diff variant_effect_predictor/Bio/AnnotationCollectionI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/AnnotationCollectionI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,177 @@
+# $Id: AnnotationCollectionI.pm,v 1.9 2002/10/22 07:38:24 lapp Exp $
+
+#
+# BioPerl module for Bio::AnnotationCollectionI
+#
+# Cared for by Ewan Birney <[e-mail]>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::AnnotationCollectionI - Interface for annotation collections
+
+=head1 SYNOPSIS
+
+   # get an AnnotationCollectionI somehow, eg
+
+   $ac = $seq->annotation();
+
+   foreach $key ( $ac->get_all_annotation_keys() ) {
+       @values = $ac->get_Annotations($key);
+       foreach $value ( @values ) {
+          # value is an Bio::AnnotationI, and defines a "as_text" method
+          print "Annotation ",$key," stringified value ",$value->as_text,"\n";
+
+          # also defined hash_tree method, which allows data orientated
+          # access into this object
+          $hash = $value->hash_tree();
+       }
+   } 
+
+=head1 DESCRIPTION
+
+Annotation Collections are a way of storing a series of "interesting
+facts" about something. We call an "interesting fact" in Bioperl an
+Annotation (this differs from a Sequence Feature, which is called
+a Sequence Feature and may or may not have an Annotation Collection).
+
+The trouble about this is we are not that sure what "interesting
+facts" someone might want to store: the possibility is endless. 
+
+Bioperl's approach is that the "interesting facts" are represented by
+Bio::AnnotationI objects. The interface Bio::AnnotationI guarentees
+two methods
+
+   $obj->as_text(); # string formated to display to users
+
+and
+
+   $obj->hash_tree(); # hash with defined rules for data-orientated discovery
+
+The hash_tree method is designed to play well with XML output and
+other "nested-tag-of-data-values" think BoulderIO and/or Ace stuff. For more
+info read Bio::AnnotationI docs
+
+Annotations are stored in AnnotationCollections, each Annotation under a
+different "tag". The tags allow simple discovery of the available annotations,
+and in some cases (like the tag "gene_name") indicate how to interpret the
+data underneath the tag. The tag is only one tag deep and each tag can have an
+array of values.
+
+In addition, AnnotationCollectionI's are guarentee to maintain a consistent
+set object values under each tag - at least that each object complies to one
+interface. The "standard" AnnotationCollection insists the following rules
+are set up
+
+  Tag         Object
+  ---         ------
+  reference   Bio::Annotation::Reference
+  comment     Bio::Annotation::Comment
+  dblink      Bio::Annotation::DBLink
+  gene_name   Bio::Annotation::SimpleValue
+  description Bio::Annotation::SimpleValue
+
+These tags are the implict tags that the SeqIO system needs to round-trip
+GenBank/EMBL/Swissprot.
+
+However, you as a user and us collectively as a community can grow the
+"standard" tag mapping over time and specifically for a particular
+area.
+
+
+=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]
+
+=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 - Ewan Birney
+
+Email [e-mail]
+
+Describe contact details 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::AnnotationCollectionI;
+use vars qw(@ISA);
+use strict;
+
+# Interface preamble - inherits from Bio::Root::RootI
+
+use Bio::Root::RootI;
+
+@ISA = qw(Bio::Root::RootI);
+
+
+=head2 get_all_annotation_keys
+
+ Title   : get_all_annotation_keys
+ Usage   : $ac->get_all_annotation_keys()
+ Function: gives back a list of annotation keys, which are simple text strings
+ Returns : list of strings
+ Args    : none
+
+=cut
+
+sub get_all_annotation_keys{
+    shift->throw_not_implemented();
+}
+
+
+=head2 get_Annotations
+
+ Title   : get_Annotations
+ Usage   : my @annotations = $collection->get_Annotations('key')
+ Function: Retrieves all the Bio::AnnotationI objects for a specific key
+ Returns : list of Bio::AnnotationI - empty if no objects stored for a key
+ Args    : string which is key for annotations
+
+=cut
+
+sub get_Annotations{
+    shift->throw_not_implemented();    
+}
+
+=head2 get_num_of_annotations
+
+ Title   : get_num_of_annotations
+ Usage   : my $count = $collection->get_num_of_annotations()
+ Function: Returns the count of all annotations stored in this collection 
+ Returns : integer
+ Args    : none
+
+
+=cut
+
+sub get_num_of_annotations{
+    shift->throw_not_implemented();
+}
+
+1;