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Bio::Annotation::StrucUserdContributed PerlBio::Annotation::StructuredValue(3)

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

perl v5.32.0			  2019-12-0Bio::Annotation::StructuredValue(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Hilmar Lapp | APPENDIX | AnnotationI implementing functions | Specific accessors for StructuredValue

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