diff variant_effect_predictor/Bio/Annotation/Comment.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Annotation/Comment.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,176 @@
+# $Id: Comment.pm,v 1.8 2002/09/25 18:11:33 lapp Exp $
+#
+# BioPerl module for Bio::Annotation::Comment
+#
+# 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::Annotation::Comment - A comment object, holding text
+
+=head1 SYNOPSIS
+
+
+    $comment = Bio::Annotation::Comment->new();
+    $comment->text("This is the text of this comment");
+    $annotation->add_Annotation('comment', $comment);
+
+
+=head1 DESCRIPTION
+
+A holder for comments in annotations, just plain text. This is a very simple
+object, and justifiably so.
+
+=head1 CONTACT
+
+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::Annotation::Comment;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::AnnotationI;
+
+@ISA = qw(Bio::Root::Root Bio::AnnotationI);
+
+=head2 new
+
+ Title   : new
+ Usage   : $comment = Bio::Annotation::Comment->new( '-text' => 'some text for this comment');
+ Function: This returns a new comment object, optionally with
+           text filed
+ Example :
+ Returns : a Bio::Annotation::Comment object
+ Args    : a hash with -text optionally set
+
+
+=cut
+
+
+sub new {
+  my($class,@args) = @_;
+
+  my $self = $class->SUPER::new(@args);
+  my ($text,$tag) = $self->_rearrange([qw(TEXT TAGNAME)], @args);
+
+  defined $text && $self->text($text);
+  defined $tag && $self->tagname($tag);
+
+  return $self;
+}
+
+=head1 AnnotationI implementing functions
+
+=cut
+
+=head2 as_text
+
+ Title   : as_text
+ Usage   :
+ Function:
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub as_text{
+   my ($self) = @_;
+
+   return "Comment: ".$self->text;
+}
+
+=head2 hash_tree
+
+ Title   : hash_tree
+ Usage   :
+ Function:
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub hash_tree{
+   my ($self) = @_;
+   
+   my $h = {};
+   $h->{'text'} = $self->text;
+}
+
+=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{
+    my ($self,$value) = @_;
+    if( defined $value) {
+	$self->{'tagname'} = $value;
+    }
+    return $self->{'tagname'};
+}
+
+=head1 Specific accessors for Comments
+
+=cut
+
+
+=head2 text
+
+ Title   : text
+ Usage   : $value = $self->text($newval)
+ Function: get/set for the text field. A comment object
+           just holds a single string which is accessible through
+           this method
+ Example : 
+ Returns : value of text
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub text{
+   my ($self,$value) = @_;
+   if( defined $value) {
+      $self->{'text'} = $value;
+    }
+    return $self->{'text'};
+
+}
+
+
+
+1;