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d71100ed |
1 | package Text::Tradition::Analysis; |
2 | |
3 | use strict; |
4 | use warnings; |
428bcf0b |
5 | use Algorithm::Diff; # for word similarity measure |
e4386ba9 |
6 | use Benchmark; |
88a6bac5 |
7 | use Encode qw/ encode_utf8 /; |
d1348d38 |
8 | use Exporter 'import'; |
b4cb2d60 |
9 | use Graph; |
88a6bac5 |
10 | use JSON qw/ encode_json decode_json /; |
11 | use LWP::UserAgent; |
d71100ed |
12 | use Text::Tradition; |
13 | use Text::Tradition::Stemma; |
d120c995 |
14 | use TryCatch; |
d71100ed |
15 | |
d1348d38 |
16 | use vars qw/ @EXPORT_OK /; |
a2cf85dd |
17 | @EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /; |
d1348d38 |
18 | |
5c44c598 |
19 | my $SOLVER_URL = 'http://byzantini.st/cgi-bin/graphcalc.cgi'; |
20 | |
21 | |
7f52eac8 |
22 | =head1 NAME |
23 | |
24 | Text::Tradition::Analysis - functions for stemma analysis of a tradition |
25 | |
26 | =head1 SYNOPSIS |
27 | |
28 | use Text::Tradition; |
29 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
30 | my $t = Text::Tradition->new( |
31 | 'name' => 'this is a text', |
32 | 'input' => 'TEI', |
33 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
34 | $t->add_stemma( 'dotfile' => $stemmafile ); |
35 | |
36 | my $variant_data = run_analysis( $tradition ); |
37 | # Recalculate rank $n treating all orthographic variants as equivalent |
38 | my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' ); |
39 | |
40 | =head1 DESCRIPTION |
41 | |
42 | Text::Tradition is a library for representation and analysis of collated |
43 | texts, particularly medieval ones. The Collation is the central feature of |
44 | a Tradition, where the text, its sequence of readings, and its relationships |
45 | between readings are actually kept. |
46 | |
47 | =head1 SUBROUTINES |
48 | |
88a6bac5 |
49 | =head2 run_analysis( $tradition, %opts ) |
7f52eac8 |
50 | |
88a6bac5 |
51 | Runs the analysis described in analyze_variant_location on every location in the |
52 | collation of the given tradition, with the given options. These include: |
7f52eac8 |
53 | |
88a6bac5 |
54 | =over 4 |
55 | |
56 | =item * stemma_id - Specify which of the tradition's stemmata to use. Default |
57 | is 0 (i.e. the first). |
58 | |
59 | =item * ranks - Specify a list of location ranks to analyze; exclude the rest. |
60 | |
61 | =item * merge_types - Specify a list of relationship types, where related readings |
62 | should be treated as identical for the purposes of analysis. |
63 | |
ffa22d6f |
64 | =item * exclude_type1 - Exclude those ranks whose groupings have only type-1 variants. |
65 | |
88a6bac5 |
66 | =back |
7f52eac8 |
67 | |
68 | =begin testing |
69 | |
70 | use Text::Tradition; |
71 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
72 | |
73 | my $datafile = 't/data/florilegium_tei_ps.xml'; |
74 | my $tradition = Text::Tradition->new( 'input' => 'TEI', |
75 | 'name' => 'test0', |
76 | 'file' => $datafile ); |
77 | my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' ); |
78 | is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" ); |
79 | |
f00cefe8 |
80 | my %expected_genealogical = ( |
a44aaf2a |
81 | 1 => 0, |
f00cefe8 |
82 | 2 => 1, |
a44aaf2a |
83 | 3 => 0, |
84 | 5 => 0, |
85 | 7 => 0, |
86 | 8 => 0, |
87 | 10 => 0, |
f00cefe8 |
88 | 13 => 1, |
a44aaf2a |
89 | 33 => 0, |
90 | 34 => 0, |
91 | 37 => 0, |
92 | 60 => 0, |
f00cefe8 |
93 | 81 => 1, |
a44aaf2a |
94 | 84 => 0, |
95 | 87 => 0, |
96 | 101 => 0, |
97 | 102 => 0, |
f00cefe8 |
98 | 122 => 1, |
a44aaf2a |
99 | 157 => 0, |
f00cefe8 |
100 | 166 => 1, |
101 | 169 => 1, |
a44aaf2a |
102 | 200 => 0, |
f00cefe8 |
103 | 216 => 1, |
104 | 217 => 1, |
105 | 219 => 1, |
106 | 241 => 1, |
107 | 242 => 1, |
108 | 243 => 1, |
109 | ); |
110 | |
7f52eac8 |
111 | my $data = run_analysis( $tradition ); |
7234b01d |
112 | my $c = $tradition->collation; |
f00cefe8 |
113 | foreach my $row ( @{$data->{'variants'}} ) { |
a44aaf2a |
114 | # Account for rows that used to be "not useful" |
115 | unless( exists $expected_genealogical{$row->{'id'}} ) { |
116 | $expected_genealogical{$row->{'id'}} = 1; |
117 | } |
18f48b82 |
118 | my $gen_bool = $row->{'genealogical'} ? 1 : 0; |
119 | is( $gen_bool, $expected_genealogical{$row->{'id'}}, |
f00cefe8 |
120 | "Got correct genealogical flag for row " . $row->{'id'} ); |
7234b01d |
121 | # Check that we have the right row with the right groups |
122 | my $rank = $row->{'id'}; |
123 | foreach my $rdghash ( @{$row->{'readings'}} ) { |
124 | # Skip 'readings' that aren't really |
125 | next unless $c->reading( $rdghash->{'readingid'} ); |
126 | # Check the rank |
127 | is( $c->reading( $rdghash->{'readingid'} )->rank, $rank, |
128 | "Got correct reading rank" ); |
129 | # Check the witnesses |
130 | my @realwits = sort $c->reading_witnesses( $rdghash->{'readingid'} ); |
131 | my @sgrp = sort @{$rdghash->{'group'}}; |
132 | is_deeply( \@sgrp, \@realwits, "Reading analyzed with correct groups" ); |
133 | } |
f00cefe8 |
134 | } |
a44aaf2a |
135 | is( $data->{'variant_count'}, 58, "Got right total variant number" ); |
b4cb2d60 |
136 | # TODO Make something meaningful of conflict count, maybe test other bits |
7f52eac8 |
137 | |
138 | =end testing |
139 | |
140 | =cut |
141 | |
d71100ed |
142 | sub run_analysis { |
88a6bac5 |
143 | my( $tradition, %opts ) = @_; |
f00cefe8 |
144 | my $c = $tradition->collation; |
88a6bac5 |
145 | |
146 | my $stemma_id = $opts{'stemma_id'} || 0; |
1d73ecad |
147 | my @ranks = ref( $opts{'ranks'} ) eq 'ARRAY' ? @{$opts{'ranks'}} : (); |
148 | my @collapse = ref( $opts{'merge_types'} ) eq 'ARRAY' ? @{$opts{'merge_types'}} : (); |
88a6bac5 |
149 | |
150 | # Get the stemma |
151 | my $stemma = $tradition->stemma( $stemma_id ); |
b4cb2d60 |
152 | |
4ce27d42 |
153 | # Figure out which witnesses we are working with - that is, the ones that |
154 | # appear both in the stemma and in the tradition. All others are 'lacunose' |
155 | # for our purposes. |
88a6bac5 |
156 | my @lacunose = $stemma->hypotheticals; |
fae07016 |
157 | my @tradition_wits = map { $_->sigil } $tradition->witnesses; |
fae07016 |
158 | push( @lacunose, _symmdiff( [ $stemma->witnesses ], \@tradition_wits ) ); |
88a6bac5 |
159 | |
160 | # Find and mark 'common' ranks for exclusion, unless they were |
161 | # explicitly specified. |
162 | unless( @ranks ) { |
163 | my %common_rank; |
a44aaf2a |
164 | foreach my $rdg ( $c->common_readings ) { |
88a6bac5 |
165 | $common_rank{$rdg->rank} = 1; |
166 | } |
167 | @ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-1 ); |
d71100ed |
168 | } |
7f52eac8 |
169 | |
88a6bac5 |
170 | # Group the variants to send to the solver |
171 | my @groups; |
f629cb3b |
172 | my @use_ranks; |
a44aaf2a |
173 | my %lacunae; |
94654e27 |
174 | my $moved = {}; |
88a6bac5 |
175 | foreach my $rank ( @ranks ) { |
a44aaf2a |
176 | my $missing = [ @lacunose ]; |
94654e27 |
177 | my $rankgroup = group_variants( $tradition, $rank, $missing, $moved, \@collapse ); |
178 | # Filter out any empty rankgroups |
179 | # (e.g. from the later rank for a transposition) |
180 | next unless keys %$rankgroup; |
ffa22d6f |
181 | if( $opts{'exclude_type1'} ) { |
182 | # Check to see whether this is a "useful" group. |
183 | my( $rdgs, $grps ) = _useful_variant( $rankgroup, |
184 | $stemma->graph, $c->ac_label ); |
185 | next unless @$rdgs; |
186 | } |
f629cb3b |
187 | push( @use_ranks, $rank ); |
ffa22d6f |
188 | push( @groups, $rankgroup ); |
a44aaf2a |
189 | $lacunae{$rank} = $missing; |
d71100ed |
190 | } |
4ce27d42 |
191 | # Run the solver |
e59b8faa |
192 | my $answer = solve_variants( $stemma, @groups ); |
fae07016 |
193 | |
88a6bac5 |
194 | # Do further analysis on the answer |
a44aaf2a |
195 | my $conflict_count = 0; |
7234b01d |
196 | my $aclabel = $c->ac_label; |
f629cb3b |
197 | foreach my $idx ( 0 .. $#use_ranks ) { |
88a6bac5 |
198 | my $location = $answer->{'variants'}->[$idx]; |
199 | # Add the rank back in |
94654e27 |
200 | my $rank = $use_ranks[$idx]; |
201 | $location->{'id'} = $rank; |
7234b01d |
202 | # Note what our lacunae are |
f629cb3b |
203 | my %lmiss; |
7234b01d |
204 | map { $lmiss{$_} = 1 } @{$lacunae{$use_ranks[$idx]}}; |
7234b01d |
205 | $location->{'missing'} = [ keys %lmiss ]; |
206 | |
88a6bac5 |
207 | # Run the extra analysis we need. |
428bcf0b |
208 | ## TODO We run through all the variants in this call, so |
209 | ## why not add the reading data there instead of here below? |
638e2a95 |
210 | analyze_location( $tradition, $stemma, $location, \%lmiss ); |
7234b01d |
211 | |
638e2a95 |
212 | my @layerwits; |
7234b01d |
213 | # Do the final post-analysis tidying up of the data. |
a44aaf2a |
214 | foreach my $rdghash ( @{$location->{'readings'}} ) { |
215 | $conflict_count++ |
216 | if exists $rdghash->{'conflict'} && $rdghash->{'conflict'}; |
94654e27 |
217 | # Add the reading text back in, setting display value as needed |
a44aaf2a |
218 | my $rdg = $c->reading( $rdghash->{'readingid'} ); |
94654e27 |
219 | if( $rdg ) { |
220 | $rdghash->{'text'} = $rdg->text . |
221 | ( $rdg->rank == $rank ? '' : ' [' . $rdg->rank . ']' ); |
7b7abf10 |
222 | $rdghash->{'is_ungrammatical'} = $rdg->grammar_invalid; |
