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d71100ed |
1 | package Text::Tradition::Analysis; |
2 | |
3 | use strict; |
4 | use warnings; |
e4386ba9 |
5 | use Benchmark; |
88a6bac5 |
6 | use Encode qw/ encode_utf8 /; |
d1348d38 |
7 | use Exporter 'import'; |
88a6bac5 |
8 | use JSON qw/ encode_json decode_json /; |
9 | use LWP::UserAgent; |
d71100ed |
10 | use Text::Tradition; |
11 | use Text::Tradition::Stemma; |
12 | |
d1348d38 |
13 | use vars qw/ @EXPORT_OK /; |
a2cf85dd |
14 | @EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /; |
d1348d38 |
15 | |
7f52eac8 |
16 | =head1 NAME |
17 | |
18 | Text::Tradition::Analysis - functions for stemma analysis of a tradition |
19 | |
20 | =head1 SYNOPSIS |
21 | |
22 | use Text::Tradition; |
23 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
24 | my $t = Text::Tradition->new( |
25 | 'name' => 'this is a text', |
26 | 'input' => 'TEI', |
27 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
28 | $t->add_stemma( 'dotfile' => $stemmafile ); |
29 | |
30 | my $variant_data = run_analysis( $tradition ); |
31 | # Recalculate rank $n treating all orthographic variants as equivalent |
32 | my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' ); |
33 | |
34 | =head1 DESCRIPTION |
35 | |
36 | Text::Tradition is a library for representation and analysis of collated |
37 | texts, particularly medieval ones. The Collation is the central feature of |
38 | a Tradition, where the text, its sequence of readings, and its relationships |
39 | between readings are actually kept. |
40 | |
41 | =head1 SUBROUTINES |
42 | |
88a6bac5 |
43 | =head2 run_analysis( $tradition, %opts ) |
7f52eac8 |
44 | |
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45 | Runs the analysis described in analyze_variant_location on every location in the |
46 | collation of the given tradition, with the given options. These include: |
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47 | |
88a6bac5 |
48 | =over 4 |
49 | |
50 | =item * stemma_id - Specify which of the tradition's stemmata to use. Default |
51 | is 0 (i.e. the first). |
52 | |
53 | =item * ranks - Specify a list of location ranks to analyze; exclude the rest. |
54 | |
55 | =item * merge_types - Specify a list of relationship types, where related readings |
56 | should be treated as identical for the purposes of analysis. |
57 | |
58 | =back |
7f52eac8 |
59 | |
60 | =begin testing |
61 | |
62 | use Text::Tradition; |
63 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
64 | |
65 | my $datafile = 't/data/florilegium_tei_ps.xml'; |
66 | my $tradition = Text::Tradition->new( 'input' => 'TEI', |
67 | 'name' => 'test0', |
68 | 'file' => $datafile ); |
69 | my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' ); |
70 | is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" ); |
71 | |
f00cefe8 |
72 | my %expected_genealogical = ( |
73 | 1 => '', |
74 | 2 => 1, |
75 | 3 => '', |
76 | 5 => '', |
77 | 7 => '', |
78 | 8 => '', |
79 | 10 => '', |
80 | 13 => 1, |
81 | 33 => '', |
82 | 34 => '', |
83 | 37 => '', |
84 | 60 => '', |
85 | 81 => 1, |
86 | 84 => '', |
87 | 87 => '', |
88 | 101 => '', |
89 | 102 => '', |
90 | 122 => 1, |
91 | 157 => '', |
92 | 166 => 1, |
93 | 169 => 1, |
94 | 200 => 1, |
95 | 216 => 1, |
96 | 217 => 1, |
97 | 219 => 1, |
98 | 241 => 1, |
99 | 242 => 1, |
100 | 243 => 1, |
101 | ); |
102 | |
7f52eac8 |
103 | my $data = run_analysis( $tradition ); |
f00cefe8 |
104 | foreach my $row ( @{$data->{'variants'}} ) { |
105 | is( $row->{'genealogical'}, $expected_genealogical{$row->{'id'}}, |
