use strict;
use warnings;
use Benchmark;
+use Encode qw/ encode_utf8 /;
use Exporter 'import';
+use JSON qw/ encode_json decode_json /;
+use LWP::UserAgent;
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 = {};
- bless( $self, $class );
- $self->{'data'} = [];
- foreach my $t ( @{$args->{'traditions'}} ) {
- $self->run_analysis( $t->{'file'}, $t->{'stemmadot'} );
+@EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /;
+
+=head1 NAME
+
+Text::Tradition::Analysis - functions for stemma analysis of a tradition
+
+=head1 SYNOPSIS
+
+ use Text::Tradition;
+ use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /;
+ my $t = Text::Tradition->new(
+ 'name' => 'this is a text',
+ 'input' => 'TEI',
+ 'file' => '/path/to/tei_parallel_seg_file.xml' );
+ $t->add_stemma( 'dotfile' => $stemmafile );
+
+ my $variant_data = run_analysis( $tradition );
+ # Recalculate rank $n treating all orthographic variants as equivalent
+ my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' );
+
+=head1 DESCRIPTION
+
+Text::Tradition is a library for representation and analysis of collated
+texts, particularly medieval ones. The Collation is the central feature of
+a Tradition, where the text, its sequence of readings, and its relationships
+between readings are actually kept.
+
+=head1 SUBROUTINES
+
+=head2 run_analysis( $tradition, %opts )
+
+Runs the analysis described in analyze_variant_location on every location in the
+collation of the given tradition, with the given options. These include:
+
+=over 4
+
+=item * stemma_id - Specify which of the tradition's stemmata to use. Default
+is 0 (i.e. the first).
+
+=item * ranks - Specify a list of location ranks to analyze; exclude the rest.
+
+=item * merge_types - Specify a list of relationship types, where related readings
+should be treated as identical for the purposes of analysis.
+
+=back
+
+=begin testing
+
+use Text::Tradition;
+use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /;
+
+my $datafile = 't/data/florilegium_tei_ps.xml';
+my $tradition = Text::Tradition->new( 'input' => 'TEI',
+ 'name' => 'test0',
+ 'file' => $datafile );
+my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" );
+
+my %expected_genealogical = (
+ 1 => 0,
+ 2 => 1,
+ 3 => 0,
+ 5 => 0,
+ 7 => 0,
+ 8 => 0,
+ 10 => 0,
+ 13 => 1,
+ 33 => 0,
+ 34 => 0,
+ 37 => 0,
+ 60 => 0,
+ 81 => 1,
+ 84 => 0,
+ 87 => 0,
+ 101 => 0,
+ 102 => 0,
+ 122 => 1,
+ 157 => 0,
+ 166 => 1,
+ 169 => 1,
+ 200 => 0,
+ 216 => 1,
+ 217 => 1,
+ 219 => 1,
+ 241 => 1,
+ 242 => 1,
+ 243 => 1,
+);
+
+my $data = run_analysis( $tradition );
+foreach my $row ( @{$data->{'variants'}} ) {
+ # Account for rows that used to be "not useful"
+ unless( exists $expected_genealogical{$row->{'id'}} ) {
+ $expected_genealogical{$row->{'id'}} = 1;
}
- return $self;
+ is( $row->{'genealogical'}, $expected_genealogical{$row->{'id'}},
+ "Got correct genealogical flag for row " . $row->{'id'} );
}
+is( $data->{'conflict_count'}, 34, "Got right conflict count" );
+is( $data->{'variant_count'}, 58, "Got right total variant number" );
+
+=end testing
+
+=cut
sub run_analysis {
- my( $self, $file, $stemmadot ) = @_;
- # 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,
- );
- $data->{'title'} = $tradition->name;
-
- my $stemma = Text::Tradition::Stemma->new(
- 'collation' => $tradition->collation,
- 'dot' => $stemmadot,
- );
- # We will return the stemma picture
- $svg = $stemma->as_svg( { size => "8,7.5" } );;
- $data->{'svg'} = $svg;
+ my( $tradition, %opts ) = @_;
+ my $c = $tradition->collation;
+
+ my $stemma_id = $opts{'stemma_id'} || 0;
+ my @ranks = @{$opts{'ranks'}} if ref( $opts{'ranks'} ) eq 'ARRAY';
+ my @collapse = @{$opts{'merge_types'}} if ref( $opts{'merge_types'} ) eq 'ARRAY';
+
+ # Get the stemma
+ my $stemma = $tradition->stemma( $stemma_id );
+ # Figure out which witnesses we are working with
+ my @lacunose = $stemma->hypotheticals;
+ my @tradition_wits = map { $_->sigil } $tradition->witnesses;
+ map { push( @tradition_wits, $_->sigil."_ac" ) if $_->is_layered }
+ $tradition->witnesses;
+ push( @lacunose, _symmdiff( [ $stemma->witnesses ], \@tradition_wits ) );
+
+ # Find and mark 'common' ranks for exclusion, unless they were
+ # explicitly specified.
