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

Uploaded

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+++ b/variant_effect_predictor/Bio/AnnotationI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: AnnotationI.pm,v 1.7 2002/10/22 07:38:24 lapp Exp $
+
+#
+# BioPerl module for Bio::AnnotationI
+#
+# 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::AnnotationI - Annotation interface
+
+=head1 SYNOPSIS
+
+  # generally you get AnnotationI's from AnnotationCollectionI's
+
+   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";
+          # you can also use a generic hash_tree method for getting 
+          # stuff out say into XML format
+          $hash_tree = $value->hash_tree();
+       }
+   } 
+
+
+=head1 DESCRIPTION
+
+Interface all annotations must support. There are two things that each
+annotation has to support.
+
+  $annotation->as_text()
+
+Annotations have to support an "as_text" method. This should be a
+single text string, without newlines representing the annotation,
+mainly for human readability. It is not aimed at being able to
+store/represent the annotation.
+
+The second method allows annotations to at least attempt to represent
+themselves as pure data for storage/display/whatever. The method
+hash_tree
+
+   $hash = $annotation->hash_tree();
+
+should return an anonymous hash with "XML-like" formatting. The
+formatting is as follows.
+
+  (1) For each key in the hash, if the value is a reference'd array -
+
+      (2) For each element of the array if the value is a object - 
+          Assumme the object has the method "hash_tree";
+      (3) else if the value is a referene to a hash
+          Recurse again from point (1)
+      (4) else 
+          Assumme the value is a scalar, and handle it directly as text
+
+   (5) else (if not an array) apply rules 2,3 and 4 to value
+
+The XML path in tags is represented by the keys taken in the
+hashes. When arrays are encountered they are all present in the path
+level of this tag
+
+This is a pretty "natural" representation of an object tree in an XML
+style, without forcing everything to inheriet off some super-generic
+interface for representing things in the hash.
+
+=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::AnnotationI;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use Bio::Root::RootI;
+
+
+@ISA = qw(Bio::Root::RootI);
+
+
+=head2 as_text
+
+ Title   : as_text
+ Usage   :
+ Function: single text string, without newlines representing the
+           annotation, mainly for human readability. It is not aimed
+           at being able to store/represent the annotation.
+ Example :
+ Returns : a string
+ Args    : none
+
+
+=cut
+
+sub as_text{
+    shift->throw_not_implemented();
+}
+
+=head2 hash_tree
+
+ Title   : hash_tree
+ Usage   :
+ Function: should return an anonymous hash with "XML-like" formatting
+ Example :
+ Returns : a hash reference
+ Args    : none
+
+
+=cut
+
+sub hash_tree{
+    shift->throw_not_implemented();
+}
+
+=head2 tagname
+
+ Title   : tagname
+ Usage   : $obj->tagname($newval)
+ Function: Get/set the tagname for this annotation value.
+
+           Setting this is optional. If set, it obviates the need to
+           provide a tag to Bio::AnnotationCollectionI when adding
+           this object. When obtaining an AnnotationI object from the
+           collection, the collection will set the value to the tag
+           under which it was stored unless the object has a tag
+           stored already.
+
+ Example : 
+ Returns : value of tagname (a scalar)
+ Args    : new value (a scalar, optional)
+
+
+=cut
+
+sub tagname{
+    shift->throw_not_implemented();
+}
+
+1;