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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 ) |
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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 = ( |
a44aaf2a |
73 | 1 => 0, |
f00cefe8 |
74 | 2 => 1, |
a44aaf2a |
75 | 3 => 0, |
76 | 5 => 0, |
77 | 7 => 0, |
78 | 8 => 0, |
79 | 10 => 0, |
f00cefe8 |
80 | 13 => 1, |
a44aaf2a |
81 | 33 => 0, |
82 | 34 => 0, |
83 | 37 => 0, |
84 | 60 => 0, |
f00cefe8 |
85 | 81 => 1, |
a44aaf2a |
86 | 84 => 0, |
87 | 87 => 0, |
88 | 101 => 0, |
89 | 102 => 0, |
f00cefe8 |
90 | 122 => 1, |
a44aaf2a |
91 | 157 => 0, |
f00cefe8 |
92 | 166 => 1, |
93 | 169 => 1, |
a44aaf2a |
94 | 200 => 0, |
f00cefe8 |
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'}} ) { |
a44aaf2a |
105 | # Account for rows that used to be "not useful" |
106 | unless( exists $expected_genealogical{$row->{'id'}} ) { |
107 | $expected_genealogical{$row->{'id'}} = 1; |
108 | } |
f00cefe8 |
109 | is( $row->{'genealogical'}, $expected_genealogical{$row->{'id'}}, |
110 | "Got correct genealogical flag for row " . $row->{'id'} ); |
111 | } |
a44aaf2a |
112 | is( $data->{'conflict_count'}, 34, "Got right conflict count" ); |
113 | is( $data->{'variant_count'}, 58, "Got right total variant number" ); |
7f52eac8 |
114 | |
115 | =end testing |
116 | |
117 | =cut |
118 | |
d71100ed |
119 | sub run_analysis { |
88a6bac5 |
120 | my( $tradition, %opts ) = @_; |
f00cefe8 |
121 | my $c = $tradition->collation; |
88a6bac5 |
122 | |
123 | my $stemma_id = $opts{'stemma_id'} || 0; |
1d73ecad |
124 | my @ranks = ref( $opts{'ranks'} ) eq 'ARRAY' ? @{$opts{'ranks'}} : (); |
125 | my @collapse = ref( $opts{'merge_types'} ) eq 'ARRAY' ? @{$opts{'merge_types'}} : (); |
88a6bac5 |
126 | |
127 | # Get the stemma |
128 | my $stemma = $tradition->stemma( $stemma_id ); |
129 | # Figure out which witnesses we are working with |
130 | my @lacunose = $stemma->hypotheticals; |
fae07016 |
131 | my @tradition_wits = map { $_->sigil } $tradition->witnesses; |
132 | map { push( @tradition_wits, $_->sigil."_ac" ) if $_->is_layered } |
133 | $tradition->witnesses; |
134 | push( @lacunose, _symmdiff( [ $stemma->witnesses ], \@tradition_wits ) ); |
88a6bac5 |
135 | |
136 | # Find and mark 'common' ranks for exclusion, unless they were |
137 | # explicitly specified. |
138 | unless( @ranks ) { |
139 | my %common_rank; |
a44aaf2a |
140 | foreach my $rdg ( $c->common_readings ) { |
88a6bac5 |
141 | $common_rank{$rdg->rank} = 1; |
142 | } |
143 | @ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-1 ); |
d71100ed |
144 | } |
7f52eac8 |
145 | |
88a6bac5 |
146 | # Group the variants to send to the solver |
147 | my @groups; |
a44aaf2a |
148 | my %lacunae; |
88a6bac5 |
149 | foreach my $rank ( @ranks ) { |
a44aaf2a |
150 | my $missing = [ @lacunose ]; |
151 | push( @groups, group_variants( $tradition, $rank, $missing, \@collapse ) ); |
152 | $lacunae{$rank} = $missing; |
d71100ed |
153 | } |
154 | |
88a6bac5 |
155 | # Parse the answer |
e59b8faa |
156 | my $answer = solve_variants( $stemma, @groups ); |
fae07016 |
157 | |
88a6bac5 |
158 | # Do further analysis on the answer |
a44aaf2a |
159 | my $conflict_count = 0; |
88a6bac5 |
160 | foreach my $idx ( 0 .. $#ranks ) { |
161 | my $location = $answer->{'variants'}->[$idx]; |
162 | # Add the rank back in |
163 | $location->{'id'} = $ranks[$idx]; |
a44aaf2a |
164 | # Add the lacunae back in |
165 | $location->{'missing'} = $lacunae{$ranks[$idx]}; |
88a6bac5 |
166 | # Run the extra analysis we need. |
88a6bac5 |
167 | analyze_location( $tradition, $stemma->graph, $location ); |
a44aaf2a |
168 | # Add the reading text back in |
169 | foreach my $rdghash ( @{$location->{'readings'}} ) { |
170 | $conflict_count++ |
171 | if exists $rdghash->{'conflict'} && $rdghash->{'conflict'}; |
172 | my $rdg = $c->reading( $rdghash->{'readingid'} ); |
173 | $rdghash->{'text'} = $rdg ? $rdg->text : $rdghash->{'readingid'}; |
174 | } |
88a6bac5 |
175 | } |
a44aaf2a |
176 | $answer->{'conflict_count'} = $conflict_count; |
f00cefe8 |
177 | |
88a6bac5 |
178 | return $answer; |
d71100ed |
179 | } |
180 | |
7f52eac8 |
181 | =head2 group_variants( $tradition, $rank, $lacunose, @merge_relationship_types ) |
182 | |
183 | Groups the variants at the given $rank of the collation, treating any |
184 | relationships in @merge_relationship_types as equivalent. $lacunose should |
185 | be a reference to an array, to which the sigla of lacunose witnesses at this |
186 | rank will be appended. |
187 | |
188 | Returns two ordered lists $readings, $groups, where $readings->[$n] is attested |
189 | by the witnesses listed in $groups->[$n]. |
190 | |
191 | =cut |
192 | |
193 | # Return group_readings, groups, lacunose |
d1348d38 |
194 | sub group_variants { |
7f52eac8 |
195 | my( $tradition, $rank, $lacunose, $collapse ) = @_; |
196 | my $c = $tradition->collation; |
fae07016 |
197 | my $aclabel = $c->ac_label; |
7f52eac8 |
198 | # Get the alignment table readings |
199 | my %readings_at_rank; |
200 | my @gap_wits; |
1d73ecad |
201 | foreach my $tablewit ( @{$c->alignment_table->{'alignment'}} ) { |
7f52eac8 |
202 | my $rdg = $tablewit->{'tokens'}->[$rank-1]; |
fae07016 |
203 | my $wit = $tablewit->{'witness'}; |
1d73ecad |
204 | $wit =~ s/^(.*)\Q$aclabel\E$/${1}_ac/; |
7f52eac8 |
205 | if( $rdg && $rdg->{'t'}->is_lacuna ) { |
1d73ecad |
206 | _add_to_witlist( $wit, $lacunose, '_ac' ); |
7f52eac8 |
207 | } elsif( $rdg ) { |
208 | $readings_at_rank{$rdg->{'t'}->text} = $rdg->{'t'}; |
209 | } else { |
1d73ecad |
210 | _add_to_witlist( $wit, \@gap_wits, '_ac' ); |
7f52eac8 |
211 | } |
212 | } |
d1348d38 |
213 | |
7f52eac8 |
214 | # Group the readings, collapsing groups by relationship if needed |
215 | my %grouped_readings; |
216 | foreach my $rdg ( sort { $b->witnesses <=> $a->witnesses } values %readings_at_rank ) { |
217 | # Skip readings that have been collapsed into others. |
f00cefe8 |
218 | next if exists $grouped_readings{$rdg->id} && !$grouped_readings{$rdg->id}; |
7f52eac8 |
219 | my @wits = $rdg->witnesses; |
1d73ecad |
220 | map { s/\Q$aclabel\E$/_ac/ } @wits; |
7f52eac8 |
221 | if( $collapse ) { |
222 | my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; }; |
223 | foreach my $other ( $rdg->related_readings( $filter ) ) { |
fae07016 |
224 | my @otherwits = $other->witnesses; |
1d73ecad |
225 | map { s/\Q$aclabel\E$/_ac/ } @otherwits; |
fae07016 |
226 | push( @wits, @otherwits ); |
f00cefe8 |
227 | $grouped_readings{$other->id} = 0; |
d1348d38 |
228 | } |
229 | } |