+ unless( @ranks ) {
+ my %common_rank;
+ foreach my $rdg ( $c->common_readings ) {
+ $common_rank{$rdg->rank} = 1;
+ }
+ @ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-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', $wits );
+ # Group the variants to send to the solver
+ my @groups;
+ my %lacunae;
+ foreach my $rank ( @ranks ) {
+ my $missing = [ @lacunose ];
+ push( @groups, group_variants( $tradition, $rank, $missing, \@collapse ) );
+ $lacunae{$rank} = $missing;
+ }
- # 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 ( $total, $genealogical, $conflicts ) = ( 0, 0, 0 );
+ # Parse the answer
+ my $answer = solve_variants( $stemma->editable( ' ' ), @groups );
+
+ # Do further analysis on the answer
+ my $conflict_count = 0;
+ foreach my $idx ( 0 .. $#ranks ) {
+ my $location = $answer->{'variants'}->[$idx];
+ # Add the rank back in
+ $location->{'id'} = $ranks[$idx];
+ # Add the lacunae back in
+ $location->{'missing'} = $lacunae{$ranks[$idx]};
+ # Run the extra analysis we need.
+ analyze_location( $tradition, $stemma->graph, $location );
+ # Add the reading text back in
+ foreach my $rdghash ( @{$location->{'readings'}} ) {
+ $conflict_count++
+ if exists $rdghash->{'conflict'} && $rdghash->{'conflict'};
+ my $rdg = $c->reading( $rdghash->{'readingid'} );
+ $rdghash->{'text'} = $rdg ? $rdg->text : $rdghash->{'readingid'};
+ }
+ }
+ $answer->{'conflict_count'} = $conflict_count;
- # 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;
+ return $answer;
+}
+
+=head2 group_variants( $tradition, $rank, $lacunose, @merge_relationship_types )
+
+Groups the variants at the given $rank of the collation, treating any
+relationships in @merge_relationship_types as equivalent. $lacunose should
+be a reference to an array, to which the sigla of lacunose witnesses at this
+rank will be appended.
+
+Returns two ordered lists $readings, $groups, where $readings->[$n] is attested
+by the witnesses listed in $groups->[$n].
