Bio::Factory TreeFactoryI
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Summary
Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees
from/to a data stream
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
  # 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); }
Description
This interface describes the minimal functions needed to get and write
trees from a data stream. It is implemented by the Bio::TreeIO factory.
Methods
next_treeDescriptionCode
write_treeDescriptionCode
Methods description
next_treecode    nextTop
 Title   : next_tree
Usage : my $tree = $factory->next_tree;
Function: Get a tree from the factory
Returns : Bio::Tree::TreeI
Args : none
write_treecodeprevnextTop
 Title   : write_tree
Usage : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args : Bio::Tree::TreeI
Methods code
next_treedescriptionprevnextTop
sub next_tree {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
write_treedescriptionprevnextTop
sub write_tree {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _