use Benchmark;
use Encode qw/ encode_utf8 /;
use Exporter 'import';
+use Graph;
use JSON qw/ encode_json decode_json /;
use LWP::UserAgent;
use Text::Tradition;
=item * merge_types - Specify a list of relationship types, where related readings
should be treated as identical for the purposes of analysis.
+=item * exclude_type1 - Exclude those ranks whose groupings have only type-1 variants.
+
=back
=begin testing
is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" );
my %expected_genealogical = (
- 1 => '',
+ 1 => 0,
2 => 1,
- 3 => '',
- 5 => '',
- 7 => '',
- 8 => '',
- 10 => '',
+ 3 => 0,
+ 5 => 0,
+ 7 => 0,
+ 8 => 0,
+ 10 => 0,
13 => 1,
- 33 => '',
- 34 => '',
- 37 => '',
- 60 => '',
+ 33 => 0,
+ 34 => 0,
+ 37 => 0,
+ 60 => 0,
81 => 1,
- 84 => '',
- 87 => '',
- 101 => '',
- 102 => '',
+ 84 => 0,
+ 87 => 0,
+ 101 => 0,
+ 102 => 0,
122 => 1,
- 157 => '',
+ 157 => 0,
166 => 1,
169 => 1,
- 200 => 1,
+ 200 => 0,
216 => 1,
217 => 1,
219 => 1,
);
my $data = run_analysis( $tradition );
+my $c = $tradition->collation;
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;
+ }
is( $row->{'genealogical'}, $expected_genealogical{$row->{'id'}},
"Got correct genealogical flag for row " . $row->{'id'} );
+ # Check that we have the right row with the right groups
+ my $rank = $row->{'id'};
+ foreach my $rdghash ( @{$row->{'readings'}} ) {
+ # Skip 'readings' that aren't really
+ next unless $c->reading( $rdghash->{'readingid'} );
+ # Check the rank
+ is( $c->reading( $rdghash->{'readingid'} )->rank, $rank,
+ "Got correct reading rank" );
+ # Check the witnesses
+ my @realwits = sort $c->reading_witnesses( $rdghash->{'readingid'} );
+ my @sgrp = sort @{$rdghash->{'group'}};
+ is_deeply( \@sgrp, \@realwits, "Reading analyzed with correct groups" );
+ }
}
-is( $data->{'conflict_count'}, 16, "Got right conflict count" );
-is( $data->{'variant_count'}, 28, "Got right total variant number" );
+is( $data->{'variant_count'}, 58, "Got right total variant number" );
+# TODO Make something meaningful of conflict count, maybe test other bits
=end testing
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';
+ my @ranks = ref( $opts{'ranks'} ) eq 'ARRAY' ? @{$opts{'ranks'}} : ();
+ my @collapse = ref( $opts{'merge_types'} ) eq 'ARRAY' ? @{$opts{'merge_types'}} : ();
# Get the stemma
my $stemma = $tradition->stemma( $stemma_id );
+
# Figure out which witnesses we are working with
my @lacunose = $stemma->hypotheticals;
- push( @lacunose, _symmdiff( [ $stemma->witnesses ],
- [ map { $_->sigil } $tradition->witnesses ] ) );
+ my @tradition_wits = map { $_->sigil } $tradition->witnesses;
+ map { push( @tradition_wits, $_->sigil.$c->ac_label ) 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 ( $tradition->collation->common_readings ) {
+ foreach my $rdg ( $c->common_readings ) {
$common_rank{$rdg->rank} = 1;
}
@ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-1 );
# Group the variants to send to the solver
my @groups;
+ my @use_ranks;
+ my %lacunae;
foreach my $rank ( @ranks ) {
- push( @groups, group_variants( $tradition, $rank, \@lacunose, \@collapse ) );
+ my $missing = [ @lacunose ];
+ my $rankgroup = group_variants( $tradition, $rank, $missing, \@collapse );
+ if( $opts{'exclude_type1'} ) {
+ # Check to see whether this is a "useful" group.
+ my( $rdgs, $grps ) = _useful_variant( $rankgroup,
+ $stemma->graph, $c->ac_label );
+ next unless @$rdgs;
+ }
+ push( @use_ranks, $rank );
+ push( @groups, $rankgroup );
+ $lacunae{$rank} = $missing;
}
-
# Parse the answer
- my $answer = solve_variants( $stemma->editable( ' ' ), @groups );
-
+ my $answer = solve_variants( $stemma, @groups );
+
# Do further analysis on the answer
- foreach my $idx ( 0 .. $#ranks ) {
+ my $conflict_count = 0;
+ my $aclabel = $c->ac_label;
+ foreach my $idx ( 0 .. $#use_ranks ) {
my $location = $answer->{'variants'}->[$idx];
# Add the rank back in
- $location->{'id'} = $ranks[$idx];
+ $location->{'id'} = $use_ranks[$idx];
+ # Note what our lacunae are
+ my %lmiss;
+ map { $lmiss{$_} = 1 } @{$lacunae{$use_ranks[$idx]}};
+ # Run through the reading groups and add as 'lacunae' any redundant
+ # a.c. witnesses (yes, we have to do this before the analysis, thus
+ # identical loops before and after. Boo.)
+ # TODO Consider making these callbacks to analyze_location
+ foreach my $rdghash ( @{$location->{'readings'}} ) {
+ my %rwits;
+ map { $rwits{$_} = 1 } @{$rdghash->{'group'}};
+ foreach my $rw ( keys %rwits ) {
+ if( $rw =~ /^(.*)\Q$aclabel\E$/ ) {
+ if( exists $rwits{$1} ) {
+ $lmiss{$rw} = 1;
+ delete $rwits{$rw};
+ }
+ }
+ }
+ $rdghash->{'group'} = [ keys %rwits ];
+ }
+ $location->{'missing'} = [ keys %lmiss ];
+
# Run the extra analysis we need.
- # For each reading we need missing, conflict, reading_parents,
- # independent_occurrence, followed, not_followed, follow_unknown
analyze_location( $tradition, $stemma->graph, $location );
+
+ # Do the final post-analysis tidying up of the data.
+ foreach my $rdghash ( @{$location->{'readings'}} ) {
+ $conflict_count++
+ if exists $rdghash->{'conflict'} && $rdghash->{'conflict'};
+ # Add the reading text back in
+ my $rdg = $c->reading( $rdghash->{'readingid'} );
+ $rdghash->{'text'} = $rdg ? $rdg->text : $rdghash->{'readingid'};
+ # Remove lacunose witnesses from this reading's list now that the
+ # analysis is done
+ my @realgroup;
+ map { push( @realgroup, $_ ) unless $lmiss{$_} } @{$rdghash->{'group'}};
+ $rdghash->{'group'} = \@realgroup;
+ # TODO Record hypotheticals used to create group, if we end up
+ # needing it
+ }
}
+ $answer->{'conflict_count'} = $conflict_count;
return $answer;
}
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].
+Returns a hash $group_readings where $rdg is attested by the witnesses listed
+in $group_readings->{$rdg}.
=cut
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 %is_lacunose; # lookup table for $lacunose
+ map { $is_lacunose{$_} = 1 } @$lacunose;
my @gap_wits;
- foreach my $tablewit ( @{$tradition->collation->alignment_table->{'alignment'}} ) {
+ foreach my $tablewit ( @{$c->alignment_table->{'alignment'}} ) {
my $rdg = $tablewit->{'tokens'}->[$rank-1];
+ my $wit = $tablewit->{'witness'};
+ # Exclude the witness if it is "lacunose" which if we got here
+ # means "not in the stemma".
+ next if $is_lacunose{$wit};
if( $rdg && $rdg->{'t'}->is_lacuna ) {
- _add_to_witlist( $tablewit->{'witness'}, $lacunose,
- $tradition->collation->ac_label );
+ _add_to_witlist( $wit, $lacunose, $aclabel );
} elsif( $rdg ) {
$readings_at_rank{$rdg->{'t'}->text} = $rdg->{'t'};
} else {
- _add_to_witlist( $tablewit->{'witness'}, \@gap_wits,
- $tradition->collation->ac_label );
+ _add_to_witlist( $wit, \@gap_wits, $aclabel );
}
}
# Group the readings, collapsing groups by relationship if needed
my %grouped_readings;
- foreach my $rdg ( sort { $b->witnesses <=> $a->witnesses } values %readings_at_rank ) {
+ 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;
if( $collapse ) {
my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; };
foreach my $other ( $rdg->related_readings( $filter ) ) {
- push( @wits, $other->witnesses );
+ my @otherwits = $other->witnesses;
+ push( @wits, @otherwits );
$grouped_readings{$other->id} = 0;
}
}
- $grouped_readings{$rdg->id} = \@wits;
+ my @use_wits = grep { !$is_lacunose{$_} } @wits;
+ $grouped_readings{$rdg->id} = \@use_wits;
}
$grouped_readings{'(omitted)'} = \@gap_wits if @gap_wits;
# Get rid of our collapsed readings
=cut
sub solve_variants {
- my( $graph, @groups ) = @_;
+ my( $stemma, @groups ) = @_;
# Make the json with stemma + groups
- my $jsonstruct = { 'graph' => $graph, 'groupings' => [] };
+ my $groupings = [];
foreach my $ghash ( @groups ) {
my @grouping;
foreach my $k ( sort keys %$ghash ) {
push( @grouping, $ghash->{$k} );
}
- push( @{$jsonstruct->{'groupings'}}, \@grouping );
+ push( @$groupings, \@grouping );
}
- my $json = encode_json( $jsonstruct );
+ ## Witness map is a HACK to get around limitations in node names from IDP
+ my $witness_map = {};
+ my $json = encode_json( _safe_wit_strings( $stemma, $groupings, $witness_map ) );
# Send it off and get the result
my $solver_url = 'http://byzantini.st/cgi-bin/graphcalc.cgi';
'Content' => $json );
my $answer;
+ my $used_idp;
if( $resp->is_success ) {
- $answer = decode_json( $resp->content );
+ $answer = _desanitize_names( decode_json( $resp->content ), $witness_map );
+ $used_idp = 1;
} else {
- # Either throw an error or fall back to the old method.
- die "Solver returned " . $resp->status_line . " / " . $resp->content;
+ # Fall back to the old method.
+ warn "IDP solver returned " . $resp->status_line . " / " . $resp->content
+ . "; falling back to perl method";
+ $answer = perl_solver( $stemma, @$groupings );
}
# Fold the result back into what we know about the groups.
my $genealogical = 0;
foreach my $idx ( 0 .. $#groups ) {
my( $calc_groups, $result ) = @{$answer->[$idx]};
- $genealogical++ if $result;
+ if( $result ) {
+ $genealogical++;
+ # Prune the calculated groups, in case the IDP solver failed to.
+ if( $used_idp ) {
+ my @pruned_groups;
+ foreach my $cg ( @$calc_groups ) {
+ my @pg = _prune_group( $cg, $stemma );
+ push( @pruned_groups, \@pg );
+ }
+ $calc_groups = \@pruned_groups;
+ }
+ }
my $input_group = $groups[$idx];
foreach my $k ( sort keys %$input_group ) {
my $cg = shift @$calc_groups;
my $vstruct = {
'genealogical' => $result,
'readings' => [],
- }
- foreach my $k ( keys %$input_group ) {
+ };
+ foreach my $k ( sort { @{$input_group->{$b}} <=> @{$input_group->{$a}} }
+ keys %$input_group ) {
push( @{$vstruct->{'readings'}},
- { 'readingid' => $k, 'group' => $dg } );
+ { 'readingid' => $k, 'group' => $input_group->{$k}} );
}
push( @$variants, $vstruct );
}
'genealogical_count' => $genealogical };
}
-=head2 analyze_variant_location( $tradition, $rank, $stemma_id, @merge_relationship_types )
+#### HACKERY to cope with IDP's limited idea of what a node name looks like ###
+
+sub _safe_wit_strings {
+ my( $stemma, $groupings, $witness_map ) = @_;
+ my $safegraph = Graph->new();
+ # Convert the graph to a safe representation and store the conversion.