+
+=cut
+
+# Return group_readings, groups, lacunose
+sub group_variants {
+ my( $tradition, $rank, $lacunose, $collapse ) = @_;
+ my $c = $tradition->collation;
+ my $aclabel = $c->ac_label;
+ # Get the alignment table readings
+ my %readings_at_rank;
+ my @gap_wits;
+ foreach my $tablewit ( @{$tradition->collation->alignment_table->{'alignment'}} ) {
+ my $rdg = $tablewit->{'tokens'}->[$rank-1];
+ my $wit = $tablewit->{'witness'};
+ $wit =~ s/^(.*)\Q$aclabel\E$/${1}_ac/;
+ if( $rdg && $rdg->{'t'}->is_lacuna ) {
+ _add_to_witlist( $wit, $lacunose, '_ac' );
+ } elsif( $rdg ) {
+ $readings_at_rank{$rdg->{'t'}->text} = $rdg->{'t'};
+ } else {
+ _add_to_witlist( $wit, \@gap_wits, '_ac' );
+ }
+ }
- # 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 }
- my $rank = 0;
- my $t0 = Benchmark->new();
- 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],
- $tradition->collation->ac_label );
+ # Group the readings, collapsing groups by relationship if needed
+ my %grouped_readings;
+ foreach my $rdg ( sort { $b->witnesses <=> $a->witnesses } values %readings_at_rank ) {
+ # Skip readings that have been collapsed into others.
+ next if exists $grouped_readings{$rdg->id} && !$grouped_readings{$rdg->id};
+ my @wits = $rdg->witnesses;
+ map { s/\Q$aclabel\E$/_ac/ } @wits;
+ if( $collapse ) {
+ my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; };
+ foreach my $other ( $rdg->related_readings( $filter ) ) {
+ my @otherwits = $other->witnesses;
+ map { s/\Q$aclabel\E$/_ac/ } @otherwits;
+ push( @wits, @otherwits );
+ $grouped_readings{$other->id} = 0;
}
}
-
- # 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;
- $rank++;
-
- # 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];
+ $grouped_readings{$rdg->id} = \@wits;
+ }
+ $grouped_readings{'(omitted)'} = \@gap_wits if @gap_wits;
+ # Get rid of our collapsed readings
+ map { delete $grouped_readings{$_} unless $grouped_readings{$_} }
+ keys %grouped_readings
+ if $collapse;
+
+ return \%grouped_readings;
+}
+
+=head2 solve_variants( $graph, @groups )
+
+Sends the set of groups to the external graph solver service and returns
+a cleaned-up answer, adding the rank IDs back where they belong.
+
+The JSON has the form
+ { "graph": [ stemmagraph DOT string without newlines ],
+ "groupings": [ array of arrays of groups, one per rank ] }
+
+The answer has the form
+ { "variants" => [ array of variant location structures ],
+ "variant_count" => total,
+ "conflict_count" => number of conflicts detected,
+ "genealogical_count" => number of solutions found }
+
+=cut
+
+sub solve_variants {
+ my( $graph, @groups ) = @_;
+
+ # Make the json with stemma + groups
+ my $jsonstruct = { 'graph' => $graph, 'groupings' => [] };
+ foreach my $ghash ( @groups ) {
+ my @grouping;
+ foreach my $k ( sort keys %$ghash ) {
+ push( @grouping, $ghash->{$k} );
}
-
- # For all the groups with more than one member, collect the list of all
- # contiguous vertices needed to connect them.
- my $variant_row = analyze_variant_location( $group_readings, $groups,
- $stemma->graph, $lacunose );
- $variant_row->{'id'} = $rank;
- $genealogical++ if $variant_row->{'genealogical'};
- $conflicts += grep { $_->{'conflict'} } @{$variant_row->{'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
-# }
-# }
-# }
+ push( @{$jsonstruct->{'groupings'}}, \@grouping );
+ }
+ my $json = encode_json( $jsonstruct );
- # Record that we used this variant in an analysis
- push( @$variants, $variant_row );
+ # Send it off and get the result
+ my $solver_url = 'http://byzantini.st/cgi-bin/graphcalc.cgi';
+ my $ua = LWP::UserAgent->new();
+ my $resp = $ua->post( $solver_url, 'Content-Type' => 'application/json',
+ 'Content' => $json );
+
+ my $answer;
+ if( $resp->is_success ) {
+ $answer = decode_json( $resp->content );
+ } else {
+ # Fall back to the old method.
