Bio::AlignIO::xmfa.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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)