Bio::Annotation SimpleValue
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Annotation::SimpleValue - A simple scalar
Package variables
Privates (from "my" definitions)
$DEFAULT_CB = sub { $_[0]->value}
Inherit
Bio::AnnotationI Bio::Root::Root
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);
Description
Scalar value annotation object
Methods
newDescriptionCode
as_textDescriptionCode
display_textDescriptionCode
hash_treeDescriptionCode
tagnameDescriptionCode
valueDescriptionCode
tag_termDescriptionCode
Methods description
newcode    nextTop
 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]
as_textcodeprevnextTop
 Title   : as_text
 Usage   : my $text = $obj->as_text
 Function: return the string "Value: $v" where $v is the value
 Returns : string
 Args    : none
display_textcodeprevnextTop
 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
hash_treecodeprevnextTop
 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
tagnamecodeprevnextTop
 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)
valuecodeprevnextTop
 Title   : value
 Usage   : $obj->value($newval)
 Function: Get/Set the value for simplevalue
 Returns : value of value
 Args    : newvalue (optional)
tag_termcodeprevnextTop
 Title   : tag_term
 Usage   : $obj->tag_term($newval)
 Function: Get/set the 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 Bio::Ontology::TermI compliant object, or undef
 Args    : on set, new value (a Bio::Ontology::TermI compliant
           object or undef, optional)
Methods code
newdescriptionprevnextTop
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 $self;
}
as_textdescriptionprevnextTop
sub as_text {
   my ($self) = @_;

   return "Value: ".$self->value;
}
display_textdescriptionprevnextTop
sub display_text {
    my ($self, $cb) = @_;
    $cb ||= $DEFAULT_CB;
    $self->throw("Callback must be a code reference") if ref $cb ne 'CODE';
    return $cb->($self);
  }
}
hash_treedescriptionprevnextTop
sub hash_tree {
    my $self = shift;

    my $h = {};
    $h->{'value'} = $self->value;
    return $h;
}
tagnamedescriptionprevnextTop
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 $self->{'tagname'};
}
valuedescriptionprevnextTop
sub value {
   my ($self,$value) = @_;

   if( defined $value) {
      $self->{'value'} = $value;
    }
    return $self->{'value'};
}
tag_termdescriptionprevnextTop
sub tag_term {
    my $self = shift;

    return $self->{'_tag_term'} = shift if @_;
    return $self->{'_tag_term'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Reporting BugsTop
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/
AUTHOR - Ewan Birney Top
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
AnnotationI implementing functionsTop
Specific accessors for SimpleValueTop