Raw content of Bio::Annotation::SimpleValue
<![CDATA[# $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 <bioperl-l@bio.perl.org>
#
# 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.
bioperl-l@bioperl.org - 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:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - bioperl
Email bioperl-l@bio.perl.org
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;
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