lib/Bio/Taxonomy/FactoryI.pm

   1 #
   2 #
   3 # BioPerl interface of Bio::Taxnomoy::FactoryI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Juguang Xiao
   8 #
   9 # You may distribute this module under the same terms as Perl itself
  10 #
  11 # POD documentation - main does before the code
  12
  13 =head1 NAME
  14
  15 Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy
  16
  17 =head1 DESCRIPTION
  18
  19 NB: This module has been deprecated.
  20
  21 $factory-E<gt>fetch is a general method to fetch Taxonomy by either NCBI
  22 taxid or any types of names.
  23
  24 $factory-E<gt>fetch_parent($taxonomy), returns a Taxonomy that is
  25 one-step higher rank of the taxonomy specified as argument.
  26
  27 $factory-E<gt>fetch_children($taxonomy), reports an array of Taxonomy
  28 those are one-step lower rank of the taxonomy specified as the
  29 argument.
  30
  31 =head1 AUTHOR - Juguang Xiao
  32
  33 juguang@tll.org.sg
  34
  35 =head1 CONTRIBUTORS
  36
  37 Additional contributors' names and emails here
  38
  39 =head1 APPENDIX
  40
  41 The rest of the documentation details each of the object methods.
  42 Internal methods are usually preceded with a _
  43
  44 =cut
  45
  46 package Bio::Taxonomy::FactoryI;
  47 use strict;
  48
  49
  50 use base qw(Bio::Root::Root);
  51
  52 =head2 fetch
  53
  54   Title:    fetch
  55   Usage:    my $taxonomy = $factory->fetch(-taxon_id => 9605);
  56             my $taxonomy = $factory->fetch(-common_name => 'mammals');
  57   Fuctnion: Fetch taxonomy by taxon_id, common name or scientific name.
  58   Returns:  an instance of Bio::Taxonomy
  59   Args:     -taxon_id => NCBI taxonomy ID
  60             -common_name => comon name, such as 'human', 'mammals'
  61             -scientifc_name => specitic name, such as 'sapiens', 'Mammalia'
  62
  63 =cut
  64
  65 sub fetch {
  66     shift->throw_not_implemented;
  67 }
  68
  69 =head2 fuzzy_fetch
  70
  71   Title:    fuzzy_fetch
  72   Usage:    my @taxonomy = $factory->fuzzy_fetch(-name => 'mouse');
  73   Function: Fuzzy fetch by name, or any text information found in DB
  74   Returns:  an array reference of Bio::Taxonomy objects
  75   Args:     -name => any name, such as common name, variant, scientific name
  76             -description, or -desc => any text information
  77
  78 =cut
  79
  80 sub fuzzy_fetch {
  81     shift->throw_not_implemented;
  82 }
  83
  84 =head2 fetch_parent
  85
  86   Title:    fetch_parent
  87   Usage:    my $parent_taxonomy = $factory->fetch_parent($taxonomy);
  88   Function: Fetch the parent that is one-rank higher than the argument.
  89   Returns:  an instance of Bio::Taxonomy, or undef if the arg is the top one.
  90   Args:     a Bio::Taxonomy object.
  91
  92 =cut
  93
  94 sub fetch_parent {
  95     shift->throw_not_implemented;
  96 }
  97
  98 =head2 fetch_children
  99
 100   Title:    fetch_children
 101   Usage:    my @children_taxonomy = $factory->fetch_children($taxonomy);
 102   Function: Fetch all children those are one-rank lower than the argument.
 103   Returns:  an array reference of Bio::Taxonomy objects
 104   Args:     a Bio::Taxonomy object.
 105
 106 =cut
 107
 108 sub fetch_children {
 109     shift->throw_not_implemented;
 110 }
 111
 112 1;