+ foreach my $n ( $stemma->graph->vertices ) {
+ my $sn = _safe_witstr( $n );
+ warn "Ambiguous stringification $sn for $n and " . $witness_map->{$sn}
+ if exists $witness_map->{$sn};
+ $witness_map->{$sn} = $n;
+ $safegraph->add_vertex( $sn );
+ $safegraph->set_vertex_attributes( $sn,
+ $stemma->graph->get_vertex_attributes( $n ) );
+ }
+ foreach my $e ( $stemma->graph->edges ) {
+ my @safe_e = ( _safe_witstr( $e->[0] ), _safe_witstr( $e->[1] ) );
+ $safegraph->add_edge( @safe_e );
+ }
+ my $safe_stemma = Text::Tradition::Stemma->new(
+ 'collation' => $stemma->collation, 'graph' => $safegraph );
+
+ # Now convert the witness groupings to a safe representation.
+ my $safe_groupings = [];
+ foreach my $grouping ( @$groupings ) {
+ my $safe_grouping = [];
+ foreach my $group ( @$grouping ) {
+ my $safe_group = [];
+ foreach my $n ( @$group ) {
+ my $sn = _safe_witstr( $n );
+ warn "Ambiguous stringification $sn for $n and " . $witness_map->{$sn}
+ if exists $witness_map->{$sn} && $witness_map->{$sn} ne $n;
+ $witness_map->{$sn} = $n;
+ push( @$safe_group, $sn );
+ }
+ push( @$safe_grouping, $safe_group );
+ }
+ push( @$safe_groupings, $safe_grouping );
+ }
+
+ # Return it all in the struct we expect. We have stored the reductions
+ # in the $witness_map that we were passed.
+ return { 'graph' => $safe_stemma->editable( ' ' ), 'groupings' => $safe_groupings };
+}
+
+sub _safe_witstr {
+ my $witstr = shift;
+ $witstr =~ s/\s+/_/g;
+ $witstr =~ s/[^\w\d-]//g;
+ return $witstr;
+}
+
+sub _desanitize_names {
+ my( $jsonstruct, $witness_map ) = @_;
+ my $result = [];
+ foreach my $grouping ( @$jsonstruct ) {
+ my $real_grouping = [];
+ foreach my $element ( @$grouping ) {
+ if( ref( $element ) eq 'ARRAY' ) {
+ # it's the groupset.
+ my $real_groupset = [];
+ foreach my $group ( @$element ) {
+ my $real_group = [];
+ foreach my $n ( @$group ) {
+ my $rn = $witness_map->{$n};
+ push( @$real_group, $rn );
+ }
+ push( @$real_groupset, $real_group );
+ }
+ push( @$real_grouping, $real_groupset );
+ } else {
+ # It is the boolean, not actually a group.
+ push( @$real_grouping, $element );
+ }
+ }
+ push( @$result, $real_grouping );
+ }
+ return $result;
+}
+
+### END HACKERY ###
+
+=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 ) = @_;
+
+ # 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;
+ }
+ }
+ $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;
+
+ # Now say whether this reading represents a conflict.
+ unless( $variant_row->{'genealogical'} ) {
+ $rdghash->{'conflict'} = @roots != 1;
+ }
+ }
+}
+
+
+=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 data structure as follows:
+Returns a nested array data structure as follows:
- { 'id' => $rank,
- 'genealogical' => boolean,
- 'readings => [ { readingid => $reading_id,
- group => [ witnesses ],
- conflict => [ conflicting ],
- missing => [ excluded ] }, ... ]
- }
-where 'conflicting' is the list of witnesses whose readings conflict with
-this group, and 'excluded' is the list of witnesses either not present in
-the stemma or lacunose at this location.