+ warn "IDP solver returned " . $resp->status_line . " / " . $resp->content
+ . "; falling back to perl method";
+ $answer = perl_solver( $graph, @groups );
}
- my $t1 = Benchmark->new();
- print STDERR "Analysis of graph for " . $tradition->name . " took "
- . timestr( timediff( $t1, $t0 ) ) . "seconds\n";
- # Go through our variant rows, after we have seen all of them once,
- # and add the number of empty columns needed by each.
- foreach my $row ( @$variants ) {
- my $empty = $html_columns - scalar @{$row->{'readings'}};
- $row->{'empty'} = $empty;
+ # Fold the result back into what we know about the groups.
+ my $variants = [];
+ my $genealogical = 0;
+ foreach my $idx ( 0 .. $#groups ) {
+ my( $calc_groups, $result ) = @{$answer->[$idx]};
+ $genealogical++ if $result;
+ my $input_group = $groups[$idx];
+ foreach my $k ( sort keys %$input_group ) {
+ my $cg = shift @$calc_groups;
+ $input_group->{$k} = $cg;
+ }
+ my $vstruct = {
+ 'genealogical' => $result,
+ 'readings' => [],
+ };
+ foreach my $k ( keys %$input_group ) {
+ push( @{$vstruct->{'readings'}},
+ { 'readingid' => $k, 'group' => $input_group->{$k}} );
+ }
+ push( @$variants, $vstruct );
}
- # Populate self with our analysis data.
- $data->{'variants'} = $variants;
- $data->{'variant_count'} = $total;
- $data->{'conflict_count'} = $conflicts;
- $data->{'genealogical_count'} = $genealogical;
- push( @{$self->{'data'}}, $data );
+ return { 'variants' => $variants,
+ 'variant_count' => scalar @$variants,
+ 'genealogical_count' => $genealogical };
}
-sub group_variants {
- my( $c, $wits ) = @_;
- my $variant_groups = [];
+=head2 analyze_location ( $tradition, $graph, $location_hash )
+
+Given the tradition, its stemma graph, and the solution from the graph solver,
+work out the rest of the information we want. For each reading we need missing,
+conflict, reading_parents, independent_occurrence, followed, not_followed, and follow_unknown. Alters the location_hash in place.
+
+=cut
+
+sub analyze_location {
+ my ( $tradition, $graph, $variant_row ) = @_;
- 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;
+ # Make a hash of all known node memberships, and make the subgraphs.
+ my $contig = {};
+ my $reading_roots = {};
+ my $subgraph = {};
+ foreach my $rdghash ( @{$variant_row->{'readings'}} ) {
+ my $rid = $rdghash->{'readingid'};
+ map { $contig->{$_} = $rid } @{$rdghash->{'group'}};
+
+ # Make the subgraph.
+ my $part = $graph->copy;
+ my %these_vertices;
+ map { $these_vertices{$_} = 1 } @{$rdghash->{'group'}};
+ $part->delete_vertices( grep { !$these_vertices{$_} } $part->vertices );
+ $subgraph->{$rid} = $part;
+ # Get the reading roots.
+ map { $reading_roots->{$_} = $rid } $part->predecessorless_vertices;
+ }
+
+ # Now that we have all the node group memberships, calculate followed/
+ # non-followed/unknown values for each reading. Also figure out the
+ # reading's evident parent(s).
+ foreach my $rdghash ( @{$variant_row->{'readings'}} ) {
+ # Group string key - TODO do we need this?
+ my $gst = wit_stringify( $rdghash->{'group'} );
+ my $rid = $rdghash->{'readingid'};
+ # Get the subgraph
+ my $part = $subgraph->{$rid};
+
+ # Start figuring things out.
+ my @roots = $part->predecessorless_vertices;
+ $rdghash->{'independent_occurrence'} = scalar @roots;
+ $rdghash->{'followed'} = scalar( $part->vertices ) - scalar( @roots );
+ # Find the parent readings, if any, of this reading.