223 | $rdghash->{'is_nonsense'} = $rdg->is_nonsense; |
94654e27 |
224 | } |
f629cb3b |
225 | # Remove lacunose witnesses from this reading's list now that the |
7234b01d |
226 | # analysis is done |
f629cb3b |
227 | my @realgroup; |
7234b01d |
228 | map { push( @realgroup, $_ ) unless $lmiss{$_} } @{$rdghash->{'group'}}; |
f629cb3b |
229 | $rdghash->{'group'} = \@realgroup; |
638e2a95 |
230 | # Note any layered witnesses that appear in this group |
231 | foreach( @realgroup ) { |
232 | if( $_ =~ /^(.*)\Q$aclabel\E$/ ) { |
233 | push( @layerwits, $1 ); |
234 | } |
235 | } |
a44aaf2a |
236 | } |
638e2a95 |
237 | $location->{'layerwits'} = \@layerwits if @layerwits; |
88a6bac5 |
238 | } |
a44aaf2a |
239 | $answer->{'conflict_count'} = $conflict_count; |
f00cefe8 |
240 | |
88a6bac5 |
241 | return $answer; |
d71100ed |
242 | } |
243 | |
7f52eac8 |
244 | =head2 group_variants( $tradition, $rank, $lacunose, @merge_relationship_types ) |
245 | |
246 | Groups the variants at the given $rank of the collation, treating any |
247 | relationships in @merge_relationship_types as equivalent. $lacunose should |
248 | be a reference to an array, to which the sigla of lacunose witnesses at this |
94654e27 |
249 | rank will be appended; $transposed should be a reference to a hash, wherein |
250 | the identities of transposed readings and their relatives will be stored. |
7f52eac8 |
251 | |
ffa22d6f |
252 | Returns a hash $group_readings where $rdg is attested by the witnesses listed |
253 | in $group_readings->{$rdg}. |
7f52eac8 |
254 | |
255 | =cut |
256 | |
257 | # Return group_readings, groups, lacunose |
d1348d38 |
258 | sub group_variants { |
94654e27 |
259 | my( $tradition, $rank, $lacunose, $transposed, $collapse ) = @_; |
7f52eac8 |
260 | my $c = $tradition->collation; |
335a62ef |
261 | my $aclabel = $c->ac_label; |
d120c995 |
262 | my $table = $c->alignment_table; |
7f52eac8 |
263 | # Get the alignment table readings |
264 | my %readings_at_rank; |
d120c995 |
265 | my %is_lacunose; # lookup table for witnesses not in stemma |
266 | map { $is_lacunose{$_} = 1; $is_lacunose{$_.$aclabel} = 1 } @$lacunose; |
94654e27 |
267 | my @check_for_gaps; |
268 | my %moved_wits; |
d120c995 |
269 | my $has_transposition; |
270 | foreach my $tablewit ( @{$table->{'alignment'}} ) { |
7f52eac8 |
271 | my $rdg = $tablewit->{'tokens'}->[$rank-1]; |
fae07016 |
272 | my $wit = $tablewit->{'witness'}; |
ffa22d6f |
273 | # Exclude the witness if it is "lacunose" which if we got here |
274 | # means "not in the stemma". |
275 | next if $is_lacunose{$wit}; |
94654e27 |
276 | # Note if the witness is actually in a lacuna |
7f52eac8 |
277 | if( $rdg && $rdg->{'t'}->is_lacuna ) { |
335a62ef |
278 | _add_to_witlist( $wit, $lacunose, $aclabel ); |
94654e27 |
279 | # Otherwise the witness either has a positive reading... |
7f52eac8 |
280 | } elsif( $rdg ) { |
94654e27 |
281 | # If the reading has been counted elsewhere as a transposition, ignore it. |
282 | if( $transposed->{$rdg->{'t'}->id} ) { |
d120c995 |
283 | # TODO Does this cope with three-way transpositions? |
94654e27 |
284 | map { $moved_wits{$_} = 1 } @{$transposed->{$rdg->{'t'}->id}}; |
285 | next; |
286 | } |
287 | # Otherwise, record it... |
288 | $readings_at_rank{$rdg->{'t'}->id} = $rdg->{'t'}; |
289 | # ...and grab any transpositions, and their relations. |
290 | my @transp = grep { $_->rank != $rank } $rdg->{'t'}->related_readings(); |
291 | foreach my $trdg ( @transp ) { |
d120c995 |
292 | next if exists $readings_at_rank{$trdg->id}; |
293 | $has_transposition = 1; |
294 | my @affected_wits = _table_witnesses( |
295 | $table, $trdg, \%is_lacunose, $aclabel ); |
296 | next unless @affected_wits; |
297 | map { $moved_wits{$_} = 1 } @affected_wits; |
298 | $transposed->{$trdg->id} = |
299 | [ _table_witnesses( $table, $rdg->{'t'}, \%is_lacunose, $aclabel ) ]; |
94654e27 |
300 | $readings_at_rank{$trdg->id} = $trdg; |
301 | } |
302 | # ...or it is empty, ergo a gap. |
7f52eac8 |
303 | } else { |
d120c995 |
304 | _add_to_witlist( $wit, \@check_for_gaps, $aclabel ); |
7f52eac8 |
305 | } |
306 | } |
94654e27 |
307 | my @gap_wits; |
308 | map { _add_to_witlist( $_, \@gap_wits, $aclabel ) |
309 | unless $moved_wits{$_} } @check_for_gaps; |
7f52eac8 |
310 | # Group the readings, collapsing groups by relationship if needed |
d120c995 |
311 | my $grouped_readings = {}; |
4ce27d42 |
312 | foreach my $rdg ( values %readings_at_rank ) { |
7f52eac8 |
313 | # Skip readings that have been collapsed into others. |
d120c995 |
314 | next if exists $grouped_readings->{$rdg->id} |
315 | && $grouped_readings->{$rdg->id} eq 'COLLAPSE'; |
4ce27d42 |
316 | # Get the witness list, including from readings collapsed into this one. |
d120c995 |
317 | my @wits = _table_witnesses( $table, $rdg, \%is_lacunose, $aclabel ); |
318 | if( $collapse && @$collapse ) { |
7f52eac8 |
319 | my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; }; |
320 | foreach my $other ( $rdg->related_readings( $filter ) ) { |
d120c995 |
321 | my @otherwits = _table_witnesses( |
322 | $table, $other, \%is_lacunose, $aclabel ); |
fae07016 |
323 | push( @wits, @otherwits ); |
d120c995 |
324 | $grouped_readings->{$other->id} = 'COLLAPSE'; |
d1348d38 |
325 | } |
326 | } |
d120c995 |
327 | $grouped_readings->{$rdg->id} = \@wits; |
7f52eac8 |
328 | } |
d120c995 |
329 | $grouped_readings->{'(omitted)'} = \@gap_wits if @gap_wits; |
7f52eac8 |
330 | # Get rid of our collapsed readings |
d120c995 |
331 | map { delete $grouped_readings->{$_} if $grouped_readings->{$_} eq 'COLLAPSE' } |
332 | keys %$grouped_readings |
7f52eac8 |
333 | if $collapse; |
d120c995 |
334 | |
335 | # If something was transposed, check the groups for doubled-up readings |
336 | if( $has_transposition ) { |
62a39b8f |
337 | # print STDERR "Group for rank $rank:\n"; |
338 | # map { print STDERR "\t$_: " . join( ' ' , @{$grouped_readings->{$_}} ) . "\n" } |
339 | # keys %$grouped_readings; |
d120c995 |
340 | _check_transposed_consistency( $c, $rank, $transposed, $grouped_readings ); |
341 | } |
7f52eac8 |
342 | |
4ce27d42 |
343 | # Return the result |
d120c995 |
344 | return $grouped_readings; |
345 | } |
346 | |
347 | # Helper function to query the alignment table for all witnesses (a.c. included) |
348 | # that have a given reading at its rank. |
349 | sub _table_witnesses { |
350 | my( $table, $trdg, $lacunose, $aclabel ) = @_; |
351 | my $tableidx = $trdg->rank - 1; |
352 | my @has_reading; |
353 | foreach my $row ( @{$table->{'alignment'}} ) { |
354 | my $wit = $row->{'witness'}; |
355 | next if $lacunose->{$wit}; |
356 | my $rdg = $row->{'tokens'}->[$tableidx]; |
357 | next unless exists $rdg->{'t'} && defined $rdg->{'t'}; |
358 | _add_to_witlist( $wit, \@has_reading, $aclabel ) |
359 | if $rdg->{'t'}->id eq $trdg->id; |
360 | } |
361 | return @has_reading; |
d1348d38 |
362 | } |
363 | |
335a62ef |
364 | # Helper function to ensure that X and X a.c. never appear in the same list. |
365 | sub _add_to_witlist { |
366 | my( $wit, $list, $acstr ) = @_; |
367 | my %inlist; |
368 | my $idx = 0; |
369 | map { $inlist{$_} = $idx++ } @$list; |
370 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
371 | my $acwit = $1; |
372 | unless( exists $inlist{$acwit} ) { |
373 | push( @$list, $acwit.$acstr ); |
374 | } |
375 | } else { |
376 | if( exists( $inlist{$wit.$acstr} ) ) { |
377 | # Replace the a.c. version with the main witness |
378 | my $i = $inlist{$wit.$acstr}; |
379 | $list->[$i] = $wit; |
380 | } else { |
381 | push( @$list, $wit ); |
382 | } |
383 | } |
384 | } |
385 | |
d120c995 |
386 | sub _check_transposed_consistency { |
387 | my( $c, $rank, $transposed, $groupings ) = @_; |
388 | my %seen_wits; |
389 | my %thisrank; |
390 | # Note which readings are actually at this rank, and which witnesses |
391 | # belong to which reading. |
392 | foreach my $rdg ( keys %$groupings ) { |
393 | my $rdgobj = $c->reading( $rdg ); |
394 | # Count '(omitted)' as a reading at this rank |
395 | $thisrank{$rdg} = 1 if !$rdgobj || $rdgobj->rank == $rank; |
396 | map { push( @{$seen_wits{$_}}, $rdg ) } @{$groupings->{$rdg}}; |
397 | } |
398 | # Our work is done if we have no witness belonging to more than one |
399 | # reading. |
400 | my @doubled = grep { scalar @{$seen_wits{$_}} > 1 } keys %seen_wits; |
401 | return unless @doubled; |
402 | # If we have a symmetric related transposition, drop the non-rank readings. |
403 | if( @doubled == scalar keys %seen_wits ) { |
404 | foreach my $rdg ( keys %$groupings ) { |
405 | if( !$thisrank{$rdg} ) { |
406 | my $groupstr = wit_stringify( $groupings->{$rdg} ); |
407 | my ( $matched ) = grep { $groupstr eq wit_stringify( $groupings->{$_} ) } |
408 | keys %thisrank; |
409 | delete $groupings->{$rdg}; |
410 | # If we found a group match, assume there is a symmetry happening. |
411 | # TODO think more about this |
62a39b8f |
412 | # print STDERR "*** Deleting symmetric reading $rdg\n"; |
d120c995 |
413 | unless( $matched ) { |
414 | delete $transposed->{$rdg}; |
415 | warn "Found problem in evident symmetry with reading $rdg"; |
416 | } |
417 | } |
418 | } |
419 | # Otherwise 'unhook' the transposed reading(s) that have duplicates. |
420 | } else { |
421 | foreach my $dup ( @doubled ) { |
