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Score Matrix ( score_matrix )

Definition

An instance S of the data type score_matrix is an object required by alignment computations. The object contains an alphabet representing residues and maintains a table that assigns a score to any pair of aligned residues. In addition it maintains the gap penalty values.
Remark: This data type is experimental. It can significantly change in future versions.

#include < LEDA/string/score_matrix.h >

Creation

score_matrix S(int defmatch = 1, int defmismatch = -1)

creates an instance S of type score_matrix. The alphabet is set to the standard alphabet consisting of the capital letters A - Z. The scores are initialized to defmatch if the letters are idendical (1 by default), to defmismatch otherwise (-1 by default).

score_matrix S(alphabet& alt, int defmatch = 1, int defmismatch = -1)

creates an instance S of type score_matrix. The alphabet is set to alt. The scores are initialized to defmatch if the letters are idendical (1 by default), to defmismatch otherwise (-1 by default).

Operations

void S.setScore(char a, char b, int sc)

sets the score for a and b to sc.
Precondition a and b are in the score alphabet. Otherwise an exception is thrown.

int S.getScore(char a, char b)

returns the score for a and b.
Precondition a and b are in the score alphabet. Otherwise an exception is thrown.

bool S.hasScore(char a, char b)

returns bool if score is defined for a and b, otherwise false.

void S.setScoreMatch(int sc) sets the score for all pairs a and a to sc.

void S.setScoreMismatch(int sc)

sets the score for all pairs a and b with a != b to sc.

void S.setGapPenalty(int pen) sets the penalty for starting a new gap to pen.

void S.setGapIncPenalty(int incpen)

sets the penalty for extending a gap by one position to incpen.

void S.setGapPenalty(int pen, int incpen)

sets the penalty for starting a new gap to pen and for extending a gap by 1 position to incpen.

int S.getGapPenalty() returns the penalty for starting a new gap.

int S.getGapIncPenalty() returns the penalty for extending a gap by one position.

Next: String Distance Function ( Up: Alignment Data Types Previous: String Matching Algorithms ( Contents Index

score_matrix	S(int defmatch = 1, int defmismatch = -1)
		creates an instance S of type score_matrix. The alphabet is set to the standard alphabet consisting of the capital letters A - Z. The scores are initialized to defmatch if the letters are idendical (1 by default), to defmismatch otherwise (-1 by default).
score_matrix	S(alphabet& alt, int defmatch = 1, int defmismatch = -1)
		creates an instance S of type score_matrix. The alphabet is set to alt. The scores are initialized to defmatch if the letters are idendical (1 by default), to defmismatch otherwise (-1 by default).

void	S.setScore(char a, char b, int sc)
		sets the score for a and b to sc. Precondition a and b are in the score alphabet. Otherwise an exception is thrown.
int	S.getScore(char a, char b)
		returns the score for a and b. Precondition a and b are in the score alphabet. Otherwise an exception is thrown.
bool	S.hasScore(char a, char b)
		returns bool if score is defined for a and b, otherwise false.
void	S.setScoreMatch(int sc)	sets the score for all pairs a and a to sc.
void	S.setScoreMismatch(int sc)
		sets the score for all pairs a and b with a != b to sc.
void	S.setGapPenalty(int pen)	sets the penalty for starting a new gap to pen.
void	S.setGapIncPenalty(int incpen)
		sets the penalty for extending a gap by one position to incpen.
void	S.setGapPenalty(int pen, int incpen)
		sets the penalty for starting a new gap to pen and for extending a gap by 1 position to incpen.
int	S.getGapPenalty()	returns the penalty for starting a new gap.
int	S.getGapIncPenalty()	returns the penalty for extending a gap by one position.