+ my %rdgparents;
+ foreach my $wit ( @roots ) {
+ # Look in the main stemma to find this witness's extant or known-reading
+ # immediate ancestor(s), and look up the reading that each ancestor olds.
+ my @check = $graph->predecessors( $wit );
+ while( @check ) {
+ my @next;
+ foreach my $wparent( @check ) {
+ my $preading = $contig->{$wparent};
+ if( $preading ) {
+ $rdgparents{$preading} = 1;
+ } else {
+ push( @next, $graph->predecessors( $wparent ) );
+ }
}
+ @check = @next;
}
- 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 );
+ }
+ $rdghash->{'reading_parents'} = [ keys %rdgparents ];
+
+ # Find the number of times this reading was altered, and the number of
+ # times we're not sure.
+ my( %nofollow, %unknownfollow );
+ foreach my $wit ( $part->vertices ) {
+ foreach my $wchild ( $graph->successors( $wit ) ) {
+ next if $part->has_vertex( $wchild );
+ if( $reading_roots->{$wchild} && $contig->{$wchild} ) {
+ # It definitely changed here.
+ $nofollow{$wchild} = 1;
+ } elsif( !($contig->{$wchild}) ) {
+ # The child is a hypothetical node not definitely in
+ # any group. Answer is unknown.
+ $unknownfollow{$wchild} = 1;
+ } # else it's a non-root node in a known group, and therefore
+ # is presumed to have its reading from its group, not this link.
}
}
+ $rdghash->{'not_followed'} = keys %nofollow;
+ $rdghash->{'follow_unknown'} = keys %unknownfollow;
- # 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;
+ # Now say whether this reading represents a conflict.
+ unless( $variant_row->{'genealogical'} ) {
+ $rdghash->{'conflict'} = @roots != 1;
+ }
+ }
}
-# variant_row -> genealogical
-# -> readings [ { text, group, conflict, missing } ]
-
-sub analyze_variant_location {
- my( $group_readings, $groups, $graph, $lacunose, $undirected ) = @_;
- my $contig = {};
- my $subgraph = {};
- my $is_conflicted;
- my $conflict = {};
- 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 { $contig->{$_} = $gst } @$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'}}, $reading );
- }
-
- # Now that we have gone through all the rows, check the hypothetical
- # readings for conflict if we haven't found one yet.
- if( keys %$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;
+
+=head2 perl_solver( $tradition, $rank, $stemma_id, @merge_relationship_types )
+
+** NOTE ** This method should hopefully not be called - it is not guaranteed
+to be correct. Serves as a backup for the real solver.
+
+Runs an analysis of the given tradition, at the location given in $rank,
+against the graph of the stemma specified in $stemma_id. The argument
+@merge_relationship_types is an optional list of relationship types for
+which readings so related should be treated as equivalent.
+
+Returns a nested array data structure as follows:
+
+ [ [ group_list, is_genealogical ], [ group_list, is_genealogical ] ... ]
+
+where the group list is the array of arrays passed in for each element of @groups,
+possibly with the addition of hypothetical readings.
+
+
+=cut
+
+sub perl_solver {
+ my( $graph, @groups ) = @_;
+
+ warn "Not implemented yet";
+ return [];
}
-sub prune_subtree {
+ # Now do the work.
+# my $contig = {};
+# my $subgraph = {};
+# my $is_conflicted;
+# my $conflict = {};
+# my %reading_roots;
+# my $variant_row = { 'id' => $rank, 'readings' => [] };
+# # Mark each ms as in its own group, first.
+# foreach my $g ( @$groups ) {
+# my $gst = wit_stringify( $g );
+# 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
+# # Copy the graph, and delete all non-members from the new graph.
+# my $part = $graph->copy;
+# my @group_roots;
+# $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.
+# my $reachable = {};
+# 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 ) {
+# # We have to take directionality into account.
