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Relation.pm
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Relation.pm
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# $Id: Relation.pm 14708 2008-06-10 00:08:17Z heikki $
#
# BioPerl module for Bio::Annotation::Relation
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by bioperl <bioperl-l@bioperl.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::Relation - Relationship (pairwise) with other objects SeqI and NodeI;
=head1 SYNOPSIS
use Bio::Annotation::Relation;
use Bio::Annotation::Collection;
my $col = Bio::Annotation::Collection->new();
my $sv = Bio::Annotation::Relation->new(-type => "paralogy" -to => "someSeqI");
$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://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Mira Han
Email mirhan@indiana.edu
=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::Relation;
use strict;
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::Root::Root Bio::AnnotationI);
=head2 new
Title : new
Usage : my $sv = Bio::Annotation::Relation->new();
Function: Instantiate a new Relation object
Returns : Bio::Annotation::Relation object
Args : -type => $type of relation [optional]
-to => $obj which $self is in relation to [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 = $class->SUPER::new(@args);
my ($type, $to, $tag, $term) =
$self->_rearrange([qw(TYPE TO TAGNAME TAG_TERM)], @args);
# set the term first
defined $term && $self->tag_term($term);
defined $type && $self->type($type);
defined $to && $self->to($to);
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 $self->type." to ".$self->to->id;
}
=head2 display_text
Title : display_text
Usage : my $str = $ann->display_text();
Function: returns a string. Unlike as_text(), this method returns a string
formatted as would be expected for te specific implementation.
One can pass a callback as an argument which allows custom text
generation; the callback is passed the current instance and any text
returned
Example :
Returns : a string
Args : [optional] callback
=cut
{
my $DEFAULT_CB = sub { return $_[0]->type." to ".$_[0]->to->id };
#my $DEFAULT_CB = sub { $_[0]->value};
sub display_text {
my ($self, $cb) = @_;
$cb ||= $DEFAULT_CB;
$self->throw("Callback must be a code reference") if ref $cb ne 'CODE';
return $cb->($self);
}
}
=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 = shift;
my $h = {};
$h->{'type'} = $self->type;
$h->{'to'} = $self->to;
return $h;
}
=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 Relation
=cut
=head2 type
Title : type
Usage : $obj->type($newval)
Function: Get/Set the type
Returns : type of relation
Args : newtype (optional)
=cut
sub type{
my ($self,$type) = @_;
if( defined $type) {
$self->{'type'} = $type;
}
return $self->{'type'};
}
=head2 to
Title : to
Usage : $obj->to($newval)
Function: Get/Set the object which $self is in relation to
Returns : the object which the relation applies to
Args : new target object (optional)
=cut
sub to{
my ($self,$to) = @_;
if( defined $to) {
$self->{'to'} = $to;
}
return $self->{'to'};
}
=head2 confidence
Title : confidence
Usage : $self->confidence($newval)
Function: Gives the confidence value.
Example :
Returns : value of confidence
Args : newvalue (optional)
=cut
sub confidence{
my ($self,$value) = @_;
if( defined $value) {
$self->{'confidence'} = $value;
}
return $self->{'confidence'};
}
=head2 confidence_type
Title : confidence_type
Usage : $self->confidence_type($newtype)
Function: Gives the confidence type.
Example :
Returns : type of confidence
Args : newtype (optional)
=cut
sub confidence_type{
my ($self,$type) = @_;
if( defined $type) {
$self->{'confidence_type'} = $type;
}
return $self->{'confidence_type'};
}
=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;