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revision 1.2, Thu Jun 4 18:21:46 2009 UTC revision 1.3, Tue Jun 16 21:58:36 2009 UTC
# Line 1365  Line 1365 
1365          my $sapling = $self->{sapling};          my $sapling = $self->{sapling};
1366          # Get the subsystem ID.          # Get the subsystem ID.
1367          my $subsysID = $self->{name};          my $subsysID = $self->{name};
1368            # Compute the pattern that matches all of this subsystem's machine roles.
1369            my $subsysCellPattern = ERDB::DigestKey($subsysID) . ':%';
1370          # Ask for all the subsystem's cells and their features.          # Ask for all the subsystem's cells and their features.
1371          my @resultRows = $sapling->GetAll("Describes IsImplementedBy IsMachineOf Contains",          my @resultRows = $sapling->GetAll("Contains", 'Contains(from-link) LIKE ?',
1372                                            'Describes(from-link) = ?', [$subsysID],                                            [$subsysCellPattern],
1373                                            [qw(Contains(to-link) Contains(from-link))]);                                            [qw(Contains(to-link) Contains(from-link))]);
1374          # Loop through the features.          # Loop through the features.
1375          for my $feature (@resultRows) {          for my $feature (@resultRows) {
# Line 1375  Line 1377 
1377              my ($featureID, $machineRoleID) = @$feature;              my ($featureID, $machineRoleID) = @$feature;
1378              # We need the column number and the role ID. These can be computed              # We need the column number and the role ID. These can be computed
1379              # from the role abbreviation at the end of the machine role ID.              # from the role abbreviation at the end of the machine role ID.
1380              my (undef, $roleAbbr) = split /:/, $machineRoleID;              my (undef, $genomeID, undef, $roleAbbr) = split /:/, $machineRoleID;
1381              my $column = $self->{roleHash}->{$roleAbbr};              my $column = $self->{roleHash}->{$roleAbbr};
1382              my $role = $self->{abbrHash}->{$roleAbbr};              my $role = $self->{abbrHash}->{$roleAbbr};
             # Compute the genome.  
             my $genomeID = FIG::genome_of($featureID);  
1383              # If we don't have this genome in the hash, create it.              # If we don't have this genome in the hash, create it.
1384              if (! exists $retVal->{$genomeID}) {              if (! exists $retVal->{$genomeID}) {
1385                  # The initial value is a list of empty lists. Features                  # The initial value is a list of empty lists. Features

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