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

[Hilmar Lapp]

What's the point of issuing a warning to the caller that what she just 
specifically asked for now indeed is going to happen?

Remember, the default is not to allow expansion - you have to 
specifically ask for it.

	-hilmar

On Wednesday, November 24, 2004, at 10:49  AM, 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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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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