106 | "Got correct genealogical flag for row " . $row->{'id'} ); |
107 | } |
5be0cdeb |
108 | is( $data->{'conflict_count'}, 16, "Got right conflict count" ); |
109 | is( $data->{'variant_count'}, 28, "Got right total variant number" ); |
7f52eac8 |
110 | |
111 | =end testing |
112 | |
113 | =cut |
114 | |
d71100ed |
115 | sub run_analysis { |
88a6bac5 |
116 | my( $tradition, %opts ) = @_; |
f00cefe8 |
117 | my $c = $tradition->collation; |
88a6bac5 |
118 | |
119 | my $stemma_id = $opts{'stemma_id'} || 0; |
120 | my @ranks = @{$opts{'ranks'}} if ref( $opts{'ranks'} ) eq 'ARRAY'; |
121 | my @collapse = @{$opts{'merge_types'}} if ref( $opts{'merge_types'} ) eq 'ARRAY'; |
122 | |
123 | # Get the stemma |
124 | my $stemma = $tradition->stemma( $stemma_id ); |
125 | # Figure out which witnesses we are working with |
126 | my @lacunose = $stemma->hypotheticals; |
127 | push( @lacunose, _symmdiff( [ $stemma->witnesses ], |
128 | [ map { $_->sigil } $tradition->witnesses ] ) ); |
129 | |
130 | # Find and mark 'common' ranks for exclusion, unless they were |
131 | # explicitly specified. |
132 | unless( @ranks ) { |
133 | my %common_rank; |
134 | foreach my $rdg ( $tradition->collation->common_readings ) { |
135 | $common_rank{$rdg->rank} = 1; |
136 | } |
137 | @ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-1 ); |
d71100ed |
138 | } |
7f52eac8 |
139 | |
88a6bac5 |
140 | # Group the variants to send to the solver |
141 | my @groups; |
142 | foreach my $rank ( @ranks ) { |
143 | push( @groups, group_variants( $tradition, $rank, \@lacunose, \@collapse ) ); |
d71100ed |
144 | } |
145 | |
88a6bac5 |
146 | # Parse the answer |
147 | my $answer = solve_variants( $stemma->editable( ' ' ), @groups ); |
148 | |
149 | # Do further analysis on the answer |
150 | foreach my $idx ( 0 .. $#ranks ) { |
151 | my $location = $answer->{'variants'}->[$idx]; |
152 | # Add the rank back in |
153 | $location->{'id'} = $ranks[$idx]; |
154 | # Run the extra analysis we need. |
155 | # For each reading we need missing, conflict, reading_parents, |
156 | # independent_occurrence, followed, not_followed, follow_unknown |
157 | analyze_location( $tradition, $stemma->graph, $location ); |
158 | } |
f00cefe8 |
159 | |
88a6bac5 |
160 | return $answer; |
d71100ed |
161 | } |
162 | |
7f52eac8 |
163 | =head2 group_variants( $tradition, $rank, $lacunose, @merge_relationship_types ) |
164 | |
165 | Groups the variants at the given $rank of the collation, treating any |
166 | relationships in @merge_relationship_types as equivalent. $lacunose should |
167 | be a reference to an array, to which the sigla of lacunose witnesses at this |
168 | rank will be appended. |
169 | |
170 | Returns two ordered lists $readings, $groups, where $readings->[$n] is attested |
171 | by the witnesses listed in $groups->[$n]. |
172 | |
173 | =cut |
174 | |
175 | # Return group_readings, groups, lacunose |
d1348d38 |
176 | sub group_variants { |
7f52eac8 |
177 | my( $tradition, $rank, $lacunose, $collapse ) = @_; |
178 | my $c = $tradition->collation; |
179 | # Get the alignment table readings |
180 | my %readings_at_rank; |
181 | my @gap_wits; |
182 | foreach my $tablewit ( @{$tradition->collation->alignment_table->{'alignment'}} ) { |
183 | my $rdg = $tablewit->{'tokens'}->[$rank-1]; |
184 | if( $rdg && $rdg->{'t'}->is_lacuna ) { |
5be0cdeb |
185 | _add_to_witlist( $tablewit->{'witness'}, $lacunose, |
186 | $tradition->collation->ac_label ); |
7f52eac8 |
187 | } elsif( $rdg ) { |
188 | $readings_at_rank{$rdg->{'t'}->text} = $rdg->{'t'}; |
189 | } else { |
5be0cdeb |
190 | _add_to_witlist( $tablewit->{'witness'}, \@gap_wits, |
191 | $tradition->collation->ac_label ); |
7f52eac8 |
192 | } |
193 | } |
d1348d38 |
194 | |
7f52eac8 |
195 | # Group the readings, collapsing groups by relationship if needed |
196 | my %grouped_readings; |
197 | foreach my $rdg ( sort { $b->witnesses <=> $a->witnesses } values %readings_at_rank ) { |
198 | # Skip readings that have been collapsed into others. |
f00cefe8 |
199 | next if exists $grouped_readings{$rdg->id} && !$grouped_readings{$rdg->id}; |
7f52eac8 |
200 | my @wits = $rdg->witnesses; |
201 | if( $collapse ) { |
202 | my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; }; |
203 | foreach my $other ( $rdg->related_readings( $filter ) ) { |
204 | push( @wits, $other->witnesses ); |
f00cefe8 |
205 | $grouped_readings{$other->id} = 0; |
d1348d38 |
206 | } |
207 | } |
f00cefe8 |
208 | $grouped_readings{$rdg->id} = \@wits; |
7f52eac8 |
209 | } |
210 | $grouped_readings{'(omitted)'} = \@gap_wits if @gap_wits; |
211 | # Get rid of our collapsed readings |
212 | map { delete $grouped_readings{$_} unless $grouped_readings{$_} } |
213 | keys %grouped_readings |
214 | if $collapse; |
215 | |
5be0cdeb |
216 | return \%grouped_readings; |
d1348d38 |
217 | } |
218 | |
88a6bac5 |
219 | =head2 solve_variants( $graph, @groups ) |
220 | |
221 | Sends the set of groups to the external graph solver service and returns |
222 | a cleaned-up answer, adding the rank IDs back where they belong. |
223 | |
224 | The JSON has the form |
225 | { "graph": [ stemmagraph DOT string without newlines ], |
226 | "groupings": [ array of arrays of groups, one per rank ] } |
227 | |
228 | The answer has the form |
229 | { "variants" => [ array of variant location structures ], |
230 | "variant_count" => total, |
231 | "conflict_count" => number of conflicts detected, |
232 | "genealogical_count" => number of solutions found } |
233 | |
234 | =cut |
235 | |
236 | sub solve_variants { |
237 | my( $graph, @groups ) = @_; |
238 | |
239 | # Make the json with stemma + groups |
240 | my $jsonstruct = { 'graph' => $graph, 'groupings' => [] }; |
241 | foreach my $ghash ( @groups ) { |
242 | my @grouping; |
243 | foreach my $k ( sort keys %$ghash ) { |
244 | push( @grouping, $ghash->{$k} ); |
245 | } |
246 | push( @{$jsonstruct->{'groupings'}}, \@grouping ); |
247 | } |
248 | my $json = encode_json( $jsonstruct ); |
249 | |
250 | # Send it off and get the result |
251 | my $solver_url = 'http://byzantini.st/cgi-bin/graphcalc.cgi'; |
252 | my $ua = LWP::UserAgent->new(); |
253 | my $resp = $ua->post( $solver_url, 'Content-Type' => 'application/json', |
254 | 'Content' => $json ); |
255 | |
256 | my $answer; |
257 | if( $resp->is_success ) { |
258 | $answer = decode_json( $resp->content ); |
259 | } else { |
260 | # Either throw an error or fall back to the old method. |
261 | die "Solver returned " . $resp->status_line . " / " . $resp->content; |
262 | } |
263 | |
264 | # Fold the result back into what we know about the groups. |
265 | my $variants = []; |
266 | my $genealogical = 0; |
267 | foreach my $idx ( 0 .. $#groups ) { |
268 | my( $calc_groups, $result ) = @{$answer->[$idx]}; |
269 | $genealogical++ if $result; |
270 | my $input_group = $groups[$idx]; |
271 | foreach my $k ( sort keys %$input_group ) { |
272 | my $cg = shift @$calc_groups; |
273 | $input_group->{$k} = $cg; |
274 | } |
275 | my $vstruct = { |
276 | 'genealogical' => $result, |
277 | 'readings' => [], |
278 | } |
279 | foreach my $k ( keys %$input_group ) { |
280 | push( @{$vstruct->{'readings'}}, |
281 | { 'readingid' => $k, 'group' => $dg } ); |
282 | } |
283 | push( @$variants, $vstruct ); |
284 | } |
285 | |
286 | return { 'variants' => $variants, |
287 | 'variant_count' => scalar @$variants, |
288 | 'genealogical_count' => $genealogical }; |
289 | } |
290 | |
7f52eac8 |
291 | =head2 analyze_variant_location( $tradition, $rank, $stemma_id, @merge_relationship_types ) |
f6c8ea08 |
292 | |
7f52eac8 |
293 | Runs an analysis of the given tradition, at the location given in $rank, |
294 | against the graph of the stemma specified in $stemma_id. The argument |
295 | @merge_relationship_types is an optional list of relationship types for |
296 | which readings so related should be treated as equivalent. |
f6c8ea08 |
297 | |
7f52eac8 |
298 | Returns a data structure as follows: |
299 | |
300 | { 'id' => $rank, |
301 | 'genealogical' => boolean, |
f00cefe8 |
302 | 'readings => [ { readingid => $reading_id, |
7f52eac8 |
303 | group => [ witnesses ], |
304 | conflict => [ conflicting ], |
305 | missing => [ excluded ] }, ... ] |
306 | } |
307 | where 'conflicting' is the list of witnesses whose readings conflict with |
308 | this group, and 'excluded' is the list of witnesses either not present in |
309 | the stemma or lacunose at this location. |
310 | |
311 | =cut |
732152b1 |
312 | |
d71100ed |
313 | sub analyze_variant_location { |
7f52eac8 |
314 | my( $tradition, $rank, $sid, @collapse ) = @_; |
7f52eac8 |
315 | # Get the readings in this tradition at this rank |
316 | my @rank_rdgs = grep { $_->rank == $rank } $tradition->collation->readings; |
317 | # Get the applicable stemma |
318 | my $undirected; # TODO Allow undirected distance tree analysis too |
319 | my $stemma = $tradition->stemma( $sid ); |
320 | my $graph = $stemma->graph; |
321 | # Figure out which witnesses we are working with |
bebec0e9 |
322 | my @lacunose = $stemma->hypotheticals; |
323 | push( @lacunose, _symmdiff( [ $stemma->witnesses ], |
324 | [ map { $_->sigil } $tradition->witnesses ] ) ); |
7f52eac8 |
325 | |
326 | # Now group the readings |
5be0cdeb |
327 | my( $readings, $groups ) = _useful_variant( |
328 | group_variants( $tradition, $rank, \@lacunose, \@collapse ), |
329 | $graph, $tradition->collation->ac_label ); |
330 | return unless scalar @$readings; |
7f52eac8 |
331 | my $group_readings = {}; |
332 | # Lookup table group string -> readings |
333 | foreach my $x ( 0 .. $#$groups ) { |
334 | $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x]; |
335 | } |
336 | |
337 | # Now do the work. |
231d71fc |
338 | my $contig = {}; |
339 | my $subgraph = {}; |
c4a4fb1b |
340 | my $is_conflicted; |
d71100ed |
341 | my $conflict = {}; |
bebec0e9 |
342 | my %reading_roots; |
7f52eac8 |
343 | my $variant_row = { 'id' => $rank, 'readings' => [] }; |
94a077d6 |
344 | # Mark each ms as in its own group, first. |
f00cefe8 |
345 | $DB::single = 1 if $rank == 81; |
94a077d6 |
346 | foreach my $g ( @$groups ) { |
347 | my $gst = wit_stringify( $g ); |
231d71fc |
348 | map { $contig->{$_} = $gst } @$g; |
94a077d6 |
349 | } |
c4a4fb1b |
350 | # Now for each unmarked node in the graph, initialize an array |
351 | # for possible group memberships. We will use this later to |
352 | # resolve potential conflicts. |
231d71fc |
353 | map { $contig->{$_} = [] unless $contig->{$_} } $graph->vertices; |
d71100ed |
354 | foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) { |
c4a4fb1b |
355 | my $gst = wit_stringify( $g ); # This is the group name |
08e0fb85 |
356 | # Copy the graph, and delete all non-members from the new graph. |
c4a4fb1b |
357 | my $part = $graph->copy; |
bebec0e9 |
358 | my @group_roots; |
c4a4fb1b |
359 | $part->delete_vertices( |
231d71fc |
360 | grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices ); |
c4a4fb1b |
361 | |
362 | # Now look to see if our group is connected. |
363 | if( $undirected ) { # For use with distance trees etc. |
364 | # Find all vertices reachable from the first (arbitrary) group |
bebec0e9 |
365 | # member. If we are genealogical this should include them all. |
366 | my $reachable = {}; |
c4a4fb1b |
367 | map { $reachable->{$_} = 1 } $part->all_reachable( $g->[0] ); |
368 | # TODO This is a terrible way to do distance trees, since all |
369 | # non-leaf nodes are included in every graph part now. We may |
370 | # have to go back to SPDP. |
371 | } else { |
372 | if( @$g > 1 ) { |
c4a4fb1b |
373 | # We have to take directionality into account. |
374 | # How many root nodes do we have? |
231d71fc |
375 | my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst } |
bebec0e9 |
376 | $part->predecessorless_vertices; |
c4a4fb1b |
377 | # Assuming that @$g > 1, find the first root node that has at |
378 | # least one successor belonging to our group. If this reading |
379 | # is genealogical, there should be only one, but we will check |
380 | # that implicitly later. |
c4a4fb1b |
381 | foreach my $root ( @roots ) { |
231d71fc |
382 | # Prune the tree to get rid of extraneous hypotheticals. |
7f52eac8 |
383 | $root = _prune_subtree( $part, $root, $contig ); |
bebec0e9 |
384 | next unless $root; |
385 | # Save this root for our group. |
386 | push( @group_roots, $root ); |
c4a4fb1b |
387 | # Get all the successor nodes of our root. |
c4a4fb1b |
388 | } |
bebec0e9 |
389 | } else { |
390 | # Dispense with the trivial case of one reading. |
f00cefe8 |
391 | my $wit = pop @$g; |
392 | @group_roots = ( $wit ); |
393 | foreach my $v ( $part->vertices ) { |
394 | $part->delete_vertex( $v ) unless $v eq $wit; |
395 | } |
bebec0e9 |
396 | } |
c4a4fb1b |
397 | } |
398 | |
bebec0e9 |
399 | map { $reading_roots{$_} = 1 } @group_roots; |
400 | if( @group_roots > 1 ) { |
401 | $conflict->{$group_readings->{$gst}} = 1; |
402 | $is_conflicted = 1; |
08e0fb85 |
403 | } |
bebec0e9 |
404 | # Paint the 'hypotheticals' with our group. |
405 | foreach my $wit ( $part->vertices ) { |
406 | if( ref( $contig->{$wit} ) ) { |
407 | push( @{$contig->{$wit}}, $gst ); |
408 | } elsif( $contig->{$wit} ne $gst ) { |
409 | warn "How did we get here?"; |
410 | } |
411 | } |
08e0fb85 |
412 | |
c4a4fb1b |
413 | |
bebec0e9 |
414 | # Start to write the reading, and save the group subgraph. |
f00cefe8 |
415 | my $reading = { 'readingid' => $group_readings->{$gst}, |
7f52eac8 |
416 | 'missing' => wit_stringify( \@lacunose ), |
c4a4fb1b |
417 | 'group' => $gst }; # This will change if we find no conflict |
bebec0e9 |
418 | # Save the relevant subgraph. |
419 | $subgraph->{$gst} = $part; |
732152b1 |
420 | push( @{$variant_row->{'readings'}}, $reading ); |
d71100ed |
421 | } |
c4a4fb1b |
422 | |
bebec0e9 |
423 | # For each of our hypothetical readings, flatten its 'contig' array if |
424 | # the array contains zero or one group. If we have any unflattened arrays, |
425 | # we may need to run the resolution process. If the reading is already known |
426 | # to have a conflict, flatten the 'contig' array to nothing; we won't resolve |
427 | # it. |
