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revision 1.43, Sun Jun 25 07:34:46 2006 UTC revision 1.44, Sun Jun 25 07:51:04 2006 UTC
# Line 1438  Line 1438 
1438      } else {      } else {
1439          Trace("Generating synonym group data.") if T(2);          Trace("Generating synonym group data.") if T(2);
1440          # Loop through the genomes.          # Loop through the genomes.
1441          for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1442              Trace("Processing $genomeID.") if T(3);              Trace("Processing $genomeID.") if T(3);
1443              # Get all of the features for this genome. The only method that does this is              # Get all of the features for this genome. The only method that does this is
1444              # all_features_detailed, which returns extra baggage that we discard.              # all_features_detailed, which returns extra baggage that we discard.
1445              my @fids = map { $_->[0] } $fig->all_features_detailed($genomeID);              my @fids = map { $_->[0] } $fig->all_features_detailed($genomeID);
1446                Trace(scalar(@fids) . " features found for genome $genomeID.") if T(3);
1447              # Loop through the feature IDs.              # Loop through the feature IDs.
1448              for my $fid (@fids) {              for my $fid (@fids) {
1449                  # Get the group for this feature.                  # Get the group for this feature.
1450                  my $synonym = $fig->maps_to_id($fid);                  my $synonym = $fig->maps_to_id($fid);
1451                    Trace("$synonym is synonym of $fid.") if T(4);
1452                  # Only proceed if the synonym is a real group.                  # Only proceed if the synonym is a real group.
1453                  if ($synonym ne $fid) {                  if ($synonym ne $fid) {
1454                      $loadSynonymGroup->Put($synonym);                      $loadSynonymGroup->Put($synonym);

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