--- SearchHelper.pm	2007/05/17 23:43:30	1.32
+++ SearchHelper.pm	2007/06/19 21:28:21	1.33
@@ -19,6 +19,7 @@
     use FeatureQuery;
     use URI::Escape;
     use PageBuilder;
+    use POSIX;
 
 =head1 Search Helper Base Class
 
@@ -875,7 +876,7 @@
 
 =head3 OrganismData
 
-C<< my ($orgName, $group) = $shelp->Organism($genomeID); >>
+C<< my ($orgName, $group, $domain) = $shelp->Organism($genomeID); >>
 
 Return the name and status of the organism corresponding to the specified genome ID.
 For performance reasons, this information is cached in a special hash table, so we
@@ -1097,7 +1098,7 @@
                 $fastaLabel = $fid;
             }
             # Now proceed according to the sequence type.
-            if ($desiredType eq 'prot') {
+            if ($desiredType =~ /prot/) {
                 # We want protein, so get the translation.
                 $fastaData = $sprout->FeatureTranslation($figID);
                 Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);
@@ -1166,13 +1167,18 @@
     Trace("FASTA data sequence: $fastaData") if T(4);
     # Only proceed if no error was detected.
     if ($okFlag) {
-        # We need to format the sequence into 60-byte chunks. We use the infamous
-        # grep-split trick. The split, because of the presence of the parentheses,
-        # includes the matched delimiters in the output list. The grep strips out
-        # the empty list items that appear between the so-called delimiters, since
-        # the delimiters are what we want.
-        my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;
-        $retVal = join("\n", ">$fastaLabel", @chunks, "");
+        if ($desiredType =~ /pattern/i) {
+            # We're doing a scan, so only the data is passed in.
+            $retVal = $fastaData;
+        } else {
+            # We need to format the sequence into 60-byte chunks. We use the infamous
+            # grep-split trick. The split, because of the presence of the parentheses,
+            # includes the matched delimiters in the output list. The grep strips out
+            # the empty list items that appear between the so-called delimiters, since
+            # the delimiters are what we want.
+            my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;
+            $retVal = join("\n", ">$fastaLabel", @chunks, "");
+        }
     }
     # Return the result.
     return $retVal;
@@ -2774,6 +2780,79 @@
                                        $dockString);
             }
         }
+    } elsif ($type eq 'role') {
+        # Here the caller wants a functional role assignment. The key is the feature ID.
+        $retVal = $sprout->FunctionOf($text);
+    } elsif ($type eq 'loc') {
+        # This is a tough one. We need to find the nearest feature in the appropriate direction
+        # on the contig, and then output its id, functional role, and link button.
+        if ($text =~ /^(.)\/(.+)/) {
+            my ($direction, $locString) = ($1, $2);
+            Trace("Location request of type $direction for $locString.") if T(3);
+            # Convert the location string into a location object.
+            my $loc = BasicLocation->new($locString);
+            # Get the contig ID.
+            my $contigID = $loc->Contig;
+            # Compute the contig length.
+            my $contigLen = $sprout->ContigLength($contigID);
+            # Widen by the area to search in both directions.
+            $loc->Widen(5000);
+            # Now, if we're doing a before (-) search, we set the end point to the area's mid point.
+            # If we're doing an after (+) search, we set the begin point to the area's mid point.
+            my $mid = ($loc->Left + $loc->Right) / 2;
+            # Compute the search direction.
+            my $searchDir = ($direction eq $loc->Dir ? 1 : -1);
+            # Adjust the midpoint so that it is different in the before direction from what it would
+            # be in the after direction.
+            if ($mid != int($mid)) {
+                # Here we need to round. The thing here is we want to round in a way that separates
+                # the after-search choice from the before-search choice.
+                if ($direction eq $loc->Dir) {
+                    $mid = ceil($mid);
+                } else {
+                    $mid = floor($mid);
+                }
+            } elsif ($direction eq '+') {
+                # Here the midpoint is on a nucleotide and we are doing the after search. We bump the
+                # midpoint toward the end point.
+                $mid += $loc->NumDirection;
+            }
+            # Now put the midpoint on the proper end of the region.
+            if ($direction eq '+') {
+                $loc->SetBegin($mid);
+            } else {
+                $loc->SetEnd($mid);
+            }
+            Trace("Search region is " . $loc->String . ".") if T(3);
+            # Find all the genes in the region.
+            my ($fidList, $beg, $end) = $sprout->GenesInRegion($loc->Contig, $loc->Left, $loc->Right);
+            Trace(scalar(@{$fidList}) . " features found.") if T(3);
+            # Look for the best match.
+            my $distance = 5000;
+            my $chosenFid = undef;
+            for my $fid (@{$fidList}) {
+                # Get the feature's location.
+                my ($locString) = $sprout->FeatureLocation($fid);
+                my $locObject = BasicLocation->new($locString);
+                # Check its begin point to see if we should keep it.
+                my $newDistance = ($mid - $locObject->Begin) * $searchDir;
+                Trace("Distance from $mid to $locString is $newDistance.") if T(4);
+                if ($newDistance > 0 && $newDistance < $distance) {
+                    $distance = $newDistance;
+                    $chosenFid = $fid;
+                }
+            }
+            # Only proceed if we found something.
+            if (defined $chosenFid) {
+                my $role = $sprout->FunctionOf($chosenFid);
+                my $linkButton = SearchHelper::FakeButton('NMPDR', "protein.cgi", undef,
+                                                           prot => $chosenFid, SPROUT => 1,
+                                                           new_framework => 0, user => '');
+                $retVal = "$chosenFid&nbsp;$linkButton&nbsp;$role";
+            }
+        } else {
+            Confess("Invalid location request %%loc=$text.");
+        }
     }
     # Return the result.
     return $retVal;
@@ -2947,7 +3026,7 @@
     # Compute the target-frame HTML.
     my $targetHtml = ($target ? " target=\"$target\"" : "");
     # Assemble the result.
-    return "<a href=\"$targetUrl\" $targetHtml><div class=\"button2 button\">$caption</div></a>";
+    return "<a href=\"$targetUrl\" $targetHtml><span class=\"button2 button\">$caption</span></a>";
 }
 
 =head3 Formlet