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Bio::AlignIO::xmfa(3) User Contributed Perl DocumentationBio::AlignIO::xmfa(3)

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)

perl v5.32.1			  2019-12-07		 Bio::AlignIO::xmfa(3)

NAME | SYNOPSIS | DESCRIPTION | TODO | FEEDBACK | AUTHORS | APPENDIX

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