422 | foreach my $rdg ( @{$seen_wits{$dup}} ) { |
423 | next if $thisrank{$rdg}; |
424 | next unless exists $groupings->{$rdg}; |
62a39b8f |
425 | # print STDERR "*** Deleting asymmetric doubled-up reading $rdg\n"; |
d120c995 |
426 | delete $groupings->{$rdg}; |
427 | delete $transposed->{$rdg}; |
428 | } |
429 | } |
430 | # and put any now-orphaned readings into an 'omitted' reading. |
431 | foreach my $wit ( keys %seen_wits ) { |
432 | unless( grep { exists $groupings->{$_} } @{$seen_wits{$wit}} ) { |
433 | $groupings->{'(omitted)'} = [] unless exists $groupings->{'(omitted)'}; |
434 | _add_to_witlist( $wit, $groupings->{'(omitted)'}, $c->ac_label ); |
435 | } |
436 | } |
437 | } |
438 | } |
439 | |
88a6bac5 |
440 | =head2 solve_variants( $graph, @groups ) |
441 | |
442 | Sends the set of groups to the external graph solver service and returns |
443 | a cleaned-up answer, adding the rank IDs back where they belong. |
444 | |
445 | The JSON has the form |
446 | { "graph": [ stemmagraph DOT string without newlines ], |
447 | "groupings": [ array of arrays of groups, one per rank ] } |
448 | |
449 | The answer has the form |
450 | { "variants" => [ array of variant location structures ], |
451 | "variant_count" => total, |
452 | "conflict_count" => number of conflicts detected, |
453 | "genealogical_count" => number of solutions found } |
454 | |
455 | =cut |
456 | |
457 | sub solve_variants { |
e59b8faa |
458 | my( $stemma, @groups ) = @_; |
335a62ef |
459 | |
460 | # Filter the groups down to distinct groups, and work out what graph |
461 | # should be used in the calculation of each group. We want to send each |
462 | # distinct problem to the solver only once. |
463 | # We need a whole bunch of lookup tables for this. |
5c44c598 |
464 | my( $index_groupkeys, $group_indices, $graph_problems ) = _prepare_groups( @_ ); |
335a62ef |
465 | |
335a62ef |
466 | ## For each distinct graph, send its groups to the solver. |
88a6bac5 |
467 | my $ua = LWP::UserAgent->new(); |
335a62ef |
468 | ## Witness map is a HACK to get around limitations in node names from IDP |
469 | my $witness_map = {}; |
470 | ## Variables to store answers as they come back |
471 | my $variants = [ ( undef ) x ( scalar keys %$index_groupkeys ) ]; |
88a6bac5 |
472 | my $genealogical = 0; |
335a62ef |
473 | foreach my $graphkey ( keys %$graph_problems ) { |
474 | my $graph = $graph_problems->{$graphkey}->{'object'}; |
5c44c598 |
475 | my $groupings = [ values %{$graph_problems->{$graphkey}->{'groups'}} ]; |
c30a4fdb |
476 | my $req = _safe_wit_strings( $graph, $stemma->collation, |
477 | $groupings, $witness_map ); |
478 | $req->{'command'} = 'findGroupings'; |
479 | my $json = encode_json( $req ); |
335a62ef |
480 | # Send it off and get the result |
5c44c598 |
481 | # print STDERR "Sending request: " . to_json( $req ) . "\n"; |
482 | my $resp = $ua->post( $SOLVER_URL, 'Content-Type' => 'application/json', |
335a62ef |
483 | 'Content' => $json ); |
484 | my $answer; |
335a62ef |
485 | if( $resp->is_success ) { |
486 | $answer = _desanitize_names( decode_json( $resp->content ), $witness_map ); |
335a62ef |
487 | } else { |
488 | # Fall back to the old method. |
5c44c598 |
489 | die "IDP solver returned " . $resp->status_line . " / " . $resp->content |
490 | . "; cannot run graph analysis"; |
335a62ef |
491 | } |
5c44c598 |
492 | |
493 | ## If IDP worked, asked it the other two questions for this dataset. |
494 | my $more_eval = {}; |
495 | foreach my $test ( qw/ findSources findClasses / ) { |
496 | $req->{'command'} = $test; |
497 | $json = encode_json( $req ); |
498 | $resp = $ua->post( $SOLVER_URL, 'Content-Type' => 'application/json', |
499 | 'Content' => $json ); |
500 | if( $resp->is_success ) { |
501 | $more_eval->{$test} = _desanitize_names( |
502 | decode_json( $resp->content ), $witness_map ); |
503 | } else { |
504 | warn "IDP solver for $test returned " . $resp->status_line . |
505 | " / " . $resp->content; |
506 | # TODO arrange fallback |
507 | } |
508 | } |
509 | |
335a62ef |
510 | ## The answer is the evaluated groupings, plus a boolean for whether |
511 | ## they were genealogical. Reconstruct our original groups. |
512 | foreach my $gidx ( 0 .. $#{$groupings} ) { |
513 | my( $calc_groups, $result ) = @{$answer->[$gidx]}; |
5c44c598 |
514 | # Keep track of the total # of genealogical readings |
515 | $genealogical++ if $result; |
516 | |
517 | my( $sources, $classes ); |
518 | # Use the expanded groups from findSources if that got calculated. |
519 | if( exists( $more_eval->{'findSources'} ) ) { |
