revert, should be on new seqstore

modules/Bio/EnsEMBL/Mapper.pm

@@ -149,91 +149,70 @@ sub map_coordinates{
    my $last_used_pair;
    my @result;
 
-   my ( $start_idx, $end_idx, $mid_idx, $pair, $self_coord );
-   my $lr = $hash->{uc($id)};
-   
-   $start_idx = 0;
-   $end_idx = $#$lr;
-   
-   # binary search the relevant pairs
-   # helps if the list is big
-   while(( $end_idx - $start_idx ) <= 1 ) {
-     $mid_idx = ($start_idx+$end_idx)>>1;
-     $pair = $lr->[$mid_idx];
-     $self_coord   = $pair->{$from};
-     if( $self_coord->{'end'} < $start ) {
-       $start_idx = $mid_idx;
-     } else {
-       $end_idx = $mid_idx;
-     }
-   }
+   foreach my $pair ( @{$hash->{uc($id)}} ) {
+       my $self_coord   = $pair->{$from};
+       my $target_coord = $pair->{$to};
 
-   my $i = $start_idx;
-   for( my $i = $start_idx; $i<=$#$lr; $i++ ) {
-     $pair = $lr->[$i];
-     my $self_coord   = $pair->{$from};
-     my $target_coord = $pair->{$to};
+       # if we haven't even reached the start, move on
+       if( $self_coord->{'end'} < $start ) {
+	   next;
+       }
 
-     # if we haven't even reached the start, move on
-     if( $self_coord->{'end'} < $start ) {
-       next;
-     }
-     
-     # if we have over run, break
-     if( $self_coord->{'start'} > $end ) {
-       last;
-     }
+       # if we have over run, break
+       if( $self_coord->{'start'} > $end ) {
+	   last;
+       }
 
-     if( $start < $self_coord->{'start'} ) {
-       # gap detected
-       my $gap = Bio::EnsEMBL::Mapper::Gap->new($start, 
-                                                $self_coord->{'start'}-1);
-       
-       push(@result,$gap);
-       $start = $gap->{'end'}+1;
-     }
-     
-     my ($target_start,$target_end,$target_ori);
-     
-     # start is somewhere inside the region
-     if( $pair->{'ori'} == 1 ) {
-       $target_start = 
-	   $target_coord->{'start'} + ($start - $self_coord->{'start'});
-     } else {
-       $target_end = 
-	   $target_coord->{'end'} - ($start - $self_coord->{'start'});
-     }
-     
-     # either we are enveloping this map or not. If yes, then end
-     # point (self perspective) is determined solely by target. If not
-     # we need to adjust
+       if( $start < $self_coord->{'start'} ) {
+	   # gap detected
+	   my $gap = Bio::EnsEMBL::Mapper::Gap->new($start, 
+						    $self_coord->{'start'}-1);
+	
+	   push(@result,$gap);
+           $start = $gap->{'end'}+1;
+       }
+
+       my ($target_start,$target_end,$target_ori);
 
-     if( $end > $self_coord->{'end'} ) {
-       # enveloped
+       # start is somewhere inside the region
        if( $pair->{'ori'} == 1 ) {
-         $target_end = $target_coord->{'end'};
+	 $target_start = 
+	   $target_coord->{'start'} + ($start - $self_coord->{'start'});
        } else {
-         $target_start = $target_coord->{'start'};
+	 $target_end = 
+	   $target_coord->{'end'} - ($start - $self_coord->{'start'});
        }
-     } else {
-       # need to adjust end
-       if( $pair->{'ori'} == 1 ) {
-         $target_end = 
-             $target_coord->{'start'} + ($end - $self_coord->{'start'});
+
+       # either we are enveloping this map or not. If yes, then end
+       # point (self perspective) is determined solely by target. If not
+       # we need to adjust
+
+       if( $end > $self_coord->{'end'} ) {
+	   # enveloped
+	   if( $pair->{'ori'} == 1 ) {
+	       $target_end = $target_coord->{'end'};
+	   } else {
+	       $target_start = $target_coord->{'start'};
+	   }
        } else {
-         $target_start = 
-             $target_coord->{'end'} - ($end - $self_coord->{'start'});
+	   # need to adjust end
+	   if( $pair->{'ori'} == 1 ) {
+	     $target_end = 
+	       $target_coord->{'start'} + ($end - $self_coord->{'start'});
+	   } else {
+	     $target_start = 
+	       $target_coord->{'end'} - ($end - $self_coord->{'start'});
+	   }
        }
-     }
 
-     my $res = Bio::EnsEMBL::Mapper::Coordinate->new($target_coord->{'id'},
+       my $res = Bio::EnsEMBL::Mapper::Coordinate->new($target_coord->{'id'},
 						     $target_start,
 						     $target_end,
 						     $pair->{'ori'} * $strand);
-     push(@result,$res);
-     
-     $last_used_pair = $pair;
-     $start = $self_coord->{'end'}+1;
+       push(@result,$res);
+
+       $last_used_pair = $pair;
+       $start = $self_coord->{'end'}+1;
    }
 
    if( !defined $last_used_pair ) {