score

Function

score

Returns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme.

score(score, value1, value2) [deprecated]

score(score, pos1, pos2, seq1, seq2)

Include Headers

seqan/score.h

Parameters

score	A scoring scheme. The scoring scheme to use. Types: Score, Score
value1	Aligned character in the first sequence.
value2	Aligned character in the second sequence.
pos1	Position of the aligned character in seq1.
pos2	Position of the aligned character in seq2.
seq1	First sequence.
seq2	Second sequence.

Status

The version that explicitely requires two characters is deprecated. For using (or defining) custom scoring schemes better use the functions score, scoreGapOpenVertical, scoreGapExtendVertical, scoreGapOpenHorizontal and scoreGapExtendHorizontal as they require character positions and sequences and allow for position-dependent scoring schemes.

Member of

SeqAn - Sequence Analysis Library - www.seqan.de