520 | ( $calc_groups, $sources ) = @{$more_eval->{'findSources'}->[$gidx]}; |
521 | } |
522 | # Use the (same) expanded groups from findClasses if that got calculated |
523 | # and is relevant. |
524 | if( exists( $more_eval->{'findClasses'} ) && !$result ) { |
c6b011b3 |
525 | my $throwaway_groups; |
526 | ( $throwaway_groups, $classes ) = @{$more_eval->{'findClasses'}->[$gidx]}; |
335a62ef |
527 | } |
5c44c598 |
528 | |
529 | # Convert the source list into a lookup hash |
530 | my $roots = {}; |
531 | map { $roots->{$_} = 1 } @$sources; |
532 | # Convert the class list into a lookup hash |
533 | if( $classes ) { |
534 | $classes = _invert_hash( $classes ); |
535 | } |
536 | |
335a62ef |
537 | # Retrieve the key for the original group that went to the solver |
538 | my $input_group = wit_stringify( $groupings->[$gidx] ); |
5c44c598 |
539 | |
540 | # Make the variant hash for each location that had this particular |
541 | # grouping on this particular stemma situation |
335a62ef |
542 | foreach my $oidx ( @{$group_indices->{$input_group}} ) { |
543 | my @readings = @{$index_groupkeys->{$oidx}}; |
544 | my $vstruct = { |
545 | 'genealogical' => $result, |
546 | 'readings' => [], |
547 | }; |
548 | foreach my $ridx ( 0 .. $#readings ) { |
549 | push( @{$vstruct->{'readings'}}, |
550 | { 'readingid' => $readings[$ridx], |
551 | 'group' => $calc_groups->[$ridx] } ); |
552 | } |
5c44c598 |
553 | $vstruct->{'reading_roots'} = $roots if $roots; |
554 | $vstruct->{'reading_types'} = $classes if $classes; |
335a62ef |
555 | $variants->[$oidx] = $vstruct; |
6d25a3a0 |
556 | } |
557 | } |
88a6bac5 |
558 | } |
559 | |
560 | return { 'variants' => $variants, |
561 | 'variant_count' => scalar @$variants, |
562 | 'genealogical_count' => $genealogical }; |
563 | } |
564 | |
5c44c598 |
565 | sub _prepare_groups { |
566 | my( $stemma, @groups ) = @_; |
567 | my $aclabel = $stemma->collation->ac_label; |
568 | |
569 | my $index_groupkeys = {}; # Save the order of readings |
570 | my $group_indices = {}; # Save the indices that have a given grouping |
571 | my $graph_problems = {}; # Save the groupings for the given graph |
572 | |
573 | foreach my $idx ( 0..$#groups ) { |
574 | my $ghash = $groups[$idx]; |
575 | my @grouping; |
576 | # Sort the groupings from big to little, and scan for a.c. witnesses |
577 | # that would need an extended graph. |
578 | my @acwits; # note which AC witnesses crop up at this rank |
579 | my $extant; # note which witnesses crop up at this rank full stop |
580 | my @idxkeys = sort { scalar @{$ghash->{$b}} <=> scalar @{$ghash->{$a}} } |
581 | keys %$ghash; |
582 | foreach my $rdg ( @idxkeys ) { |
583 | my @sg = sort @{$ghash->{$rdg}}; |
584 | push( @acwits, grep { $_ =~ /\Q$aclabel\E$/ } @sg ); |
585 | map { $extant->{$_} = 1 } @sg; |
586 | push( @grouping, \@sg ); |
587 | } |
588 | # Save the reading order |
589 | $index_groupkeys->{$idx} = \@idxkeys; |
590 | |
591 | # Now associate the distinct group with this index |
592 | my $gstr = wit_stringify( \@grouping ); |
593 | push( @{$group_indices->{$gstr}}, $idx ); |
594 | |
595 | # Finally, add the group to the list to be calculated for this graph. |
596 | map { s/\Q$aclabel\E$// } @acwits; |
597 | my $graph; |
598 | ## TODO When we get rid of the safe_wit_strings HACK we should also |
599 | ## be able to save the graph here as a dotstring rather than as an |
600 | ## object, thus simplifying life enormously. |
601 | try { |
602 | $graph = $stemma->situation_graph( $extant, \@acwits ); |
603 | } catch { |
5c44c598 |
604 | die "Unable to extend graph with @acwits"; |
605 | } |
606 | my $graphkey = "$graph || " . wit_stringify( [ sort keys %$extant ] ); |
607 | unless( exists $graph_problems->{$graphkey} ) { |
608 | $graph_problems->{$graphkey} = { 'object' => $graph, 'groups' => {} }; |
609 | } |
610 | $graph_problems->{$graphkey}->{'groups'}->{wit_stringify( \@grouping )} = \@grouping; |
611 | } |
612 | say STDERR "Created " . scalar( keys %$graph_problems ). " distinct graph(s)"; |
613 | return( $index_groupkeys, $group_indices, $graph_problems ); |
614 | } |
615 | |
b4cb2d60 |
616 | #### HACKERY to cope with IDP's limited idea of what a node name looks like ### |
617 | |
618 | sub _safe_wit_strings { |
335a62ef |
619 | my( $graph, $c, $groupings, $witness_map ) = @_; |
b4cb2d60 |
620 | # Convert the graph to a safe representation and store the conversion. |
5c44c598 |
621 | my $safegraph = Graph->new(); |
335a62ef |
622 | foreach my $n ( $graph->vertices ) { |
b4cb2d60 |
623 | my $sn = _safe_witstr( $n ); |
335a62ef |
624 | if( exists $witness_map->{$sn} ) { |
