NAME

Bio::Annotation::StructuredValue - A scalar with embedded structured information

SYNOPSIS

   use Bio::Annotation::StructuredValue;
   use Bio::Annotation::Collection;

   my $col = Bio::Annotation::Collection->new();
   my $sv = Bio::Annotation::StructuredValue->new(-value => 'someval');
   $col->add_Annotation('tagname', $sv);

DESCRIPTION

Scalar value annotation object.

FEEDBACK

Mailing Lists

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

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 or the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Hilmar Lapp

Email hlapp-at-gmx.net

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 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]

AnnotationI implementing functions

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

display_text

 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_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)

Specific accessors for StructuredValue

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 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)

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