--- Sprout.pm	2005/09/14 13:43:31	1.34
+++ Sprout.pm	2005/10/12 03:12:24	1.40
@@ -659,7 +659,7 @@
     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
     my ($location) = @_;
     # Parse it into segments.
-    $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;
+    $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/;
     my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);
     # If the direction is an underscore, convert it to a + or -.
     if ($dir eq "_") {
@@ -790,7 +790,7 @@
             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 $len1 = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;
+            my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $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, $len1);
@@ -869,7 +869,55 @@
     # Set it from the sequence data, if any.
     if ($sequence) {
         my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
-        $retVal = $start + $len;
+        $retVal = $start + $len - 1;
+    }
+    # Return the result.
+    return $retVal;
+}
+
+=head3 ClusterPEGs
+
+C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>
+
+Cluster the PEGs in a list according to the cluster coding scheme of the specified
+subsystem. In order for this to work properly, the subsystem object must have
+been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.
+This causes the cluster numbers to be pulled into the subsystem's color hash.
+If a PEG is not found in the color hash, it will not appear in the output
+sequence.
+
+=over 4
+
+=item sub
+
+Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
+method.
+
+=item pegs
+
+Reference to the list of PEGs to be clustered.
+
+=item RETURN
+
+Returns a list of the PEGs, grouped into smaller lists by cluster number.
+
+=back
+
+=cut
+#: Return Type $@@;
+sub ClusterPEGs {
+    # Get the parameters.
+    my ($self, $sub, $pegs) = @_;
+    # Declare the return variable.
+    my $retVal = [];
+    # Loop through the PEGs, creating arrays for each cluster.
+    for my $pegID (@{$pegs}) {
+        my $clusterNumber = $sub->get_cluster_number($pegID);
+        # Only proceed if the PEG is in a cluster.
+        if ($clusterNumber >= 0) {
+            # Push this PEG onto the sub-list for the specified cluster number.
+            push @{$retVal->[$clusterNumber]}, $pegID;
+        }
     }
     # Return the result.
     return $retVal;
@@ -1019,7 +1067,7 @@
 
 =head3 FeatureAnnotations
 
-C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>
+C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
 
 Return the annotations of a feature.
 
@@ -1029,13 +1077,18 @@
 
 ID of the feature whose annotations are desired.
 
+=item rawFlag
+
+If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
+will be returned in human-readable form.
+
 =item RETURN
 
 Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
 
 * B<featureID> ID of the relevant feature.
 
-* B<timeStamp> time the annotation was made, in user-friendly format.
+* B<timeStamp> time the annotation was made.
 
 * B<user> ID of the user who made the annotation
 
@@ -1047,7 +1100,7 @@
 #: Return Type @%;
 sub FeatureAnnotations {
     # Get the parameters.
-    my ($self, $featureID) = @_;
+    my ($self, $featureID, $rawFlag) = @_;
     # Create a query to get the feature's annotations and the associated users.
     my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
                            "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
@@ -1060,9 +1113,13 @@
             $annotation->Values(['IsTargetOfAnnotation(from-link)',
                                  'Annotation(time)', 'MadeAnnotation(from-link)',
                                  'Annotation(annotation)']);
+        # Convert the time, if necessary.
+        if (! $rawFlag) {
+            $timeStamp = FriendlyTimestamp($timeStamp);
+        }
         # Assemble them into a hash.
         my $annotationHash = { featureID => $featureID,
-                               timeStamp => FriendlyTimestamp($timeStamp),
+                               timeStamp => $timeStamp,
                                user => $user, text => $text };
         # Add it to the return list.
         push @retVal, $annotationHash;
@@ -1266,12 +1323,12 @@
         my $query = $self->Get(['IsBidirectionalBestHitOf'],
                                "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
                                [$featureID, $genomeID]);
-        # Look for the best hit.
-        my $bbh = $query->Fetch;
-        if ($bbh) {
-            my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');
-            $retVal{$featureID} = $targetFeature;
+        # Peel off the BBHs found.
+        my @found = ();
+        while (my $bbh = $query->Fetch) {
+            push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
         }
+        $retVal{$featureID} = \@found;
     }
     # Return the mapping.
     return \%retVal;
@@ -3154,7 +3211,7 @@
 
 sub FriendlyTimestamp {
     my ($timeValue) = @_;
-    my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));
+    my $retVal = localtime($timeValue);
     return $retVal;
 }