625 | warn "Ambiguous stringification $sn for $n and " . $witness_map->{$sn} |
626 | if $witness_map->{$sn} ne $n; |
627 | } else { |
628 | $witness_map->{$sn} = $n; |
629 | } |
b4cb2d60 |
630 | $safegraph->add_vertex( $sn ); |
631 | $safegraph->set_vertex_attributes( $sn, |
335a62ef |
632 | $graph->get_vertex_attributes( $n ) ); |
b4cb2d60 |
633 | } |
335a62ef |
634 | foreach my $e ( $graph->edges ) { |
b4cb2d60 |
635 | my @safe_e = ( _safe_witstr( $e->[0] ), _safe_witstr( $e->[1] ) ); |
636 | $safegraph->add_edge( @safe_e ); |
637 | } |
b4cb2d60 |
638 | |
639 | # Now convert the witness groupings to a safe representation. |
640 | my $safe_groupings = []; |
641 | foreach my $grouping ( @$groupings ) { |
642 | my $safe_grouping = []; |
643 | foreach my $group ( @$grouping ) { |
644 | my $safe_group = []; |
645 | foreach my $n ( @$group ) { |
646 | my $sn = _safe_witstr( $n ); |
647 | warn "Ambiguous stringification $sn for $n and " . $witness_map->{$sn} |
648 | if exists $witness_map->{$sn} && $witness_map->{$sn} ne $n; |
649 | $witness_map->{$sn} = $n; |
650 | push( @$safe_group, $sn ); |
651 | } |
652 | push( @$safe_grouping, $safe_group ); |
653 | } |
654 | push( @$safe_groupings, $safe_grouping ); |
655 | } |
656 | |
657 | # Return it all in the struct we expect. We have stored the reductions |
658 | # in the $witness_map that we were passed. |
5c44c598 |
659 | return { 'graph' => Text::Tradition::Stemma::editable_graph( |
660 | $safegraph, { 'linesep' => ' ' } ), |
335a62ef |
661 | 'groupings' => $safe_groupings }; |
b4cb2d60 |
662 | } |
663 | |
664 | sub _safe_witstr { |
665 | my $witstr = shift; |
666 | $witstr =~ s/\s+/_/g; |
667 | $witstr =~ s/[^\w\d-]//g; |
668 | return $witstr; |
669 | } |
670 | |
671 | sub _desanitize_names { |
5c44c598 |
672 | my( $element, $witness_map ) = @_; |
b4cb2d60 |
673 | my $result = []; |
5c44c598 |
674 | if( ref( $element ) eq 'ARRAY' ) { |
675 | foreach my $n ( @$element ) { |
676 | push( @$result, _desanitize_names( $n, $witness_map ) ); |
b4cb2d60 |
677 | } |
5c44c598 |
678 | } elsif( ref( $element ) eq 'HASH' ) { |
679 | my $real_hash = {}; |
680 | map { $real_hash->{$_} = _desanitize_names( $element->{$_}, $witness_map ) } |
681 | keys %$element; |
682 | $result = $real_hash; |
683 | } elsif( exists $witness_map->{$element} ) { |
684 | $result = $witness_map->{$element} |
685 | } else { |
686 | $result = $element; |
b4cb2d60 |
687 | } |
688 | return $result; |
689 | } |
690 | |
5c44c598 |
691 | sub _invert_hash { |
692 | my( $hash ) = @_; |
693 | my $newhash; |
694 | foreach my $k ( keys %$hash ) { |
695 | if( ref( $hash->{$k} ) eq 'ARRAY' ) { |
696 | foreach my $v ( @{$hash->{$k}} ) { |
697 | $newhash->{$v} = $k; |
698 | } |
699 | } else { |
700 | $newhash->{$hash->{$k}} = $k; |
701 | } |
702 | } |
703 | return $newhash; |
704 | } |
705 | |
b4cb2d60 |
706 | ### END HACKERY ### |
707 | |
fae07016 |
708 | =head2 analyze_location ( $tradition, $graph, $location_hash ) |
7f52eac8 |
709 | |
fae07016 |
710 | Given the tradition, its stemma graph, and the solution from the graph solver, |
711 | work out the rest of the information we want. For each reading we need missing, |
5c44c598 |
712 | conflict, reading_parents, independent_occurrence, followed, not_followed, |
713 | and follow_unknown. Alters the location_hash in place. |
7f52eac8 |
714 | |
715 | =cut |
732152b1 |
716 | |
fae07016 |
717 | sub analyze_location { |
638e2a95 |
718 | my ( $tradition, $stemma, $variant_row, $lacunose ) = @_; |
94654e27 |
719 | my $c = $tradition->collation; |
fae07016 |
720 | |
721 | # Make a hash of all known node memberships, and make the subgraphs. |
722 | my $contig = {}; |
723 | my $reading_roots = {}; |
724 | my $subgraph = {}; |
638e2a95 |
725 | my $acstr = $c->ac_label; |
726 | my @acwits; |
5c44c598 |
727 | |
728 | my $NO_IDP; |
729 | if( exists $variant_row->{'reading_roots'} ) { |
730 | $reading_roots = delete $variant_row->{'reading_roots'}; |
731 | } else { |
732 | warn "No reading source information from IDP - proceed at your own risk"; |
733 | $NO_IDP = 1; |
734 | } |
735 | |
736 | # Note which witnesses positively belong to which group. This information |
737 | # comes ultimately from the IDP solver. |
738 | # Also make a note of the reading's roots. |
fae07016 |
739 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
740 | my $rid = $rdghash->{'readingid'}; |
5c44c598 |
741 | my @roots; |
638e2a95 |
742 | foreach my $wit ( @{$rdghash->{'group'}} ) { |
743 | $contig->{$wit} = $rid; |
744 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
745 | push( @acwits, $1 ); |
746 | } |