+# # How many root nodes do we have?
+# my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst }
+# $part->predecessorless_vertices;
+# # Assuming that @$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.
+# foreach my $root ( @roots ) {
+# # Prune the tree to get rid of extraneous hypotheticals.
+# $root = _prune_subtree( $part, $root, $contig );
+# next unless $root;
+# # Save this root for our group.
+# push( @group_roots, $root );
+# # Get all the successor nodes of our root.
+# }
+# } else {
+# # Dispense with the trivial case of one reading.
+# my $wit = pop @$g;
+# @group_roots = ( $wit );
+# foreach my $v ( $part->vertices ) {
+# $part->delete_vertex( $v ) unless $v eq $wit;
+# }
+# }
+# }
+#
+# map { $reading_roots{$_} = 1 } @group_roots;
+# if( @group_roots > 1 ) {
+# $conflict->{$group_readings->{$gst}} = 1;
+# $is_conflicted = 1;
+# }
+# # Paint the 'hypotheticals' with our group.
+# foreach my $wit ( $part->vertices ) {
+# if( ref( $contig->{$wit} ) ) {
+# push( @{$contig->{$wit}}, $gst );
+# } elsif( $contig->{$wit} ne $gst ) {
+# warn "How did we get here?";
+# }
+# }
+#
+#
+# # Start to write the reading, and save the group subgraph.
+# my $reading = { 'readingid' => $group_readings->{$gst},
+# 'missing' => wit_stringify( \@lacunose ),
+# 'group' => $gst }; # This will change if we find no conflict
+# # Save the relevant subgraph.
+# $subgraph->{$gst} = $part;
+# push( @{$variant_row->{'readings'}}, $reading );
+# }
+#
+# # For each of our hypothetical readings, flatten its 'contig' array if
+# # the array contains zero or one group. If we have any unflattened arrays,
+# # we may need to run the resolution process. If the reading is already known
+# # to have a conflict, flatten the 'contig' array to nothing; we won't resolve
+# # it.
+# my @resolve;
+# foreach my $wit ( keys %$contig ) {
+# next unless ref( $contig->{$wit} );
+# if( @{$contig->{$wit}} > 1 ) {
+# if( $is_conflicted ) {
+# $contig->{$wit} = ''; # We aren't going to decide.
+# } else {
+# push( @resolve, $wit );
+# }
+# } else {
+# my $gst = pop @{$contig->{$wit}};
+# $contig->{$wit} = $gst || '';
+# }
+# }
+#
+# if( @resolve ) {
+# 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}->copy();
+# # If we have come this far, there is only one root and everything
+# # is reachable from it.
+# my( $root ) = $gpart->predecessorless_vertices;
+# my $reachable = {};
+# map { $reachable->{$_} = 1 } $gpart->vertices;
+#
+# # Try deleting the hypothetical node.
+# $gpart->delete_vertex( $h );
+# if( $h eq $root ) {
+# # See if we still have a single root.
+# my @roots = $gpart->predecessorless_vertices;
+# warn "This shouldn't have happened" unless @roots;
+# if( @roots > 1 ) {
+# # $h is needed by this group.
+# if( exists( $still_contig->{$h} ) ) {
+# # Conflict!
+# $conflict->{$group_readings->{$gst}} = 1;
+# $still_contig->{$h} = '';
+# } else {
+# $still_contig->{$h} = $gst;
+# }
+# }
+# } else {
+# # $h is somewhere in the middle. See if everything
+# # else can still be reached from the root.
+# my %still_reachable = ( $root => 1 );
+# map { $still_reachable{$_} = 1 }
+# $gpart->all_successors( $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}} = 1;
+# $still_contig->{$h} = '';
+# } else {
+# $still_contig->{$h} = $gst;
+# }
+# last;
+# } # else we don't need $h in this group.
+# } # end foreach $v
+# } # endif $h eq $root
+# } # end foreach $gst
+# } # end foreach $h
+#
+# # Now we have some hypothetical vertices in $still_contig that are the
+# # "real" group memberships. Replace these in $contig.
+# foreach my $v ( keys %$contig ) {
+# next unless ref $contig->{$v};
+# $contig->{$v} = $still_contig->{$v};
+# }
+# } # end if @resolve
+#
+#
+# $variant_row->{'genealogical'} = !( keys %$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;
}
# Then delete a hypothetical root with only one successor, moving the
- # root to the child.
+ # root to the first child that has no other predecessors.
while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) {
my @nextroot = $tree->successors( $root );
$tree->delete_vertex( $root );
- $root = $nextroot[0];
+ ( $root ) = grep { $tree->is_predecessorless_vertex( $_ ) } @nextroot;
}
# The tree has been modified in place, but we need to know the new root.
+ $root = undef unless $root && $tree->has_vertex( $root );
return $root;
}
# Add the variant, subject to a.c. representation logic.
push( @$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 );
+sub _useful_variant {
+ my( $group_readings, $graph, $acstr ) = @_;
+
+ # TODO Decide what to do with AC witnesses
+
+ # Sort by group size and return
+ my $is_useful = 0;
+ my( @readings, @groups ); # The sorted groups for our answer.
+ foreach my $rdg ( sort { @{$group_readings->{$b}} <=> @{$group_readings->{$a}} }
+ keys %$group_readings ) {
+ push( @readings, $rdg );
+ push( @groups, $group_readings->{$rdg} );
+ if( @{$group_readings->{$rdg}} > 1 ) {
+ $is_useful++;
+ } else {
+ my( $wit ) = @{$group_readings->{$rdg}};
+ $wit =~ s/^(.*)\Q$acstr\E$/$1/;
+ $is_useful++ unless( $graph->is_sink_vertex( $wit ) );
+ }
+ }
+ if( $is_useful > 1 ) {
+ return( \@readings, \@groups );
+ } else {
+ return( [], [] );
+ }
}
-# Take an array of witness groupings and produce a string like
-# ['A','B'] / ['C','D','E'] / ['F']
+=head2 wit_stringify( $groups )
+
+Takes an array of witness groupings and produces a string like
+['A','B'] / ['C','D','E'] / ['F']
+
+=cut
sub wit_stringify {
my $groups = shift;
}
return join( ' / ', @gst );
}
-
-1;
\ No newline at end of file
+
+# Helper function to ensure that X and X a.c. never appear in the same list.
+sub _add_to_witlist {
+ my( $wit, $list, $acstr ) = @_;
+ my %inlist;
+ my $idx = 0;
+ map { $inlist{$_} = $idx++ } @$list;
+ if( $wit =~ /^(.*)\Q$acstr\E$/ ) {
+ my $acwit = $1;
+ unless( exists $inlist{$acwit} ) {
+ push( @$list, $acwit.$acstr );
+ }
+ } else {
+ if( exists( $inlist{$wit.$acstr} ) ) {
+ # Replace the a.c. version with the main witness
+ my $i = $inlist{$wit.$acstr};
+ $list->[$i] = $wit;
+ } else {
+ push( @$list, $wit );
+ }
+ }
+}
+
+sub _symmdiff {
+ my( $lista, $listb ) = @_;
+ my %union;
+ my %scalars;
+ map { $union{$_} = 1; $scalars{$_} = $_ } @$lista;
+ map { $union{$_} += 1; $scalars{$_} = $_ } @$listb;
+ my @set = grep { $union{$_} == 1 } keys %union;
+ return map { $scalars{$_} } @set;
+}
+
+1;
+
+=head1 LICENSE
+
+This package is free software and is provided "as is" without express
+or implied warranty. You can redistribute it and/or modify it under
+the same terms as Perl itself.
+
+=head1 AUTHOR
+
+Tara L Andrews E<lt>aurum@cpan.orgE<gt>