get transposition a.c. gap recognized as a gap

diff --git a/analysis/lib/Text/Tradition/Analysis.pm b/analysis/lib/Text/Tradition/Analysis.pm
index 44a8b73..aa02e85 100644 (file)
--- a/analysis/lib/Text/Tradition/Analysis.pm
+++ b/analysis/lib/Text/Tradition/Analysis.pm
@@ -321,6 +321,7 @@ sub group_variants {
        my $check_for_gaps = Set::Scalar->new();
        my %moved_wits;
        my $has_transposition;
+       my @transp_acgap;
        foreach my $tablewit ( @{$table->{'alignment'}} ) {
                my $rdg = $tablewit->{'tokens'}->[$rank-1];
                my $wit = $tablewit->{'witness'};
@@ -346,19 +347,21 @@ sub group_variants {
                                next if exists $readings_at_rank{$trdg->id};
                                $has_transposition = 1;
                                my @affected_wits = _table_witnesses( 
-                                       $table, $trdg, $lacunose, $aclabel );
+                                       $table, $trdg->rank, $trdg, $lacunose, $aclabel );
                                next unless @affected_wits;
                                map { $moved_wits{$_} = 1 } @affected_wits;
-                               my @thisloc_wits = _table_witnesses( $table, $rdg->{'t'}, 
+                               my @thisloc_wits = _table_witnesses( $table, $rank, $rdg->{'t'}, 
                                        $lacunose, $aclabel );
                                # Check to see if our affected wits have layers that do something
                                # wacky.
                                my %transploc_gaps;
                                map { $transploc_gaps{$_} = 1 } 
-                                       _table_witnesses( $table, undef, $lacunose, $aclabel );
+                                       _table_witnesses( $table, $trdg->rank, undef, $lacunose, $aclabel );
                                foreach my $aw ( @affected_wits ) {
-                                       push( @thisloc_wits, $aw.$aclabel ) 
-                                               if $transploc_gaps{$aw.$aclabel};
+                                       if( $transploc_gaps{$aw.$aclabel} ) {
+                                               push( @thisloc_wits, $aw.$aclabel );
+                                               push( @transp_acgap, $aw.$aclabel );
+                                       }
                                }
                                # Record which witnesses we should count as already analyzed when we 
                                # get to the transposed reading's own rank.
@@ -370,6 +373,9 @@ sub group_variants {
                        _add_to_witlist( $wit, $check_for_gaps, $aclabel );
                }
        }
+       # Push all the transposition layer gaps onto our list
+       $check_for_gaps->insert( @transp_acgap );
+       # Now remove from our 'gaps' any witnesses known to have been dealt with elsewhere.
        my $gap_wits = Set::Scalar->new();
        map { _add_to_witlist( $_, $gap_wits, $aclabel ) 
                unless $moved_wits{$_} } $check_for_gaps->members;
@@ -381,11 +387,11 @@ sub group_variants {
                next if exists $grouped_readings->{$rdg->id} 
                        && $grouped_readings->{$rdg->id} eq 'COLLAPSE';
                # Get the witness list, including from readings collapsed into this one.
-               my @wits = _table_witnesses( $table, $rdg, $lacunose, $aclabel );
+               my @wits = _table_witnesses( $table, $rdg->rank, $rdg, $lacunose, $aclabel );
                if( $collapse && $collapse->size ) {
                        my $filter = sub { $collapse->has( $_[0]->type ) };
                        foreach my $other ( $rdg->related_readings( $filter ) ) {
-                               my @otherwits = _table_witnesses( $table, $other, $lacunose, $aclabel );
+                               my @otherwits = _table_witnesses( $table, $other->rank, $other, $lacunose, $aclabel );
                                push( @wits, @otherwits );
                                $grouped_readings->{$other->id} = 'COLLAPSE';
                        }
@@ -439,8 +445,8 @@ sub _all_related {
 # Helper function to query the alignment table for all witnesses (a.c. included)
 # that have a given reading at its rank.
 sub _table_witnesses {
-       my( $table, $trdg, $lacunose, $aclabel ) = @_;
-       my $tableidx = $trdg->rank - 1;
+       my( $table, $rank, $trdg, $lacunose, $aclabel ) = @_;
+       my $tableidx = $rank - 1;
        my $has_reading = Set::Scalar->new();
        foreach my $row ( @{$table->{'alignment'}} ) {
                my $wit = $row->{'witness'};