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Summary

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

Package variables

Inherit

Bio::AnnotationI Bio::Range Bio::Root::Root

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

Methods

Methods description

 Title   : as_text
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

 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

 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)

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

  my ($target_id, $tstart, $tend, $tstrand) =
      $self->_rearrange([ qw(
                              TARGET_ID
                              START
                              END
                              STRAND ) ], @args);

  $target_id    && $self->target_id($target_id);
  $tstart       && $self->start($tstart);
  $tend         && $self->end($tend);
  $tstrand      && $self->strand($tstrand);

  return $self;

}

sub as_text {

  my ($self) = @_;

  my $target = $self->target_id || '';
  my $start  = $self->start     || '';
  my $end    = $self->end       || '';
  my $strand = $self->strand    || '';

   return "Target=".$target." ".$start." ".$end." ".$strand;

}

sub display_text {

    my ($self, $cb) = @_;
    $cb ||= $DEFAULT_CB;
    $self->throw("Callback must be a code reference") if ref $cb ne 'CODE';
    return $cb->($self);
  }

}

sub tagname {

    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'tagname'} = $value;
    }
    return $self->{'tagname'};

}

sub target_id {

    my $self = shift;
    return $self->{'target_id'} = shift if defined($_[0]);
    return $self->{'target_id'};
}

1;

}

General documentation

Scott Cain - cain@cshl.org

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