SA_alignmentMatrix
Usage:
ScoreMatrix = SA_alignmentMatrix(VecArr1, VecArr2, Alignment, GapPenalty,
ScoreTreshold)
VecArr1: SA_VectorArray; First list of strings.
VecArr2: SA_VectorArray; Second list of strings.
Alignment: uint; The alignment function that should be used.
GapPenalty: double; Gap penalty used in the alignment process.
ScoreTreshold: double; Treshold used in the alignment process.
ScoreMatrix: [U x V] Matrix; Matrix containing the alignment scores.
Description
SA_alignmentMatrix computes a matrix of scores from the alignment of each string in VecArr1 against each
one of VecArr2. The used alignment algorithm is encoded in Alignment:
1 = SA_localAlignment
2 = SA_globalAlignment
3 = SA_repeatedMatchesAlignment
4 = SA_overlapMatchesAlignment
The parameters GapPenalty and ScoreTreshold are used in the specified alignment algorithm.
SA_localAlignment and
SA_globalAlignment only use GapPenalty, thus ScoreTreshold will
be ignored.
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