Commit 9edf71c8 authored by Patrick Meidl's avatar Patrick Meidl
Browse files

added check for same seq_region to overlaps(), now method is no longer deprectated

parent fad9b099
......@@ -1038,6 +1038,35 @@ sub get_all_alt_locations {
}
=head2 overlaps
Arg [1] : Bio::EnsEMBL::Feature $f
The other feature you want to check overlap with this feature
for.
Description: This method does a range comparison of this features start and
end and compares it with another features start and end. It will
return true if these ranges overlap and the features are on the
same seq_region.
Returntype : TRUE if features overlap, FALSE if they don't
Exceptions : warning if features are on different seq_regions
Caller : general
Status : At Risk
=cut
sub overlaps {
my $self = shift;
my $f = shift;
unless ($self->slice->seq_region_name eq $f->slice->seq_region_name) {
warning("Bio::EnsEMBL::Feature->overlaps(): features are on different seq_regions.");
return undef;
}
return ($self->end >= $f->start and $self->start <= $f->end);
}
##############################################
......@@ -1157,24 +1186,4 @@ sub id {
}
=head2 overlaps
Description: This method is only for backwards compatibility and should not
be used. It does a range comparison of this features start and
and and compares it with another features start and end. It
Will return true if these ranges overlap but even if these
features are on different sequence regions! Do yourself a
favour and use a simple one line comparison instead:
$overlaps = ($f1->end() >= $f2->start() &&
$f1->start() <= $f2->end());
Status : At Risk
=cut
sub overlaps {
my $self = shift;
my $f = shift;
return ($self->end() >= $f->start() && $self->start() <= $f->end());
}
1;
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