next up previous contents index
Next: String Distance Function ( Up: Alignment Data Types Previous: String Matching Algorithms (   Contents   Index


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/core/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 up previous contents index
Next: String Distance Function ( Up: Alignment Data Types Previous: String Matching Algorithms (   Contents   Index
root 2008-01-09