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";
'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
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 = {};
# 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'} = $rank;
push( @{$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 } ]
projects / scpubgit/stemmatology.git / commitdiff