NAME¶
Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver
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:
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://github.com/bioperl/bioperl-live/issues
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 : 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