Bio::Annotation::TargeUser Contributed Perl DocumentBio::Annotation::Target(3)NAMEBio::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 v5.14.1 2011-07-22 Bio::Annotation::Target(3)
