SYNOPSIS

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

DESCRIPTION

This object can transform Bio::SimpleAlign objects to and from NeXML format. For more information on NeXML, visit <http://www.nexml.org>.

FEEDBACK

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

Chase Miller

CONTRIBUTORS

Mark Jensen, [email protected] Rutger Vos, [email protected]

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    :

See Bio::Align::AlignI

rewind

 Title   : rewind
 Usage   : $alnio->rewind
 Function: Resets the stream
 Returns : none
 Args    : none

doc

 Title   : doc
 Usage   : $treeio->doc
 Function: Returns the biophylo nexml document object
 Returns : Bio::Phylo::Project
 Args    : none or Bio::Phylo::Project object

write_aln

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in nexml format
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object

See Bio::Align::AlignI