/ 
BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::AlignIO::xmfa

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)