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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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 the web:

         https://github.com/bioperl/bioperl-live/issues

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
                  $aln->map_chars('~','-')
        Returns : 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    : Bio::Align::AlignI object