--- GenomeStats.pl	2006/06/18 07:53:45	1.8
+++ GenomeStats.pl	2006/08/24 17:29:45	1.19
@@ -61,6 +61,14 @@
 
 Style to use for small-text markers (e.g. NEW!)
 
+=item numStyle
+
+Style to use for numeric cells.
+
+=item counterStyle
+
+Style to use for counter cells.
+
 =item linkCGI
 
 Path to the CGI script for displaying detailed statistics.
@@ -90,6 +98,8 @@
                                             evenStyle => ['even', 'style for even rows'],
                                             tableStyle => ['genomestats', 'style for whole table'],
                                             markerStyle => ['tinytext', 'style for markers'],
+                                            numStyle => ['numcell', 'style for cells with numeric values'],
+                                            counterStyle => ['countercell', 'style for cells with counter values'],
                                             linkCGI => ['../FIG/genome_statistics.cgi',
                                                         'path to CGI script for detailed statistics'],
                                            },
@@ -102,7 +112,7 @@
 } elsif (! -d $targetDir) {
     Confess("Target directory $targetDir not found.");
 } else {
-    # *Get the old Sprout.
+    # Get the old Sprout.
     my $oldSprout = SFXlate->new_sprout_only($FIG_Config::oldSproutDB);
     # Extract the genome group data from the old Sprout.
     my %oldGroupHash = $oldSprout->GetGroups();
@@ -127,23 +137,27 @@
             %oldGenomes = map { $_ => 1 } @{$oldGroupHash{$groupID}};
         }
         # Create the output file.
-        Open(\*GROUPFILE, ">$targetDir/$groupID.inc");
+        my $outFileName = "stats-" . lc($groupID) . ".inc";
+        Open(\*GROUPFILE, ">$targetDir/$outFileName");
         # Get the styles.
         my ($tableStyle, $markerStyle, @rowStyle) = ($options->{tableStyle}, $options->{markerStyle},
                                                      $options->{evenStyle}, $options->{oddStyle});
+        my ($numStyle, $counterStyle) = ($options->{numStyle}, $options->{counterStyle});
         # Start the table.
         print GROUPFILE "<table class=\"$tableStyle\">\n";
         # Create the header row.
-        print GROUPFILE Tr( { class => 'odd' }, th("Strain annotated in NMPDR",
+        print GROUPFILE Tr( { class => 'odd' }, th(["Strain annotated in NMPDR",
                                                  "Genome size, bp",
                                                  "Protein Encoding Genes (PEGs)",
                                                  "Named genes in subsystems",            # s0
                                                  "Named genes not in subsystems",        # n0
                                                  "Hypothetical genes in subsystems",     # s1
                                                  "Hypothetical genes not in subsystems", # n1
-                                                 "RNAs")) . "\n";
+                                                 "",
+                                                 "RNAs",
+                                                   ])) . "\n";
         # Set up some useful stuff for the four count columns.
-        my %linkParms = ( s0 => "nohypo_sub", n0 => "nohypo_nosub",
+        my %linkParms = ( s0 => "nothypo_sub", n0 => "nothypo_nosub",
                           s1 => "hypo_sub", n1 => "hypo_nosub" );
         my @columnTypes = ('s0', 'n0', 's1', 'n1');
         # The data rows will be built next. We'll be putting them into a hash keyed by
@@ -161,21 +175,24 @@
                 $new = " <span class=\"$markerStyle\">NEW!</span>";
             }
             # Get the genome length.
-            my $genomeLen = $sprout->GenomeLength($genomeID);
+            my $genomeLen = Tracer::CommaFormat($sprout->GenomeLength($genomeID));
             # Get the number of PEGs.
-            my $pegCount = $sprout->FeatureCount($genomeID, 'peg');
+            my $pegCount = Tracer::CommaFormat($sprout->FeatureCount($genomeID, 'peg'));
             # Get the number of RNAs.
-            my $rnaCount = $sprout->FeatureCount($genomeID, 'rna');
+            my $rnaCount = Tracer::CommaFormat($sprout->FeatureCount($genomeID, 'rna'));
+            # If there are no RNAs, we say we don't know the number, since we know there
+            # must be RNAs somewhere.
+            if (! $rnaCount) {
+                $rnaCount = "n/d";
+            }
             # Now we have four categories of features to work with, for each
             # combination of named or hypothetical vs. in-subsystem or
             # not-in-subsystem. First, we get all of the feature assignments for
             # the genome.
             my $assignHash = $sprout->GenomeAssignments($genomeID);
             # Next, we get all of the features in the genome that belong to a
-            # subsystem. This involves a query via the subsystem spreadsheet.
-            my %ssHash = map { $_ => 1 } $sprout->GetFlat(['IsGenomeOf', 'ContainsFeature'],
-                                                    "IsGenomeOf(from-link) = ?",
-                                                    [$genomeID], 'ContainsFeature(to-link)');
+            # subsystem.
+            my %ssHash = $sprout->GenomeSubsystemData($genomeID);
             # Create a hash to track the four categories. "s" or "n" indicates
             # in or out of a subsystem. "1" or "0" indicates hypothetical or
             # real.
@@ -200,12 +217,20 @@
                                      sprintf("%d(%.1f%%)", $counters{$type},
                                              Tracer::Percent($counters{$type}, $totalFeatures)));
             }
-            # Create the row text. We use a list reference to distribute the TD tag
-            # across all the cells.
-            my $rowHtml = td(["$genomeName$new", $genomeLen, $pegCount,
-                              map { $counters{$_} } @columnTypes,
-                              $rnaCount,
-                             ]);
+            my @counterValues = map { $counters{$_} } @columnTypes;
+            # The last link is a button to look at the subsystem summaries.
+            my $ssLink = "$options->{linkCGI}?user=\&genome=$genomeID&SPROUT=1&show_subsystems=1";
+            my $ssCol = "<a href=\"$ssLink\"><img src=\"../images/button-ss.gif\"></a>";
+            # Create the row text. Note that we use the distributive capability of the TD
+            # function to apply the same style to each one.
+            my $rowHtml = join("",
+                               td("$genomeName$new"),
+                               td({ class => $numStyle }, $genomeLen),
+                               td({ class => $numStyle }, $pegCount),
+                               td({ class => $counterStyle }, \@counterValues),
+                               td($ssCol),
+                               td({ class => $numStyle }, $rnaCount),
+                              );
             # Put it in the row hash.
             $rows{$genomeName} = $rowHtml;
         }