debian man page for bio::annotation::target

Bio::Annotation::Target(3pm)				User Contributed Perl Documentation			      Bio::Annotation::Target(3pm)

NAME
       Bio::Annotation::Target - Provides an object which represents a target (ie, a similarity hit) from one object to something in another
       database

SYNOPSIS
	  $target1 = Bio::Annotation::Target->new(-target_id  => 'F321966.1',
						 -start      => 1,
						 -end	     => 200,
						 -strand     => 1,   # or -1
						);

	  # or

	  $target2 = Bio::Annotation::Target->new();
	  $target2->target_id('Q75IM5');
	  $target2->start(7);
	  # ... etc ...

	  # Target is-a Bio::AnnotationI object, can be added to annotation
	  # collections, e.g. the one on features or seqs
	  $feat->annotation->add_Annotation('Target', $target2);

DESCRIPTION
       Provides an object which represents a target (ie, a similarity hit) from one object to something in another database without prescribing
       what is in the other database

AUTHOR - Scott Cain
       Scott Cain - cain@cshl.org

APPENDIX
       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

AnnotationI implementing functions
   as_text
	Title	: as_text
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   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

   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 Bio::AnnotationCollectionI when adding
		  this object. When obtaining an AnnotationI object from the
		  collection, the collection will set the value to the tag
		  under which it was stored unless the object has a tag
		  stored already.

	Example :
	Returns : value of tagname (a scalar)
	Args	: new value (a scalar, optional)

Specific accessors for Targets
   target_id
       Usage
	     $obj->target_id()	      #get existing value
	     $obj->target_id($newval) #set new value

       Function
       Returns
	   value of target_id (a scalar)

       Arguments
	   new value of target_id (to set)

perl v5.14.2							    2012-03-02					      Bio::Annotation::Target(3pm)