Bio::Annotation SimpleValue
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Summary
Bio::Annotation::SimpleValue - A simple scalar
Package variables
No package variables defined.
Included modules
Bio::AnnotationI
Bio::Root::Root
Inherit
Bio::AnnotationI Bio::Root::Root
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);
Description
Scalar value annotation object
Methods
as_textDescriptionCode
hash_treeDescriptionCode
newDescriptionCode
tag_termDescriptionCode
tagnameDescriptionCode
valueDescriptionCode
Methods description
as_textcode    nextTop
 Title   : as_text
Usage : my $text = $obj->as_text
Function: return the string "Value: $v" where $v is the value
Returns : string
Args : none
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
newcodeprevnextTop
 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]
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)
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)
Methods code
as_textdescriptionprevnextTop
sub as_text {
   my ($self) = @_;

   return "Value: ".$self->value;
}
hash_treedescriptionprevnextTop
sub hash_tree {
   my ($self) = @_;
   
   my $h = {};
   $h->{'value'} = $self->value;
}
newdescriptionprevnextTop
sub new {
   my ($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;
}
tag_termdescriptionprevnextTop
sub tag_term {
    my $self = shift;

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

1;
}
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'};
}
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://bio.perl.org/MailList.html - 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 email
or the web:
  bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
AUTHOR - bioperlTop
Email bioperl-l@bio.perl.org
Describe contact details here
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