X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2FText%2FTradition%2FAnalysis.pm;h=910f9947e1f368ef7f76398cf7c197b0aab28b52;hb=b979e2e269da9877011d671af5b2857f2189fc6e;hp=c74b96d99f8b65fe7ce083b1bafb19d44884e049;hpb=9c52877edc72b6e277432b2c5bed47569a626b79;p=scpubgit%2Fstemmatology.git diff --git a/lib/Text/Tradition/Analysis.pm b/lib/Text/Tradition/Analysis.pm index c74b96d..910f994 100644 --- a/lib/Text/Tradition/Analysis.pm +++ b/lib/Text/Tradition/Analysis.pm @@ -2,166 +2,343 @@ package Text::Tradition::Analysis; use strict; use warnings; +use Benchmark; +use Exporter 'import'; use Text::Tradition; use Text::Tradition::Stemma; -sub new { - my( $class, $args ) = @_; - my $self = {}; - # Our object needs to have a stemma graph and a variant table. - my( $svg, $variants ) = run_analysis( $args->{'file'}, $args->{'stemmadot'} ); - $self->{'svg'} = $svg; - $self->{'variants'} = $variants; - - bless( $self, $class ); - return $self; -} +use vars qw/ @EXPORT_OK /; +@EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /; sub run_analysis { - my( $file, $stemmadot ) = @_; + my( $tradition ) = @_; # What we will return - my $svg; my $variants = []; + my $data = {}; - # Read in the file and stemma - my $tradition = Text::Tradition->new( - 'input' => 'Self', - 'file' => $file, - 'linear' => 1, - ); - my $stemma = Text::Tradition::Stemma->new( - 'collation' => $tradition->collation, - 'dot' => $stemmadot, - ); - # We will return the stemma picture - $svg = $stemma->as_svg; - ### DIRTY HACK - $svg =~ s/transform=\"scale\(1 1\)/transform=\"scale\(0.7 0.7\)/; - + # We need a stemma in order to run this... + unless( $tradition->stemma_count ) { + warn "Tradition '" . $tradition->name . "' has no stemma to analyze"; + return undef; + } + my $stemma = $tradition->stemma(0); # TODO allow multiple + # 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; + # For each column in the alignment table, we want to see if the existing + # groupings of witnesses match our stemma hypothesis. We also need to keep + # track of the maximum number of variants at any one location. + my $max_variants = 0; + my ( $genealogical, $conflicts ) = ( 0, 0, 0 ); - my $all_wits_table = $tradition->collation->make_alignment_table( 'refs' ); + my $variant_groups = group_variants( $tradition->collation, $wits ); + foreach my $rank ( 0 .. $#{$variant_groups} ) { + my $groups = $variant_groups->[$rank]->{'groups'}; + my $readings = $variant_groups->[$rank]->{'readings'}; + my $lacunose = $variant_groups->[$rank]->{'lacunose'}; + + $max_variants = scalar @$groups if scalar @$groups > $max_variants; + + # 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. + my $variant_loc = analyze_variant_location( $group_readings, $groups, + $stemma->graph, $lacunose ); + $variant_loc->{'id'} = $rank; + $genealogical++ if $variant_loc->{'genealogical'}; + $conflicts += grep { $_->{'conflict'} } @{$variant_loc->{'readings'}}; + + # Now run the same analysis given the calculated distance tree(s). +# my @trees = @{$stemma->distance_trees}; +# if( @trees ) { +# foreach my $tree ( 0 .. $#trees ) { +# my $dc = analyze_variant_location( $group_readings, $groups, $tree, $lacunose, 'undirected' ); +# foreach my $rdg ( keys %$dc ) { +# my $var = $dc->{$rdg}; +# # TODO Do something with this +# } +# } +# } + + # Record that we used this variant in an analysis + push( @$variants, $variant_loc ); + } + + # Go through our variant locations, after we have seen all of them once, + # and add the number of empty columns needed by each. + foreach my $row ( @$variants ) { + my $empty = $max_variants - scalar @{$row->{'readings'}}; + $row->{'empty'} = $empty; + } - # 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 + $data->{'variants'} = $variants; + $data->{'variant_count'} = $tradition->collation->end->rank - 1; + $data->{'conflict_count'} = $conflicts; + $data->{'genealogical_count'} = $genealogical; + return $data; +} + +sub group_variants { + my( $c, $wits ) = @_; + my $variant_groups = []; + # 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 = $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; - - # We will return a data structure, an array for each row that looks like: - # { id = X, genealogical = Y, readings = [ text = X, group = Y], empty = N } - foreach my $i ( 0 .. $#$all_wits_table ) { + my @table_wits = map { $_->{'witness'} } @{$all_wits_table->{'alignment'}}; + # Any witness in the stemma that has no row should be noted. + foreach ( @table_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->{'length'} - 1 ) { # 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 = []; - foreach my $j ( 0 .. $#{$col_rdgs} ) { - my $rdg = $col_rdgs->[$j]; + my @col_rdgs = map { $_->{tokens}->[$i] } @{$all_wits_table->{'alignment'}}; + 