Bio::Annotation::StructuredValue - A scalar with embedded structured information
my $col = Bio::Annotation::Collection->new();
my $sv = Bio::Annotation::StructuredValue->new(-value => 'someval');
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::StructuredValue->new();
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]
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
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.
Returns : value of tagname (a scalar)
Args : new value (a scalar, optional)
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
In get mode, this implementation allows one 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)
Title : get_values
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.
Returns : an array
Args : none
Title : get_all_values
Function: Flattens all values in this structured annotation and
returns them as an array.
Returns : the (flat) array of values
Args : none
Title : add_value
Function: Adds the given value to the structured annotation at the
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.
Returns : none
Args : the index at which to add (a reference to an array)
the value(s) to add