lib/Bio/Factory/TreeFactoryI.pm

   1 #
   2 # BioPerl module for Bio::Factory::TreeFactoryI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees
  17   from/to a data stream
  18
  19 =head1 SYNOPSIS
  20
  21   # get a $factory from somewhere Bio::TreeIO likely
  22   my $treeio = Bio::TreeIO->new(-format => 'newick', #this is phylip/newick format
  23                                -file   => 'file.tre');
  24   my $treeout = Bio::TreeIO->new(-format => 'nexus',
  25                                 -file   => ">file.nexus");
  26
  27   # convert tree formats from newick/phylip to nexus
  28   while(my $tree = $treeio->next_tree) {
  29       $treeout->write_tree($tree);
  30   }
  31
  32 =head1 DESCRIPTION
  33
  34 This interface describes the minimal functions needed to get and write
  35 trees from a data stream.  It is implemented by the L<Bio::TreeIO> factory.
  36
  37 =head1 FEEDBACK
  38
  39 =head2 Mailing Lists
  40
  41 User feedback is an integral part of the evolution of this and other
  42 Bioperl modules. Send your comments and suggestions preferably to
  43 the Bioperl mailing list.  Your participation is much appreciated.
  44
  45   bioperl-l@bioperl.org                  - General discussion
  46   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  47
  48 =head2 Support
  49
  50 Please direct usage questions or support issues to the mailing list:
  51
  52 I<bioperl-l@bioperl.org>
  53
  54 rather than to the module maintainer directly. Many experienced and
  55 reponsive experts will be able look at the problem and quickly
  56 address it. Please include a thorough description of the problem
  57 with code and data examples if at all possible.
  58
  59 =head2 Reporting Bugs
  60
  61 Report bugs to the Bioperl bug tracking system to help us keep track
  62 of the bugs and their resolution. Bug reports can be submitted via the
  63 web:
  64
  65   https://github.com/bioperl/bioperl-live/issues
  66
  67 =head1 AUTHOR - Jason Stajich
  68
  69 Email jason@bioperl.org
  70
  71 =head1 APPENDIX
  72
  73 The rest of the documentation details each of the object methods.
  74 Internal methods are usually preceded with a _
  75
  76 =cut
  77
  78
  79 # Let the code begin...
  80
  81
  82 package Bio::Factory::TreeFactoryI;
  83 use strict;
  84
  85 use base qw(Bio::Root::RootI);
  86
  87 =head2 next_tree
  88
  89  Title   : next_tree
  90  Usage   : my $tree = $factory->next_tree;
  91  Function: Get a tree from the factory
  92  Returns : L<Bio::Tree::TreeI>
  93  Args    : none
  94
  95 =cut
  96
  97 sub next_tree{
  98    my ($self,@args) = @_;
  99    $self->throw_not_implemented();
 100 }
 101
 102 =head2 write_tree
 103
 104  Title   : write_tree
 105  Usage   : $treeio->write_tree($tree);
 106  Function: Writes a tree onto the stream
 107  Returns : none
 108  Args    : L<Bio::Tree::TreeI>
 109
 110
 111 =cut
 112
 113 sub write_tree{
 114    my ($self,@args) = @_;
 115    $self->throw_not_implemented();
 116 }
 117
 118 1;