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revision 1.87, Mon Sep 10 18:16:54 2007 UTC revision 1.88, Mon Nov 5 22:52:06 2007 UTC
# Line 12  Line 12 
12      use Stats;      use Stats;
13      use BasicLocation;      use BasicLocation;
14      use HTML;      use HTML;
15        use AliasAnalysis;
16    
17  =head1 Sprout Load Methods  =head1 Sprout Load Methods
18    
# Line 102  Line 103 
103              # Here we want all the complete genomes and an access code of 1.              # Here we want all the complete genomes and an access code of 1.
104              my @genomeList = $fig->genomes(1);              my @genomeList = $fig->genomes(1);
105              %genomes = map { $_ => 1 } @genomeList;              %genomes = map { $_ => 1 } @genomeList;
106                Trace(scalar(keys %genomes) . " genomes found.") if T(3);
107          } else {          } else {
108              my $type = ref $genomeFile;              my $type = ref $genomeFile;
109              Trace("Genome file parameter type is \"$type\".") if T(3);              Trace("Genome file parameter type is \"$type\".") if T(3);
# Line 397  Line 399 
399      } else {      } else {
400          Trace("Generating feature data.") if T(2);          Trace("Generating feature data.") if T(2);
401          # Now we loop through the genomes, generating the data for each one.          # Now we loop through the genomes, generating the data for each one.
402          for my $genomeID (sort keys %{$genomeHash}) {          my @allGenomes = sort keys %{$genomeHash};
403            Trace(scalar(@allGenomes) . " genomes found in list.") if T(3);
404            for my $genomeID (@allGenomes) {
405              Trace("Loading features for genome $genomeID.") if T(3);              Trace("Loading features for genome $genomeID.") if T(3);
406              $loadFeature->Add("genomeIn");              $loadFeature->Add("genomeIn");
407              # Get the feature list for this genome.              # Get the feature list for this genome.
# Line 409  Line 413 
413              Trace("$count features found for genome $genomeID.") if T(3);              Trace("$count features found for genome $genomeID.") if T(3);
414              # Get the attributes for this genome and put them in a hash by feature ID.              # Get the attributes for this genome and put them in a hash by feature ID.
415              my $attributes = GetGenomeAttributes($fig, $genomeID, \@fids, $propKeys);              my $attributes = GetGenomeAttributes($fig, $genomeID, \@fids, $propKeys);
416                Trace("Looping through features for $genomeID.") if T(3);
417              # Set up for our duplicate-feature check.              # Set up for our duplicate-feature check.
418              my $oldFeatureID = "";              my $oldFeatureID = "";
419              # Loop through the features.              # Loop through the features.
# Line 615  Line 620 
620                      $loadFeature->Put($featureID, 1, $user, $quality, $celloValue, $type, $assignment, $cleanWords, $locations);                      $loadFeature->Put($featureID, 1, $user, $quality, $celloValue, $type, $assignment, $cleanWords, $locations);
621                  }                  }
622              }              }
623                Trace("Genome $genomeID processed.") if T(3);
624          }          }
625      }      }
626      # Finish the loads.      # Finish the loads.

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