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Bio::Annotation::RelatUser3Contributed Perl DocumeBio::Annotation::Relation(3)

NAME
       Bio::Annotation::Relation - Relationship	(pairwise) with	other objects
       SeqI and	NodeI;

SYNOPSIS
	  use Bio::Annotation::Relation;
	  use Bio::Annotation::Collection;

	  my $col = Bio::Annotation::Collection->new();
	  my $sv = Bio::Annotation::Relation->new(-type	=> "paralogy" -to => "someSeqI");
	  $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	the
       web:

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

AUTHOR	- Mira Han
       Email mirhan@indiana.edu

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::Relation->new();
	Function: Instantiate a	new Relation object
	Returns	: Bio::Annotation::Relation object
	Args	: -type	   => $type of relation	[optional]
		  -to	  => $obj which	$self is in relation to	[optional]
		  -tagname  => $tag to initialize the tagname [optional]
		  -tag_term => ontology	term representation of the tag [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 Relation
   type
	Title	: type
	Usage	: $obj->type($newval)
	Function: Get/Set the type
	Returns	: type of relation
	Args	: newtype (optional)

   to
	Title	: to
	Usage	: $obj->to($newval)
	Function: Get/Set the object which $self is in relation	to
	Returns	: the object which the relation	applies	to
	Args	: new target object (optional)

   confidence
	Title	: confidence
	Usage	: $self->confidence($newval)
	Function: Gives	the confidence value.
	Example	:
	Returns	: value	of confidence
	Args	: newvalue (optional)

   confidence_type
	Title	: confidence_type
	Usage	: $self->confidence_type($newtype)
	Function: Gives	the confidence type.
	Example	:
	Returns	: type of confidence
	Args	: newtype (optional)

   tag_term
	Title	: tag_term
	Usage	: $obj->tag_term($newval)
	Function: Get/set the L<Bio::Ontology::TermI> object representing
		  the tag name.

		  This is so you can specifically relate the tag of this
		  annotation to	an entry in an ontology. You may want to do
		  this to associate an identifier with the tag,	or a
		  particular category, such that you can better	match the tag
		  against a controlled vocabulary.

		  This accessor	will return undef if it	has never been set
		  before in order to allow this	annotation to stay
		  light-weight if an ontology term representation of the tag
		  is not needed. Once it is set	to a valid value, tagname()
		  will actually	delegate to the	name() of this term.

	Example	:
	Returns	: a L<Bio::Ontology::TermI> compliant object, or undef
	Args	: on set, new value (a L<Bio::Ontology::TermI> compliant
		  object or undef, optional)

perl v5.32.0			  2019-12-07	  Bio::Annotation::Relation(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Mira Han | APPENDIX | AnnotationI implementing functions | Specific accessors for Relation

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