Raw content of Bio::Annotation::Comment
<![CDATA[# $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 <birney@ebi.ac.uk>
#
# 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;
]]>