handle features that only have seqnames (and no slices!)

modules/Bio/EnsEMBL/Feature.pm

@@ -792,9 +792,11 @@ sub seq {
   Example    : if( $this_feature->overlaps( $otherfeature ) ...
   Description: Test if two features overlap. Strandedness is ignored. Both features have
                to have slices. If they are not on the same coordinate system they need
-               as well database connection.
-  Returntype : boolean 0,1
-  Exceptions : on no slices, wrong argument type, more if not on same coord_system
+               as well database connection. Calculates how many bases overlap.
+               There is some backward compatibility for unsliced features built in here.
+               Its worth checking once a while wether this can go.
+  Returntype : int
+  Exceptions : wrong argument type, if not on same coord_system
   Caller     : general
 
 =cut
@@ -803,41 +805,63 @@ sub overlaps {
   my $self = shift;
   my $feature = shift;
 
-  if( ! $feature->isa( "Bio::EnsEMBL::Feature" )) {
-    throw( "Need a Bio::EnsEMBL::Feature as argument" );
+  my ( $sstart, $astart, $send, $aend, $sname, $aname );
+  my ( $scoordsystem, $acoordsystem, $overlap );
+
+  if( defined $self->{'slice'} ) {
+    $sname = $self->seq_region_name();
+    $sstart = $self->seq_region_start();
+    $send = $self->seq_region_end();
+    $scoordsystem = $self->slice->coord_system();
+  } else {
+    $sname = $self->seqname();
+    $sstart = $self->start();
+    $send = $self->end();
   }
 
-  if( ! defined $self->slice() || ! defined $feature->slice() ) {
-    throw( "Features need to contain slices to support overlaps" );
+  if( defined $feature->{'slice'} ) {
+    $aname = $feature->seq_region_name();
+    $astart = $feature->seq_region_start();
+    $aend = $feature->seq_region_end();
+    $acoordsystem = $feature->slice()->coord_system();
+  } else {
+    $aname = $feature->seqname();
+    $astart = $feature->start();
+    $aend = $feature->end();
   }
 
 
-  if( $self->slice()->coord_system()->equals
-      ( $feature->slice()->coord_system())) {
-    if( $self->seq_region_name() eq $feature->seq_region_name() ) {
-      if( $feature->seq_region_start() <= $self->seq_region_end() &&
-	  $self->seq_region_start() <= $feature->seq_region_end() ) {
-	return 1;
-      } else {
-	return 0;
-      }
-    } else {
-      return 0;
-    }
+  # simple case
+  if( $sname eq $aname ) {
+    $overlap = (($send>$aend) ? $aend : $send ) - 
+      (($sstart>$astart) ? $sstart : $astart ) +1;
+    if( $overlap < 0 ) { $overlap = 0;}
+    return $overlap;
   }
 
-  # not same coord system
-  # have to project
-  my $projection = $self->project( $feature->slice()->coord_system()->name(),
-				   $feature->slice()->coord_system()->version());
-  for my $proj ( @$projection ) {
-    my $slice=$proj->[2];
-    if( $slice->seq_region_name() eq $feature->seq_region_name() &&
-	$slice->start() <= $feature->seq_region_end() &&
-	$feature->seq_region_start() <= $slice->end() ) {
-      return 1;
-    }
+  # full feature case
+  # if both have coord systems
 
+  if( defined $scoordsystem && defined $acoordsystem ) {
+    if( $scoordsystem->equals( $acoordsystem )) {
+      # they are really not on the same sequence
+      return 0;
+    } else {
+      my $projection = $self->project( $feature->slice()->coord_system()->name(),
+				       $feature->slice()->coord_system()->version());
+      my $total_overlap = 0;
+      for my $proj ( @$projection ) {
+	my $slice=$proj->[2];
+	if( $slice->seq_region_name() eq $feature->seq_region_name()) {
+	  $overlap = (($slice->end()>$aend) ? $aend : $slice->end() ) - 
+	    (($slice->start()>$astart) ? $slice->start() : $astart ) +1;
+	  if( $overlap < 0 ) { $overlap = 0;}
+	  $total_overlap += $overlap;
+	}
+      }
+      return $total_overlap;
+    }
+  } else {
     return 0;
   }
 }