Bio::AlignIO::largemultifasta - Largemultifasta MSA Sequence input/output stream
Do not use this module directly. Use it via the Bio::AlignIO class.
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.
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:
http://bugzilla.open-bio.org/
Email: avilella-at-gmail-dot-com, heikki-at-bioperl-dot-org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
