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1 # $Id: TreeFactoryI.pm,v 1.6 2002/10/22 07:45:14 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Factory::TreeFactoryI
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees
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16 from/to a data stream
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17
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18 =head1 SYNOPSIS
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19
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20 # get a $factory from somewhere Bio::TreeIO likely
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21 my $treeio = new Bio::TreeIO(-format => 'newick', #this is phylip/newick format
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22 -file => 'file.tre');
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23 my $treeout = new Bio::TreeIO(-format => 'nexus',
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24 -file => ">file.nexus");
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25
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26 # convert tree formats from newick/phylip to nexus
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27 while(my $tree = $treeio->next_tree) {
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28 $treeout->write_tree($treeout);
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29 }
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30
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31 =head1 DESCRIPTION
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32
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33 This interface describes the minimal functions needed to get and write
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34 trees from a data stream. It is implemented by the L<Bio::TreeIO> factory.
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35
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36 =head1 FEEDBACK
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37
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38 =head2 Mailing Lists
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39
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40 User feedback is an integral part of the evolution of this and other
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41 Bioperl modules. Send your comments and suggestions preferably to
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42 the Bioperl mailing list. Your participation is much appreciated.
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43
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44 bioperl-l@bioperl.org - General discussion
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45 http://bioperl.org/MailList.shtml - About the mailing lists
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46
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47 =head2 Reporting Bugs
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48
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49 Report bugs to the Bioperl bug tracking system to help us keep track
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50 of the bugs and their resolution. Bug reports can be submitted via
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51 email or the web:
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52
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53 bioperl-bugs@bioperl.org
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54 http://bugzilla.bioperl.org/
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55
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56 =head1 AUTHOR - Jason Stajich
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57
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58 Email jason@bioperl.org
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59
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60 Describe contact details here
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61
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62 =head1 CONTRIBUTORS
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63
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64 Additional contributors names and emails here
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65
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66 =head1 APPENDIX
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67
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68 The rest of the documentation details each of the object methods.
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69 Internal methods are usually preceded with a _
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70
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71 =cut
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72
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73
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74 # Let the code begin...
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75
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76
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77 package Bio::Factory::TreeFactoryI;
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78 use vars qw(@ISA);
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79 use strict;
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80 use Bio::Root::RootI;
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81
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82 @ISA = qw(Bio::Root::RootI);
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83
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84 =head2 next_tree
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85
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86 Title : next_tree
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87 Usage : my $tree = $factory->next_tree;
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88 Function: Get a tree from the factory
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89 Returns : L<Bio::Tree::TreeI>
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90 Args : none
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91
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92 =cut
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93
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94 sub next_tree{
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95 my ($self,@args) = @_;
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96 $self->throw_not_implemented();
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97 }
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98
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99 =head2 write_tree
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100
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101 Title : write_tree
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102 Usage : $treeio->write_tree($tree);
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103 Function: Writes a tree onto the stream
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104 Returns : none
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105 Args : L<Bio::Tree::TreeI>
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106
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107
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108 =cut
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109
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110 sub write_tree{
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111 my ($self,@args) = @_;
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112 $self->throw_not_implemented();
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113 }
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114
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115 1;
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