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revision 1.43, Sun Jun 25 07:34:46 2006 UTC revision 1.46, Mon Jun 26 19:13:16 2006 UTC
# Line 634  Line 634 
634  The following relations are loaded by this method.  The following relations are loaded by this method.
635    
636      Subsystem      Subsystem
637        SubsystemClass
638      Role      Role
639      RoleEC      RoleEC
640      SSCell      SSCell
# Line 696  Line 697 
697      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
698      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
699      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
700        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
701      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
702          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
703      } else {      } else {
# Line 721  Line 723 
723                  my $curator = $sub->get_curator();                  my $curator = $sub->get_curator();
724                  my $notes = $sub->get_notes();                  my $notes = $sub->get_notes();
725                  $loadSubsystem->Put($subsysID, $curator, $notes);                  $loadSubsystem->Put($subsysID, $curator, $notes);
726                    my $class = $fig->subsystem_classification($subsysID);
727                    if ($class) {
728                        $loadSubsystemClass->Put($subsysID, $class);
729                    }
730                  # Connect it to its roles. Each role is a column in the subsystem spreadsheet.                  # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
731                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
732                      # Connect to this role.                      # Connect to this role.
# Line 1438  Line 1444 
1444      } else {      } else {
1445          Trace("Generating synonym group data.") if T(2);          Trace("Generating synonym group data.") if T(2);
1446          # Loop through the genomes.          # Loop through the genomes.
1447          for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1448              Trace("Processing $genomeID.") if T(3);              Trace("Processing $genomeID.") if T(3);
1449              # 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
1450              # all_features_detailed, which returns extra baggage that we discard.              # all_features_detailed, which returns extra baggage that we discard.
1451              my @fids = map { $_->[0] } $fig->all_features_detailed($genomeID);              my $featureData = $fig->all_features_detailed($genomeID);
1452                my @fids = map { $_->[0] } @{$featureData};
1453                Trace(scalar(@fids) . " features found for genome $genomeID.") if T(3);
1454              # Loop through the feature IDs.              # Loop through the feature IDs.
1455              for my $fid (@fids) {              for my $fid (@fids) {
1456                  # Get the group for this feature.                  # Get the group for this feature.

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