Bio::AlignIO::msf(3)

NAME
Bio::AlignIO::msf - msf sequence input/output stream

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

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

FEEDBACK

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.
 Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

AUTHORS - Peter Schattner
Email: schattner@alum.mit.edu

APPENDIX
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