Bio::Annotation::StructuredValue.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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 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