Commit | Line | Data |
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 | |
88a6bac5 |
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: |
7f52eac8 |
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 = $opts{'stemma_id'} || 0; |
124 | my @ranks = @{$opts{'ranks'}} if ref( $opts{'ranks'} ) eq 'ARRAY'; |
125 | my @collapse = @{$opts{'merge_types'}} if ref( $opts{'merge_types'} ) eq 'ARRAY'; |
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; |
e59b8faa |
197 | # All the regexps here are to get rid of space characters in witness names. |
fae07016 |
198 | my $aclabel = $c->ac_label; |
e59b8faa |
199 | $aclabel =~ s/\s/_/g; |
7f52eac8 |
200 | # Get the alignment table readings |
201 | my %readings_at_rank; |
202 | my @gap_wits; |
203 | foreach my $tablewit ( @{$tradition->collation->alignment_table->{'alignment'}} ) { |
204 | my $rdg = $tablewit->{'tokens'}->[$rank-1]; |
fae07016 |
205 | my $wit = $tablewit->{'witness'}; |
e59b8faa |
206 | $wit =~ s/\s/_/g; |
7f52eac8 |
207 | if( $rdg && $rdg->{'t'}->is_lacuna ) { |
e59b8faa |
208 | _add_to_witlist( $wit, $lacunose, $aclabel ); |
7f52eac8 |
209 | } elsif( $rdg ) { |
210 | $readings_at_rank{$rdg->{'t'}->text} = $rdg->{'t'}; |
211 | } else { |
e59b8faa |
212 | _add_to_witlist( $wit, \@gap_wits, $aclabel ); |
7f52eac8 |
213 | } |
214 | } |
d1348d38 |
215 | |
7f52eac8 |
216 | # Group the readings, collapsing groups by relationship if needed |
217 | my %grouped_readings; |
218 | foreach my $rdg ( sort { $b->witnesses <=> $a->witnesses } values %readings_at_rank ) { |
219 | # Skip readings that have been collapsed into others. |
f00cefe8 |
220 | next if exists $grouped_readings{$rdg->id} && !$grouped_readings{$rdg->id}; |
7f52eac8 |
221 | my @wits = $rdg->witnesses; |
e59b8faa |
222 | map { s/\s/_/g } @wits; |
7f52eac8 |
223 | if( $collapse ) { |
224 | my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; }; |
225 | foreach my $other ( $rdg->related_readings( $filter ) ) { |
fae07016 |
226 | my @otherwits = $other->witnesses; |
e59b8faa |
227 | map { s/\s/_/g } @otherwits; |
fae07016 |
228 | push( @wits, @otherwits ); |
f00cefe8 |
229 | $grouped_readings{$other->id} = 0; |
d1348d38 |
230 | } |
231 | } |
f00cefe8 |
232 | $grouped_readings{$rdg->id} = \@wits; |
7f52eac8 |
233 | } |
234 | $grouped_readings{'(omitted)'} = \@gap_wits if @gap_wits; |
235 | # Get rid of our collapsed readings |
236 | map { delete $grouped_readings{$_} unless $grouped_readings{$_} } |
237 | keys %grouped_readings |
238 | if $collapse; |
239 | |
5be0cdeb |
240 | return \%grouped_readings; |
d1348d38 |
241 | } |
242 | |
88a6bac5 |
243 | =head2 solve_variants( $graph, @groups ) |
244 | |
245 | Sends the set of groups to the external graph solver service and returns |
246 | a cleaned-up answer, adding the rank IDs back where they belong. |
247 | |
248 | The JSON has the form |
249 | { "graph": [ stemmagraph DOT string without newlines ], |
250 | "groupings": [ array of arrays of groups, one per rank ] } |
251 | |
252 | The answer has the form |
253 | { "variants" => [ array of variant location structures ], |
254 | "variant_count" => total, |
255 | "conflict_count" => number of conflicts detected, |
256 | "genealogical_count" => number of solutions found } |
257 | |
258 | =cut |
259 | |
260 | sub solve_variants { |
e59b8faa |
261 | my( $stemma, @groups ) = @_; |
88a6bac5 |
262 | |
263 | # Make the json with stemma + groups |
e59b8faa |
264 | my $jsonstruct = { 'graph' => $stemma->editable( ' ' ), 'groupings' => [] }; |
88a6bac5 |
265 | foreach my $ghash ( @groups ) { |
266 | my @grouping; |
267 | foreach my $k ( sort keys %$ghash ) { |
