SimpleValue.pm

class Bio::Annotation::SimpleValue {
# Object preamble - inherits from Bio::Root::Root
#use Bio::Ontology::TermI;
#use base qw(Bio::Root::Root Bio::AnnotationI);

# =head2 new

#  Title   : new
#  Usage   : my $sv = Bio::Annotation::SimpleValue->new();
#  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


# =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

method as_text() {
    return "Value: " ~ self.value;
}

# =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 $DEFAULT_CB = sub ($self) { $self.value() };

method display_text($cb? is copy) {
    $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

# method hash_tree{
#     my $self = shift;

#     my $h = {};
#     $h->{'value'} = $self->value;
#     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

has $!tagname is rw;    
method tagname($value?){
    # check for presence of an ontology term
     if ($!tag_term) {
 	# keep a copy in case the term is removed later
 	$!tagname = $value if $value;
 	# delegate to the ontology term object
 	return self.tag_term.name($value);
    }
    $!tagname = $value if $value;
    return $!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

has $!value is rw;

method value($value?){
    if ( defined $value) {
        $!value = $value;
    }
    return $!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

has $!tag_term is rw;
method tag_term($value?){
    if ( defined $value) {
        $!tag_term = $value;
    }
    return $!tag_term;
}

}


# $Id: SimpleValue.pm 16123 2009-09-17 12:57:27Z cjfields $
#
# BioPerl module for Bio::Annotation::SimpleValue
# 
# 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::SimpleValue - A simple scalar

# =head1 SYNOPSIS

#    use Bio::Annotation::SimpleValue;
#    use Bio::Annotation::Collection;

#    my $col = Bio::Annotation::Collection->new();
#    my $sv = Bio::Annotation::SimpleValue->new(-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://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:

#   http://bugzilla.open-bio.org/

# =head1 AUTHOR  - Ewan Birney 

# Email birney@ebi.ac.uk

# =head1 APPENDIX

# The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

# =cut