NAME

Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream

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 (e.g. for very large sequences from Mauve).

FEEDBACK

Support

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.

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 Fields

APPENDIX

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)