Function
localAlignment
Computes the best local alignment of two sequences.
localAlignment(graph, score, tag)
localAlignment(file, strSet, score, tag)
Include Headers
seqan/graph_align.h
Parameters
|  Alignment object to use. Types:  Align | |
|  Alignments with scores < cutoff will be discarded. | |
|  The lowest diagonal of the alignment matrix that will be computed for banded alignment. | |
|  The highest diagonal of the alignment matrix that will be computed for banded alignment. | |
|  A tag indicating the alignment algorithm to use Remarks: SmithWaterman | |
|  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 | |
|  The alignment graph having 2 sequences. Types:  Alignment Graph | |
|  A file stream or std::cout to write a textual alignment | |
|  The score values to be used for computing the alignment. Types:  Score | 
Return Values
 The maximum score of the best local alignment.
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de