vg::SpliceStats Class Reference

#include <splicing.hpp>

Public Member Functions
	SpliceStats (const GSSWAligner &aligner)
	SpliceStats (const vector< tuple< string, string, double > > &motifs, const vector< double > &lognormal_mixture_weights, const vector< pair< double, double > > &lognormal_component_params, const GSSWAligner &aligner)
size_t	motif_size () const
const string &	oriented_motif (size_t motif_num, bool left_side) const
bool	motif_is_reverse (size_t motif_num) const
string	unoriented_motif (size_t motif_num, bool left_side) const
int32_t	motif_score (size_t motif_num) const
double	motif_frequency (size_t motif_num) const
int32_t	intron_length_score (int64_t length) const
void	update_motifs (const vector< tuple< string, string, double > > &motifs, const GSSWAligner &aligner)
void	update_intron_length_distribution (const vector< double > &lognormal_mixture_weights, const vector< pair< double, double > > &lognormal_component_params, const GSSWAligner &aligner)
void	update_scoring (const GSSWAligner &aligner)

Private Member Functions
void	init (const vector< tuple< string, string, double > > &motifs, const vector< double > &lognormal_mixture_weights, const vector< pair< double, double > > &lognormal_component_params, const GSSWAligner &aligner)
double	intron_length_log_likelihood (int64_t length) const

Private Attributes
vector< tuple< string, string, int32_t > >	motif_data
vector< tuple< string, string, double > >	unaltered_motif_data
vector< double >	mixture_weights
vector< pair< double, double > >	component_params
double	mode_log_likelihood
double	log_base

Constructor & Destructor Documentation

SpliceStats() [1/2]

vg::SpliceStats::SpliceStats

(

const GSSWAligner &

aligner

)

SpliceStats() [2/2]

vg::SpliceStats::SpliceStats	(	const vector< tuple< string, string, double > > &	motifs,
		const vector< double > &	lognormal_mixture_weights,
		const vector< pair< double, double > > &	lognormal_component_params,
		const GSSWAligner &	aligner )

Member Function Documentation

init()

void vg::SpliceStats::init ( const vector< tuple< string, string, double > > & motifs, const vector< double > & lognormal_mixture_weights, const vector< pair< double, double > > & lognormal_component_params, const GSSWAligner & aligner )

private

intron_length_log_likelihood()

double vg::SpliceStats::intron_length_log_likelihood ( int64_t length ) const

private

intron_length_score()

int32_t vg::SpliceStats::intron_length_score

(

int64_t

length

)

const

motif_frequency()

double vg::SpliceStats::motif_frequency

(

size_t

motif_num

)

const

motif_is_reverse()

bool vg::SpliceStats::motif_is_reverse

(

size_t

motif_num

)

const

motif_score()

int32_t vg::SpliceStats::motif_score

(

size_t

motif_num

)

const

motif_size()

size_t vg::SpliceStats::motif_size

(

)

const

oriented_motif()

const string & vg::SpliceStats::oriented_motif	(	size_t	motif_num,
		bool	left_side ) const

unoriented_motif()

string vg::SpliceStats::unoriented_motif	(	size_t	motif_num,
		bool	left_side ) const

update_intron_length_distribution()

void vg::SpliceStats::update_intron_length_distribution	(	const vector< double > &	lognormal_mixture_weights,
		const vector< pair< double, double > > &	lognormal_component_params,
		const GSSWAligner &	aligner )

update_motifs()

void vg::SpliceStats::update_motifs	(	const vector< tuple< string, string, double > > &	motifs,
		const GSSWAligner &	aligner )

update_scoring()

void vg::SpliceStats::update_scoring

(

const GSSWAligner &

aligner

)

Member Data Documentation

component_params

vector<pair<double, double> > vg::SpliceStats::component_params

private

log_base

double vg::SpliceStats::log_base

private

mixture_weights

vector<double> vg::SpliceStats::mixture_weights

private

mode_log_likelihood

double vg::SpliceStats::mode_log_likelihood

private

motif_data

vector<tuple<string, string, int32_t> > vg::SpliceStats::motif_data

private

unaltered_motif_data

vector<tuple<string, string, double> > vg::SpliceStats::unaltered_motif_data

private

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The documentation for this class was generated from the following files:

• src/splicing.hpp
• src/splicing.cpp