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Summary

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

Package variables

Included modules

Inherit

Bio::Root::RootI

Synopsis

  # get a $factory from somewhere Bio::TreeIO likely
  my $treeio = new Bio::TreeIO(-format => 'newick', #this is phylip/newick format
  			       -file   => 'file.tre');
  my $treeout = new Bio::TreeIO(-format => 'nexus',
  				-file   => ">file.nexus");

  # convert tree formats from newick/phylip to nexus
  while(my $tree = $treeio->next_tree) {
      $treeout->write_tree($treeout);
  }

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

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