f00cefe8 |
230 | $grouped_readings{$rdg->id} = \@wits; |
7f52eac8 |
231 | } |
232 | $grouped_readings{'(omitted)'} = \@gap_wits if @gap_wits; |
233 | # Get rid of our collapsed readings |
234 | map { delete $grouped_readings{$_} unless $grouped_readings{$_} } |
235 | keys %grouped_readings |
236 | if $collapse; |
237 | |
5be0cdeb |
238 | return \%grouped_readings; |
d1348d38 |
239 | } |
240 | |
88a6bac5 |
241 | =head2 solve_variants( $graph, @groups ) |
242 | |
243 | Sends the set of groups to the external graph solver service and returns |
244 | a cleaned-up answer, adding the rank IDs back where they belong. |
245 | |
246 | The JSON has the form |
247 | { "graph": [ stemmagraph DOT string without newlines ], |
248 | "groupings": [ array of arrays of groups, one per rank ] } |
249 | |
250 | The answer has the form |
251 | { "variants" => [ array of variant location structures ], |
252 | "variant_count" => total, |
253 | "conflict_count" => number of conflicts detected, |
254 | "genealogical_count" => number of solutions found } |
255 | |
256 | =cut |
257 | |
258 | sub solve_variants { |
e59b8faa |
259 | my( $stemma, @groups ) = @_; |
88a6bac5 |
260 | |
261 | # Make the json with stemma + groups |
e59b8faa |
262 | my $jsonstruct = { 'graph' => $stemma->editable( ' ' ), 'groupings' => [] }; |
88a6bac5 |
263 | foreach my $ghash ( @groups ) { |
264 | my @grouping; |
265 | foreach my $k ( sort keys %$ghash ) { |
266 | push( @grouping, $ghash->{$k} ); |
267 | } |
268 | push( @{$jsonstruct->{'groupings'}}, \@grouping ); |
269 | } |
270 | my $json = encode_json( $jsonstruct ); |
271 | |
272 | # Send it off and get the result |
273 | my $solver_url = 'http://byzantini.st/cgi-bin/graphcalc.cgi'; |
274 | my $ua = LWP::UserAgent->new(); |
275 | my $resp = $ua->post( $solver_url, 'Content-Type' => 'application/json', |
276 | 'Content' => $json ); |
277 | |
278 | my $answer; |
279 | if( $resp->is_success ) { |
280 | $answer = decode_json( $resp->content ); |
281 | } else { |
fae07016 |
282 | # Fall back to the old method. |
283 | warn "IDP solver returned " . $resp->status_line . " / " . $resp->content |
284 | . "; falling back to perl method"; |
e59b8faa |
285 | $answer = perl_solver( $stemma, @{$jsonstruct->{'groupings'}} ); |
88a6bac5 |
286 | } |
287 | |
288 | # Fold the result back into what we know about the groups. |
289 | my $variants = []; |
290 | my $genealogical = 0; |
291 | foreach my $idx ( 0 .. $#groups ) { |
292 | my( $calc_groups, $result ) = @{$answer->[$idx]}; |
293 | $genealogical++ if $result; |
294 | my $input_group = $groups[$idx]; |
295 | foreach my $k ( sort keys %$input_group ) { |
296 | my $cg = shift @$calc_groups; |
297 | $input_group->{$k} = $cg; |
298 | } |
299 | my $vstruct = { |
300 | 'genealogical' => $result, |
301 | 'readings' => [], |
fae07016 |
302 | }; |
88a6bac5 |
303 | foreach my $k ( keys %$input_group ) { |
304 | push( @{$vstruct->{'readings'}}, |
fae07016 |
305 | { 'readingid' => $k, 'group' => $input_group->{$k}} ); |
88a6bac5 |
306 | } |
307 | push( @$variants, $vstruct ); |
308 | } |
309 | |
310 | return { 'variants' => $variants, |
311 | 'variant_count' => scalar @$variants, |
312 | 'genealogical_count' => $genealogical }; |
313 | } |
314 | |
fae07016 |
315 | =head2 analyze_location ( $tradition, $graph, $location_hash ) |
7f52eac8 |
316 | |
fae07016 |
317 | Given the tradition, its stemma graph, and the solution from the graph solver, |
318 | work out the rest of the information we want. For each reading we need missing, |
319 | conflict, reading_parents, independent_occurrence, followed, not_followed, and follow_unknown. Alters the location_hash in place. |
7f52eac8 |
320 | |
321 | =cut |
732152b1 |
322 | |
fae07016 |
323 | sub analyze_location { |
324 | my ( $tradition, $graph, $variant_row ) = @_; |
325 | |
326 | # Make a hash of all known node memberships, and make the subgraphs. |
327 | my $contig = {}; |
328 | my $reading_roots = {}; |
329 | my $subgraph = {}; |
330 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
331 | my $rid = $rdghash->{'readingid'}; |
332 | map { $contig->{$_} = $rid } @{$rdghash->{'group'}}; |
c4a4fb1b |
333 | |
fae07016 |
334 | # Make the subgraph. |
335 | my $part = $graph->copy; |
336 | my %these_vertices; |
337 | map { $these_vertices{$_} = 1 } @{$rdghash->{'group'}}; |
338 | $part->delete_vertices( grep { !$these_vertices{$_} } $part->vertices ); |
339 | $subgraph->{$rid} = $part; |
340 | # Get the reading roots. |
341 | map { $reading_roots->{$_} = $rid } $part->predecessorless_vertices; |
bebec0e9 |
342 | } |
343 | |
fae07016 |
344 | # Now that we have all the node group memberships, calculate followed/ |
bebec0e9 |
345 | # non-followed/unknown values for each reading. Also figure out the |
346 | # reading's evident parent(s). |
347 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
fae07016 |
348 | # Group string key - TODO do we need this? |
349 | my $gst = wit_stringify( $rdghash->{'group'} ); |
350 | my $rid = $rdghash->{'readingid'}; |
351 | # Get the subgraph |
352 | my $part = $subgraph->{$rid}; |
353 | |
354 | # Start figuring things out. |
bebec0e9 |
355 | my @roots = $part->predecessorless_vertices; |
356 | $rdghash->{'independent_occurrence'} = scalar @roots; |
357 | $rdghash->{'followed'} = scalar( $part->vertices ) - scalar( @roots ); |
358 | # Find the parent readings, if any, of this reading. |
f00cefe8 |
359 | my %rdgparents; |
bebec0e9 |
360 | foreach my $wit ( @roots ) { |
f00cefe8 |
361 | # Look in the main stemma to find this witness's extant or known-reading |
362 | # immediate ancestor(s), and look up the reading that each ancestor olds. |
363 | my @check = $graph->predecessors( $wit ); |
364 | while( @check ) { |
365 | my @next; |
366 | foreach my $wparent( @check ) { |
fae07016 |
367 | my $preading = $contig->{$wparent}; |
368 | if( $preading ) { |
369 | $rdgparents{$preading} = 1; |
f00cefe8 |
370 | } else { |
371 | push( @next, $graph->predecessors( $wparent ) ); |
372 | } |
373 | } |
374 | @check = @next; |
375 | } |
bebec0e9 |
376 | } |
f00cefe8 |
377 | $rdghash->{'reading_parents'} = [ keys %rdgparents ]; |
bebec0e9 |
378 | |
379 | # Find the number of times this reading was altered, and the number of |
380 | # times we're not sure. |
381 | my( %nofollow, %unknownfollow ); |
382 | foreach my $wit ( $part->vertices ) { |
383 | foreach my $wchild ( $graph->successors( $wit ) ) { |
384 | next if $part->has_vertex( $wchild ); |
fae07016 |
385 | if( $reading_roots->{$wchild} && $contig->{$wchild} ) { |
bebec0e9 |
386 | # It definitely changed here. |
387 | $nofollow{$wchild} = 1; |
388 | } elsif( !($contig->{$wchild}) ) { |
389 | # The child is a hypothetical node not definitely in |
390 | # any group. Answer is unknown. |
391 | $unknownfollow{$wchild} = 1; |
392 | } # else it's a non-root node in a known group, and therefore |
393 | # is presumed to have its reading from its group, not this link. |
394 | } |
395 | } |
396 | $rdghash->{'not_followed'} = keys %nofollow; |
397 | $rdghash->{'follow_unknown'} = keys %unknownfollow; |
fae07016 |
398 | |
399 | # Now say whether this reading represents a conflict. |
400 | unless( $variant_row->{'genealogical'} ) { |
401 | $rdghash->{'conflict'} = @roots != 1; |
402 | } |
c4a4fb1b |
403 | } |
d71100ed |
404 | } |
405 | |
fae07016 |
406 | |
407 | =head2 perl_solver( $tradition, $rank, $stemma_id, @merge_relationship_types ) |
408 | |
409 | ** NOTE ** This method should hopefully not be called - it is not guaranteed |
410 | to be correct. Serves as a backup for the real solver. |
411 | |
412 | Runs an analysis of the given tradition, at the location given in $rank, |
413 | against the graph of the stemma specified in $stemma_id. The argument |
414 | @merge_relationship_types is an optional list of relationship types for |
415 | which readings so related should be treated as equivalent. |
416 | |
417 | Returns a nested array data structure as follows: |
418 | |
419 | [ [ group_list, is_genealogical ], [ group_list, is_genealogical ] ... ] |
420 | |
421 | where the group list is the array of arrays passed in for each element of @groups, |
422 | possibly with the addition of hypothetical readings. |
423 | |
424 | |
425 | =cut |
426 | |
427 | sub perl_solver { |
e59b8faa |
428 | my( $stemma, @groups ) = @_; |
429 | my $graph = $stemma->graph; |
430 | my @answer; |
431 | foreach my $g ( @groups ) { |
432 | push( @answer, _solve_variant_location( $graph, $g ) ); |
433 | } |
434 | return \@answer; |
fae07016 |
435 | } |
436 | |
e59b8faa |
437 | sub _solve_variant_location { |
438 | my( $graph, $groups ) = @_; |
fae07016 |
439 | # Now do the work. |
e59b8faa |
440 | my $contig = {}; |
441 | my $subgraph = {}; |
442 | my $is_conflicted; |
443 | my $conflict = {}; |
444 | |
445 | # Mark each ms as in its own group, first. |
446 | foreach my $g ( @$groups ) { |
447 | my $gst = wit_stringify( $g ); |
448 | map { $contig->{$_} = $gst } @$g; |
449 | } |
450 | |
451 | # Now for each unmarked node in the graph, initialize an array |
452 | # for possible group memberships. We will use this later to |
453 | # resolve potential conflicts. |
454 | map { $contig->{$_} = [] unless $contig->{$_} } $graph->vertices; |
455 | foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) { |
456 | my $gst = wit_stringify( $g ); # This is the group name |
457 | # Copy the graph, and delete all non-members from the new graph. |
458 | my $part = $graph->copy; |
459 | my @group_roots; |
460 | $part->delete_vertices( |
461 | grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices ); |
462 | |
463 | # Now look to see if our group is connected. |
464 | if( @$g > 1 ) { |
465 | # We have to take directionality into account. |
466 | # How many root nodes do we have? |
467 | my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst } |
468 | $part->predecessorless_vertices; |
469 | # Assuming that @$g > 1, find the first root node that has at |
470 | # least one successor belonging to our group. If this reading |
471 | # is genealogical, there should be only one, but we will check |
472 | # that implicitly later. |
473 | foreach my $root ( @roots ) { |
474 | # Prune the tree to get rid of extraneous hypotheticals. |
475 | $root = _prune_subtree( $part, $root, $contig ); |
476 | next unless $root; |
477 | # Save this root for our group. |
478 | push( @group_roots, $root ); |
479 | # Get all the successor nodes of our root. |
480 | } |
481 | } else { |
482 | # Dispense with the trivial case of one reading. |
483 | my $wit = $g->[0]; |
484 | @group_roots = ( $wit ); |
485 | foreach my $v ( $part->vertices ) { |
486 | $part->delete_vertex( $v ) unless $v eq $wit; |
487 | } |
488 | } |
489 | |
490 | if( @group_roots > 1 ) { |
491 | $conflict->{$gst} = 1; |
492 | $is_conflicted = 1; |
493 | } |
494 | # Paint the 'hypotheticals' with our group. |
495 | foreach my $wit ( $part->vertices ) { |
496 | if( ref( $contig->{$wit} ) ) { |
497 | push( @{$contig->{$wit}}, $gst ); |
498 | } elsif( $contig->{$wit} ne $gst ) { |
499 | warn "How did we get here?"; |
500 | } |
501 | } |
502 | |
503 | |
504 | # Save the relevant subgraph. |
505 | $subgraph->{$gst} = $part; |
506 | } |
507 | |
508 | # For each of our hypothetical readings, flatten its 'contig' array if |
509 | # the array contains zero or one group. If we have any unflattened arrays, |
510 | # we may need to run the resolution process. If the reading is already known |
511 | # to have a conflict, flatten the 'contig' array to nothing; we won't resolve |
512 | # it. |
513 | my @resolve; |
514 | foreach my $wit ( keys %$contig ) { |
515 | next unless ref( $contig->{$wit} ); |
516 | if( @{$contig->{$wit}} > 1 ) { |
517 | if( $is_conflicted ) { |
518 | $contig->{$wit} = ''; # We aren't going to decide. |
519 | } else { |
520 | push( @resolve, $wit ); |
521 | } |
522 | } else { |
523 | my $gst = pop @{$contig->{$wit}}; |
524 | $contig->{$wit} = $gst || ''; |
525 | } |
526 | } |
527 | |
528 | if( @resolve ) { |
529 | my $still_contig = {}; |
530 | foreach my $h ( @resolve ) { |
531 | # For each of the hypothetical readings with more than one possibility, |
532 | # try deleting it from each of its member subgraphs in turn, and see |
533 | # if that breaks the contiguous grouping. |
534 | # TODO This can still break in a corner case where group A can use |
535 | # either vertex 1 or 2, and group B can use either vertex 2 or 1. |
536 | # Revisit this if necessary; it could get brute-force nasty. |
537 | foreach my $gst ( @{$contig->{$h}} ) { |
538 | my $gpart = $subgraph->{$gst}->copy(); |
539 | # If we have come this far, there is only one root and everything |
540 | # is reachable from it. |
541 | my( $root ) = $gpart->predecessorless_vertices; |
542 | my $reachable = {}; |
543 | map { $reachable->{$_} = 1 } $gpart->vertices; |
544 | |
545 | # Try deleting the hypothetical node. |
546 | $gpart->delete_vertex( $h ); |
547 | if( $h eq $root ) { |
548 | # See if we still have a single root. |
549 | my @roots = $gpart->predecessorless_vertices; |
550 | warn "This shouldn't have happened" unless @roots; |
551 | if( @roots > 1 ) { |
552 | # $h is needed by this group. |
553 | if( exists( $still_contig->{$h} ) ) { |
554 | # Conflict! |
555 | $conflict->{$gst} = 1; |
556 | $still_contig->{$h} = ''; |
557 | } else { |
558 | $still_contig->{$h} = $gst; |
559 | } |
560 | } |
561 | } else { |
562 | # $h is somewhere in the middle. See if everything |
563 | # else can still be reached from the root. |
564 | my %still_reachable = ( $root => 1 ); |
565 | map { $still_reachable{$_} = 1 } |
566 | $gpart->all_successors( $root ); |
567 | foreach my $v ( keys %$reachable ) { |
568 | next if $v eq $h; |
569 | if( !$still_reachable{$v} |
570 | && ( $contig->{$v} eq $gst |
571 | || ( exists $still_contig->{$v} |
572 | && $still_contig->{$v} eq $gst ) ) ) { |
573 | # We need $h. |
574 | if( exists $still_contig->{$h} ) { |
575 | # Conflict! |
576 | $conflict->{$gst} = 1; |
577 | $still_contig->{$h} = ''; |
578 | } else { |
579 | $still_contig->{$h} = $gst; |
580 | } |
581 | last; |
582 | } # else we don't need $h in this group. |
583 | } # end foreach $v |
584 | } # endif $h eq $root |
585 | } # end foreach $gst |
586 | } # end foreach $h |
587 | |
588 | # Now we have some hypothetical vertices in $still_contig that are the |
589 | # "real" group memberships. Replace these in $contig. |
590 | foreach my $v ( keys %$contig ) { |
591 | next unless ref $contig->{$v}; |
592 | $contig->{$v} = $still_contig->{$v}; |
593 | } |
594 | } # end if @resolve |
595 | |
596 | my $is_genealogical = keys %$conflict ? JSON::false : JSON::true; |
597 | my $variant_row = [ [], $is_genealogical ]; |
598 | # Fill in the groupings from $contig. |
599 | foreach my $g ( @$groups ) { |
600 | my $gst = wit_stringify( $g ); |
601 | my @realgroup = grep { $contig->{$_} eq $gst } keys %$contig; |
602 | push( @{$variant_row->[0]}, \@realgroup ); |
603 | } |
604 | return $variant_row; |
605 | } |
fae07016 |
606 | |
7f52eac8 |
607 | sub _prune_subtree { |
231d71fc |
608 | my( $tree, $root, $contighash ) = @_; |
609 | # First, delete hypothetical leaves / orphans until there are none left. |
610 | my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } |
611 | $tree->successorless_vertices; |
612 | while( @orphan_hypotheticals ) { |
613 | $tree->delete_vertices( @orphan_hypotheticals ); |
614 | @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } |
615 | $tree->successorless_vertices; |
616 | } |
617 | # Then delete a hypothetical root with only one successor, moving the |
bebec0e9 |
618 | # root to the first child that has no other predecessors. |
231d71fc |
619 | while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) { |
620 | my @nextroot = $tree->successors( $root ); |
621 | $tree->delete_vertex( $root ); |
bebec0e9 |
622 | ( $root ) = grep { $tree->is_predecessorless_vertex( $_ ) } @nextroot; |
231d71fc |
623 | } |
624 | # The tree has been modified in place, but we need to know the new root. |
bebec0e9 |
625 | $root = undef unless $root && $tree->has_vertex( $root ); |
231d71fc |
626 | return $root; |
627 | } |
d71100ed |
628 | # Add the variant, subject to a.c. representation logic. |
629 | # This assumes that we will see the 'main' version before the a.c. version. |
630 | sub add_variant_wit { |
631 | my( $arr, $wit, $acstr ) = @_; |
632 | my $skip; |
633 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
634 | my $real = $1; |
635 | $skip = grep { $_ =~ /^\Q$real\E$/ } @$arr; |
636 | } |
637 | push( @$arr, $wit ) unless $skip; |
638 | } |
639 | |
5be0cdeb |
640 | sub _useful_variant { |
641 | my( $group_readings, $graph, $acstr ) = @_; |
642 | |
643 | # TODO Decide what to do with AC witnesses |
644 | |
645 | # Sort by group size and return |
646 | my $is_useful = 0; |
647 | my( @readings, @groups ); # The sorted groups for our answer. |
648 | foreach my $rdg ( sort { @{$group_readings->{$b}} <=> @{$group_readings->{$a}} } |
649 | keys %$group_readings ) { |
650 | push( @readings, $rdg ); |
651 | push( @groups, $group_readings->{$rdg} ); |
652 | if( @{$group_readings->{$rdg}} > 1 ) { |
653 | $is_useful++; |
654 | } else { |
655 | my( $wit ) = @{$group_readings->{$rdg}}; |
656 | $wit =~ s/^(.*)\Q$acstr\E$/$1/; |
657 | $is_useful++ unless( $graph->is_sink_vertex( $wit ) ); |
658 | } |
659 | } |
660 | if( $is_useful > 1 ) { |
661 | return( \@readings, \@groups ); |
662 | } else { |
663 | return( [], [] ); |
664 | } |
665 | } |
666 | |
7f52eac8 |
667 | =head2 wit_stringify( $groups ) |
668 | |
669 | Takes an array of witness groupings and produces a string like |
670 | ['A','B'] / ['C','D','E'] / ['F'] |
d71100ed |
671 | |
7f52eac8 |
672 | =cut |
d71100ed |
673 | |
674 | sub wit_stringify { |
675 | my $groups = shift; |
676 | my @gst; |
677 | # If we were passed an array of witnesses instead of an array of |
678 | # groupings, then "group" the witnesses first. |
679 | unless( ref( $groups->[0] ) ) { |
680 | my $mkgrp = [ $groups ]; |
681 | $groups = $mkgrp; |
682 | } |
683 | foreach my $g ( @$groups ) { |
684 | push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' ); |
685 | } |
686 | return join( ' / ', @gst ); |
687 | } |
7f52eac8 |
688 | |
5be0cdeb |
689 | # Helper function to ensure that X and X a.c. never appear in the same list. |
690 | sub _add_to_witlist { |
691 | my( $wit, $list, $acstr ) = @_; |
692 | my %inlist; |
693 | my $idx = 0; |
694 | map { $inlist{$_} = $idx++ } @$list; |
695 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
696 | my $acwit = $1; |
697 | unless( exists $inlist{$acwit} ) { |
698 | push( @$list, $acwit.$acstr ); |
699 | } |
700 | } else { |
701 | if( exists( $inlist{$wit.$acstr} ) ) { |
702 | # Replace the a.c. version with the main witness |
703 | my $i = $inlist{$wit.$acstr}; |
704 | $list->[$i] = $wit; |
705 | } else { |
706 | push( @$list, $wit ); |
707 | } |
708 | } |
709 | } |
710 | |
bebec0e9 |
711 | sub _symmdiff { |
712 | my( $lista, $listb ) = @_; |
7f52eac8 |
713 | my %union; |
714 | my %scalars; |
715 | map { $union{$_} = 1; $scalars{$_} = $_ } @$lista; |
716 | map { $union{$_} += 1; $scalars{$_} = $_ } @$listb; |
bebec0e9 |
717 | my @set = grep { $union{$_} == 1 } keys %union; |
7f52eac8 |
718 | return map { $scalars{$_} } @set; |
719 | } |
720 | |
721 | 1; |
722 | |
723 | =head1 LICENSE |
724 | |
725 | This package is free software and is provided "as is" without express |
726 | or implied warranty. You can redistribute it and/or modify it under |
727 | the same terms as Perl itself. |
728 | |
729 | =head1 AUTHOR |
730 | |
731 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |