NAME

       Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)

SYNOPSIS

           # do not use the object directly
           use Bio::AlignIO;
           # read in an alignment from the EMBOSS program water
           my $in = Bio::AlignIO->new(-format => 'emboss',
                                     -file   => 'seq.water');
           while( my $aln = $in->next_aln ) {
           # do something with the alignment
           }

DESCRIPTION

       This object handles parsing and writing pairwise sequence alignments from the EMBOSS
       suite.

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 the Bioperl mailing list.  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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

       Email jason@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.
        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 emboss format
        Returns : 1 for success and 0 for error
        Args    : L<Bio::Align::AlignI> object