NAME

       Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream

SYNOPSIS

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

DESCRIPTION

       This object can transform Bio::SimpleAlign objects from XMFA flat file databases.  For
       more information, see:

         http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html

       This module is based on the AlignIO::fasta parser written by Peter Schattner

TODO

       Finish write_aln(), clean up code, allow LargeLocatableSeq (ie for very large sequences
       a'la Mauve)

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://redmine.open-bio.org/projects/bioperl/

AUTHORS

       Chris Fields

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.
        Returns : Bio::Align::AlignI object - returns 0 on end of file
                   or on error
        Args    : -width => optional argument to specify the width sequence
                  will be written (60 chars by default)

       See Bio::Align::AlignI

   write_aln
        Title   : write_aln
        Usage   : $stream->write_aln(@aln)
        Function: writes the $aln object into the stream in xmfa format
        Returns : 1 for success and 0 for error
        Args    : L<Bio::Align::AlignI> object

       See Bio::Align::AlignI

   _get_len
        Title   : _get_len
        Usage   :
        Function: determine number of alphabetic chars
        Returns : integer
        Args    : sequence string

   width
        Title   : width
        Usage   : $obj->width($newwidth)
                  $width = $obj->width;
        Function: Get/set width of alignment
        Returns : integer value of width
        Args    : on set, new value (a scalar or undef, optional)