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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Annotation/SimpleValue.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,237 @@
+# $Id: SimpleValue.pm,v 1.9.2.1 2003/03/10 22:04:56 lapp Exp $
+#
+# BioPerl module for Bio::Annotation::SimpleValue
+#
+# Cared for by bioperl <[e-mail]>
+#
+# Copyright bioperl
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Annotation::SimpleValue - A simple scalar 
+
+=head1 SYNOPSIS
+
+   use Bio::Annotation::SimpleValue;
+   use Bio::Annotation::Collection;
+
+   my $col = new Bio::Annotation::Collection;
+   my $sv = new Bio::Annotation::SimpleValue(-value => 'someval');   
+   $col->add_Annotation('tagname', $sv);
+
+=head1 DESCRIPTION
+
+Scalar value annotation object 
+
+=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://bio.perl.org/MailList.html  - 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 - bioperl
+
+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::Annotation::SimpleValue;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use Bio::AnnotationI;
+#use Bio::Ontology::TermI;
+use Bio::Root::Root;
+
+@ISA = qw(Bio::Root::Root Bio::AnnotationI);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $sv = new Bio::Annotation::SimpleValue;
+ Function: Instantiate a new SimpleValue object
+ Returns : Bio::Annotation::SimpleValue object
+ Args    : -value    => $value to initialize the object data field [optional]
+           -tagname  => $tag to initialize the tagname [optional]
+           -tag_term => ontology term representation of the tag [optional]
+
+=cut
+
+sub new{
+   my ($class,@args) = @_;
+
+   my $self = $class->SUPER::new(@args);
+
+   my ($value,$tag,$term) =
+       $self->_rearrange([qw(VALUE TAGNAME TAG_TERM)], @args);
+
+   # set the term first
+   defined $term   && $self->tag_term($term);
+   defined $value  && $self->value($value);
+   defined $tag    && $self->tagname($tag);
+
+   return $self;
+}
+
+
+=head1 AnnotationI implementing functions
+
+=cut
+
+=head2 as_text
+
+ Title   : as_text
+ Usage   : my $text = $obj->as_text
+ Function: return the string "Value: $v" where $v is the value 
+ Returns : string
+ Args    : none
+
+
+=cut
+
+sub as_text{
+   my ($self) = @_;
+
+   return "Value: ".$self->value;
+}
+
+=head2 hash_tree
+
+ Title   : hash_tree
+ Usage   : my $hashtree = $value->hash_tree
+ Function: For supporting the AnnotationI interface just returns the value
+           as a hashref with the key 'value' pointing to the value
+ Returns : hashrf
+ Args    : none
+
+
+=cut
+
+sub hash_tree{
+   my ($self) = @_;
+   
+   my $h = {};
+   $h->{'value'} = $self->value;
+}
+
+=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 AnnotationCollection when adding this
+           object.
+
+ Example : 
+ Returns : value of tagname (a scalar)
+ Args    : new value (a scalar, optional)
+
+
+=cut
+
+sub tagname{
+    my $self = shift;
+
+    # check for presence of an ontology term
+    if($self->{'_tag_term'}) {
+	# keep a copy in case the term is removed later
+	$self->{'tagname'} = $_[0] if @_;
+	# delegate to the ontology term object
+	return $self->tag_term->name(@_);
+    }
+    return $self->{'tagname'} = shift if @_;
+    return $self->{'tagname'};
+}
+
+
+=head1 Specific accessors for SimpleValue
+
+=cut
+
+=head2 value
+
+ Title   : value
+ Usage   : $obj->value($newval)
+ Function: Get/Set the value for simplevalue
+ Returns : value of value
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub value{
+   my ($self,$value) = @_;
+   
+   if( defined $value) {
+      $self->{'value'} = $value;
+    }
+    return $self->{'value'};
+}
+
+=head2 tag_term
+
+ Title   : tag_term
+ Usage   : $obj->tag_term($newval)
+ Function: Get/set the L<Bio::Ontology::TermI> object representing
+           the tag name.
+
+           This is so you can specifically relate the tag of this
+           annotation to an entry in an ontology. You may want to do
+           this to associate an identifier with the tag, or a
+           particular category, such that you can better match the tag
+           against a controlled vocabulary.
+
+           This accessor will return undef if it has never been set
+           before in order to allow this annotation to stay
+           light-weight if an ontology term representation of the tag
+           is not needed. Once it is set to a valid value, tagname()
+           will actually delegate to the name() of this term.
+
+ Example : 
+ Returns : a L<Bio::Ontology::TermI> compliant object, or undef
+ Args    : on set, new value (a L<Bio::Ontology::TermI> compliant
+           object or undef, optional)
+
+
+=cut
+
+sub tag_term{
+    my $self = shift;
+
+    return $self->{'_tag_term'} = shift if @_;
+    return $self->{'_tag_term'};
+}
+
+1;