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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:

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

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)

   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 v5.14.1			  2011-07-22	  Bio::Annotation::Relation(3)
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