Ewan Birney

NAME

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

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.

FEEDBACK

Mailing Lists

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/MailList.shtml  - About the mailing lists

Reporting Bugs

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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

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

next_tree

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

write_tree

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