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revision 1.30, Fri Dec 12 23:43:13 2008 UTC revision 1.31, Mon Feb 23 10:28:43 2009 UTC
# Line 4261  Line 4261 
4261      my $subsystem = $fig->get_subsystem($ss_name);      my $subsystem = $fig->get_subsystem($ss_name);
4262      my %genome_reactions = ();      my %genome_reactions = ();
4263      my %hope_reactions = $subsystem->get_hope_reactions;      my %hope_reactions = $subsystem->get_hope_reactions;
     my $index = $subsystem->get_genome_index($genome_id);  
4264    
     if (defined $index)  
     {  
         foreach my $role (keys %hope_reactions)  
         {  
             my @peg_list = $subsystem->get_pegs_from_cell($genome_id,$role);  
   
             if (scalar @peg_list > 0)  
             {  
                 foreach my $reaction (@{$hope_reactions{$role}})  
                 {  
                     push @{$genome_reactions{$reaction}}, @peg_list;  
                 }  
             }  
         }  
     }  
     else  
     {  
         # the genome is not in the subsystem, but we can check for role assignments anyhow;  
4265          foreach my $role (keys %hope_reactions)          foreach my $role (keys %hope_reactions)
4266          {          {
4267              my @peg_list = $fig->seqs_with_role($role, "", $genome_id);              my @peg_list = $fig->seqs_with_role($role, "", $genome_id);
# Line 4293  Line 4274 
4274                  }                  }
4275              }              }
4276          }          }
     }  
4277    
4278      # assume that the hope_supersets.txt has been loaded      # assume that the hope_supersets.txt has been loaded
4279      my $superset = $ss_to_superset{$ss_name};      my $superset = $ss_to_superset{$ss_name};

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