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AMEN: v.1.1.2 released, four changes & three bugs fixed !
07-25-2008
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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)