Bio/Ontology/TermFactory.pm

   1 #
   2 # BioPerl module for Bio::Ontology::TermFactory
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Hilmar Lapp <hlapp at gmx.net>
   7 #
   8 # Copyright Hilmar Lapp
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 #
  13 # (c) Hilmar Lapp, hlapp at gmx.net, 2002.
  14 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
  15 #
  16 # You may distribute this module under the same terms as perl itself.
  17 # Refer to the Perl Artistic License (see the license accompanying this
  18 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  19 # for the terms under which you may use, modify, and redistribute this module.
  20 #
  21 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  22 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  23 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  24 #
  25
  26 # POD documentation - main docs before the code
  27
  28 =head1 NAME
  29
  30 Bio::Ontology::TermFactory - Instantiates a new
  31 Bio::Ontology::TermI (or derived class) through a factory
  32
  33 =head1 SYNOPSIS
  34
  35     use Bio::Ontology::TermFactory;
  36
  37     # the default type is Bio::Ontology::Term
  38     my $factory = Bio::Ontology::TermFactory->new(
  39                         -type => 'Bio::Ontology::GOterm');
  40     my $term = $factory->create_object(-name => 'peroxisome',
  41                                        -ontology => 'Gene Ontology',
  42                                        -identifier => 'GO:0005777');
  43
  44
  45 =head1 DESCRIPTION
  46
  47 This object will build L<Bio::Ontology::TermI> objects generically.
  48
  49 =head1 FEEDBACK
  50
  51 =head2 Mailing Lists
  52
  53 User feedback is an integral part of the evolution of this and other
  54 Bioperl modules. Send your comments and suggestions preferably to
  55 the Bioperl mailing list.  Your participation is much appreciated.
  56
  57   bioperl-l@bioperl.org                  - General discussion
  58   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  59
  60 =head2 Support
  61
  62 Please direct usage questions or support issues to the mailing list:
  63
  64 I<bioperl-l@bioperl.org>
  65
  66 rather than to the module maintainer directly. Many experienced and
  67 reponsive experts will be able look at the problem and quickly
  68 address it. Please include a thorough description of the problem
  69 with code and data examples if at all possible.
  70
  71 =head2 Reporting Bugs
  72
  73 Report bugs to the Bioperl bug tracking system to help us keep track
  74 of the bugs and their resolution. Bug reports can be submitted via
  75 the web:
  76
  77   https://github.com/bioperl/bioperl-live/issues
  78
  79 =head1 AUTHOR - Hilmar Lapp
  80
  81 Email hlapp at gmx.net
  82
  83
  84 =head1 APPENDIX
  85
  86 The rest of the documentation details each of the object methods.
  87 Internal methods are usually preceded with a _
  88
  89 =cut
  90
  91
  92 # Let the code begin...
  93
  94
  95 package Bio::Ontology::TermFactory;
  96 use strict;
  97
  98 use Bio::Root::Root;
  99
 100 use base qw(Bio::Factory::ObjectFactory);
 101
 102 =head2 new
 103
 104  Title   : new
 105  Usage   : my $obj = Bio::Ontology::TermFactory->new();
 106  Function: Builds a new Bio::Ontology::TermFactory object
 107  Returns : Bio::Ontology::TermFactory
 108  Args    : -type => string, name of a Bio::Ontology::TermI derived class.
 109                     The default is Bio::Ontology::Term.
 110
 111 See L<Bio::Ontology::TermI>, L<Bio::Ontology::Term>.
 112
 113 =cut
 114
 115 sub new {
 116     my($class,@args) = @_;
 117
 118     my $self = $class->SUPER::new(@args);
 119
 120     # make sure this matches our requirements
 121     $self->interface("Bio::Ontology::TermI");
 122     $self->type($self->type() || "Bio::Ontology::Term");
 123
 124     return $self;
 125 }
 126
 127
 128 =head2 create_object
 129
 130  Title   : create_object
 131  Usage   : my $term = $factory->create_object(<named parameters>);
 132  Function: Instantiates new Bio::Ontology::TermI (or one of its child classes)
 133
 134            This object allows us to genericize the instantiation of
 135            Term objects.
 136
 137  Returns : Bio::Ontology::TermI compliant object
 138            The return type is configurable using new(-type =>"...").
 139  Args    : initialization parameters specific to the type of term
 140            object we want.  Typically
 141            -name        => $name
 142            -identifier  => identifier for the term
 143            -ontology    => ontology for the term
 144
 145 See L<Bio::Ontology::TermI>.
 146
 147 =cut
 148
 149 1;