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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/AnnotatableI.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,107 @@
+# $Id: AnnotatableI.pm,v 1.2 2002/12/31 13:09:06 birney Exp $
+#
+# BioPerl module for Bio::AnnotatableI
+#
+# Cared for by Hilmar Lapp <hlapp at gmx.net>
+#
+# Copyright Hilmar Lapp
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::AnnotatableI - the base interface an annotatable object must implement
+
+=head1 SYNOPSIS
+
+    use Bio::SeqIO;
+    # get an annotatable object somehow: for example, Bio::SeqI objects
+    # are annotatable
+    my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank);
+    while (my $seq = $seqio->next_seq()) {
+        # $seq is-a Bio::AnnotatableI, hence:
+        my $ann_coll = $seq->annotation();
+        # $ann_coll is-a Bio::AnnotationCollectionI, hence:
+        my @all_anns = $ann_coll->get_Annotations();
+        # do something with the annotation objects
+    }
+
+=head1 DESCRIPTION
+
+This is the base interface that all annotatable objects must implement. A good
+example is Bio::Seq which is an AnnotableI object; if you are a little confused
+about what this module does, start a Bio::Seq.
+
+=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://bioperl.org/bioperl-bugs/
+
+=head1 AUTHOR - Hilmar Lapp
+
+Email hlapp at gmx.net
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=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::AnnotatableI;
+use vars qw(@ISA);
+use strict;
+use Carp;
+use Bio::Root::RootI;
+
+@ISA = qw( Bio::Root::RootI );
+
+=head2 annotation
+
+ Title   : annotation
+ Usage   : $obj->annotation($newval)
+ Function: Get the annotation collection (see L<Bio::AnnotationCollectionI>)
+           for this annotatable object.
+ Example : 
+ Returns : a Bio::AnnotationCollectionI implementing object, or undef
+ Args    : on set, new value (a Bio::AnnotationCollectionI
+           implementing object, optional) (an implementation may not
+           support changing the annotation collection)
+
+
+=cut
+
+sub annotation{
+    shift->throw_not_implemented();
+}
+
+
+
+1;