NAME

       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 (http://proda.stanford.edu)

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 proda files.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   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 - Albert Vilella

       Email: avilella-at-gmail-dot-com

APPENDIX

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

   new
        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)

   next_aln
        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

   write_aln
        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

   percentages
        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)

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

   no_header
        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)