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 ) { + if( $rdg->{'t'}->is_lacuna ) { $rdg_text = undef; # Don't count lacunae - push( @$lacunose, $col_wits->[$j] ); + push( @$lacunose, $table_wits[$j] ); } else { - $rdg_text = $rdg->text; - # Get the rank from any real reading; they should be identical. - $rank = $rdg->rank; + $rdg_text = $rdg->{'t'}->text; } } 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], - $tradition->collation->ac_label ); + add_variant_wit( $rdg_wits->{$rdg_text}, $table_wits[$j], + $c->ac_label ); } } # 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; - - # Initialize the data structure for the row that we will return - my $variant_row = {'id' => $rank, 'readings' => [] }; - # Keep track of our widest row - $html_columns = scalar @$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 $conflict = analyze_variant_location( - $group_readings, $groups, $stemma->apsp ); - $variant_row->{'genealogical'} = keys %$conflict ? undef : 1; - foreach my $grp ( sort keys %$group_readings ) { - my $rdg = $group_readings->{$grp}; - my $in_conflict = exists $conflict->{$grp}; - push( @{$variant_row->{'readings'}}, - { 'text' => $rdg, 'group' => $grp, 'conflict' => $in_conflict, - 'missing' => wit_stringify( $lacunose ) } ); - } - - # 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}; -# } -# } - - # Record that we used this variant in an analysis - push( @$variants, $variant_row ); - } - - # Go through our variant rows and add the number of empty columns we need. - foreach my $row ( @$variants ) { - my $empty = $html_columns - scalar @{$row->{'readings'}}; - $row->{'empty'} = $empty; + + push( @$variant_groups, + { 'groups' => $groups, 'readings' => $readings, 'lacunose' => $lacunose } ); } - - return( $svg, $variants ); + return $variant_groups; } + + +# variant_row -> genealogical +# -> readings [ { text, group, conflict, missing } ] + sub analyze_variant_location { - my( $group_readings, $groups, $apsp ) = @_; - my %contig; + my( $group_readings, $groups, $graph, $lacunose, $undirected ) = @_; + my $contig = {}; + my $subgraph = {}; + my $is_conflicted; my $conflict = {}; - foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) { - my @members = @$g; + my $missing = {}; + map { $missing->{$_} = 1 } @$lacunose; + my $variant_row = { 'readings' => [] }; + # Mark each ms as in its own group, first. + foreach my $g ( @$groups ) { 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}}; + map { $contig->{$_} = $gst } @$g; + } + # Now for each unmarked node in the graph, initialize an array + # for possible group memberships. We will use this later to + # resolve potential conflicts. + map { $contig->{$_} = [] unless $contig->{$_} } $graph->vertices; + foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) { + my $gst = wit_stringify( $g ); # This is the group name + my $reachable = { $g->[0] => 1 }; + # Copy the graph, and delete all non-members from the new graph. + my $part = $graph->copy; + my $group_root; + $part->delete_vertices( + grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices ); + + # Now look to see if our group is connected. + if( $undirected ) { # For use with distance trees etc. + # Find all vertices reachable from the first (arbitrary) group + # member. If we are genealogical this should include them all. + map { $reachable->{$_} = 1 } $part->all_reachable( $g->[0] ); + # TODO This is a terrible way to do distance trees, since all + # non-leaf nodes are included in every graph part now. We may + # have to go back to SPDP. + } else { + if( @$g > 1 ) { + # Dispense with the trivial case of one reading. + # We have to take directionality into account. + # How many root nodes do we have? + my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst } + $part->source_vertices; + # Assuming that @$g > 1, find the first root node that has at + # least one successor belonging to our group. If this reading + # is genealogical, there should be only one, but we will check + # that implicitly later. + my $nodes_in_subtree = 0; + foreach my $root ( @roots ) { + # Prune the tree to get rid of extraneous hypotheticals. + $root = prune_subtree( $part, $root, $contig ); + # Get all the successor nodes of our root. + my $tmp_reach = { $root => 1 }; + map { $tmp_reach->{$_} = 1 } $part->all_successors( $root ); + # Skip this root if none of our successors are in our group + # (e.g. isolated 'hypothetical' witnesses with no group) + next unless grep { $contig->{$_} } keys %$tmp_reach; + if( keys %$tmp_reach > $nodes_in_subtree ) { + $nodes_in_subtree = keys %$tmp_reach; + $reachable = $tmp_reach; + $group_root = $root; + } + } + } # else it is a single-node group, nothing to calculate. + } + + # None of the 'reachable' nodes