Bio::AlignIO::largemultifasta(3pm)			User Contributed Perl Documentation			Bio::AlignIO::largemultifasta(3pm)

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

perl v5.14.2							    2012-03-02					Bio::AlignIO::largemultifasta(3pm)