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revision 1.71, Wed Sep 27 13:25:53 2006 UTC revision 1.72, Sat Oct 14 18:12:14 2006 UTC
# Line 163  Line 163 
163                  Confess("Invalid subsystem parameter in SproutLoad constructor.");                  Confess("Invalid subsystem parameter in SproutLoad constructor.");
164              }              }
165          }          }
166            # Go through the subsys hash again, creating the keyword list for each subsystem.
167            for my $subsystem (keys %subsystems) {
168                my $name = $subsystem;
169                $name =~ s/_/ /g;
170                my $classes = $fig->subsystem_classification($subsystem);
171                my @classList = map { " $_" } @{$classes};
172                $name .= join("", @classList);
173                $subsystems{$subsystem} = $name;
174            }
175      }      }
176      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
177      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
# Line 475  Line 484 
484  sub LoadFeatureData {  sub LoadFeatureData {
485      # Get this object instance.      # Get this object instance.
486      my ($self) = @_;      my ($self) = @_;
487      # Get the FIG object.      # Get the FIG and Sprout objects.
488      my $fig = $self->{fig};      my $fig = $self->{fig};
489        my $sprout = $self->{sprout};
490      # Get the table of genome IDs.      # Get the table of genome IDs.
491      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
492      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
# Line 488  Line 498 
498      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
499      my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);      my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);
500      my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);      my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);
501        # Get the subsystem hash.
502        my $subHash = $self->{subsystems};
503      # 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
504      # locations.      # locations.
505      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 520  Line 532 
532                      $loadFeature->Add("featureIn");                      $loadFeature->Add("featureIn");
533                      # Get the functional assignment.                      # Get the functional assignment.
534                      my $assignment = $fig->function_of($featureID);                      my $assignment = $fig->function_of($featureID);
535                      # Create the feature record.                      # Begin building the keywords.
536                      $loadFeature->Put($featureID, 1, $type, $assignment);                      my $keywords = "$assignment $genomeID";
537                      # Link it to the parent genome.                      # Link this feature to the parent genome.
538                      $loadHasFeature->Put($genomeID, $featureID, $type);                      $loadHasFeature->Put($genomeID, $featureID, $type);
539                      # Create the aliases.                      # Create the aliases.
540                      for my $alias ($fig->feature_aliases($featureID)) {                      for my $alias ($fig->feature_aliases($featureID)) {
541                          $loadFeatureAlias->Put($featureID, $alias);                          $loadFeatureAlias->Put($featureID, $alias);
542                            $keywords .= " $alias";
543                      }                      }
544                      # Get the links.                      # Get the links.
545                      my @links = $fig->fid_links($featureID);                      my @links = $fig->fid_links($featureID);
# Line 547  Line 560 
560                          }                          }
561                      }                      }
562                      # Now we need to find the subsystems this feature participates in.                      # Now we need to find the subsystems this feature participates in.
563                        # We also add the subsystems to the keyword list. Before we do that,
564                        # we must convert underscores to spaces and tack on the classifications.
565                      my @subsystems = $fig->peg_to_subsystems($featureID);                      my @subsystems = $fig->peg_to_subsystems($featureID);
566                      for my $subsystem (@subsystems) {                      for my $subsystem (@subsystems) {
567                            # Only proceed if we like this subsystem.
568                            if (exists $subHash->{$subsystem}) {
569                                # Store the has-role link.
570                          $loadHasRoleInSubsystem->Put($featureID, $subsystem, $genomeID, $type);                          $loadHasRoleInSubsystem->Put($featureID, $subsystem, $genomeID, $type);
571                                # Save the subsystem's keyword data.
572                                my $subKeywords = $subHash->{$subsystem};
573                                $keywords .= " $subKeywords";
574                            }
575                        }
576                        # The final task is to add virulence and essentiality attributes.
577                        if ($fig->virulent($featureID)) {
578                            $keywords .= " virulent";
579                        }
580                        if ($fig->essential($featureID)) {
581                            $keywords .= " essential";
582                      }                      }
583                        # Clean the keyword list.
584                        my $cleanWords = $sprout->CleanKeywords($keywords);
585                        # Create the feature record.
586                        $loadFeature->Put($featureID, 1, $type, $assignment, $cleanWords);
587                      # 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
588                      # 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
589                      # the maximum segment size. This simplifies the genes_in_region processing                      # the maximum segment size. This simplifies the genes_in_region processing
# Line 762  Line 795 
795                  my $curator = $sub->get_curator();                  my $curator = $sub->get_curator();
796                  my $notes = $sub->get_notes();                  my $notes = $sub->get_notes();
797                  $loadSubsystem->Put($subsysID, $curator, $notes);                  $loadSubsystem->Put($subsysID, $curator, $notes);
798                    # Now for the classification string. This comes back as a list
799                    # reference and we convert it to a space-delimited string.
800                  my $classList = $fig->subsystem_classification($subsysID);                  my $classList = $fig->subsystem_classification($subsysID);
801                  my @classes = @$classList;                  my $classString = join(" ", grep { $_ } @$classList);
802                  if (@classes) {                  $loadSubsystemClass->Put($subsysID, $classString);
                     for my $class (@classes) {  
                         $loadSubsystemClass->Put($subsysID, $class);  
                     }  
                 }  
803                  # Connect it to its roles. Each role is a column in the subsystem spreadsheet.                  # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
804                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
805                      # Connect to this role.                      # Connect to this role.
# Line 985  Line 1016 
1016                  # Get all attributes for this feature. We do this one feature at a time                  # Get all attributes for this feature. We do this one feature at a time
1017                  # to insure we do not get any genome attributes.                  # to insure we do not get any genome attributes.
1018                  my @attributeList = $fig->get_attributes($fid, '', '', '');                  my @attributeList = $fig->get_attributes($fid, '', '', '');
1019                    # Add essentiality and virulence attributes.
1020                    if ($fig->essential($fid)) {
1021                        push @attributeList, [$fid, 'essential', 1, ''];
1022                    }
1023                    if ($fig->virulent($fid)) {
1024                        push @attributeList, [$fid, 'virulent', 1, ''];
1025                    }
1026                  if (scalar @attributeList) {                  if (scalar @attributeList) {
1027                      $featureCount++;                      $featureCount++;
1028                  }                  }
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