| Bio::AlignIO::xmfa(3pm) | User Contributed Perl Documentation | Bio::AlignIO::xmfa(3pm) |
Bio::AlignIO::xmfa - XMFA 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 from XMFA flat file databases. For more information, see:
http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html
This module is based on the AlignIO::fasta parser written by Peter Schattner
Finish write_aln(), clean up code, allow LargeLocatableSeq (e.g. for very large sequences from Mauve).
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.
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://github.com/bioperl/bioperl-live/issues
Chris Fields
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_aln
Usage : $aln = $stream->next_aln
Function: returns the next alignment in the stream.
Returns : Bio::Align::AlignI object - returns 0 on end of file
or on error
Args : -width => optional argument to specify the width sequence
will be written (60 chars by default)
See Bio::Align::AlignI
Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in xmfa format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object
See Bio::Align::AlignI
Title : _get_len Usage : Function: determine number of alphabetic chars Returns : integer Args : sequence string
Title : width
Usage : $obj->width($newwidth)
$width = $obj->width;
Function: Get/set width of alignment
Returns : integer value of width
Args : on set, new value (a scalar or undef, optional)
| 2021-08-15 | perl v5.32.1 |