);
# 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;
return $self->csv;
}
-# TODO Make an alignment table at the end of initialization to check for
-# duplicate nodes from mis-collation.
-
-
+# Make an alignment table - $noderefs controls whether the objects
+# in the table are the nodes or simply their readings.
sub make_alignment_table {
- my( $self, $in_rows ) = shift;
+ my( $self, $noderefs ) = @_;
unless( $self->linear ) {
warn "Need a linear graph in order to make an alignment table";
return;
my @all_pos = sort { $a <=> $b } $self->possible_positions;
foreach my $wit ( $self->tradition->witnesses ) {
# print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
- my @row = _make_witness_row( $wit->path, \@all_pos );
+ my @row = _make_witness_row( $wit->path, \@all_pos, $noderefs );
unshift( @row, $wit->sigil );
push( @$table, \@row );
if( $wit->has_ante_corr ) {
- my @ac_row = _make_witness_row( $wit->uncorrected_path, \@all_pos );
+ my @ac_row = _make_witness_row( $wit->uncorrected_path, \@all_pos, $noderefs );
unshift( @ac_row, $wit->sigil . $self->ac_label );
push( @$table, \@ac_row );
}
}
- return $table if $in_rows;
-
+
# Return a table where the witnesses read in columns rather than rows.
my $turned = _turn_table( $table );
return $turned;
}
sub _make_witness_row {
- my( $path, $positions ) = @_;
+ my( $path, $positions, $noderefs ) = @_;
my %char_hash;
map { $char_hash{$_} = undef } @$positions;
foreach my $rdg ( @$path ) {
my $rtext = $rdg->text;
$rtext = '#LACUNA#' if $rdg->is_lacuna;
- $char_hash{$rdg->rank} = $rtext;
+ $char_hash{$rdg->rank} = $noderefs ? $rdg : $rtext;
}
my @row = map { $char_hash{$_} } @$positions;
# Fill in lacuna markers for undef spots in the row
my $last_el = shift @row;
my @filled_row = ( $last_el );
foreach my $el ( @row ) {
- if( $last_el && $last_el eq '#LACUNA#' && !defined $el ) {
- $el = '#LACUNA#';
+ # If we are using node reference, make the lacuna node appear many times
+ # in the table. If not, use the lacuna tag.
+ if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
+ $el = $noderefs ? $last_el : '#LACUNA#';
}
push( @filled_row, $el );
$last_el = $el;
return @filled_row;
}
+# Tiny utility function to say if a table element is a lacuna
+sub _el_is_lacuna {
+ my $el = shift;
+ return 1 if $el eq '#LACUNA#';
+ return 1 if ref( $el ) eq 'Text::Tradition::Collation::Reading'
+ && $el->is_lacuna;
+ return 0;
+}
+
# Helper to turn the witnesses along columns rather than rows. Assumes
# equal-sized rows.
sub _turn_table {
return @next_nodes;
}
+# Another method to make up for rough collation methods. If the same reading
+# appears multiple times at the same rank, collapse the nodes.
+sub flatten_ranks {
+ my $self = shift;
+ my %unique_rank_rdg;
+ foreach my $rdg ( $self->readings ) {
+ next unless $rdg->has_rank;
+ my $key = $rdg->rank . "||" . $rdg->text;
+ if( exists $unique_rank_rdg{$key} ) {
+ # Combine!
+ print STDERR "Combining readings at same rank: $key\n";
+ $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
+ } else {
+ $unique_rank_rdg{$key} = $rdg;
+ }
+ }
+}
+
+
sub possible_positions {
my $self = shift;
my %all_pos;
projects / scpubgit/stemmatology.git / commitdiff