428 | my @resolve; |
429 | foreach my $wit ( keys %$contig ) { |
430 | next unless ref( $contig->{$wit} ); |
431 | if( @{$contig->{$wit}} > 1 ) { |
432 | if( $is_conflicted ) { |
433 | $contig->{$wit} = ''; # We aren't going to decide. |
434 | } else { |
435 | push( @resolve, $wit ); |
436 | } |
437 | } else { |
438 | my $gst = pop @{$contig->{$wit}}; |
439 | $contig->{$wit} = $gst || ''; |
440 | } |
441 | } |
442 | |
443 | if( @resolve ) { |
231d71fc |
444 | my $still_contig = {}; |
c4a4fb1b |
445 | foreach my $h ( @resolve ) { |
446 | # For each of the hypothetical readings with more than one possibility, |
447 | # try deleting it from each of its member subgraphs in turn, and see |
448 | # if that breaks the contiguous grouping. |
449 | # TODO This can still break in a corner case where group A can use |
450 | # either vertex 1 or 2, and group B can use either vertex 2 or 1. |
451 | # Revisit this if necessary; it could get brute-force nasty. |
231d71fc |
452 | foreach my $gst ( @{$contig->{$h}} ) { |
bebec0e9 |
453 | my $gpart = $subgraph->{$gst}->copy(); |
454 | # If we have come this far, there is only one root and everything |
455 | # is reachable from it. |
456 | my( $root ) = $gpart->predecessorless_vertices; |
457 | my $reachable = {}; |
458 | map { $reachable->{$_} = 1 } $gpart->vertices; |
459 | |
460 | # Try deleting the hypothetical node. |
c4a4fb1b |
461 | $gpart->delete_vertex( $h ); |
bebec0e9 |
462 | if( $h eq $root ) { |
463 | # See if we still have a single root. |
464 | my @roots = $gpart->predecessorless_vertices; |
465 | warn "This shouldn't have happened" unless @roots; |
466 | if( @roots > 1 ) { |
467 | # $h is needed by this group. |
468 | if( exists( $still_contig->{$h} ) ) { |
469 | # Conflict! |
470 | $conflict->{$group_readings->{$gst}} = 1; |
471 | $still_contig->{$h} = ''; |
472 | } else { |
473 | $still_contig->{$h} = $gst; |
474 | } |
475 | } |
476 | } else { |
477 | # $h is somewhere in the middle. See if everything |
478 | # else can still be reached from the root. |
479 | my %still_reachable = ( $root => 1 ); |
480 | map { $still_reachable{$_} = 1 } |
481 | $gpart->all_successors( $root ); |
482 | foreach my $v ( keys %$reachable ) { |
483 | next if $v eq $h; |
484 | if( !$still_reachable{$v} |
485 | && ( $contig->{$v} eq $gst |
486 | || ( exists $still_contig->{$v} |
487 | && $still_contig->{$v} eq $gst ) ) ) { |
488 | # We need $h. |
489 | if( exists $still_contig->{$h} ) { |
490 | # Conflict! |
491 | $conflict->{$group_readings->{$gst}} = 1; |
492 | $still_contig->{$h} = ''; |
493 | } else { |
494 | $still_contig->{$h} = $gst; |
495 | } |
496 | last; |
497 | } # else we don't need $h in this group. |
498 | } # end foreach $v |
499 | } # endif $h eq $root |
500 | } # end foreach $gst |
501 | } # end foreach $h |
c4a4fb1b |
502 | |
bebec0e9 |
503 | # Now we have some hypothetical vertices in $still_contig that are the |
504 | # "real" group memberships. Replace these in $contig. |
505 | foreach my $v ( keys %$contig ) { |
506 | next unless ref $contig->{$v}; |
507 | $contig->{$v} = $still_contig->{$v}; |
508 | } |
509 | } # end if @resolve |
510 | |
511 | # Now that we have all the node group memberships, calculate followed/ |
512 | # non-followed/unknown values for each reading. Also figure out the |
513 | # reading's evident parent(s). |
514 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
515 | my $gst = $rdghash->{'group'}; |
516 | my $part = $subgraph->{$gst}; |
517 | my @roots = $part->predecessorless_vertices; |
518 | $rdghash->{'independent_occurrence'} = scalar @roots; |
519 | $rdghash->{'followed'} = scalar( $part->vertices ) - scalar( @roots ); |
520 | # Find the parent readings, if any, of this reading. |
f00cefe8 |
521 | my %rdgparents; |
bebec0e9 |
522 | foreach my $wit ( @roots ) { |
f00cefe8 |
523 | # Look in the main stemma to find this witness's extant or known-reading |
524 | # immediate ancestor(s), and look up the reading that each ancestor olds. |
525 | my @check = $graph->predecessors( $wit ); |
526 | while( @check ) { |
527 | my @next; |
528 | foreach my $wparent( @check ) { |
529 | my $pgroup = $contig->{$wparent}; |
530 | if( $pgroup ) { |
531 | $rdgparents{$group_readings->{$pgroup}} = 1; |
532 | } else { |
533 | push( @next, $graph->predecessors( $wparent ) ); |
534 | } |
535 | } |
536 | @check = @next; |
537 | } |
bebec0e9 |
538 | } |
f00cefe8 |
539 | $rdghash->{'reading_parents'} = [ keys %rdgparents ]; |
bebec0e9 |
540 | |
541 | # Find the number of times this reading was altered, and the number of |
542 | # times we're not sure. |
543 | my( %nofollow, %unknownfollow ); |
544 | foreach my $wit ( $part->vertices ) { |
545 | foreach my $wchild ( $graph->successors( $wit ) ) { |
546 | next if $part->has_vertex( $wchild ); |
547 | if( $reading_roots{$wchild} && $contig->{$wchild} ) { |
548 | # It definitely changed here. |
549 | $nofollow{$wchild} = 1; |
550 | } elsif( !($contig->{$wchild}) ) { |
551 | # The child is a hypothetical node not definitely in |
552 | # any group. Answer is unknown. |
553 | $unknownfollow{$wchild} = 1; |
554 | } # else it's a non-root node in a known group, and therefore |
555 | # is presumed to have its reading from its group, not this link. |
556 | } |
557 | } |
558 | $rdghash->{'not_followed'} = keys %nofollow; |
559 | $rdghash->{'follow_unknown'} = keys %unknownfollow; |
c4a4fb1b |
560 | } |
bebec0e9 |
561 | |
c4a4fb1b |
562 | # Now write the group and conflict information into the respective rows. |
bebec0e9 |
563 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
f00cefe8 |
564 | $rdghash->{'conflict'} = $conflict->{$rdghash->{'readingid'}}; |
bebec0e9 |
565 | my @members = grep { $contig->{$_} eq $rdghash->{'group'} } keys %$contig; |
566 | $rdghash->{'group'} = wit_stringify( \@members ); |
c4a4fb1b |
567 | } |
568 | |
08e0fb85 |
569 | $variant_row->{'genealogical'} = !( keys %$conflict ); |
732152b1 |
570 | return $variant_row; |
d71100ed |
571 | } |
572 | |
7f52eac8 |
573 | sub _prune_subtree { |
231d71fc |
574 | my( $tree, $root, $contighash ) = @_; |
575 | # First, delete hypothetical leaves / orphans until there are none left. |
576 | my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } |
577 | $tree->successorless_vertices; |
578 | while( @orphan_hypotheticals ) { |
579 | $tree->delete_vertices( @orphan_hypotheticals ); |
580 | @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } |
581 | $tree->successorless_vertices; |
582 | } |
583 | # Then delete a hypothetical root with only one successor, moving the |
bebec0e9 |
584 | # root to the first child that has no other predecessors. |
231d71fc |
585 | while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) { |
586 | my @nextroot = $tree->successors( $root ); |
587 | $tree->delete_vertex( $root ); |
bebec0e9 |
588 | ( $root ) = grep { $tree->is_predecessorless_vertex( $_ ) } @nextroot; |
231d71fc |
589 | } |
590 | # The tree has been modified in place, but we need to know the new root. |
bebec0e9 |
591 | $root = undef unless $root && $tree->has_vertex( $root ); |
231d71fc |
592 | return $root; |
593 | } |
d71100ed |
594 | # Add the variant, subject to a.c. representation logic. |
595 | # This assumes that we will see the 'main' version before the a.c. version. |
596 | sub add_variant_wit { |
597 | my( $arr, $wit, $acstr ) = @_; |
598 | my $skip; |
599 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
600 | my $real = $1; |
601 | $skip = grep { $_ =~ /^\Q$real\E$/ } @$arr; |
602 | } |
603 | push( @$arr, $wit ) unless $skip; |
604 | } |
605 | |
5be0cdeb |
606 | sub _useful_variant { |
607 | my( $group_readings, $graph, $acstr ) = @_; |
608 | |
609 | # TODO Decide what to do with AC witnesses |
610 | |
611 | # Sort by group size and return |
612 | my $is_useful = 0; |
613 | my( @readings, @groups ); # The sorted groups for our answer. |
614 | foreach my $rdg ( sort { @{$group_readings->{$b}} <=> @{$group_readings->{$a}} } |
615 | keys %$group_readings ) { |
616 | push( @readings, $rdg ); |
617 | push( @groups, $group_readings->{$rdg} ); |
618 | if( @{$group_readings->{$rdg}} > 1 ) { |
619 | $is_useful++; |
620 | } else { |
621 | my( $wit ) = @{$group_readings->{$rdg}}; |
622 | $wit =~ s/^(.*)\Q$acstr\E$/$1/; |
623 | $is_useful++ unless( $graph->is_sink_vertex( $wit ) ); |
624 | } |
625 | } |
626 | if( $is_useful > 1 ) { |
627 | return( \@readings, \@groups ); |
628 | } else { |
629 | return( [], [] ); |
630 | } |
631 | } |
632 | |
7f52eac8 |
633 | =head2 wit_stringify( $groups ) |
634 | |
635 | Takes an array of witness groupings and produces a string like |
636 | ['A','B'] / ['C','D','E'] / ['F'] |
d71100ed |
637 | |
7f52eac8 |
638 | =cut |
d71100ed |
639 | |
640 | sub wit_stringify { |
641 | my $groups = shift; |
642 | my @gst; |
643 | # If we were passed an array of witnesses instead of an array of |
644 | # groupings, then "group" the witnesses first. |
645 | unless( ref( $groups->[0] ) ) { |
646 | my $mkgrp = [ $groups ]; |
647 | $groups = $mkgrp; |
648 | } |
649 | foreach my $g ( @$groups ) { |
650 | push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' ); |
651 | } |
652 | return join( ' / ', @gst ); |
653 | } |
7f52eac8 |
654 | |
5be0cdeb |
655 | # Helper function to ensure that X and X a.c. never appear in the same list. |
656 | sub _add_to_witlist { |
657 | my( $wit, $list, $acstr ) = @_; |
658 | my %inlist; |
659 | my $idx = 0; |
660 | map { $inlist{$_} = $idx++ } @$list; |
661 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
662 | my $acwit = $1; |
663 | unless( exists $inlist{$acwit} ) { |
664 | push( @$list, $acwit.$acstr ); |
665 | } |
666 | } else { |
667 | if( exists( $inlist{$wit.$acstr} ) ) { |
668 | # Replace the a.c. version with the main witness |
669 | my $i = $inlist{$wit.$acstr}; |
670 | $list->[$i] = $wit; |
671 | } else { |
672 | push( @$list, $wit ); |
673 | } |
674 | } |
675 | } |
676 | |
bebec0e9 |
677 | sub _symmdiff { |
678 | my( $lista, $listb ) = @_; |
7f52eac8 |
679 | my %union; |
680 | my %scalars; |
681 | map { $union{$_} = 1; $scalars{$_} = $_ } @$lista; |
682 | map { $union{$_} += 1; $scalars{$_} = $_ } @$listb; |
bebec0e9 |
683 | my @set = grep { $union{$_} == 1 } keys %union; |
7f52eac8 |
684 | return map { $scalars{$_} } @set; |
685 | } |
686 | |
687 | 1; |
688 | |
689 | =head1 LICENSE |
690 | |
691 | This package is free software and is provided "as is" without express |
692 | or implied warranty. You can redistribute it and/or modify it under |
693 | the same terms as Perl itself. |
694 | |
695 | =head1 AUTHOR |
696 | |
697 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |