Bio/Taxonomy/FactoryI.pm

   1 #
   2 #
   3 # BioPerl interface of Bio::Taxnomoy::FactoryI
   4 #
   5 # Cared for by Juguang Xiao
   6 #
   7 # You may distribute this module under the same terms as Perl itself
   8 #
   9 # POD documentation - main does before the code
  10
  11 =head1 NAME
  12
  13 Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy
  14
  15 =head1 DESCRIPTION
  16
  17 NB: This module has been deprecated.
  18
  19 $factory-E<gt>fetch is a general method to fetch Taxonomy by either NCBI
  20 taxid or any types of names.
  21
  22 $factory-E<gt>fetch_parent($taxonomy), returns a Taxonomy that is
  23 one-step higher rank of the taxonomy specified as argument.
  24
  25 $factory-E<gt>fetch_children($taxonomy), reports an array of Taxonomy
  26 those are one-step lower rank of the taxonomy specified as the
  27 argument.
  28
  29 =head1 AUTHOR - Juguang Xiao
  30
  31 juguang@tll.org.sg
  32
  33 =head1 CONTRIBUTORS
  34
  35 Additional contributors' names and emails here
  36
  37 =head1 APPENDIX
  38
  39 The rest of the documentation details each of the object methods.
  40 Internal methods are usually preceded with a _
  41
  42 =cut
  43
  44 package Bio::Taxonomy::FactoryI;
  45 use strict;
  46
  47
  48 use base qw(Bio::Root::Root);
  49
  50 =head2 fetch
  51
  52   Title:    fetch
  53   Usage:    my $taxonomy = $factory->fetch(-taxon_id => 9605);
  54             my $taxonomy = $factory->fetch(-common_name => 'mammals');
  55   Fuctnion: Fetch taxonomy by taxon_id, common name or scientific name.
  56   Returns:  an instance of Bio::Taxonomy
  57   Args:     -taxon_id => NCBI taxonomy ID
  58             -common_name => comon name, such as 'human', 'mammals'
  59             -scientifc_name => specitic name, such as 'sapiens', 'Mammalia'
  60
  61 =cut
  62
  63 sub fetch {
  64     shift->throw_not_implemented;
  65 }
  66
  67 =head2 fuzzy_fetch
  68
  69   Title:    fuzzy_fetch
  70   Usage:    my @taxonomy = $factory->fuzzy_fetch(-name => 'mouse');
  71   Function: Fuzzy fetch by name, or any text information found in DB
  72   Returns:  an array reference of Bio::Taxonomy objects
  73   Args:     -name => any name, such as common name, variant, scientific name
  74             -description, or -desc => any text information
  75
  76 =cut
  77
  78 sub fuzzy_fetch {
  79     shift->throw_not_implemented;
  80 }
  81
  82 =head2 fetch_parent
  83
  84   Title:    fetch_parent
  85   Usage:    my $parent_taxonomy = $factory->fetch_parent($taxonomy);
  86   Function: Fetch the parent that is one-rank higher than the argument.
  87   Returns:  an instance of Bio::Taxonomy, or undef if the arg is the top one.
  88   Args:     a Bio::Taxonomy object.
  89
  90 =cut
  91
  92 sub fetch_parent {
  93     shift->throw_not_implemented;
  94 }
  95
  96 =head2 fetch_children
  97
  98   Title:    fetch_children
  99   Usage:    my @children_taxonomy = $factory->fetch_children($taxonomy);
 100   Function: Fetch all children those are one-rank lower than the argument.
 101   Returns:  an array reference of Bio::Taxonomy objects
 102   Args:     a Bio::Taxonomy object.
 103
 104 =cut
 105
 106 sub fetch_children {
 107     shift->throw_not_implemented;
 108 }
 109
 110 1;