--- SproutLoad.pm 2007/09/10 18:16:54 1.87 +++ SproutLoad.pm 2007/11/05 22:52:06 1.88 @@ -12,6 +12,7 @@ use Stats; use BasicLocation; use HTML; + use AliasAnalysis; =head1 Sprout Load Methods @@ -102,6 +103,7 @@ # Here we want all the complete genomes and an access code of 1. my @genomeList = $fig->genomes(1); %genomes = map { $_ => 1 } @genomeList; + Trace(scalar(keys %genomes) . " genomes found.") if T(3); } else { my $type = ref $genomeFile; Trace("Genome file parameter type is \"$type\".") if T(3); @@ -397,7 +399,9 @@ } else { Trace("Generating feature data.") if T(2); # Now we loop through the genomes, generating the data for each one. - for my $genomeID (sort keys %{$genomeHash}) { + my @allGenomes = sort keys %{$genomeHash}; + Trace(scalar(@allGenomes) . " genomes found in list.") if T(3); + for my $genomeID (@allGenomes) { Trace("Loading features for genome $genomeID.") if T(3); $loadFeature->Add("genomeIn"); # Get the feature list for this genome. @@ -409,6 +413,7 @@ Trace("$count features found for genome $genomeID.") if T(3); # Get the attributes for this genome and put them in a hash by feature ID. my $attributes = GetGenomeAttributes($fig, $genomeID, \@fids, $propKeys); + Trace("Looping through features for $genomeID.") if T(3); # Set up for our duplicate-feature check. my $oldFeatureID = ""; # Loop through the features. @@ -615,6 +620,7 @@ $loadFeature->Put($featureID, 1, $user, $quality, $celloValue, $type, $assignment, $cleanWords, $locations); } } + Trace("Genome $genomeID processed.") if T(3); } } # Finish the loads.