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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq