lib/Bio/Annotation/TypeManager.pm

   1 #
   2 # BioPerl module for Bio::Annotation::TypeManager
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   7 #
   8 # Copyright Ewan Birney
   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::Annotation::TypeManager - Manages types for annotation collections
  17
  18 =head1 SYNOPSIS
  19
  20     # default type manager
  21
  22     $tm = Bio::Annotation::TypeManager->new();
  23
  24     # $key is a string or a Bio::Ontology::TermI compliant object
  25     print "The type for $key is ",$tm->type_for_key($key),"\n";
  26
  27     if( !$tm->is_valid($key,$object) ) {
  28         $self->throw("Invalid object for key $key");
  29     }
  30
  31 =head1 DESCRIPTION
  32
  33 Manages types for annotation collections.
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this
  40 and other Bioperl modules. Send your comments and suggestions preferably
  41  to one of the Bioperl mailing lists.
  42 Your participation is much appreciated.
  43
  44   bioperl-l@bioperl.org
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 the bugs and their resolution.
  61 Bug reports can be submitted via the web:
  62
  63   https://github.com/bioperl/bioperl-live/issues
  64
  65 =head1 AUTHOR - Ewan Birney
  66
  67 Email birney@ebi.ac.uk
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
  72
  73 =cut
  74
  75
  76 # Let the code begin...
  77
  78
  79 package Bio::Annotation::TypeManager;
  80
  81 use strict;
  82
  83 # Object preamble - inherits from Bio::Root::Root
  84
  85
  86
  87 use base qw(Bio::Root::Root);
  88 # new() can be inherited from Bio::Root::Root
  89
  90 =head2 new
  91
  92  Title   : new
  93  Usage   :
  94  Function:
  95  Example :
  96  Returns :
  97  Args    :
  98
  99
 100 =cut
 101
 102 sub new{
 103    my ($class,@args) = @_;
 104
 105    my $self = $class->SUPER::new(@args);
 106
 107    $self->{'_type'} = {};
 108
 109    $self->_add_type_map('reference',"Bio::Annotation::Reference");
 110    $self->_add_type_map('comment',"Bio::Annotation::Comment");
 111    $self->_add_type_map('dblink',"Bio::Annotation::DBLink");
 112
 113    return $self;
 114 }
 115
 116
 117 =head2 type_for_key
 118
 119  Title   : type_for_key
 120  Usage   :
 121  Function:
 122  Example :
 123  Returns :
 124  Args    :
 125
 126
 127 =cut
 128
 129 sub type_for_key{
 130    my ($self,$key) = @_;
 131
 132    $key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI");
 133    return $self->{'_type'}->{$key};
 134 }
 135
 136
 137 =head2 is_valid
 138
 139  Title   : is_valid
 140  Usage   :
 141  Function:
 142  Example :
 143  Returns :
 144  Args    :
 145
 146
 147 =cut
 148
 149 sub is_valid{
 150    my ($self,$key,$object) = @_;
 151
 152    if( !defined $object || !ref $object ) {
 153        $self->throw("Cannot type an object [$object]!");
 154    }
 155
 156    if( !$object->isa($self->type_for_key($key)) ) {
 157        return 0;
 158    } else {
 159        return 1;
 160    }
 161 }
 162
 163
 164 =head2 _add_type_map
 165
 166  Title   : _add_type_map
 167  Usage   :
 168  Function:
 169  Example :
 170  Returns :
 171  Args    :
 172
 173
 174 =cut
 175
 176 sub _add_type_map{
 177    my ($self,$key,$type) = @_;
 178
 179    $key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI");
 180    $self->{'_type'}->{$key} = $type;
 181 }
 182
 183 1;