[Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.16, 1.17

[Steffen Grossmann]

As it is now, the expansion only takes place, when you explicitly say 
'EXPAND'. If you don't do this and try to add a feature, which is not 
contained, you get a warning

("$val is not contained within parent feature, ignoring.")

and nothing is added.


Allen Day wrote:

>i'd like a warning issued if the range expands.  i see expansion as a 
>convenience feature, and want to know when it happens because i don't 
>generally expect it.
>
>On Wed, 24 Nov 2004, Steffen Grossman wrote:
>
>  
>
>>Update of /home/repository/bioperl/bioperl-live/Bio/SeqFeature
>>In directory pub.open-bio.org:/tmp/cvs-serv19535
>>
>>Modified Files:
>>	Annotated.pm 
>>Log Message:
>>Added support for the 'EXPAND' option in 'add_SeqFeature'.
>>
>>
>>Index: Annotated.pm
>>===================================================================
>>RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Annotated.pm,v
>>retrieving revision 1.16
>>retrieving revision 1.17
>>diff -C2 -d -r1.16 -r1.17
>>*** Annotated.pm	24 Nov 2004 02:14:06 -0000	1.16
>>--- Annotated.pm	24 Nov 2004 16:31:59 -0000	1.17
>>***************
>>*** 604,617 ****
>>  =head2 add_SeqFeature()
>>  
>>!  Usage   : $obj->add_SeqFeature($feat);
>>!  Function: Returns : nothing
>>!  Args    : A Bio::SeqFeatureI object.  Objects not implementing Bio::SeqFeatureI
>>!            and those whose bounds are not within those of the called object are
>>!            ignored with a warning.
>>  
>>  =cut
>>  
>>  sub add_SeqFeature {
>>!   my ($self,$val) = @_;
>>  
>>    return undef unless $val;
>>--- 604,625 ----
>>  =head2 add_SeqFeature()
>>  
>>!  Usage   : $feat->add_SeqFeature($subfeat);
>>!            $feat->add_SeqFeature($subfeat,'EXPAND')
>>!  Function: adds a SeqFeature into the subSeqFeature array.
>>!            with no 'EXPAND' qualifer, subfeat will be tested
>>!            as to whether it lies inside the parent, and throw
>>!            an exception if not.
>>! 
>>!            If EXPAND is used, the parent''s start/end/strand will
>>!            be adjusted so that it grows to accommodate the new
>>!            subFeature
>>!  Example :
>>!  Returns : nothing
>>!  Args    : a Bio::SeqFeatureI object
>>  
>>  =cut
>>  
>>  sub add_SeqFeature {
>>!   my ($self,$val, $expand) = @_;
>>  
>>    return undef unless $val;
>>***************
>>*** 619,626 ****
>>    if ( !$val->isa('Bio::SeqFeatureI') ) {
>>      $self->warn("$val does not implement Bio::SeqFeatureI, ignoring.");
>>    }
>>  
>>!   if ( !$self->contains($val) ) {
>>!     $self->warn("$val is not contained within parent feature, ignoring.");
>>    }
>>  
>>--- 627,640 ----
>>    if ( !$val->isa('Bio::SeqFeatureI') ) {
>>      $self->warn("$val does not implement Bio::SeqFeatureI, ignoring.");
>>+     return undef;
>>    }
>>  
>>!   if($expand && ($expand eq 'EXPAND')) {
>>!       $self->_expand_region($val);
>>!   } else {
>>!       if ( !$self->contains($val) ) {
>>! 	  $self->warn("$val is not contained within parent feature, and expansion is not valid, ignoring.");
>>! 	  return undef;
>>!       }
>>    }
>>  
>>***************
>>*** 734,737 ****
>>--- 748,785 ----
>>    my ($self) = @_;
>>    return $self->{'targets'} ? @{ $self->{'targets'} } : ();
>>+ }
>>+ 
>>+ =head2 _expand_region
>>+ 
>>+  Title   : _expand_region
>>+  Usage   : $self->_expand_region($feature);
>>+  Function: Expand the total region covered by this feature to
>>+            accomodate for the given feature.
>>+ 
>>+            May be called whenever any kind of subfeature is added to this
>>+            feature. add_SeqFeature() already does this.
>>+  Returns : 
>>+  Args    : A Bio::SeqFeatureI implementing object.
>>+ 
>>+ 
>>+ =cut
>>+ 
>>+ sub _expand_region {
>>+     my ($self, $feat) = @_;
>>+     if(! $feat->isa('Bio::SeqFeatureI')) {
>>+         $self->warn("$feat does not implement Bio::SeqFeatureI");
>>+     }
>>+     # if this doesn't have start/end set - forget it!
>>+     if((! defined($self->start())) && (! defined $self->end())) {
>>+         $self->start($feat->start());
>>+         $self->end($feat->end());
>>+         $self->strand($feat->strand) unless defined($self->strand());
>>+ #        $self->strand($feat->strand) unless $self->strand();
>>+     } else {
>>+         my $range = $self->union($feat);
>>+         $self->start($range->start);
>>+         $self->end($range->end);
>>+         $self->strand($range->strand);
>>+     }
>>  }
>>  
>>
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>>
>>    
>>
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>


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