diff variant_effect_predictor/Bio/Ontology/TermFactory.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Ontology/TermFactory.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,134 @@
+# $Id: TermFactory.pm,v 1.1.2.2 2003/03/27 10:07:56 lapp Exp $
+#
+# BioPerl module for Bio::Ontology::TermFactory
+#
+# Cared for by Hilmar Lapp <hlapp at gmx.net>
+#
+# Copyright Hilmar Lapp
+#
+# You may distribute this module under the same terms as perl itself
+
+#
+# (c) Hilmar Lapp, hlapp at gmx.net, 2002.
+# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
+#
+# You may distribute this module under the same terms as perl itself.
+# Refer to the Perl Artistic License (see the license accompanying this
+# software package, or see http://www.perl.com/language/misc/Artistic.html)
+# for the terms under which you may use, modify, and redistribute this module.
+# 
+# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
+# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+#
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Ontology::TermFactory - Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
+
+=head1 SYNOPSIS
+
+    use Bio::Ontology::TermFactory;
+
+    # the default type is Bio::Ontology::Term
+    my $factory = new Bio::Ontology::TermFactory(-type => 'Bio::Ontology::GOterm');
+    my $term = $factory->create_object(-name => 'peroxisome',
+                                       -ontology => 'Gene Ontology',
+                                       -identifier => 'GO:0005777');
+
+
+=head1 DESCRIPTION
+
+This object will build L<Bio::Ontology::TermI> objects generically.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Hilmar Lapp
+
+Email hlapp at gmx.net
+
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Ontology::TermFactory;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::Factory::ObjectFactory;
+
+@ISA = qw(Bio::Factory::ObjectFactory);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Ontology::TermFactory();
+ Function: Builds a new Bio::Ontology::TermFactory object 
+ Returns : Bio::Ontology::TermFactory
+ Args    : -type => string, name of a L<Bio::Ontology::TermI> derived class.
+                    The default is L<Bio::Ontology::Term>.
+
+=cut
+
+sub new {
+    my($class,@args) = @_;
+
+    my $self = $class->SUPER::new(@args);
+  
+    # make sure this matches our requirements
+    $self->interface("Bio::Ontology::TermI");
+    $self->type($self->type() || "Bio::Ontology::Term");
+
+    return $self;
+}
+
+
+=head2 create_object
+
+ Title   : create_object
+ Usage   : my $term = $factory->create_object(<named parameters>);
+ Function: Instantiates new Bio::Ontology::TermI (or one of its child classes)
+
+           This object allows us to genericize the instantiation of
+           Term objects.
+
+ Returns : L<Bio::Ontology::TermI> compliant object
+           The return type is configurable using new(-type =>"...").
+ Args    : initialization parameters specific to the type of term
+           object we want.  Typically 
+           -name        => $name
+           -identifier  => identifier for the term
+           -ontology    => ontology for the term
+
+=cut
+
+1;