[Bio] / FigKernelPackages / UnvSubsys.pm Repository:
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revision 1.17, Fri Nov 3 15:53:51 2006 UTC revision 1.18, Wed Nov 29 15:19:19 2006 UTC
# Line 150  Line 150 
150      $ssa =~ s/ /_/g;      $ssa =~ s/ /_/g;
151      # Get the FIG object. At this point in time, we're only getting data from the SEED. On      # Get the FIG object. At this point in time, we're only getting data from the SEED. On
152      # a future pass through the code, we'll get data from a SEED or Sprout.      # a future pass through the code, we'll get data from a SEED or Sprout.
153      if ((ref($fig) eq "FIG") || (ref($fig) eq 'SFXlate')) {      if ((ref($fig) eq "FIG") || (ref($fig) eq "FIGV") || (ref($fig) eq 'SFXlate')) {
154          # Create a subsystem object. The "get_subsystem" method is provided by both FIG          # Create a subsystem object. The "get_subsystem" method is provided by both FIG
155          # and SFXlate; however, the object returned in each case is different: FIG          # and SFXlate; however, the object returned in each case is different: FIG
156          # returns a "Subsystem" object; SFXlate returns a "SproutSubsys" object.          # returns a "Subsystem" object; SFXlate returns a "SproutSubsys" object.
# Line 474  Line 474 
474      foreach $pair (@$taxonomic_groups)      foreach $pair (@$taxonomic_groups)
475      {      {
476          ($id,$members) = @$pair;          ($id,$members) = @$pair;
477    #       warn "Group $id is @$members\n";
478    #       if ($id eq 'All')
479    #       {
480    #           push(@$members, '372461.6');
481    #       }
482    
483          # Extract the genomes in the member list that participate in this          # Extract the genomes in the member list that participate in this
484          # subsystem. To do this, we convert each genome ID to its row          # subsystem. To do this, we convert each genome ID to its row
485          # index. If no row index exists, the GREP condition discards the          # index. If no row index exists, the GREP condition discards the

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