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1 # $Id: TermFactory.pm,v 1.1.2.2 2003/03/27 10:07:56 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Ontology::TermFactory
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4 #
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5 # Cared for by Hilmar Lapp <hlapp at gmx.net>
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6 #
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7 # Copyright Hilmar Lapp
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 #
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12 # (c) Hilmar Lapp, hlapp at gmx.net, 2002.
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13 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
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14 #
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15 # You may distribute this module under the same terms as perl itself.
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16 # Refer to the Perl Artistic License (see the license accompanying this
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17 # software package, or see http://www.perl.com/language/misc/Artistic.html)
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18 # for the terms under which you may use, modify, and redistribute this module.
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19 #
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20 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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21 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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22 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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23 #
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24
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25 # POD documentation - main docs before the code
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26
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27 =head1 NAME
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28
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29 Bio::Ontology::TermFactory - Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
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30
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31 =head1 SYNOPSIS
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32
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33 use Bio::Ontology::TermFactory;
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34
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35 # the default type is Bio::Ontology::Term
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36 my $factory = new Bio::Ontology::TermFactory(-type => 'Bio::Ontology::GOterm');
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37 my $term = $factory->create_object(-name => 'peroxisome',
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38 -ontology => 'Gene Ontology',
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39 -identifier => 'GO:0005777');
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40
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41
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42 =head1 DESCRIPTION
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43
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44 This object will build L<Bio::Ontology::TermI> objects generically.
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45
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46 =head1 FEEDBACK
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47
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48 =head2 Mailing Lists
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49
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50 User feedback is an integral part of the evolution of this and other
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51 Bioperl modules. Send your comments and suggestions preferably to
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52 the Bioperl mailing list. Your participation is much appreciated.
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53
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54 bioperl-l@bioperl.org - General discussion
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55 http://bioperl.org/MailList.shtml - About the mailing lists
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56
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57 =head2 Reporting Bugs
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58
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59 Report bugs to the Bioperl bug tracking system to help us keep track
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60 of the bugs and their resolution. Bug reports can be submitted via
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61 email or the web:
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62
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63 bioperl-bugs@bioperl.org
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64 http://bugzilla.bioperl.org/
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65
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66 =head1 AUTHOR - Hilmar Lapp
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67
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68 Email hlapp at gmx.net
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69
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70
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71 =head1 APPENDIX
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72
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73 The rest of the documentation details each of the object methods.
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74 Internal methods are usually preceded with a _
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75
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76 =cut
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77
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78
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79 # Let the code begin...
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80
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81
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82 package Bio::Ontology::TermFactory;
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83 use vars qw(@ISA);
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84 use strict;
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85
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86 use Bio::Root::Root;
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87 use Bio::Factory::ObjectFactory;
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88
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89 @ISA = qw(Bio::Factory::ObjectFactory);
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90
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91 =head2 new
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92
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93 Title : new
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94 Usage : my $obj = new Bio::Ontology::TermFactory();
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95 Function: Builds a new Bio::Ontology::TermFactory object
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96 Returns : Bio::Ontology::TermFactory
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97 Args : -type => string, name of a L<Bio::Ontology::TermI> derived class.
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98 The default is L<Bio::Ontology::Term>.
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99
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100 =cut
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101
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102 sub new {
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103 my($class,@args) = @_;
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104
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105 my $self = $class->SUPER::new(@args);
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106
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107 # make sure this matches our requirements
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108 $self->interface("Bio::Ontology::TermI");
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109 $self->type($self->type() || "Bio::Ontology::Term");
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110
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111 return $self;
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112 }
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113
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114
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115 =head2 create_object
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116
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117 Title : create_object
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118 Usage : my $term = $factory->create_object(<named parameters>);
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119 Function: Instantiates new Bio::Ontology::TermI (or one of its child classes)
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120
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121 This object allows us to genericize the instantiation of
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122 Term objects.
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123
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124 Returns : L<Bio::Ontology::TermI> compliant object
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125 The return type is configurable using new(-type =>"...").
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126 Args : initialization parameters specific to the type of term
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127 object we want. Typically
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128 -name => $name
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129 -identifier => identifier for the term
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130 -ontology => ontology for the term
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131
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132 =cut
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133
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134 1;
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