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

[Allen Day]

yeah, you're right.  i was thinking this was the default behaviour.

-allen

On Fri, 26 Nov 2004, Hilmar Lapp wrote:

> 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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