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revision 1.68, Sun Sep 24 17:14:16 2006 UTC revision 1.69, Wed Sep 27 12:34:46 2006 UTC
# Line 460  Line 460 
460      FeatureUpstream      FeatureUpstream
461      IsLocatedIn      IsLocatedIn
462      HasFeature      HasFeature
463        HasRoleInSubsystem
464    
465  =over 4  =over 4
466    
# Line 485  Line 486 
486      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
487      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
488      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
489      my $loadHasFeature = $self->_TableLoader('HasFeature');      my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);
490        my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);
491      # Get the maximum sequence size. We need this later for splitting up the      # Get the maximum sequence size. We need this later for splitting up the
492      # locations.      # locations.
493      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 544  Line 546 
546                              $loadFeatureUpstream->Put($featureID, $upstream);                              $loadFeatureUpstream->Put($featureID, $upstream);
547                          }                          }
548                      }                      }
549                        # Now we need to find the subsystems this feature participates in.
550                        my @subsystems = $fig->peg_to_subsystems($featureID);
551                        for my $subsystem (@subsystems) {
552                            $loadHasRoleInSubsystem->Put($featureID, $subsystem);
553                        }
554                      # This part is the roughest. We need to relate the features to contig                      # This part is the roughest. We need to relate the features to contig
555                      # locations, and the locations must be split so that none of them exceed                      # locations, and the locations must be split so that none of them exceed
556                      # the maximum segment size. This simplifies the genes_in_region processing                      # the maximum segment size. This simplifies the genes_in_region processing
# Line 1572  Line 1579 
1579      return $retVal;      return $retVal;
1580  }  }
1581    
1582    
1583    
1584  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1585    
1586  =head3 TableLoader  =head3 TableLoader

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