--- Sprout.pm	2005/09/11 17:29:52	1.25
+++ Sprout.pm	2005/09/14 13:43:31	1.34
@@ -622,8 +622,10 @@
         }
         # Remember this specifier for the adjacent-segment test the next time through.
         ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);
+        # Compute the initial base pair.
+        my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
         # Add the specifier to the list.
-        push @retVal, "${contigID}_$beg$dir$len";
+        push @retVal, "${contigID}_$start$dir$len";
     }
     # Return the list in the format indicated by the context.
     return (wantarray ? @retVal : join(',', @retVal));
@@ -765,13 +767,15 @@
         # the start point is the ending. Note that in the latter case we must reverse the DNA string
         # before putting it in the return value.
         my ($start, $stop);
+        Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
         if ($dir eq "+") {
             $start = $beg;
             $stop = $beg + $len - 1;
         } else {
-            $start = $beg + $len + 1;
+            $start = $beg - $len + 1;
             $stop = $beg;
         }
+        Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
         my $query = $self->Get(['IsMadeUpOf','Sequence'],
             "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
             " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
@@ -783,18 +787,19 @@
                 $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
                                    'IsMadeUpOf(len)']);
             my $stopPosition = $startPosition + $sequenceLength;
+            Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
             # Figure out the start point and length of the relevant section.
             my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
-            my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;
+            my $len1 = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;
+            Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
             # Add the relevant data to the location data.
-            $locationDNA .= substr($sequenceData, $pos1, $len);
+            $locationDNA .= substr($sequenceData, $pos1, $len1);
         }
         # Add this location's data to the return string. Note that we may need to reverse it.
         if ($dir eq '+') {
             $retVal .= $locationDNA;
         } else {
-            $locationDNA = join('', reverse split //, $locationDNA);
-            $retVal .= $locationDNA;
+            $retVal .= FIG::reverse_comp($locationDNA);
         }
     }
     # Return the result.
@@ -2048,6 +2053,7 @@
     # Get the parameters.
     my ($self, $entityName, $entityID) = @_;
     # Check for the entity instance.
+    Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
     my $testInstance = $self->GetEntity($entityName, $entityID);
     # Return an existence indicator.
     my $retVal = ($testInstance ? 1 : 0);