SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.DESCRIPTION
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
TODO
Finish write_aln(), clean up code, allow LargeLocatableSeq (ie for very large sequences a'la Mauve)FEEDBACK
Support
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.
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://github.com/bioperl/bioperl-live/issues
AUTHORS
Chris FieldsAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _next_aln
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
write_aln
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
_get_len
Title : _get_len Usage : Function: determine number of alphabetic chars Returns : integer Args : sequence string
width
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)