--- Sprout.pm	2006/06/14 19:47:19	1.60
+++ Sprout.pm	2006/06/18 05:38:12	1.62
@@ -793,6 +793,128 @@
     return @retVal;
 }
 
+=head3 GenomeLength
+
+C<< my $length = $sprout->GenomeLength($genomeID); >>
+
+Return the length of the specified genome in base pairs.
+
+=over 4
+
+=item genomeID
+
+ID of the genome whose base pair count is desired.
+
+=item RETURN
+
+Returns the number of base pairs in all the contigs of the specified
+genome.
+
+=back
+
+=cut
+
+sub GenomeLength {
+    # Get the parameters.
+    my ($self, $genomeID) = @_;
+    # Declare the return variable.
+    my $retVal = 0;
+    # Get the genome's contig sequence lengths.
+    my @lens = GetFlat(['HasContig', 'IsMadeUpOf'], 'HasContig(from-link) = ?',
+                       [$genomeID], 'IsMadeUpOf(len)');
+    # Sum the lengths.
+    map { $retVal += $_ } @lens;
+    # Return the result.
+    return $retVal;
+}
+
+=head3 FeatureCount
+
+C<< my $count = $sprout->FeatureCount($genomeID, $type); >>
+
+Return the number of features of the specified type in the specified genome.
+
+=over 4
+
+=genomeID
+
+ID of the genome whose feature count is desired.
+
+=item type
+
+Type of feature to count (eg. C<peg>, C<rna>, etc.).
+
+=item RETURN
+
+Returns the number of features of the specified type for the specified genome.
+
+=back
+
+=cut
+
+sub FeatureCount {
+    # Get the parameters.
+    my ($self, $genomeID, $type) = @_;
+    # Compute the count.
+    my $retVal = $self->GetCount(['HasFeature', 'Feature'],
+                                "HasFeature(from-link) = ? AND Feature(type) = ?",
+                                [$genomeID, $type]);
+    # Return the result.
+    return $retVal;
+}
+
+=head3 GenomeAssignments
+
+C<< my $fidHash = $sprout->GenomeAssignments($genomeID); >>
+
+Return a list of a genome's assigned features. The return hash will contain each
+assigned feature of the genome mapped to the text of its most recent functional
+assignment.
+
+=over 4
+
+=item genomeID
+
+ID of the genome whose functional assignments are desired.
+
+=item RETURN
+
+Returns a reference to a hash which maps each feature to its most recent
+functional assignment.
+
+=back
+
+=cut
+
+sub GenomeAssignments {
+    # Get the parameters.
+    my ($self, $genomeID) = @_;
+    # Declare the return variable.
+    my $retVal = {};
+    # Query the genome's features and annotations. We'll put the oldest annotations
+    # first so that the last assignment to go into the hash will be the correct one.
+    my $query = $self->Get(['HasFeature', 'IsTargetOfAnnotation', 'Annotation'],
+                           "HasFeature(from-link) = ? ORDER BY Annotation(time)",
+                           [$genomeID]);
+    # Loop through the annotations.
+    while (my $data = $query->Fetch) {
+        # Get the feature ID and annotation text.
+        my ($fid, $annotation) = $data->Values(['HasFeature(from-link)',
+                                                'Annotation(text)']);
+        # Check to see if this is an assignment. Note that the user really
+        # doesn't matter to us, other than we use it to determine whether or
+        # not this is an assignment.
+        my ($user, $assignment) = $self->_ParseAssignment('fig', $annotation);
+        if ($user) {
+            # Here it's an assignment. We put it in the return hash, overwriting
+            # any older assignment that might be present.
+            $retVal->{$fid} = $assignment;
+        }
+    }
+    # Return the result.
+    return $retVal;
+}
+
 =head3 ContigLength
 
 C<< my $length = $sprout->ContigLength($contigID); >>
@@ -1546,7 +1668,7 @@
         # Get the other feature that participates in the coupling.
         my ($otherFeatureID) = $self->GetFlat(['ParticipatesInCoupling'],
                                            "ParticipatesInCoupling(to-link) = ? AND ParticipatesInCoupling(from-link) <> ?",
-                                           [$couplingID, $featureID], 'ParticipatesInCoupling(to-link)');
+                                           [$couplingID, $featureID], 'ParticipatesInCoupling(from-link)');
         # Attach the other feature's score to its ID.
         $retVal{$otherFeatureID} = $score;
         $found = 1;