| Bio::Factory::TreeFactoryI(3pm) | User Contributed Perl Documentation | Bio::Factory::TreeFactoryI(3pm) |
Bio::Factory::TreeFactoryI - Factory Interface for getting and
writing trees
from/to a data stream
# get a $factory from somewhere Bio::TreeIO likely
my $treeio = Bio::TreeIO->new(-format => 'newick', #this is phylip/newick format
-file => 'file.tre');
my $treeout = Bio::TreeIO->new(-format => 'nexus',
-file => ">file.nexus");
# convert tree formats from newick/phylip to nexus
while(my $tree = $treeio->next_tree) {
$treeout->write_tree($tree);
}
This interface describes the minimal functions needed to get and write trees from a data stream. It is implemented by the Bio::TreeIO factory.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
Email jason@bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_tree Usage : my $tree = $factory->next_tree; Function: Get a tree from the factory Returns : L<Bio::Tree::TreeI> Args : none
Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : L<Bio::Tree::TreeI>
| 2018-10-27 | perl v5.26.2 |