NAME

       Bio::AlignIO::largemultifasta - Largemultifasta MSA Sequence input/output stream

SYNOPSIS

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

DESCRIPTION

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

       Reimplementation of Bio::AlignIO::fasta modules so that creates temporary files instead of
       keeping the whole sequences in memory.

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 - Albert Vilella, Heikki Lehvaslaiho

       Email: avilella-at-gmail-dot-com, heikki-at-bioperl-dot-org

APPENDIX

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

   next_seq
        Title   : next_seq
        Usage   : $seq = $stream->next_seq()
        Function: returns the next sequence in the stream while taking care
                  of the length
        Returns : Bio::Seq object
        Args    : NONE

   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 largemultifasta format
        Returns : 1 for success and 0 for error
        Args    : L<Bio::Align::AlignI> object