+ [ [ 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 analyze_variant_location {
- my( $tradition, $rank, $sid, @collapse ) = @_;
- # Get the readings in this tradition at this rank
- my @rank_rdgs = grep { $_->rank == $rank } $tradition->collation->readings;
- # Get the applicable stemma
- my $undirected; # TODO Allow undirected distance tree analysis too
- my $stemma = $tradition->stemma( $sid );
+sub perl_solver {
+ my( $stemma, @groups ) = @_;
my $graph = $stemma->graph;
- # Figure out which witnesses we are working with
- my @lacunose = $stemma->hypotheticals;
- push( @lacunose, _symmdiff( [ $stemma->witnesses ],
- [ map { $_->sigil } $tradition->witnesses ] ) );
-
- # Now group the readings
- my( $readings, $groups ) = _useful_variant(
- group_variants( $tradition, $rank, \@lacunose, \@collapse ),
- $graph, $tradition->collation->ac_label );
- return unless scalar @$readings;
- my $group_readings = {};
- # Lookup table group string -> readings
- foreach my $x ( 0 .. $#$groups ) {
- $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x];
+ my @answer;
+ foreach my $g ( @groups ) {
+ push( @answer, _solve_variant_location( $graph, $g ) );
}
+ return \@answer;
+}
+sub _solve_variant_location {
+ my( $graph, $groups ) = @_;
# 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.
- $DB::single = 1 if $rank == 81;
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.
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 $wit;
- }
- }
+ if( @$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 = $g->[0];
+ @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;
+ $conflict->{$gst} = 1;
$is_conflicted = 1;
}
# Paint the 'hypotheticals' with our group.
}
- # 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
# $h is needed by this group.
if( exists( $still_contig->{$h} ) ) {
# Conflict!
- $conflict->{$group_readings->{$gst}} = 1;
+ $conflict->{$gst} = 1;
$still_contig->{$h} = '';
} else {
$still_contig->{$h} = $gst;
# We need $h.
if( exists $still_contig->{$h} ) {
# Conflict!
- $conflict->{$group_readings->{$gst}} = 1;
+ $conflict->{$gst} = 1;
$still_contig->{$h} = '';
} else {
$still_contig->{$h} = $gst;
}
} # end if @resolve
- # 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'}} ) {
- my $gst = $rdghash->{'group'};
- my $part = $subgraph->{$gst};
- 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 $pgroup = $contig->{$wparent};
- if( $pgroup ) {
- $rdgparents{$group_readings->{$pgroup}} = 1;
- } else {
- push( @next, $graph->predecessors( $wparent ) );
- }
- }
- @check = @next;
- }
- }
- $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;
+ my $is_genealogical = keys %$conflict ? JSON::false : JSON::true;
+ my $variant_row = [ [], $is_genealogical ];
+ # Fill in the groupings from $contig.
+ foreach my $g ( @$groups ) {
+ my $gst = wit_stringify( $g );
+ my @realgroup = grep { $contig->{$_} eq $gst } keys %$contig;
+ push( @{$variant_row->[0]}, \@realgroup );
}
-
- # Now write the group and conflict information into the respective rows.
- foreach my $rdghash ( @{$variant_row->{'readings'}} ) {
- $rdghash->{'conflict'} = $conflict->{$rdghash->{'readingid'}};
- my @members = grep { $contig->{$_} eq $rdghash->{'group'} } keys %$contig;
- $rdghash->{'group'} = wit_stringify( \@members );
- }
-
- $variant_row->{'genealogical'} = !( keys %$conflict );
return $variant_row;
}
+sub _prune_group {
+ my( $group, $stemma ) = @_;
+ # Get these into a form prune_subtree will recognize. Make a "contighash"
+ my $hypohash = {};
+ map { $hypohash->{$_} = 1 } @$group;
+ # ...with reference values for hypotheticals.
+ map { $hypohash->{$_} = [] } $stemma->hypotheticals;
+ # Make our subgraph
+ my $subgraph = $stemma->graph->copy;
+ map { $subgraph->delete_vertex( $_ ) unless exists $hypohash->{$_} }
+ $subgraph->vertices;
+ # ...and find the root.
+ my( $root ) = $subgraph->predecessorless_vertices;
+ # Now prune and return the remaining vertices.
+ _prune_subtree( $subgraph, $root, $hypohash );
+ return $subgraph->vertices;
+}
+
sub _prune_subtree {
my( $tree, $root, $contighash ) = @_;
# First, delete hypothetical leaves / orphans until there are none left.
projects / scpubgit/stemmatology.git / blobdiff