Inheritance diagram for LocARNA::PairHMMMatchProbs:

Collaboration diagram for LocARNA::PairHMMMatchProbs:

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Classes
class	PairHMMParams
	Maintains parameter for computing match probabilities. More...

Public Member Functions
	PairHMMMatchProbs (const Sequence &seqA, const Sequence &seqB, const PairHMMParams &params)
	construct predicting pair probs by pairHMM More...

Public Member Functions inherited from LocARNA::MatchProbs
	MatchProbs (std::istream &in, size_type lenA, size_type lenB)
	construct from input stream (sparse format)

Public Member Functions inherited from LocARNA::EdgeProbs
	EdgeProbs (std::istream &in, size_type lenA, size_type lenB)
	construct from input stream (sparse format)

std::ostream &	write_sparse (std::ostream &out, double threshold) const

size_type	lenA () const
	get the length of the first sequence

size_type	lenB () const
	get the length of the second sequence

double	prob (size_t i, size_t j) const
	return the match probability for the two bases

Protected Member Functions
void	pairHMM_probs (const Sequence &seqA, const Sequence &seqB, const PairHMMParams &params)

Protected Member Functions inherited from LocARNA::EdgeProbs
std::istream &	read_sparse (std::istream &in, size_type lenA, size_type lenB)

void	read_sparse (const std::string &filename, size_type lenA, size_type lenB)

Additional Inherited Members
Public Types inherited from LocARNA::EdgeProbs
using	size_type = size_t
	size

Protected Attributes inherited from LocARNA::EdgeProbs
Matrix< double >	probs_
	the base match probabilities

Constructor & Destructor Documentation

◆ PairHMMMatchProbs()

LocARNA::PairHMMMatchProbs::PairHMMMatchProbs	(	const Sequence &	seqA,
		const Sequence &	seqB,
		const PairHMMParams &	params
	)

inline

construct predicting pair probs by pairHMM

Parameters

seqA	sequence A
seqB	sequence B
params	pairHMM (probcons) parameter object

void LocARNA::PairHMMMatchProbs::pairHMM_probs	(	const Sequence &	seqA,
		const Sequence &	seqB,
		const PairHMMParams &	params
	)

protected

read probcons parameter file and compute match probabilities for the two given sequences

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