From: Tara L Andrews <tla@mit.edu>
Date: Sat, 5 Nov 2011 11:16:58 +0000 (+0100)
Subject: just export variants; Analysis really needs a refactor now.
X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?p=scpubgit%2Fstemmatology.git;a=commitdiff_plain;h=d1348d38c3cbf26ac9ea4f3e598e9a0922333d01

just export variants; Analysis really needs a refactor now.
---

diff --git a/group_vars.pl b/group_vars.pl
index a6f7a5e..229ff79 100644
--- a/group_vars.pl
+++ b/group_vars.pl
@@ -3,7 +3,9 @@
 use lib 'lib';
 use strict;
 use warnings;
+use JSON;
 use Text::Tradition;
+use Text::Tradition::Analysis qw/ group_variants /;
 use Text::Tradition::Stemma;
 
 binmode STDERR, ":utf8";
@@ -17,163 +19,15 @@ my %args = ( 'input' => $informat,
              'file'  => $ARGV[0] );
 my $tradition = Text::Tradition->new( %args );
 
-# Parse the stemma hypothesis
-my $stemma = Text::Tradition::Stemma->new( 
-    'collation' => $tradition->collation,
-    'dot' => $ARGV[1],
-    );
+# Parse the stemma data
+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.
-# Also return the reading objects in the table, rather than just the words.
+my $wits = {};
+map { $wits->{$_} = 1 } $stemma->witnesses;
 
-my $all_wits_table = $tradition->collation->make_alignment_table( 'refs' );
+my $variant_groups = group_variants( $tradition->collation, $wits );
 
-# For each column in the alignment table, we want to see if the existing
-# groupings of witnesses match our stemma hypothesis. We also want, at the
-# end, to produce an HTML table with all the variants.
-my $html_columns = 0;
-my $html_data = [];
-my $total = 0; # Keep track of the total number of variant locations
-
-# Strip the list of sigla and save it for correlation to the readings.
-my $col_wits = shift @$all_wits_table;
-    
-foreach my $i ( 0 .. $#$all_wits_table ) {
-    # For each column in the table, group the readings by witness.
-    my $rdg_wits = {};
-    my $col_rdgs = shift @$all_wits_table;
-    my $rank;
-    foreach my $j ( 0 .. $#{$col_rdgs} ) {
-        my $rdg = $col_rdgs->[$j];
-        $rank = $rdg->rank if $rdg;  # Save the rank for later display
-        my $rdg_text = '(omitted)';  # Initialize in case of empty reading
-        if( $rdg ) {
-            $rdg_text = $rdg->is_lacuna ? undef : $rdg->text; # Don't count lacunae
-        }
-        if( defined $rdg_text ) {
-            # Initialize the witness array if we haven't got one yet
-            $rdg_wits->{$rdg_text} = [] unless $rdg_wits->{$rdg_text};
-            # Add the relevant witness, subject to a.c. logic
-            add_variant_wit( $rdg_wits->{$rdg_text}, $col_wits->[$j] );
-        }
-    }
-    
-    # See if this column has any potentially genealogical variants.
-    # If not, skip to the next.
-    $total++ unless scalar keys %$rdg_wits == 1;
-    my( $groups, $readings ) = useful_variant( $rdg_wits );
-    next unless $groups && $readings;  
-    $html_columns = scalar @$groups if scalar @$groups > $html_columns;
-    
-    # We can already look up witnesses for a reading; we also want to look
-    # up readings for a given witness.
-    my $group_readings = {};
-    foreach my $x ( 0 .. $#$groups ) {
-        $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x];
-    }
-    
-    # For all the groups with more than one member, collect the list of all
-    # contiguous vertices needed to connect them.
-    # TODO: deal with a.c. reading logic
-    my $sc = analyze_variant_location( $group_readings, $groups, $stemma->apsp );
-    print wit_stringify( $groups ) . ' - ' . join( " / ", @$readings ) . "\n";
-    foreach my $rdg ( keys %$sc ) {
-        my $var = $sc->{$rdg};
-        print "\tReadings '$rdg' and '$var' are not genealogical\n";
-    }
-    
-    # Now run the same analysis given the calculated distance tree(s).
-    foreach my $tree ( 0 .. $#{$stemma->distance_trees} ) {
-        my $dc = analyze_variant_location( $group_readings, $groups,    
-                                           $stemma->distance_apsps->[$tree] );
-        foreach my $rdg ( keys %$dc ) {
-            my $var = $dc->{$rdg};
-            print "\tReadings '$rdg' and '$var' disregarded by parsimony on tree $tree\n";
-        }
-    }
-
-    # Record that we used this variant in an analysis
-    push( @$html_data, [ $rank, $readings, $sc ] );
-}
-
-# Save the stemma picture
-open( STEMMA, ">stemma_graph.svg" ) or die "Could not open stemma graph to write";
-binmode STEMMA, ":utf8";
-print STEMMA $stemma->as_svg;
-close STEMMA;
-
-printf( "Ran analysis on %d / %d variant locations\n", scalar @$html_data, $total );
-
-sub analyze_variant_location {
-    my( $group_readings, $groups, $apsp ) = @_;
-    my %contig;
-    my $conflict = {};
-    foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) {
-        my @members = @$g;
-        my $gst = wit_stringify( $g );
-        map { $contig{$_} = $gst } @members; # The witnesses need themselves to be 
-                                             # in their collection.
-        next unless @members > 1;
-        my $curr = pop @members;
-        foreach my $m ( @members ) {
-            foreach my $v ( $apsp->path_vertices( $curr, $m ) ) {
-                $contig{$v} = $gst unless exists $contig{$v};
-                next if $contig{$v} eq $gst;
-                # print STDERR "Conflict at $v between group $gst and group " 
-                #     . $contig{$v} . "\n";
-                # Record what is conflicting.
-                $conflict->{$group_readings->{$gst}} = $group_readings->{$contig{$v}};
-            }
-        }
-    }
-    return $conflict;
-}
-
-# 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, $readings->{$var} );
-        push( @$text, $var );
-    }
-    return( $groups, $text );
-}
-
-# Take an array of witness groupings and produce a string like
-# A,B / C,D,E / F
-
-sub wit_stringify {
-    my $groups = shift;
-    my @gst;
-    # If we were passed an array of witnesses instead of an array of 
-    # groupings, then "group" the witnesses first.
-    unless( ref( $groups->[0] ) ) {
-        my $mkgrp = [ $groups ];
-        $groups = $mkgrp;
-    }
-    foreach my $g ( @$groups ) {
-        push( @gst, join( ',', @$g ) );
-    }
-    return join( ' / ', @gst );
-}
-    
\ No newline at end of file
+print encode_json( $variant_groups );
\ No newline at end of file
diff --git a/lib/Text/Tradition/Analysis.pm b/lib/Text/Tradition/Analysis.pm
index a717529..5d4e335 100644
--- a/lib/Text/Tradition/Analysis.pm
+++ b/lib/Text/Tradition/Analysis.pm
@@ -2,9 +2,13 @@ package Text::Tradition::Analysis;
 
