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