[ENSCORESW-448]. new overlap algorithm and better test cases. supports...

[ENSCORESW-448]. new overlap algorithm and better test cases. supports overlaps when you do not want to normalise WRT the backing slice

modules/Bio/EnsEMBL/Feature.pm

@@ -1367,10 +1367,13 @@ sub get_all_alt_locations {
   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.
+  Description: This method does a range comparison of this feature's C<seq_region_start> and
+               C<seq_region_end> and compares it with another feature's C<seq_region_start>
+               and C<seq_region_end>. It will return true if these ranges overlap 
+               and the features are on the same seq_region.
+
+               For local coordinate overlaps tests (those values returned from
+               start and end) use C<overlaps_local()>.
   Returntype : TRUE if features overlap, FALSE if they don't
   Exceptions : warning if features are on different seq_regions
   Caller     : general
@@ -1379,21 +1382,47 @@ sub get_all_alt_locations {
 =cut
 
 sub overlaps {
-  my $self = shift;
-  my $f = shift;
+  my ($self, $f) = @_;
+  my ($sr1, $sr2) = ($self->seq_region_name, $f->seq_region_name);
+  if($sr1 && $sr2 && ($sr1 ne $sr2)) {
+    warning("Bio::EnsEMBL::Feature->overlaps(): features are on different seq regions. \$self is on $sr1 and \$feature is on $sr2");
+    return 0;
+  }
+  return ($self->seq_region_end >= $f->seq_region_start and $self->seq_region_start <= $f->seq_region_end) ? 1 : 0;
+}
 
-  my $sr1_name = $self->seq_region_name;
-  my $sr2_name = $f->seq_region_name;
+=head2 overlaps_local
 
-  if ($sr1_name and $sr2_name and ($sr1_name ne $sr2_name)) {
-    warning("Bio::EnsEMBL::Feature->overlaps(): features are on different seq regions.");
-    return undef;
+  Arg [1]    : Bio::EnsEMBL::Feature $f
+               The other feature you want to check overlap with this feature
+               for.
+  Description: This method does a range comparison of this feature's start and
+               end and compares it with another feature's and end. It will 
+               return true if these ranges overlap and the features are 
+               on the same seq_region.
+
+               This method will not attempt to resolve starts and ends with 
+               reference to the feature's backing Slice.
+
+               For global coordinate overlaps tests (with reference to the feature's 
+               backing sequence region) use C<overlaps()>.
+  Returntype : TRUE if features overlap, FALSE if they don't
+  Exceptions : warning if features are on different seq_regions
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub overlaps_local {
+  my ($self, $f) = @_;
+  my ($sr1, $sr2) = ($self->seq_region_name, $f->seq_region_name);
+  if($sr1 && $sr2 && ($sr1 ne $sr2)) {
+    warning("Bio::EnsEMBL::Feature->overlaps_local(): features are on different seq regions. \$self is on $sr1 and \$feature is on $sr2");
+    return;
   }
-  
-  return ($self->seq_region_end >= $f->seq_region_start and $self->seq_region_start <= $f->seq_region_end);
+  return ($self->end >= $f->start and $self->start <= $f->end) ? 1 : 0;
 }
 
-
 =head2 get_overlapping_Genes
 
   Description: Get all the genes that overlap this feature.

modules/t/feature.t

@@ -463,6 +463,12 @@ my $chr_slice = $db->get_SliceAdaptor->fetch_by_region('chromosome',
 						       '20',
 						       30_249_935,
 						       31_000_000);
+my $all_chr_slice =  $db->get_SliceAdaptor->fetch_by_region('chromosome', 20);
+
+my $hap_chr_slice = $db->get_SliceAdaptor->fetch_by_region('chromosome',
+                   '20_HAP1',
+                   30_249_935,
+                   31_000_000);
 
 # my $sctg_slice  = $db->get_SliceAdaptor->fetch_by_region('supercontig',
 # 							 'NT_028392');
@@ -490,8 +496,8 @@ my $f2 = new Bio::EnsEMBL::Feature( -start => 10,
 # simple same coord system overlap
 #
 
-debug( "f1<->f2 overlap = ".($f1->overlaps( $f2 )));
-ok( $f1->overlaps( $f2 ));
+ok( $f1->overlaps( $f2 ), 'Overlaps: feature 1 <-> feature 2 overlap (1 ends @ 10. 2 starts @ 10)');
+ok( $f1->overlaps_local( $f2 ), 'Overlaps Local: feature 1 <-> feature 2 overlap (1 ends @ 10. 2 starts @ 10)');
 
 $f2 = new Bio::EnsEMBL::Feature( -start => 11,
 				 -end => 20,
@@ -500,10 +506,29 @@ $f2 = new Bio::EnsEMBL::Feature( -start => 11,
 				 -analysis => $analysis
 			       );
 
-ok( ! $f2->overlaps( $f1 ));
+ok( ! $f1->overlaps( $f2 ), 'Overlaps: feature 1 <-> new feature 2 do not overlap (1 ends @ 10. 2 starts @ 11)');
+ok( ! $f1->overlaps_local( $f2 ), 'Overlaps Local: feature 1 <-> feature 2 overlap (1 ends @ 10. 2 starts @ 10)');
 
+#
+# Testing when seq_region overlaps do not return true but local ones do
+#
+my $f1_absolute = Bio::EnsEMBL::Feature->new(-start => 30_249_935, -end => 30_249_945, -strand => 1, -slice => $all_chr_slice);
+ok($f1->overlaps($f1_absolute), 'Overlaps: feature 1 overlaps as both it and absolute feature are on the same chromsomal coordinate');
+ok(!$f1->overlaps_local($f1_absolute), 'Overlaps Local: feature 1 does not overlap absolute feature; their starts and ends are different');
 
+# 
+# Testing alternative seq region overlap
+#
+my $hap_feature_1 = Bio::EnsEMBL::Feature->new(-start => 1, -end => 10, -strand => 1, -slice => $hap_chr_slice);
+warns_like 
+  { ok( ! $hap_feature_1->overlaps( $f1 ), 'Overlaps: feature 1 <-> new feature 2 do not overlap (different seq regions)') }
+  qr/different seq regions/,
+  'Error when using different seq regions as expected';
 
+warns_like 
+  { ok( ! $hap_feature_1->overlaps_local( $f1 ), 'Overlaps Local: feature 1 <-> feature 2 overlap (different seq regions)') }
+  qr/different seq regions/,
+  'Error when using different seq regions as expected';
 
 #
 # test get_all_alt_locations