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.
Please direct usage questions or support issues to the mailing list:
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.
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:
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