Toolbar

Summary

Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees
from/to a data stream

Package variables

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

Methods description

 Title   : next_tree
 Usage   : my $tree = $factory->next_tree;
 Function: Get a tree from the factory
 Returns : Bio::Tree::TreeI
 Args    : none

 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Writes a tree onto the stream
 Returns : none
 Args    : Bio::Tree::TreeI

Methods code

sub next_tree {

   my ($self,@args) = @_;
   $self->throw_not_implemented();

}

sub write_tree {

   my ($self,@args) = @_;
   $self->throw_not_implemented();
}

1;

}

General documentation

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://redmine.open-bio.org/projects/bioperl/

Email jason@bioperl.org

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _