrossLinkSpectrumMatch::percTIC, OPXLDataStructs::CrossLinkSpectrumMatch::pre_score, OPXLDataStructs::CrossLinkSpectrumMatch::PScoreAlpha, OPXLDataStructs::CrossLinkSpectrumMatch::PScoreBeta, OPXLDataStructs::CrossLinkSpectrumMatch::PScoreBoth, OPXLDataStructs::CrossLinkSpectrumMatch::PScoreCommon, OPXLDataStructs::CrossLinkSpectrumMatch::PScoreXlink, OPXLDataStructs::CrossLinkSpectrumMatch::rank, OPXLDataStructs::CrossLinkSpectrumMatch::scan_index_heavy, OPXLDataStructs::CrossLinkSpectrumMatch::scan_index_light, OPXLDataStructs::CrossLinkSpectrumMatch::score, OPXLDataStructs::CrossLinkSpectrumMatch::wTIC, OPXLDataStructs::CrossLinkSpectrumMatch::xcorrc, OPXLDataStructs::CrossLinkSpectrumMatch::xcorrc_max, OPXLDataStructs::CrossLinkSpectrumMatch::xcorrx, and OPXLDataStructs::CrossLinkSpectrumMatch::xcorrx_max.

Member Data Documentation

cross_link

ProteinProteinCrossLink cross_link

structure of the cross-link

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

frag_annotations

std::vector<PeptideHit::PeakAnnotation> frag_annotations

Referenced by TOPPOpenPepXLLF::main_(), and TOPPOpenPepXL::main_().

HyperAlpha

double HyperAlpha

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

HyperBeta

double HyperBeta

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

HyperBoth

double HyperBoth

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

HyperCommon

double HyperCommon

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

HyperXlink

double HyperXlink

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

int_sum

double int_sum

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

match_odds

double match_odds

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

matched_common_alpha

Size matched_common_alpha

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

matched_common_beta

Size matched_common_beta

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

matched_xlink_alpha

Size matched_xlink_alpha

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

matched_xlink_beta

Size matched_xlink_beta

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

peptide_id_index

Size peptide_id_index

percTIC

double percTIC

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

pre_score

double pre_score

counts, scores and other data for xQuest-like output

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

PScoreAlpha

double PScoreAlpha

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

PScoreBeta

double PScoreBeta

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

PScoreBoth

double PScoreBoth

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

PScoreCommon

double PScoreCommon

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

PScoreXlink

double PScoreXlink

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

rank

Size rank

rank among the matches to the same spectrum

Referenced by OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

scan_index_heavy

Size scan_index_heavy

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

scan_index_light

Size scan_index_light

reference to pair of spectra

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

score

double score

final score

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), OPXLDataStructs::CrossLinkSpectrumMatch::operator<(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

wTIC

double wTIC

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

xcorrc

std::vector< double > xcorrc

Referenced by OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

xcorrc_max

double xcorrc_max

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

xcorrx

std::vector< double > xcorrx

Referenced by OPXLDataStructs::CrossLinkSpectrumMatch::operator==().

xcorrx_max

double xcorrx_max

Referenced by TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and OPXLDataStructs::CrossLinkSpectrumMatch::operator==().