268 | push( @grouping, $ghash->{$k} ); |
269 | } |
270 | push( @{$jsonstruct->{'groupings'}}, \@grouping ); |
271 | } |
272 | my $json = encode_json( $jsonstruct ); |
273 | |
274 | # Send it off and get the result |
275 | my $solver_url = 'http://byzantini.st/cgi-bin/graphcalc.cgi'; |
276 | my $ua = LWP::UserAgent->new(); |
277 | my $resp = $ua->post( $solver_url, 'Content-Type' => 'application/json', |
278 | 'Content' => $json ); |
279 | |
280 | my $answer; |
281 | if( $resp->is_success ) { |
282 | $answer = decode_json( $resp->content ); |
283 | } else { |
fae07016 |
284 | # Fall back to the old method. |
285 | warn "IDP solver returned " . $resp->status_line . " / " . $resp->content |
286 | . "; falling back to perl method"; |
e59b8faa |
287 | $answer = perl_solver( $stemma, @{$jsonstruct->{'groupings'}} ); |
88a6bac5 |
288 | } |
289 | |
290 | # Fold the result back into what we know about the groups. |
291 | my $variants = []; |
292 | my $genealogical = 0; |
293 | foreach my $idx ( 0 .. $#groups ) { |
294 | my( $calc_groups, $result ) = @{$answer->[$idx]}; |
295 | $genealogical++ if $result; |
296 | my $input_group = $groups[$idx]; |
297 | foreach my $k ( sort keys %$input_group ) { |
298 | my $cg = shift @$calc_groups; |
299 | $input_group->{$k} = $cg; |
300 | } |
301 | my $vstruct = { |
302 | 'genealogical' => $result, |
303 | 'readings' => [], |
fae07016 |
304 | }; |
88a6bac5 |
305 | foreach my $k ( keys %$input_group ) { |
306 | push( @{$vstruct->{'readings'}}, |
fae07016 |
307 | { 'readingid' => $k, 'group' => $input_group->{$k}} ); |
88a6bac5 |
308 | } |
309 | push( @$variants, $vstruct ); |
310 | } |
311 | |
312 | return { 'variants' => $variants, |
313 | 'variant_count' => scalar @$variants, |
314 | 'genealogical_count' => $genealogical }; |
315 | } |
316 | |
fae07016 |
317 | =head2 analyze_location ( $tradition, $graph, $location_hash ) |
7f52eac8 |
318 | |
fae07016 |
319 | Given the tradition, its stemma graph, and the solution from the graph solver, |
320 | work out the rest of the information we want. For each reading we need missing, |
321 | conflict, reading_parents, independent_occurrence, followed, not_followed, and follow_unknown. Alters the location_hash in place. |
7f52eac8 |
322 | |
323 | =cut |
732152b1 |
324 | |
fae07016 |
325 | sub analyze_location { |
326 | my ( $tradition, $graph, $variant_row ) = @_; |
327 | |
328 | # Make a hash of all known node memberships, and make the subgraphs. |
329 | my $contig = {}; |
330 | my $reading_roots = {}; |
331 | my $subgraph = {}; |
332 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
333 | my $rid = $rdghash->{'readingid'}; |
334 | map { $contig->{$_} = $rid } @{$rdghash->{'group'}}; |
c4a4fb1b |
335 | |
fae07016 |
336 | # Make the subgraph. |
337 | my $part = $graph->copy; |
338 | my %these_vertices; |
339 | map { $these_vertices{$_} = 1 } @{$rdghash->{'group'}}; |
340 | $part->delete_vertices( grep { !$these_vertices{$_} } $part->vertices ); |
341 | $subgraph->{$rid} = $part; |
342 | # Get the reading roots. |
343 | map { $reading_roots->{$_} = $rid } $part->predecessorless_vertices; |
bebec0e9 |
344 | } |
345 | |
fae07016 |
346 | # Now that we have all the node group memberships, calculate followed/ |
bebec0e9 |
347 | # non-followed/unknown values for each reading. Also figure out the |
348 | # reading's evident parent(s). |
349 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
fae07016 |
350 | # Group string key - TODO do we need this? |
351 | my $gst = wit_stringify( $rdghash->{'group'} ); |
352 | my $rid = $rdghash->{'readingid'}; |
353 | # Get the subgraph |
354 | my $part = $subgraph->{$rid}; |
355 | |
356 | # Start figuring things out. |
bebec0e9 |
357 | my @roots = $part->predecessorless_vertices; |
358 | $rdghash->{'independent_occurrence'} = scalar @roots; |
359 | $rdghash->{'followed'} = scalar( $part->vertices ) - scalar( @roots ); |
360 | # Find the parent readings, if any, of this reading. |
f00cefe8 |
361 | my %rdgparents; |
bebec0e9 |
362 | foreach my $wit ( @roots ) { |
f00cefe8 |
363 | # Look in the main stemma to find this witness's extant or known-reading |
364 | # immediate ancestor(s), and look up the reading that each ancestor olds. |
365 | my @check = $graph->predecessors( $wit ); |
366 | while( @check ) { |
367 | my @next; |
368 | foreach my $wparent( @check ) { |
fae07016 |
369 | my $preading = $contig->{$wparent}; |
370 | if( $preading ) { |
371 | $rdgparents{$preading} = 1; |
f00cefe8 |
372 | } else { |
373 | push( @next, $graph->predecessors( $wparent ) ); |
374 | } |
375 | } |
376 | @check = @next; |
377 | } |
bebec0e9 |
378 | } |
f00cefe8 |
379 | $rdghash->{'reading_parents'} = [ keys %rdgparents ]; |
bebec0e9 |
380 | |
381 | # Find the number of times this reading was altered, and the number of |
382 | # times we're not sure. |
383 | my( %nofollow, %unknownfollow ); |
384 | foreach my $wit ( $part->vertices ) { |
385 | foreach my $wchild ( $graph->successors( $wit ) ) { |
386 | next if $part->has_vertex( $wchild ); |
fae07016 |
387 | if( $reading_roots->{$wchild} && $contig->{$wchild} ) { |
bebec0e9 |
388 | # It definitely changed here. |
389 | $nofollow{$wchild} = 1; |
390 | } elsif( !($contig->{$wchild}) ) { |
391 | # The child is a hypothetical node not definitely in |
392 | # any group. Answer is unknown. |
393 | $unknownfollow{$wchild} = 1; |
394 | } # else it's a non-root node in a known group, and therefore |
395 | # is presumed to have its reading from its group, not this link. |
396 | } |
397 | } |
398 | $rdghash->{'not_followed'} = keys %nofollow; |
399 | $rdghash->{'follow_unknown'} = keys %unknownfollow; |
fae07016 |
400 | |
401 | # Now say whether this reading represents a conflict. |
402 | unless( $variant_row->{'genealogical'} ) { |
403 | $rdghash->{'conflict'} = @roots != 1; |
404 | } |
c4a4fb1b |
405 | } |
d71100ed |
406 | } |
407 | |
fae07016 |
408 | |
409 | =head2 perl_solver( $tradition, $rank, $stemma_id, @merge_relationship_types ) |
410 | |
411 | ** NOTE ** This method should hopefully not be called - it is not guaranteed |
412 | to be correct. Serves as a backup for the real solver. |
413 | |
414 | Runs an analysis of the given tradition, at the location given in $rank, |
415 | against the graph of the stemma specified in $stemma_id. The argument |
416 | @merge_relationship_types is an optional list of relationship types for |
417 | which readings so related should be treated as equivalent. |
418 | |
419 | Returns a nested array data structure as follows: |
420 | |
421 | [ [ group_list, is_genealogical ], [ group_list, is_genealogical ] ... ] |
422 | |
423 | where the group list is the array of arrays passed in for each element of @groups, |
424 | possibly with the addition of hypothetical readings. |
425 | |
426 | |
427 | =cut |
428 | |
429 | sub perl_solver { |
e59b8faa |
430 | my( $stemma, @groups ) = @_; |
431 | my $graph = $stemma->graph; |
432 | my @answer; |
433 | foreach my $g ( @groups ) { |
434 | push( @answer, _solve_variant_location( $graph, $g ) ); |
435 | } |
436 | return \@answer; |
fae07016 |
437 | } |
438 | |
e59b8faa |
439 | sub _solve_variant_location { |
440 | my( $graph, $groups ) = @_; |
fae07016 |
441 | # Now do the work. |
e59b8faa |
442 | my $contig = {}; |
443 | my $subgraph = {}; |
444 | my $is_conflicted; |
445 | my $conflict = {}; |
446 | |
447 | # Mark each ms as in its own group, first. |
448 | foreach my $g ( @$groups ) { |
449 | my $gst = wit_stringify( $g ); |
450 | map { $contig->{$_} = $gst } @$g; |
451 | } |
452 | |
453 | # Now for each unmarked node in the graph, initialize an array |
454 | # for possible group memberships. We will use this later to |
455 | # resolve potential conflicts. |
456 | map { $contig->{$_} = [] unless $contig->{$_} } $graph->vertices; |
457 | foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) { |
458 | my $gst = wit_stringify( $g ); # This is the group name |
459 | # Copy the graph, and delete all non-members from the new graph. |
460 | my $part = $graph->copy; |
461 | my @group_roots; |
462 | $part->delete_vertices( |
463 | grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices ); |
464 | |
465 | # Now look to see if our group is connected. |
466 | if( @$g > 1 ) { |
467 | # We have to take directionality into account. |
468 | # How many root nodes do we have? |
469 | my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst } |
470 | $part->predecessorless_vertices; |
471 | # Assuming that @$g > 1, find the first root node that has at |
472 | # least one successor belonging to our group. If this reading |
473 | # is genealogical, there should be only one, but we will check |
474 | # that implicitly later. |
475 | foreach my $root ( @roots ) { |
476 | # Prune the tree to get rid of extraneous hypotheticals. |
477 | $root = _prune_subtree( $part, $root, $contig ); |
478 | next unless $root; |
479 | # Save this root for our group. |
480 | push( @group_roots, $root ); |
481 | # Get all the successor nodes of our root. |
482 | } |
483 | } else { |
484 | # Dispense with the trivial case of one reading. |
485 | my $wit = $g->[0]; |
486 | @group_roots = ( $wit ); |
487 | foreach my $v ( $part->vertices ) { |
488 | $part->delete_vertex( $v ) unless $v eq $wit; |
489 | } |
490 | } |
491 | |
492 | if( @group_roots > 1 ) { |
493 | $conflict->{$gst} = 1; |
494 | $is_conflicted = 1; |
495 | } |
496 | # Paint the 'hypotheticals' with our group. |
497 | foreach my $wit ( $part->vertices ) { |
498 | if( ref( $contig->{$wit} ) ) { |
499 | push( @{$contig->{$wit}}, $gst ); |
500 | } elsif( $contig->{$wit} ne $gst ) { |
501 | warn "How did we get here?"; |
502 | } |
503 | } |
504 | |
505 | |
506 | # Save the relevant subgraph. |
507 | $subgraph->{$gst} = $part; |
508 | } |
509 | |
510 | # For each of our hypothetical readings, flatten its 'contig' array if |
511 | # the array contains zero or one group. If we have any unflattened arrays, |
512 | # we may need to run the resolution process. If the reading is already known |
513 | # to have a conflict, flatten the 'contig' array to nothing; we won't resolve |
514 | # it. |
515 | my @resolve; |
516 | foreach my $wit ( keys %$contig ) { |
517 | next unless ref( $contig->{$wit} ); |
518 | if( @{$contig->{$wit}} > 1 ) { |
519 | if( $is_conflicted ) { |
520 | $contig->{$wit} = ''; # We aren't going to decide. |
521 | } else { |
522 | push( @resolve, $wit ); |
523 | } |
524 | } else { |
525 | my $gst = pop @{$contig->{$wit}}; |
526 | $contig->{$wit} = $gst || ''; |
527 | } |
528 | } |
529 | |
530 | if( @resolve ) { |
531 | my $still_contig = {}; |
532 | foreach my $h ( @resolve ) { |
533 | # For each of the hypothetical readings with more than one possibility, |
534 | # try deleting it from each of its member subgraphs in turn, and see |
535 | # if that breaks the contiguous grouping. |
536 | # TODO This can still break in a corner case where group A can use |
537 | # either vertex 1 or 2, and group B can use either vertex 2 or 1. |
538 | # Revisit this if necessary; it could get brute-force nasty. |
539 | foreach my $gst ( @{$contig->{$h}} ) { |
540 | my $gpart = $subgraph->{$gst}->copy(); |
541 | # If we have come this far, there is only one root and everything |
542 | # is reachable from it. |
543 | my( $root ) = $gpart->predecessorless_vertices; |
544 | my $reachable = {}; |
545 | map { $reachable->{$_} = 1 } $gpart->vertices; |
546 | |
547 | # Try deleting the hypothetical node. |
548 | $gpart->delete_vertex( $h ); |
549 | if( $h eq $root ) { |
550 | # See if we still have a single root. |
551 | my @roots = $gpart->predecessorless_vertices; |
552 | warn "This shouldn't have happened" unless @roots; |
553 | if( @roots > 1 ) { |
554 | # $h is needed by this group. |
555 | if( exists( $still_contig->{$h} ) ) { |
556 | # Conflict! |
557 | $conflict->{$gst} = 1; |
558 | $still_contig->{$h} = ''; |
559 | } else { |
560 | $still_contig->{$h} = $gst; |
561 | } |
562 | } |
563 | } else { |
564 | # $h is somewhere in the middle. See if everything |
565 | # else can still be reached from the root. |
566 | my %still_reachable = ( $root => 1 ); |
567 | map { $still_reachable{$_} = 1 } |
568 | $gpart->all_successors( $root ); |
569 | foreach my $v ( keys %$reachable ) { |
570 | next if $v eq $h; |
571 | if( !$still_reachable{$v} |
572 | && ( $contig->{$v} eq $gst |
573 | || ( exists $still_contig->{$v} |
574 | && $still_contig->{$v} eq $gst ) ) ) { |
575 | # We need $h. |
576 | if( exists $still_contig->{$h} ) { |
577 | # Conflict! |
578 | $conflict->{$gst} = 1; |
579 | $still_contig->{$h} = ''; |
580 | } else { |
581 | $still_contig->{$h} = $gst; |
582 | } |
583 | last; |
584 | } # else we don't need $h in this group. |
585 | } # end foreach $v |
586 | } # endif $h eq $root |
587 | } # end foreach $gst |
588 | } # end foreach $h |
589 | |
590 | # Now we have some hypothetical vertices in $still_contig that are the |
591 | # "real" group memberships. Replace these in $contig. |
592 | foreach my $v ( keys %$contig ) { |
593 | next unless ref $contig->{$v}; |
594 | $contig->{$v} = $still_contig->{$v}; |
595 | } |
596 | } # end if @resolve |
597 | |
598 | my $is_genealogical = keys %$conflict ? JSON::false : JSON::true; |
599 | my $variant_row = [ [], $is_genealogical ]; |
600 | # Fill in the groupings from $contig. |
601 | foreach my $g ( @$groups ) { |
602 | my $gst = wit_stringify( $g ); |
603 | my @realgroup = grep { $contig->{$_} eq $gst } keys %$contig; |
604 | push( @{$variant_row->[0]}, \@realgroup ); |
605 | } |
606 | return $variant_row; |
607 | } |
fae07016 |
608 | |
7f52eac8 |
609 | sub _prune_subtree { |
231d71fc |
610 | my( $tree, $root, $contighash ) = @_; |
611 | # First, delete hypothetical leaves / orphans until there are none left. |
612 | my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } |
613 | $tree->successorless_vertices; |
614 | while( @orphan_hypotheticals ) { |
615 | $tree->delete_vertices( @orphan_hypotheticals ); |
616 | @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } |
617 | $tree->successorless_vertices; |
618 | } |
619 | # Then delete a hypothetical root with only one successor, moving the |
bebec0e9 |
620 | # root to the first child that has no other predecessors. |
231d71fc |
621 | while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) { |
622 | my @nextroot = $tree->successors( $root ); |
623 | $tree->delete_vertex( $root ); |
bebec0e9 |
624 | ( $root ) = grep { $tree->is_predecessorless_vertex( $_ ) } @nextroot; |
231d71fc |
625 | } |
626 | # The tree has been modified in place, but we need to know the new root. |
bebec0e9 |
627 | $root = undef unless $root && $tree->has_vertex( $root ); |
231d71fc |
628 | return $root; |
629 | } |
d71100ed |
630 | # Add the variant, subject to a.c. representation logic. |
631 | # This assumes that we will see the 'main' version before the a.c. version. |
632 | sub add_variant_wit { |
633 | my( $arr, $wit, $acstr ) = @_; |
634 | my $skip; |
635 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
636 | my $real = $1; |
637 | $skip = grep { $_ =~ /^\Q$real\E$/ } @$arr; |
638 | } |
639 | push( @$arr, $wit ) unless $skip; |
640 | } |
641 | |
5be0cdeb |
642 | sub _useful_variant { |
643 | my( $group_readings, $graph, $acstr ) = @_; |
644 | |
645 | # TODO Decide what to do with AC witnesses |
646 | |
647 | # Sort by group size and return |
648 | my $is_useful = 0; |
649 | my( @readings, @groups ); # The sorted groups for our answer. |
650 | foreach my $rdg ( sort { @{$group_readings->{$b}} <=> @{$group_readings->{$a}} } |
651 | keys %$group_readings ) { |
652 | push( @readings, $rdg ); |
653 | push( @groups, $group_readings->{$rdg} ); |
654 | if( @{$group_readings->{$rdg}} > 1 ) { |
655 | $is_useful++; |
656 | } else { |
657 | my( $wit ) = @{$group_readings->{$rdg}}; |
658 | $wit =~ s/^(.*)\Q$acstr\E$/$1/; |
659 | $is_useful++ unless( $graph->is_sink_vertex( $wit ) ); |
660 | } |
661 | } |
662 | if( $is_useful > 1 ) { |
663 | return( \@readings, \@groups ); |
664 | } else { |
665 | return( [], [] ); |
666 | } |
667 | } |
668 | |
7f52eac8 |
669 | =head2 wit_stringify( $groups ) |
670 | |
671 | Takes an array of witness groupings and produces a string like |
672 | ['A','B'] / ['C','D','E'] / ['F'] |
d71100ed |
673 | |
7f52eac8 |
674 | =cut |
d71100ed |
675 | |
676 | sub wit_stringify { |
677 | my $groups = shift; |
678 | my @gst; |
679 | # If we were passed an array of witnesses instead of an array of |
680 | # groupings, then "group" the witnesses first. |
681 | unless( ref( $groups->[0] ) ) { |
682 | my $mkgrp = [ $groups ]; |
683 | $groups = $mkgrp; |
684 | } |
685 | foreach my $g ( @$groups ) { |
686 | push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' ); |
687 | } |
688 | return join( ' / ', @gst ); |
689 | } |
7f52eac8 |
690 | |
5be0cdeb |
691 | # Helper function to ensure that X and X a.c. never appear in the same list. |
692 | sub _add_to_witlist { |
693 | my( $wit, $list, $acstr ) = @_; |
694 | my %inlist; |
695 | my $idx = 0; |
696 | map { $inlist{$_} = $idx++ } @$list; |
697 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
698 | my $acwit = $1; |
699 | unless( exists $inlist{$acwit} ) { |
700 | push( @$list, $acwit.$acstr ); |
701 | } |
702 | } else { |
703 | if( exists( $inlist{$wit.$acstr} ) ) { |
704 | # Replace the a.c. version with the main witness |
705 | my $i = $inlist{$wit.$acstr}; |
706 | $list->[$i] = $wit; |
707 | } else { |
708 | push( @$list, $wit ); |
709 | } |
710 | } |
711 | } |
712 | |
bebec0e9 |
713 | sub _symmdiff { |
714 | my( $lista, $listb ) = @_; |
7f52eac8 |
715 | my %union; |
716 | my %scalars; |
717 | map { $union{$_} = 1; $scalars{$_} = $_ } @$lista; |
718 | map { $union{$_} += 1; $scalars{$_} = $_ } @$listb; |
bebec0e9 |
719 | my @set = grep { $union{$_} == 1 } keys %union; |
7f52eac8 |
720 | return map { $scalars{$_} } @set; |
721 | } |
722 | |
723 | 1; |
724 | |
725 | =head1 LICENSE |
726 | |
727 | This package is free software and is provided "as is" without express |
728 | or implied warranty. You can redistribute it and/or modify it under |
729 | the same terms as Perl itself. |
730 | |
731 | =head1 AUTHOR |
732 | |
733 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |