Provided by: libbio-perl-perl_1.7.6-3_all bug


       Bio::AlignIO::proda - proda sequence input/output stream

       This provides the basic capabilities to parse the output alignments from the ProDA
       multiple sequence alignment program (


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


       This object can transform Bio::Align::AlignI objects to and from proda files.


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AUTHORS - Albert Vilella

       Email: avilella-at-gmail-dot-com


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

        Title   : new
        Usage   : $alignio = Bio::AlignIO->new(-format => 'proda',
                              -file => 'filename');
        Function: returns a new Bio::AlignIO object to handle proda files
        Returns : Bio::AlignIO::proda object
        Args    : -verbose => verbosity setting (-1, 0, 1, 2)
                  -file    => name of file to read in or to write, with ">"
                  -fh      => alternative to -file param - provide a filehandle
                              to read from or write to
                  -format  => alignment format to process or produce
                  -percentages => display a percentage of identity
                                  in each line of the alignment (proda only)
                  -linelength=> alignment output line length (default 60)

        Title   : next_aln
        Usage   : $aln = $stream->next_aln()
        Function: returns the next alignment in the stream
        Returns : Bio::Align::AlignI object
        Args    : NONE

       See Bio::Align::AlignI for details

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

        Title   : percentages
        Usage   : $obj->percentages($newval)
        Function: Set the percentages flag - whether or not to show percentages in
                  each output line
        Returns : value of percentages
        Args    : newvalue (optional)

        Title   : line_length
        Usage   : $obj->line_length($newval)
        Function: Set the alignment output line length
        Returns : value of line_length
        Args    : newvalue (optional)

        Title   : no_header
        Usage   : $obj->no_header($newval)
        Function: Set if the alignment input has a CLUSTAL header or not
        Returns : value of no_header
        Args    : newvalue (optional)