Christopher Fields > BioPerl-1.6.923 > Bio::Annotation::Target

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Source   Latest Release: BioPerl-1.6.924

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)

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