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.\" ========================================================================
.\"
.IX Title "Bio::AlignIO::largemultifasta 3pm"
.TH Bio::AlignIO::largemultifasta 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::AlignIO::largemultifasta \- Largemultifasta MSA Sequence
input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Do not use this module directly.  Use it via the Bio::AlignIO class.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object can transform Bio::SimpleAlign objects to and from
largemultifasta flat file databases.  This is for the fasta sequence
format \s-1NOT\s0 FastA analysis program.  To process the pairwise alignments
from a FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO
module.
.PP
Reimplementation of Bio::AlignIO::fasta modules so that creates
temporary files instead of keeping the whole sequences in memory.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHORS \- Albert Vilella, Heikki Lehvaslaiho"
.IX Header "AUTHORS - Albert Vilella, Heikki Lehvaslaiho"
Email: avilella-at-gmail-dot-com, heikki-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 6
\& 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
.Ve
.SS "next_aln"
.IX Subsection "next_aln"
.Vb 6
\& 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
.Ve
.SS "write_aln"
.IX Subsection "write_aln"
.Vb 5
\& 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
.Ve