should be marked as being in another + # group. Paint the 'hypotheticals' with our group while we are at it, + # unless there is a conflict present. + foreach ( keys %$reachable ) { + if( ref $contig->{$_} ) { + push( @{$contig->{$_}}, $gst ); + } elsif( $contig->{$_} ne $gst ) { + $conflict->{$group_readings->{$gst}} = $group_readings->{$contig->{$_}}; + } # else it is an 'extant' node marked with our group already. + } + # None of the unreachable nodes should be in our group either. + foreach ( $part->vertices ) { + next if $reachable->{$_}; + if( $contig->{$_} eq $gst ) { + $conflict->{$group_readings->{$gst}} = $group_readings->{$gst}; + last; } } + + # Now, if we have a conflict, we can write the reading in full. If not, + # we have to save the subgraph so that we can resolve possible conflicts + # on hypothetical nodes. + $is_conflicted = 1 if exists $conflict->{$group_readings->{$gst}}; + + # Write the reading. + my $reading = { 'text' => $group_readings->{$gst}, + 'missing' => wit_stringify( $lacunose ), + 'group' => $gst }; # This will change if we find no conflict + if( $is_conflicted ) { + $reading->{'conflict'} = $conflict->{$group_readings->{$gst}} + } else { + # Save the relevant subgraph. + $subgraph->{$gst} = { 'graph' => $part, + 'root' => $group_root, + 'reachable' => $reachable }; + } + push( @{$variant_row->{'readings'}}, $reading ); } - return $conflict; + + # Now that we have gone through all the rows, check the hypothetical + # readings for conflict if we haven't found one yet. + if( keys %$subgraph && !keys %$conflict ) { + my @resolve; + foreach ( keys %$contig ) { + next unless ref $contig->{$_}; + if( scalar @{$contig->{$_}} > 1 ) { + push( @resolve, $_ ); + } else { + $contig->{$_} = scalar @{$contig->{$_}} ? $contig->{$_}->[0] : ''; + } + } + # Do we still have a possible conflict? + my $still_contig = {}; + foreach my $h ( @resolve ) { + # For each of the hypothetical readings with more than one possibility, + # try deleting it from each of its member subgraphs in turn, and see + # if that breaks the contiguous grouping. + # TODO This can still break in a corner case where group A can use + # either vertex 1 or 2, and group B can use either vertex 2 or 1. + # Revisit this if necessary; it could get brute-force nasty. + foreach my $gst ( @{$contig->{$h}} ) { + my $gpart = $subgraph->{$gst}->{'graph'}->copy; + my $reachable = $subgraph->{$gst}->{'reachable'}; + $gpart->delete_vertex( $h ); + # Is everything else still reachable from the root? + # TODO If $h was the root, see if we still have a single root. + my %still_reachable = ( $subgraph->{$gst}->{'root'} => 1 ); + map { $still_reachable{$_} = 1 } + $gpart->all_successors( $subgraph->{$gst}->{'root'} ); + foreach my $v ( keys %$reachable ) { + next if $v eq $h; + if( !$still_reachable{$v} + && ( $contig->{$v} eq $gst + || ( exists $still_contig->{$v} + && $still_contig->{$v} eq $gst ) ) ) { + # We need $h. + if( exists $still_contig->{$h} ) { + # Conflict! + $conflict->{$group_readings->{$gst}} = + $group_readings->{$still_contig->{$h}}; + } else { + $still_contig->{$h} = $gst; + } + last; + } # else we don't need $h in this group. + } + } + } + + # Now, assuming no conflict, we have some hypothetical vertices in + # $still_contig that are the "real" group memberships. Replace these + # in $contig. + unless ( keys %$conflict ) { + foreach my $v ( keys %$contig ) { + next unless ref $contig->{$v}; + $contig->{$v} = $still_contig->{$v}; + } + } + } + + # Now write the group and conflict information into the respective rows. + foreach my $rdg ( @{$variant_row->{'readings'}} ) { + $rdg->{'conflict'} = $conflict->{$rdg->{'text'}}; + next if $rdg->{'conflict'}; + my @members = grep { $contig->{$_} eq $rdg->{'group'} && !$missing->{$_} } + keys %$contig; + $rdg->{'group'} = wit_stringify( \@members ); + } + + $variant_row->{'genealogical'} = !( keys %$conflict ); + return $variant_row; } +sub prune_subtree { + my( $tree, $root, $contighash ) = @_; + # First, delete hypothetical leaves / orphans until there are none left. + my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } + $tree->successorless_vertices; + while( @orphan_hypotheticals ) { + $tree->delete_vertices( @orphan_hypotheticals ); + @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } + $tree->successorless_vertices; + } + # Then delete a hypothetical root with only one successor, moving the + # root to the child. + while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) { + my @nextroot = $tree->successors( $root ); + $tree->delete_vertex( $root ); + $root = $nextroot[0]; + } + # The tree has been modified in place, but we need to know the new root. + return $root; +} # 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 {