CawalignSimpleScores Class Reference

Inheritance diagram for CawalignSimpleScores:

Public Member Functions
	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)

Public Attributes
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

CawalignSimpleScores() [1/2]

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
	)

Constructs a CawalignSimpleScores object with a custom alphabet and scoring matrix.

This constructor initializes the scoring system with a user-specified alphabet and scoring matrix, as well as gap penalties for both reference and query sequences. Throws an error if the alphabet is empty.

Parameters

_alphabet	The alphabet for scoring (e.g., nucleotides or amino acids).
_scoring_matrix	A pointer to the scoring matrix values.
_open_gap_reference	Gap opening penalty for reference sequences.
_open_gap_query	Gap opening penalty for query sequences.
_extend_gap_reference	Gap extension penalty for reference sequences.
_extend_gap_query	Gap extension penalty for query sequences.

CawalignSimpleScores() [2/2]

CawalignSimpleScores::CawalignSimpleScores

(

ConfigParser *

settings

)

Constructs a CawalignSimpleScores object using configuration settings.

This constructor reads configuration values from a ConfigParser to initialize the alphabet, scoring matrix, and gap penalties. Throws errors if the alphabet is missing or the scoring matrix dimensions are incorrect.

Parameters

settings

A pointer to a ConfigParser object containing configuration settings.

Member Function Documentation

_init_alphabet()

void CawalignSimpleScores::_init_alphabet

(

long

not_found = -1

)

Initializes the character map for the scoring matrix.

This function populates the char_map array, mapping each character in the alphabet to its index in the scoring matrix. Characters not in the alphabet are assigned a value of not_found.

Parameters

not_found

The value to assign for characters not found in the alphabet.

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

• src/scoring.hpp
• src/scoring.cpp