Bio::Annotation::StructuredValue - A scalar with embedded structured information use Bio::Annotation::StructuredValue; use Bio::Annotation::Collection; my $col = new Bio::Annotation::Collection; my $sv = new Bio::Annotation::StructuredValue(-value => 'someval'); $col->add_Annotation('tagname', $sv); Scalar value annotation object

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email bioperl-l@bio.perl.org Describe contact details here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $sv = new Bio::Annotation::StructuredValue; Function: Instantiate a new StructuredValue object Returns : Bio::Annotation::StructuredValue object Args : -value => $value to initialize the object data field [optional] -tagname => $tag to initialize the tagname [optional]

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

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

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)

value
Title : value Usage : $obj->value($newval) Function: Get/set the value for this annotation. Set mode is here only to retain compatibility with SimpleValue. It is equivalent to calling add_value([0], $newval). In get mode, this implementation allows to pass additional parameters that control how the structured annotation components will be joined together to form a string. Recognized are presently -joins a reference to an array of join strings, the elements at index i applying to joining annotations at dimension i. The last element will be re-used for dimensions higher than i. Defaults to ['; ']. -brackets a reference to an array of two strings denoting the opening and closing brackets for the elements of one dimension, if there is more than one element in the dimension. Defaults to ['(',')']. Returns : value of value Args : newvalue (optional)

get_values
Title : get_values Usage : Function: Get the top-level array of values. Each of the elements will recursively be a reference to an array or a scalar, depending on the depth of this structured value annotation. Example : Returns : an array Args : none

get_all_values
Title : get_all_values Usage : Function: Flattens all values in this structured annotation and returns them as an array. Example : Returns : the (flat) array of values Args : none

add_value
Title : add_value Usage : Function: Adds the given value to the structured annotation at the given index. The index is multi-dimensional, with the first dimension applying to the first level, and so forth. If a particular dimension or a particular index does not exist yet, it will be created. If it does exist and adding the value would mean replacing a scalar with an array reference, we throw an exception to prevent unintended damage. An index of -1 at any dimension means append. If an array of values is to be added, it will create an additional dimension at the index specified, unless the last index value is -1, in which case they will all be appended to the last dimension. Example : Returns : none Args : the index at which to add (a reference to an array) the value(s) to add