| Function localAlignment Computes the best local alignment of two sequences. localAlignment(strSet, score, tag) localAlignment(graph, score, tag) localAlignment(file, strSet, score, tag) Parameters
strSet | A string set with 2 sequences. Types: StringSet Remarks: If an alignment graph is used that graph must contain a string set with two sequences
graph | The alignment graph having 2 sequences. Types: Alignment Graph
file | A file stream or std::cout to write a textual alignment
score | The score values to be used for computing the alignment. Types: Score
tag | A tag indicating the alignment algorithm to use Remarks: SmithWaterman
Return Values The maximum score of the best local alignment. Example Programs Local Alignments, Smith-Waterman Algorithm See Also Local Alignment Algorithms, smithWaterman, smithWatermanGetNext SeqAn - Sequence Analysis Library - www.seqan.de