NAME

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

SYNOPSIS

         # Do not use this module directly.  Use it via the L<Bio::AlignIO> class.

         use Bio::AlignIO;
         use strict;

         my $in = Bio::AlignIO->new(-format => 'selex',
                                    -file   => 't/data/testaln.selex');
         while( my $aln = $in->next_aln ) {

         }

DESCRIPTION

       This object can transform Bio::Align::AlignI objects to and from selex flat file
       databases.

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 - Peter Schattner

       Email: schattner@alum.mit.edu

CONTRIBUTORS

       Jason Stajich, jason-at-bioperl.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. Tries to read *all* selex
                 It reads all non whitespace characters in the alignment
                 area. For selexs with weird gaps (eg ~~~) map them by using
                 $al->map_chars('~','-')
        Returns : L<Bio::Align::AlignI> object
        Args    : NONE

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