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

NAME

       Bio::AlignIO::msf - msf sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::AlignIO class.

DESCRIPTION

       This object can transform Bio::Align::AlignI objects to and from msf flat file databases.

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 - Peter Schattner
       Email: schattner@alum.mit.edu

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. Tries to read *all* MSF
		  It reads all non whitespace characters in the alignment
		  area. For MSFs with weird gaps (eg ~~~) map them by using
		  $aln->map_chars('~','-')
	Returns : Bio::Align::AlignI object
	Args	: NONE

   write_aln
	Title	: write_aln
	Usage	: $stream->write_aln(@aln)
	Function: writes the $aln object into the stream in MSF format
		  Sequence type of the alignment is determined by the first sequence.
	Returns : 1 for success and 0 for error
	Args	: Bio::Align::AlignI object

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