Raw content of Bio::Factory::TreeFactoryI
<![CDATA[# $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;
]]>