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revision 1.749, Wed Feb 4 17:46:02 2009 UTC revision 1.750, Thu Feb 5 16:32:57 2009 UTC
# Line 16356  Line 16356 
16356              $ans = $taxonomy->{$genome};              $ans = $taxonomy->{$genome};
16357          }          }
16358      }      }
16359      if (!$ans)  
16360      {      if (!$ans) {
16361          warn "No taxonomy found for $genome\n";          #warn "No taxonomy found for $genome\n";
16362      }      }
16363    
16364      $ans =~ s/^\s*//o;      $ans =~ s/^\s*//o;
# Line 18420  Line 18420 
18420      }      }
18421  }  }
18422    
18423    =head3 subsystems_for_pegs_complete
18424    
18425     Return the list of subsystems, roles and variants that the pegs appear in.
18426     Returns a hash keyed by peg. Each item in the hash is a reference to a tuple
18427     of subsystem, role and variant. If the last argument ($include_aux)
18428     is "true", also roles playing auxiliary roles will be returned.
18429    
18430    =cut
18431    
18432    sub subsystems_for_pegs_complete {
18433        my ($self, $pegs, $include_aux) = @_;
18434    
18435        my $rdbH = $self->db_handle;
18436        my %results;
18437    
18438        my $q = "SELECT subsystem, role, variant, protein FROM (SELECT subsystem, role, variant, protein FROM subsystem_index WHERE protein IN ('".join("', '", @$pegs)."')) AS t1 LEFT JOIN deleted_fids ON t1.protein=deleted_fids.fid WHERE deleted_fids.fid IS NULL";
18439        unless ($include_aux) {
18440            $q = "SELECT t2.subsystem, t2.role, t2.variant, t2.protein FROM (".$q.") AS t2 LEFT JOIN aux_roles ON (t2.subsystem=aux_roles.subsystem AND t2.role=aux_roles.role) WHERE aux_roles.role IS NULL";
18441        }
18442        my $ret = $rdbH->SQL($q);
18443    
18444        foreach my $row (@$ret) {
18445            if (exists($results{$row->[3]})) {
18446                push(@{$results{$row->[3]}}, [ $row->[0], $row->[1], $row->[2] ]);
18447            } else {
18448                $results{$row->[3]} = [ [ $row->[0], $row->[1], $row->[2] ] ];
18449            }
18450        }
18451    
18452        return %results;
18453    }
18454    
18455  =head3 subsystems_for_peg  =head3 subsystems_for_peg
18456    
18457   Return the list of subsystems and roles that this peg appears in.   Return the list of subsystems and roles that this peg appears in.

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