Bio::AlignIO::msf 1.4

Bio::AlignIO::msf is a Perl module with msf sequence input/output stream.

SYNOPSIS

Do not use this module directly. Use it via the Bio::AlignIO class.

This object can transform Bio::Align::AlignI objects to and from msf flat file databases.

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_aln

Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream. Tries to read *all* MSF
It reads all non whitespace characters in the alignment
area. For MSFs with weird gaps (eg ~~~) map them by using
$al->map_chars(~,-)
Returns : L< Bio::Align::AlignI > object
Args : NONE

write_aln

Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in MSF format
Sequence type of the alignment is determined by the first sequence.
Returns : 1 for success and 0 for error
Args : L< Bio::Align::AlignI > object