#include <alignment_scorer.hpp>

Inheritance diagram for vg::AlignmentScorer:

Public Member Functions
virtual	~AlignmentScorer ()=default

virtual int32_t	score_alignment (const Alignment &aln) const =0
	Compute a single integer score for the alignment under this scorer's scheme. More...

virtual double	get_log_base () const =0

Static Protected Member Functions
static double	recover_log_base (const double matrix[16], double gc_content, double tol=1e-12)

Static Private Member Functions
static bool	verify_valid_log_odds_score_matrix (const double matrix[16], const double nt_freqs[4])
	Check a score matrix to make sure it has negative scores for random sequence. More...

static double	alignment_score_partition_function (double lambda, const double matrix[16], const double nt_freqs[4])

Detailed Description

Base interface for computing scores for alignments under some (not necessarily affine-gap) scoring scheme.

Constructor & Destructor Documentation

◆ ~AlignmentScorer()

virtual vg::AlignmentScorer::~AlignmentScorer ( )

virtualdefault

Member Function Documentation

◆ alignment_score_partition_function()

double vg::AlignmentScorer::alignment_score_partition_function	(	double	lambda,
		const double	matrix[16],
		const double	nt_freqs[4]
	)

staticprivate

Partition function used for recovering the log base for a scoring scheme. TODO: What is a partition function exactly?

◆ get_log_base()

virtual double vg::AlignmentScorer::get_log_base ( ) const

pure virtual

Get the log base value used to probabilistically interpret scores. Implementations probably need to have a stores GC content to implement this.

Implemented in vg::LoggedGapAlignmentScorer, and vg::MatrixAlignmentScorer.

◆ recover_log_base()

double vg::AlignmentScorer::recover_log_base	(	const double	matrix[16],
		double	gc_content,
		double	tol = `1e-12`
	)

staticprotected

Bisects to find the log base under which the partition function over the given 4x4 substitution matrix and nucleotide frequencies (from GC content) equals 1.

Useful for implementing the recover_log_base operation for a derived class, if that class can produce a scoring matrix.

◆ score_alignment()

virtual int32_t vg::AlignmentScorer::score_alignment ( const Alignment & aln ) const

pure virtual

Compute a single integer score for the alignment under this scorer's scheme.

Implemented in vg::LoggedGapAlignmentScorer, and vg::EditAlignmentScorer.

◆ verify_valid_log_odds_score_matrix()

bool vg::AlignmentScorer::verify_valid_log_odds_score_matrix	(	const double	matrix[16],
		const double	nt_freqs[4]
	)

staticprivate

Check a score matrix to make sure it has negative scores for random sequence.

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

src/alignment_scorer.hpp
src/alignment_scorer.cpp

Public Member Functions

Static Protected Member Functions

Static Private Member Functions