NAME

FAST::Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver

SYNOPSIS

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

DESCRIPTION

This object can transform FAST::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:

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

Chase Miller

CONTRIBUTORS

Mark Jensen, maj@fortinbras.us Rutger Vos, rutgeraldo@gmail.com

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 : FAST::Bio::Align::AlignI object - returns 0 on end of file
	        or on error
 Args    :

See FAST::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 : FAST::Bio::Phylo::Project
Args    : none or FAST::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<FAST::Bio::Align::AlignI> object