--- Sprout.pm	2005/09/09 20:40:41	1.21
+++ Sprout.pm	2005/09/14 13:13:25	1.30
@@ -70,6 +70,8 @@
 
 * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
 
+* B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
+
 =back
 
 For example, the following constructor call specifies a database named I<Sprout> and a user name of
@@ -98,6 +100,7 @@
                                                         # database connection port
                        maxSegmentLength => 4500,        # maximum feature segment length
                        maxSequenceLength => 8000,       # maximum contig sequence length
+                       noDBOpen     => 0,               # 1 to suppress the database open
                       }, $options);
     # Get the data directory.
     my $dataDir = $optionTable->{dataDir};
@@ -105,7 +108,11 @@
     $optionTable->{userData} =~ m!([^/]*)/(.*)$!;
     my ($userName, $password) = ($1, $2);
     # Connect to the database.
-    my $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName, $password, $optionTable->{port});
+    my $dbh;
+    if (! $optionTable->{noDBOpen}) {
+        $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
+                                $password, $optionTable->{port});
+    }
     # Create the ERDB object.
     my $xmlFileName = "$optionTable->{xmlFileName}";
     my $erdb = ERDB->new($dbh, $xmlFileName);
@@ -758,13 +765,15 @@
         # the start point is the ending. Note that in the latter case we must reverse the DNA string
         # before putting it in the return value.
         my ($start, $stop);
+        Tracer("Parsed 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)",
@@ -776,18 +785,19 @@
                 $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.
@@ -1538,6 +1548,7 @@
             Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
             push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
         }
+        Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
     }
     # Return the result.
     return @retVal;
@@ -1587,12 +1598,15 @@
                                  [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
     # Check to see if we found anything.
     if (!@pegs) {
+        Trace("No coupling found.") if T(Coupling => 4);
         # No coupling, so undefine the return value.
         $retVal = undef;
     } else {
         # We have a coupling! Get the score and check for inversion.
         $score = $pegs[0]->[1];
-        $inverted = ($pegs[0]->[0] eq $peg1);
+        my $firstFound = $pegs[0]->[0];
+        $inverted = ($firstFound ne $peg1);
+        Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
     }
     # Return the result.
     return ($retVal, $inverted, $score);
@@ -1697,13 +1711,13 @@
         if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
             # Here we have a new header. Store the current sequence if we have one.
             if ($id) {
-                $retVal{$id} = uc $sequence;
+                $retVal{$id} = lc $sequence;
             }
             # Clear the sequence accumulator and save the new ID.
             ($id, $sequence) = ("$prefix$1", "");
         } else {
             # Here we have a data line, so we add it to the sequence accumulator.
-            # First, we get the actual data out. Note that we normalize to upper
+            # First, we get the actual data out. Note that we normalize to lower
             # case.
             $line =~ /^\s*(.*?)(\s|\n)/;
             $sequence .= $1;
@@ -1711,7 +1725,7 @@
     }
     # Flush out the last sequence (if any).
     if ($sequence) {
-        $retVal{$id} = uc $sequence;
+        $retVal{$id} = lc $sequence;
     }
     # Close the file.
     close FASTAFILE;
@@ -2037,6 +2051,7 @@
     # Get the parameters.
     my ($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);