refrain from counting hypotheticals in groups; fix bugs relating to array skew

diff --git a/lib/Text/Tradition/Analysis.pm b/lib/Text/Tradition/Analysis.pm
index 30475c7..bbf3ee5 100644 (file)
--- a/lib/Text/Tradition/Analysis.pm
+++ b/lib/Text/Tradition/Analysis.pm
@@ -149,8 +149,10 @@ sub run_analysis {
        
        # Group the variants to send to the solver
        my @groups;
+       my @use_ranks;
        my %lacunae;
        foreach my $rank ( @ranks ) {
+               $DB::single = 1 if $rank == 1003;
                my $missing = [ @lacunose ];
                my $rankgroup = group_variants( $tradition, $rank, $missing, \@collapse );
                if( $opts{'exclude_type1'} ) {
@@ -159,29 +161,36 @@ sub run_analysis {
                                $stemma->graph, $c->ac_label );
                        next unless @$rdgs;
                }
+               push( @use_ranks, $rank );
                push( @groups, $rankgroup );
                $lacunae{$rank} = $missing;
        }
-       $DB::single = 1;
        # Parse the answer
        my $answer = solve_variants( $stemma, @groups );
 
        # Do further analysis on the answer
        my $conflict_count = 0;
-       foreach my $idx ( 0 .. $#ranks ) {
+       foreach my $idx ( 0 .. $#use_ranks ) {
                my $location = $answer->{'variants'}->[$idx];
                # Add the rank back in
-               $location->{'id'} = $ranks[$idx];
+               $location->{'id'} = $use_ranks[$idx];
                # Add the lacunae back in
-               $location->{'missing'} = $lacunae{$ranks[$idx]};
+               $location->{'missing'} = $lacunae{$use_ranks[$idx]};
+               my %lmiss;
+               map { $lmiss{$_} = 1 } @{$location->{'missing'}};
                # Run the extra analysis we need.
                analyze_location( $tradition, $stemma->graph, $location );
-               # Add the reading text back in
                foreach my $rdghash ( @{$location->{'readings'}} ) {
                        $conflict_count++ 
                                if exists $rdghash->{'conflict'} && $rdghash->{'conflict'};
+                       # Add the reading text back in
                        my $rdg = $c->reading( $rdghash->{'readingid'} );
                        $rdghash->{'text'} = $rdg ? $rdg->text : $rdghash->{'readingid'};
+                       # Remove lacunose witnesses from this reading's list now that the
+                       # analysis is done
+                       my @realgroup;
+                       map { push( @realgroup, $_ ) unless $lmiss{$_} } $rdghash->{'group'};
+                       $rdghash->{'group'} = \@realgroup;
                }
        }
        $answer->{'conflict_count'} = $conflict_count;
@@ -322,7 +331,7 @@ sub solve_variants {
                        }
                }
                my $input_group = $groups[$idx];
-               foreach my $k ( sort keys %$input_group ) {
+               foreach my $k ( keys %$input_group ) {
                        my $cg = shift @$calc_groups;
                        $input_group->{$k} = $cg;
                }
@@ -330,7 +339,8 @@ sub solve_variants {
                        'genealogical' => $result,
                        'readings' => [],
                };
-               foreach my $k ( keys %$input_group ) {
+               foreach my $k ( sort { @{$input_group->{$b}} <=> @{$input_group->{$a}} }
+                                                       keys %$input_group ) {
                        push( @{$vstruct->{'readings'}}, 
                                  { 'readingid' => $k, 'group' => $input_group->{$k}} );
                }