diff variant_effect_predictor/Bio/DBLinkContainerI.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DBLinkContainerI.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,106 @@
+# $Id: DBLinkContainerI.pm,v 1.8 2002/10/22 07:38:24 lapp Exp $
+#
+# BioPerl module for Bio::DBLinkContainerI
+#
+# Cared for by Heikki Lehvaslaiho <[e-mail]>
+#
+# Copyright Heikki Lehvaslaiho
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::DBLinkContainerI - Abstract interface for any object wanting to use  
+                        database cross references
+
+=head1 SYNOPSIS
+
+    # get an objects containing database cross reference
+
+        foreach $obj ( @objs ) {
+                if( $obj->isa('Bio::DBLinkContainerI') ) {
+                        foreach $dblink ( $obj->each_DBLink() ) {
+                                # do stuff
+                        }
+                }
+        }
+
+=head1 DESCRIPTION
+
+This interface defines the functions one can expect for any object
+wanting to use database cross-references. This class does not actually
+provide any implemention, it just provides the definitions of what
+methods one can call.
+
+The database cross-references are implemented as L<Bio::Annotation::DBLink>
+objects.
+
+=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 one
+of the Bioperl mailing lists.  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
+the bugs and their resolution.  Bug reports can be submitted via email
+or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Heikki Lehvaslaiho
+
+Email:  [e-mail]
+Address: 
+
+     EMBL Outstation, European Bioinformatics Institute
+     Wellcome Trust Genome Campus, Hinxton
+     Cambs. CB10 1SD, United Kingdom 
+
+=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::DBLinkContainerI;
+use vars qw(@ISA);
+use strict;
+
+use Carp;
+use Bio::Root::RootI;
+
+@ISA = qw(Bio::Root::RootI);
+
+=head2 each_DBLink
+
+ Title   : each_DBLink
+ Usage   : foreach $ref ( $self->each_DBlink() )
+ Function: gets an array of DBlink of objects
+ Example :
+ Returns : an array of Bio::Annotation::DBLink objects
+ Args    : none
+
+
+=cut
+
+sub each_DBLink{
+   my ($self) = @_;
+   my $class = ref($self) || $self;
+   $self->throw("Class $class did not define method 'each_DBLink' for interface DBLinkContainerI");
+}
+
+1;
+