Ewan Birney


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 = 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) {


This interface describes the minimal functions needed to get and write trees from a data stream. It is implemented by the Bio::TreeIO factory.


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AUTHOR - Jason Stajich

Email jason@bioperl.org

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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>