Raw content of Bio::Factory::TreeFactoryI # $Id: TreeFactoryI.pm,v 1.6 2002/10/22 07:45:14 lapp Exp $ # # BioPerl module for Bio::Factory::TreeFactoryI # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees from/to a data stream =head1 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); } =head1 DESCRIPTION This interface describes the minimal functions needed to get and write trees from a data stream. It is implemented by the L<Bio::TreeIO> factory. =head1 FEEDBACK =head2 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 =head2 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://bugzilla.bioperl.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Factory::TreeFactoryI; use vars qw(@ISA); use strict; use Bio::Root::RootI; @ISA = qw(Bio::Root::RootI); =head2 next_tree Title : next_tree Usage : my $tree = $factory->next_tree; Function: Get a tree from the factory Returns : L<Bio::Tree::TreeI> Args : none =cut sub next_tree{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : L<Bio::Tree::TreeI> =cut sub write_tree{ my ($self,@args) = @_; $self->throw_not_implemented(); } 1;