Bio::Annotation::SimpleValue - A simple scalar
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);
Scalar value annotation object
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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]
Title : as_text Usage : my $text = $obj->as_text Function: return the string "Value: $v" where $v is the value Returns : string Args : none
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
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
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)
Title : value Usage : $obj->value($newval) Function: Get/Set the value for simplevalue Returns : value of value Args : newvalue (optional)
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)