Bio/Ontology/TermFactory.pm

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