);
# 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 $all_wits_table = $tradition->collation->make_alignment_table( 1 );
+my $all_wits_table = $tradition->collation->make_alignment_table( 'refs' );
# 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.
+# 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;
-# For each column in the table, group the readings by witness.
-
-my $used_vars = 0;
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];
- $rdg = '' unless $rdg; # We care about empty readings
- $rdg = undef if $rdg eq '#LACUNA#'; # ... unless they're lacunas
+ $rank = $rdg->rank if $rdg; # Save the rank for later display
+ my $rdg_text = '(omitted)'; # Initialize in case of empty reading
if( $rdg ) {
- $rdg_wits->{$rdg} = [] unless $rdg_wits->{$rdg};
- add_variant_wit( $rdg_wits->{$rdg}, $col_wits->[$j] );
+ $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;
+ next unless $groups && $readings;
+ $html_columns = scalar @$groups if scalar @$groups > $html_columns;
- # We can look up witnesses for a reading; we also want to look up readings
- # for a given witness.
+ # 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 $conflict = analyze_variant_location( $group_readings, $groups, $stemma->apsp );
+ my $sc = analyze_variant_location( $group_readings, $groups, $stemma->apsp );
print wit_stringify( $groups ) . ' - ' . join( " / ", @$readings ) . "\n";
- foreach my $rdg ( keys %$conflict ) {
- my $var = $conflict->{$rdg};
+ foreach my $rdg ( keys %$sc ) {
+ my $var = $sc->{$rdg};
print "\tReadings '$rdg' and '$var' are not genealogical\n";
}
- # Now run the same analysis given a distance tree.
- my $distance_apsp = $stemma->distance_trees->[0]->APSP_Floyd_Warshall();
- $conflict = analyze_variant_location( $group_readings, $groups, $distance_apsp );
- foreach my $rdg ( keys %$conflict ) {
- my $var = $conflict->{$rdg};
- print "\tReadings '$rdg' and '$var' disregarded by parsimony\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
- $used_vars++;
-
+ push( @$html_data, [ $rank, $readings, $sc ] );
}
-print "Found $used_vars useful variants in this analysis\n";
+
# 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;
+# Save the used variants as an HTML table
+open( TABLE, ">variant_table.html" ) or die "Could not save variant table";
+binmode TABLE, ":utf8";
+print TABLE "<table>\n";
+foreach my $row ( @$html_data ) {
+ my( $rank, $readings, $sc ) = @$row;
+ # Do we have a stemma conflict or a distance-tree conflict?
+ my $class = scalar keys %$sc ? 'coincidental' : 'genealogical';
+ print TABLE sprintf( "\t<tr id=\"%s\" class=\"%s\">\n", "variant-$rank", $class );
+ # Table row header should be the graph rank.
+ print TABLE "\t\t<th>$rank</th>\n";
+ my $ctr = 0;
+ foreach my $rdg ( @$readings ) {
+ print TABLE sprintf( "\t\t<td id=\"%s\">%s</td>\n", "item-$rank-$ctr", $rdg );
+ $ctr++;
+ }
+ # Pad out the table - is this necessary I wonder?
+ while( $ctr++ < $html_columns ) {
+ print TABLE "\t\t<td/>\n";
+ }
+ print TABLE "\t</tr>\n";
+}
+print TABLE "</table>\n";
+
+printf( "Ran analysis on %d / %d variant locations\n", scalar @$html_data, $total );
+
sub analyze_variant_location {
my( $group_readings, $groups, $apsp ) = @_;
my %contig;
projects / scpubgit/stemmatology.git / blobdiff