asap

Bio::AlignIO::xmfa(3pm) 				User Contributed Perl Documentation				   Bio::AlignIO::xmfa(3pm)

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 (ie for very large sequences a'la 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://redmine.open-bio.org/projects/bioperl/

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)

perl v5.14.2							    2012-03-02						   Bio::AlignIO::xmfa(3pm)