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.




Copyright © 2007 Thomas Oskam, ETH Zürich. All rights reserved.