Code tidy in AssemblyExceptionFeatureAdaptor

modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm

@@ -286,7 +286,6 @@ sub _remap {
                     $features->[0]->slice == $slice)) {
     return $features;
   }
-
   # remapping has not been done, we have to do our own conversion from
   # to slice coords
 
@@ -333,14 +332,6 @@ sub _remap {
     # create new copies of successfully mapped feaatures with shifted start,
     # end and strand
     my ($new_start, $new_end);
-    # if($slice_strand == -1) {
-    #   $new_start = $slice_end - $end + 1;
-    #   $new_end = $slice_end - $start + 1;
-    # } else {
-    #   $new_start = $start - $slice_start + 1;
-    #   $new_end = $end - $slice_start + 1;
-    # }
-    
     my $seq_region_len = $slice->seq_region_length();
 
     if ($slice_strand == 1) { # Positive strand
@@ -349,92 +340,75 @@ sub _remap {
       $new_end   = $end - $slice_start + 1;
 
       if ($slice->is_circular()) {
-	# Handle circular chromosomes.
-
-	if ($new_start > $new_end) {
-	  # Looking at a feature overlapping the chromsome origin.
-
-	  if ($new_end > $slice_start) {
-
-	    # Looking at the region in the beginning of the
-	    # chromosome.
-	    $new_start -= $seq_region_len;
-	  }
-
-	  if ($new_end < 0) {
-	    $new_end += $seq_region_len;
-	  }
-
-	} else {
-
-	  if (   $slice_start > $slice_end
-		 && $new_end < 0) {
-	    # Looking at the region overlapping the chromosome
-	    # origin and a feature which is at the beginning of the
-	    # chromosome.
-	    $new_start += $seq_region_len;
-	    $new_end   += $seq_region_len;
-	  }
-	}
-
-      }			       ## end if ($dest_slice->is_circular...)
-
-    } else {			# Negative strand
+        # Handle circular chromosomes.
+
+        if ($new_start > $new_end) {
+    	  # Looking at a feature overlapping the chromsome origin.
+          if ($new_end > $slice_start) {
+            # Looking at the region in the beginning of the chromosome.
+            $new_start -= $seq_region_len;
+          }
+          if ($new_end < 0) {
+            $new_end += $seq_region_len;
+          }
+        } else {
+          if (   $slice_start > $slice_end && $new_end < 0) {
+            # Looking at the region overlapping the chromosome
+            # origin and a feature which is at the beginning of the
+            # chromosome.
+            $new_start += $seq_region_len;
+            $new_end   += $seq_region_len;
+          }
+        }
+      }   ## end if ($dest_slice->is_circular...)
+    } else {  # Negative strand
 
       my $new_start = $slice_end - $end + 1;
       my $new_end = $slice_end - $start + 1;
 
       if ($slice->is_circular()) {
 
-	if ($slice_start > $slice_end) { 
-	  # slice spans origin or replication
-
-	  if ($start >= $slice_start) {
-	    $new_end += $seq_region_len;
-	    $new_start += $seq_region_len 
-	      if $end > $slice_start;
+        if ($slice_start > $slice_end) { 
+        # slice spans origin or replication
 
-	  } elsif ($start <= $slice_end) {
-	    # do nothing
-	  } elsif ($end >= $slice_start) {
-	    $new_start += $seq_region_len;
-	    $new_end += $seq_region_len;
+          if ($start >= $slice_start) {
+            $new_end += $seq_region_len;
+            $new_start += $seq_region_len if $end > $slice_start;
 
-	  } elsif ($end <= $slice_end) {
+          } elsif ($start <= $slice_end) {
+            # do nothing
+          } elsif ($end >= $slice_start) {
+            $new_start += $seq_region_len;
+            $new_end += $seq_region_len;
 
-	    $new_end += $seq_region_len
-	      if $new_end < 0;
+          } elsif ($end <= $slice_end) {
+            $new_end += $seq_region_len if $new_end < 0;
+          } elsif ($start > $end) {
+            $new_end += $seq_region_len;
+          } else {
 
-	  } elsif ($start > $end) {
-		  
-	    $new_end += $seq_region_len;
+          }
+              
+        } else {
 
-	  } else {
-		  
-	  }
-      
-	} else {
+          if ($start <= $slice_end and $end >= $slice_start) {
+            # do nothing
+          } elsif ($start > $end) {
+            if ($start <= $slice_end) {
+          
+              $new_start -= $seq_region_len;
 
-	  if ($start <= $slice_end and $end >= $slice_start) {
-	    # do nothing
-	  } elsif ($start > $end) {
-	    if ($start <= $slice_end) {
-	  
-	      $new_start -= $seq_region_len;
+            } elsif ($end >= $slice_start) {
+              $new_end += $seq_region_len;
+            } else {
 
-	    } elsif ($end >= $slice_start) {
-	      $new_end += $seq_region_len;
-
-	    } else {
-		    
-	    }
-	  }
-	}
+            }
+          }
+        }
 
       }
 
-    }			     ## end else [ if ($dest_slice_strand...)]
-
+    }    ## end else [ if ($dest_slice_strand...)]
     push @out, Bio::EnsEMBL::AssemblyExceptionFeature->new(
             '-dbID'            => $f->dbID,
             '-start'           => $new_start,
@@ -445,7 +419,7 @@ sub _remap {
             '-alternate_slice' => $f->alternate_slice,
             '-type'            => $f->type,
     );
-  }
+  }  # end foreach assembly exception
 
   return \@out;
 }