From: Tara L Andrews <tla@mit.edu>
Date: Fri, 30 Sep 2011 00:41:22 +0000 (+0200)
Subject: first forays in variant analysis
X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=commitdiff_plain;h=a5d533773d305632e3a82278cc6be9211db53c6b;p=scpubgit%2Fstemmatology.git

first forays in variant analysis
---

diff --git a/group_vars.pl b/group_vars.pl
new file mode 100644
index 0000000..ecde4de
--- /dev/null
+++ b/group_vars.pl
@@ -0,0 +1,125 @@
+#!/usr/bin/env perl
+
+use lib 'lib';
+use strict;
+use warnings;
+use Text::Tradition;
+use Text::Tradition::Stemma;
+
+binmode STDERR, ":utf8";
+binmode STDOUT, ":utf8";
+eval { no warnings; binmode $DB::OUT, ":utf8"; };
+
+my $informat = 'TEI';
+my $inbase;
+my $linear = 1;
+
+# Parse the tradition data
+
+my $input = $ARGV[0];
+my @lines;
+open( INFILE, "$input" ) or die "Could not read $input";
+binmode INFILE, ':utf8';
+@lines = <INFILE>;
+close INFILE;
+$input = join( '', @lines );
+
+my %args = ( $informat => $input,
+             'linear' => $linear );
+$args{'base'} = $inbase if $inbase;
+ my $tradition = Text::Tradition->new( %args );
+
+# Parse the stemma hypothesis
+my $stemma = Text::Tradition::Stemma->new( 
+    'collation' => $tradition->collation,
+    'dot' => $ARGV[1],
+    );
+
+# We have the collation, so get the alignment table with witnesses in rows.
+
+my $all_wits_table = $tradition->collation->make_alignment_table( 1 );
+
+# For each column in the alignment table, we want to see if the existing
+# groupings of witnesses match our stemma hypothesis.  First let's just go 
+# through the groupings.
+
+# Strip the list of sigla and save it for correlation to the readings.
+my $col_wits = shift @$all_wits_table;
+    
+# For each column in the table, group the readings by witness.
+
+my $useful_vars = 0;
+foreach my $i ( 0 .. $#$all_wits_table ) {
+    my $rdg_wits = {};
+    my $col_rdgs = shift @$all_wits_table;
+    foreach my $j ( 0 .. $#{$col_rdgs} ) {
+        my $rdg = $col_rdgs->[$j];
+        $rdg = '' unless $rdg;   # We care about empty readings
+        $rdg = undef if $rdg eq '#LACUNA#'; # ... unless they're lacunas
+        if( $rdg ) {
+            $rdg_wits->{$rdg} = [] unless $rdg_wits->{$rdg};
+            add_variant_wit( $rdg_wits->{$rdg}, $col_wits->[$j] );
+        }
+    }
+    
+    my( $groups, $readings ) = useful_variant( $rdg_wits );
+    next unless $groups && $readings;        
+    
+    # For all the groups with more than one member, make a group that contains
+    # all contiguous vertices to connect them.
+    # TODO Need to do pairwise comparison of groups - a variant location can
+    # have both coincidental and genealogical variants!
+    my %contig;
+    my $conflict;
+    foreach my $g ( @$groups ) {
+        my @members = split( /,/, $g );
+        next unless @members > 1;
+        map { $contig{$_} = $g } @members;
+        my $curr = pop @members;
+        foreach my $m ( @members ) {
+            foreach my $v ( $stemma->apsp->path_vertices( $curr, $m ) ) {
+                $contig{$v} = $g unless exists $contig{$v};
+                next if $contig{$v} eq $g;
+                # print STDERR "Conflict at $v between group $g and group " 
+                #     . $contig{$v} . "\n";
+                $conflict = 1;
+            }
+        }
+    }
+    print join( " / ", @$groups ) . ' - ' . join( " / ", @$readings ) . ' - ';
+    print $conflict ? "coincidental" : "genealogical";
+    print "\n";
+    $useful_vars++;
+    
+}
+print "Found $useful_vars useful variants\n";
+
+# Add the variant, subject to a.c. representation logic.
+# This assumes that we will see the 'main' version before the a.c. version.
+sub add_variant_wit {
+    my( $arr, $wit ) = @_;
+    my $acstr = $tradition->collation->ac_label;
+    my $skip;
+    if( $wit =~ /^(.*)\Q$acstr\E$/ ) {
+        my $real = $1;
+        $skip = grep { $_ =~ /^\Q$real\E$/ } @$arr;
+    } 
+    push( @$arr, $wit ) unless $skip;
+}
+
+# Return an answer if the variant is useful, i.e. if there are at least 2 variants
+# with at least 2 witnesses each.
+sub useful_variant {
+    my( $readings ) = @_;
+    my $total = keys %$readings;
+    foreach my $var ( keys %$readings ) {
+        $total-- if @{$readings->{$var}} == 1;
+    }
+    return( undef, undef ) if $total <= 1;
+    my( $groups, $text );
+    foreach my $var ( keys %$readings ) {
+        push( @$groups, join( ',', @{$readings->{$var}} ) );
+        push( @$text, $var );
+    }
+    return( $groups, $text );
+}