 use strict;
 use warnings;
+use Exporter 'import';
 use Text::Tradition;
 use Text::Tradition::Stemma;
 
+use vars qw/ @EXPORT_OK /;
+@EXPORT_OK = qw/ run_analysis group_variants wit_stringify /;
+
 sub new {
 	my( $class, $args ) = @_;
 	my $self = {};
@@ -107,7 +111,6 @@ sub run_analysis {
 		
 		# For all the groups with more than one member, collect the list of all
 		# contiguous vertices needed to connect them.
-		$DB::single = 1;
 		my $variant_row = analyze_variant_location( $group_readings, $groups, 
 		    $stemma->graph, $lacunose );
 		$variant_row->{'id'} = $rank;
@@ -145,6 +148,56 @@ sub run_analysis {
 	push( @{$self->{'data'}}, $data );
 }
 
+sub group_variants {
+	my( $c, $wits ) = @_;
+	my $variant_groups = [];
+	
+	my $all_wits_table = $c->make_alignment_table( 'refs', $wits );
+	# Strip the list of sigla and save it for correlation to the readings.
+	my $col_wits = shift @$all_wits_table;
+	# Any witness in the stemma that has no row should be noted.
+    foreach ( @$col_wits ) {
+        $wits->{$_}++; # Witnesses present in table and stemma now have value 2.
+    }
+    my @not_collated = grep { $wits->{$_} == 1 } keys %$wits;	
+	foreach my $i ( 0 .. $#$all_wits_table ) {
+		# For each column in the table, group the readings by witness.
+		my $rdg_wits = {};
+		my $col_rdgs = shift @$all_wits_table;
+		my $rank;
+		my $lacunose = [ @not_collated ];
+		foreach my $j ( 0 .. $#{$col_rdgs} ) {
+			my $rdg = $col_rdgs->[$j];
+			my $rdg_text = '(omitted)';  # Initialize in case of empty reading
+			if( $rdg ) {
+			    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
+				$rdg_wits->{$rdg_text} = [] unless $rdg_wits->{$rdg_text};
+				# Add the relevant witness, subject to a.c. logic
+				add_variant_wit( $rdg_wits->{$rdg_text}, $col_wits->[$j],
+					$c->ac_label );
+			}
+		}
+		
+		# See if this column has any potentially genealogical variants.
+		# If not, skip to the next.
+		my( $groups, $readings ) = useful_variant( $rdg_wits );
+		next unless $groups && $readings;  
+
+		push( @$variant_groups, $groups );
+	}
+	return $variant_groups;
+}
+
 # variant_row -> genealogical
 #             -> readings [ { text, group, conflict, missing } ]