CawalignCodonScores Class Reference

Inheritance diagram for CawalignCodonScores:

Public Member Functions
	CawalignCodonScores (ConfigParser *, ConfigParser *)
Public Member Functions inherited from CawalignSimpleScores
	CawalignSimpleScores (const char *_alphabet, const cawlign_fp *_scoring_matrix, const cawlign_fp _open_gap_reference, const cawlign_fp _open_gap_query, const cawlign_fp _extend_gap_reference, const cawlign_fp _extend_gap_query)
	CawalignSimpleScores (ConfigParser *)
void	_init_alphabet (long not_found=-1)

Static Public Member Functions
static int	nucleotide_diff (long, long)

Public Attributes
Vector	translation_table
Vector	resolutions
VectorFP	s3x1
VectorFP	s3x2
VectorFP	s3x4
VectorFP	s3x5
cawlign_fp	frameshift_cost
cawlign_fp	synonymous_penalty
StringBuffer	amino_acids
int	stop_codon_index
int	mismatch_index
Public Attributes inherited from CawalignSimpleScores
StringBuffer	alphabet
unsigned int	D
long	char_map [255]
VectorFP	scoring_matrix
cawlign_fp	open_gap_reference
cawlign_fp	open_gap_query
cawlign_fp	extend_gap_query
cawlign_fp	extend_gap_reference
char	gap_char

Constructor & Destructor Documentation

CawalignCodonScores()

CawalignCodonScores::CawalignCodonScores	(	ConfigParser *	code_settings,
		ConfigParser *	score_settings )

Constructs a CawalignCodonScores object using configuration score_settings.

This constructor initializes the codon scoring system using values from a ConfigParser. It sets up the codon translation table, stop codon index, mismatch index, and scoring matrices for codon alignments. Throws errors if the amino acid alphabet is incomplete or the translation table is invalid.

Parameters

code_settings	A pointer to a ConfigParser object containing genetic code settings.
score_settings	A pointer to a ConfigParser object containing configuration score_settings.

Member Function Documentation

nucleotide_diff()

int CawalignCodonScores::nucleotide_diff ( long c1, long c2 )

static

Calculates the number of nucleotide differences between two codons.

---

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

• src/scoring.hpp
• src/scoring.cpp