Merge branch 'master' of github.com:tla/stemmatology

[scpubgit/stemmatology.git] / lib / Text / Tradition / Analysis.pm

diff --git a/lib/Text/Tradition/Analysis.pm b/lib/Text/Tradition/Analysis.pm
index 1de487f..7d1c7aa 100644 (file)
--- a/lib/Text/Tradition/Analysis.pm
+++ b/lib/Text/Tradition/Analysis.pm
@@ -23,15 +23,10 @@ sub run_analysis {
        my $svg;
        my $variants = [];
        
-       # Read in the file and stemma
-       my @lines;
-       open( INFILE, "$file" ) or die "Could not read $file";
-       binmode INFILE, ':utf8';
-       @lines = <INFILE>;
-       close INFILE;
-       
+       # Read in the file and stemma   
        my $tradition = Text::Tradition->new( 
-               'Self' => join( '', @lines ),
+               'input'  => 'Self',
+               'file'   => $file,
                'linear' => 1,
                );
        my $stemma = Text::Tradition::Stemma->new(
@@ -65,13 +60,19 @@ sub run_analysis {
                my $rdg_wits = {};
                my $col_rdgs = shift @$all_wits_table;
                my $rank;
+               my $lacunose = [];
                foreach my $j ( 0 .. $#{$col_rdgs} ) {
                        my $rdg = $col_rdgs->[$j];
                        my $rdg_text = '(omitted)';  # Initialize in case of empty reading
                        if( $rdg ) {
-                               $rdg_text = $rdg->is_lacuna ? undef : $rdg->text; # Don't count lacunae
-                               # Get the rank from any real reading; they should be identical.
-                               $rank = $rdg->rank unless $rank || $rdg->is_lacuna;
+                           if( $rdg->is_lacuna ) {
+                               $rdg_text = undef;   # Don't count lacunae
+                               push( @$lacunose, $col_wits->[$j] );
+                           } else {
+                               $rdg_text = $rdg->text; 
+                                   # Get the rank from any real reading; they should be identical.
+                                   $rank = $rdg->rank;
+                               }
                        }
                        if( defined $rdg_text ) {
                                # Initialize the witness array if we haven't got one yet
@@ -107,7 +108,9 @@ sub run_analysis {
                $variant_row->{'genealogical'} = keys %$sc ? 1 : undef;
                foreach my $grp ( sort keys %$group_readings ) {
                        my $rdg = $group_readings->{$grp};
-                       push( @{$variant_row->{'readings'}}, { 'text' => $rdg, 'group' => $grp } );
+                       push( @{$variant_row->{'readings'}}, 
+                             { 'text' => $rdg, 'group' => $grp,
+                               'missing' => wit_stringify( $lacunose ) } );
                }
                
                # Now run the same analysis given the calculated distance tree(s).