--- Sprout.pm	2006/06/18 07:20:33	1.65
+++ Sprout.pm	2006/06/25 02:44:43	1.73
@@ -12,6 +12,7 @@
     use DBObject;
     use Tracer;
     use FIGRules;
+    use FidCheck;
     use Stats;
     use POSIX qw(strftime);
 
@@ -104,7 +105,7 @@
                                                         # user name and password
                        port         => $FIG_Config::dbport,
                                                         # database connection port
-                       sock         => $FIG_Config::dbsock, 
+                       sock         => $FIG_Config::dbsock,
                        maxSegmentLength => 4500,        # maximum feature segment length
                        maxSequenceLength => 8000,       # maximum contig sequence length
                        noDBOpen     => 0,               # 1 to suppress the database open
@@ -375,18 +376,20 @@
     # Get the genomes.
     my @genomes = $self->GetAll(['Genome'], $filterString, $params, ['Genome(id)',
                                                                      'Genome(genus)',
-                                                                     'Genome(species)']);
+                                                                     'Genome(species)',
+                                                                     'Genome(unique-characterization)']);
     # Sort them by name.
     my @sorted = sort { lc("$a->[1] $a->[2]") cmp lc("$b->[1] $b->[2]") } @genomes;
     # Loop through the genomes, creating the option tags.
     for my $genomeData (@sorted) {
         # Get the data for this genome.
-        my ($genomeID, $genus, $species) = @{$genomeData};
+        my ($genomeID, $genus, $species, $strain) = @{$genomeData};
         # Get the contig count.
         my $count = $self->ContigCount($genomeID);
         my $counting = ($count == 1 ? "contig" : "contigs");
         # Build the option tag.
-        $retVal .= "<option value=\"$genomeID\">$genus $species ($genomeID) [$count $counting]</option>\n";
+        $retVal .= "<option value=\"$genomeID\">$genus $species $strain ($genomeID) [$count $counting]</option>\n";
+        Trace("Option tag built for $genomeID: $genus $species $strain.") if T(3);
     }
     # Close the SELECT tag.
     $retVal .= "</select>\n";
@@ -836,7 +839,7 @@
 
 =over 4
 
-=genomeID
+=item genomeID
 
 ID of the genome whose feature count is desired.
 
@@ -899,12 +902,12 @@
     # Loop through the annotations.
     while (my $data = $query->Fetch) {
         # Get the feature ID and annotation text.
-        my ($fid, $annotation) = $data->Values(['HasFeature(from-link)',
+        my ($fid, $annotation) = $data->Values(['HasFeature(to-link)',
                                                 'Annotation(annotation)']);
         # Check to see if this is an assignment. Note that the user really
         # doesn't matter to us, other than we use it to determine whether or
         # not this is an assignment.
-        my ($user, $assignment) = $self->_ParseAssignment('fig', $annotation);
+        my ($user, $assignment) = _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.
@@ -1801,7 +1804,7 @@
     my ($self, $peg1, $peg2) = @_;
     # Declare the return values. We'll start with the coupling ID and undefine the
     # flag and score until we have more information.
-    my ($retVal, $inverted, $score) = (CouplingID($peg1, $peg2), undef, undef);
+    my ($retVal, $inverted, $score) = ($self->CouplingID($peg1, $peg2), undef, undef);
     # Find the coupling data.
     my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],
                                  "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",
@@ -1824,7 +1827,7 @@
 
 =head3 CouplingID
 
-C<< my $couplingID = Sprout::CouplingID($peg1, $peg2); >>
+C<< my $couplingID = $sprout->CouplingID($peg1, $peg2); >>
 
 Return the coupling ID for a pair of feature IDs.
 
@@ -1857,7 +1860,8 @@
 =cut
 #: Return Type $;
 sub CouplingID {
-    return join " ", sort @_;
+    my ($self, @pegs) = @_;
+    return $self->DigestKey(join " ", sort @pegs);
 }
 
 =head3 ReadFasta
@@ -2216,41 +2220,6 @@
     return @retVal;
 }
 
-=head3 Exists
-
-C<< my $found = $sprout->Exists($entityName, $entityID); >>
-
-Return TRUE if an entity exists, else FALSE.
-
-=over 4
-
-=item entityName
-
-Name of the entity type (e.g. C<Feature>) relevant to the existence check.
-
-=item entityID
-
-ID of the entity instance whose existence is to be checked.
-
-=item RETURN
-
-Returns TRUE if the entity instance exists, else FALSE.
-
-=back
-
-=cut
-#: Return Type $;
-sub Exists {
-    # Get the parameters.
-    my ($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);
-    return $retVal;
-}
-
 =head3 FeatureTranslation
 
 C<< my $translation = $sprout->FeatureTranslation($featureID); >>
@@ -2788,8 +2757,6 @@
     return @retVal;
 }
 
-
-
 =head3 RelatedFeatures
 
 C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
@@ -3041,6 +3008,71 @@
     return %retVal;
 }
 
+=head3 Sims
+
+C<< my $simList = $sprout->Sims($fid, $maxN, $maxP, $select, $max_expand, $filters); >>
+
+Get a list of similarities for a specified feature. Similarity information is not kept in the
+Sprout database; rather, they are retrieved from a network server. The similarities are
+returned as B<Sim> objects. A Sim object is actually a list reference that has been blessed
+so that its elements can be accessed by name.
+
+Similarities can be either raw or expanded. The raw similarities are basic
+hits between features with similar DNA. Expanding a raw similarity drags in any
+features considered substantially identical. So, for example, if features B<A1>,
+B<A2>, and B<A3> are all substatially identical to B<A>, then a raw similarity
+B<[C,A]> would be expanded to B<[C,A] [C,A1] [C,A2] [C,A3]>.
+
+=over 4
+
+=item fid
+
+ID of the feature whose similarities are desired.
+
+=item maxN
+
+Maximum number of similarities to return.
+
+=item maxP
+
+Minumum allowable similarity score.
+
+=item select
+
+Selection criterion: C<raw> means only raw similarities are returned; C<fig>
+means only similarities to FIG features are returned; C<all> means all expanded
+similarities are returned; and C<figx> means similarities are expanded until the
+number of FIG features equals the maximum.
+
+=item max_expand
+
+The maximum number of features to expand.
+
+=item filters
+
+Reference to a hash containing filter information, or a subroutine that can be
+used to filter the sims.
+
+=item RETURN
+
+Returns a reference to a list of similarity objects, or C<undef> if an error
+occurred.
+
+=back
+
+=cut
+
+sub Sims {
+    # Get the parameters.
+    my ($self, $fid, $maxN, $maxP, $select, $max_expand, $filters) = @_;
+    # Create the shim object to test for deleted FIDs.
+    my $shim = FidCheck->new($self);
+    # Ask the network for sims.
+    my $retVal = FIGRules::GetNetworkSims($shim, $fid, {}, $maxN, $maxP, $select, $max_expand, $filters);
+    # Return the result.
+    return $retVal;
+}
+
 =head3 GetGroups
 
 C<< my %groups = $sprout->GetGroups(\@groupList); >>