NAME

       Bio::AlignIO::metafasta - Metafasta 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 to and from metafasta flat file
       databases.

       The format of a metafasta file is

         >test/1-25
         ABCDEFHIJKLMNOPQRSTUVWXYZ
         &charge
         NBNAANCNJCNNNONNCNNUNNXNZ
         &chemical
         LBSAARCLJCLSMOIMCHHULRXRZ

       where the sequence block is followed by one or several meta blocks.  Each meta block
       starts with the ampersand character '&' in the first column and is immediately followed by
       the name of the meta data which continues until the new line. The meta data follows it.
       All characters, except new line, are important in meta data.

SEE ALSO

       Bio::SeqIO::metafasta

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

AUTHOR - Heikki Lehvaslaiho

       Email heikki-at-bioperl-dot-org

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 : L<Bio::Align::AlignI> object - returns 0 on end of file
                   or on error
        Args    : NONE

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

   width
        Title   : width
        Usage   : $obj->width($newval)
        Function: Get/Set the line width for METAFASTA output
        Returns : value of width
        Args    : newvalue (optional)