Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::AlignIO::fasta - fasta MSA Sequence input/output stream


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


       This object can transform Bio::SimpleAlign objects to and from fasta flat files.  This is
       for the fasta alignment format, not for the FastA sequence analysis program.  To process
       the alignments from FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.


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

       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:


       Peter Schattner


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

        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

        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

       See Bio::Align::AlignI

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

        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)