5c44c598 |
747 | if( exists $reading_roots->{$wit} && $reading_roots->{$wit} ) { |
748 | push( @roots, $wit ); |
749 | } |
638e2a95 |
750 | } |
5c44c598 |
751 | $rdghash->{'independent_occurrence'} = \@roots; |
94654e27 |
752 | } |
5c44c598 |
753 | |
638e2a95 |
754 | # Get the actual graph we should work with |
d120c995 |
755 | my $graph; |
756 | try { |
5c44c598 |
757 | # contig contains all extant wits and all hypothetical wits |
758 | # needed to make up the groups. |
759 | $graph = $stemma->situation_graph( $contig, \@acwits ); |
760 | } catch ( Text::Tradition::Error $e ) { |
761 | die "Could not extend graph with given extant and a.c. witnesses: " |
762 | . $e->message; |
d120c995 |
763 | } catch { |
764 | die "Could not extend graph with a.c. witnesses @acwits"; |
765 | } |
638e2a95 |
766 | |
5c44c598 |
767 | |
fae07016 |
768 | # Now that we have all the node group memberships, calculate followed/ |
bebec0e9 |
769 | # non-followed/unknown values for each reading. Also figure out the |
770 | # reading's evident parent(s). |
771 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
fae07016 |
772 | my $rid = $rdghash->{'readingid'}; |
428bcf0b |
773 | my $rdg = $c->reading( $rid ); |
5c44c598 |
774 | my @roots = @{$rdghash->{'independent_occurrence'}}; |
775 | my @group = @{$rdghash->{'group'}}; |
fae07016 |
776 | |
777 | # Start figuring things out. |
5c44c598 |
778 | $rdghash->{'followed'} = scalar( @group ) - scalar( @roots ); |
bebec0e9 |
779 | # Find the parent readings, if any, of this reading. |
94654e27 |
780 | my $rdgparents = {}; |
bebec0e9 |
781 | foreach my $wit ( @roots ) { |
5c44c598 |
782 | # Look in the stemma graph to find this witness's extant or known-reading |
f00cefe8 |
783 | # immediate ancestor(s), and look up the reading that each ancestor olds. |
784 | my @check = $graph->predecessors( $wit ); |
785 | while( @check ) { |
786 | my @next; |
787 | foreach my $wparent( @check ) { |
fae07016 |
788 | my $preading = $contig->{$wparent}; |
428bcf0b |
789 | if( $preading && $preading ne $rid ) { |
94654e27 |
790 | $rdgparents->{$preading} = 1; |
f00cefe8 |
791 | } else { |
792 | push( @next, $graph->predecessors( $wparent ) ); |
793 | } |
794 | } |
795 | @check = @next; |
796 | } |
bebec0e9 |
797 | } |
94654e27 |
798 | foreach my $p ( keys %$rdgparents ) { |
799 | # Resolve the relationship of the parent to the reading, and |
800 | # save it in our hash. |
801 | my $pobj = $c->reading( $p ); |
94654e27 |
802 | my $prep = $pobj ? $pobj->id . ' (' . $pobj->text . ')' : $p; |
354cc918 |
803 | my $phash = { 'label' => $prep }; |
94654e27 |
804 | if( $pobj ) { |
805 | my $rel = $c->get_relationship( $p, $rdghash->{readingid} ); |
806 | if( $rel ) { |
428bcf0b |
807 | _add_to_hash( $rel, $phash ); |
808 | } elsif( $rdg ) { |
809 | # First check for a transposed relationship |
810 | if( $rdg->rank != $pobj->rank ) { |
811 | foreach my $ti ( $rdg->related_readings( 'transposition' ) ) { |
812 | next unless $ti->text eq $rdg->text; |
813 | $rel = $c->get_relationship( $ti, $pobj ); |
814 | if( $rel ) { |
815 | _add_to_hash( $rel, $phash, 1 ); |
816 | last; |
817 | } |
818 | } |
819 | unless( $rel ) { |
820 | foreach my $ti ( $pobj->related_readings( 'transposition' ) ) { |
821 | next unless $ti->text eq $pobj->text; |
822 | $rel = $c->get_relationship( $ti, $rdg ); |
823 | if( $rel ) { |
824 | _add_to_hash( $rel, $phash, 1 ); |
825 | last; |
826 | } |
827 | } |
828 | } |
354cc918 |
829 | } |
428bcf0b |
830 | unless( $rel ) { |
831 | # and then check for sheer word similarity. |
832 | my $rtext = $rdg->text; |
833 | my $ptext = $pobj->text; |
834 | if( similar( $rtext, $ptext ) ) { |
835 | # say STDERR "Words $rtext and $ptext judged similar"; |
836 | $phash->{relation} = { type => 'wordsimilar' }; |
837 | } |
94654e27 |
838 | } |
428bcf0b |
839 | } else { |
840 | $phash->{relation} = { type => 'deletion' }; |
94654e27 |
841 | } |
354cc918 |
842 | # Get the attributes of the parent object while we are here |
843 | $phash->{'text'} = $pobj->text if $pobj; |
844 | $phash->{'is_nonsense'} = $pobj->is_nonsense; |
845 | $phash->{'is_ungrammatical'} = $pobj->grammar_invalid; |
846 | } elsif( $p eq '(omitted)' ) { |
847 | $phash->{relation} = { type => 'addition' }; |
7b7abf10 |
848 | } |
354cc918 |
849 | # Save it |
7b7abf10 |
850 | $rdgparents->{$p} = $phash; |
94654e27 |
851 | } |
852 | |
853 | $rdghash->{'reading_parents'} = $rdgparents; |
bebec0e9 |
854 | |
855 | # Find the number of times this reading was altered, and the number of |
856 | # times we're not sure. |
857 | my( %nofollow, %unknownfollow ); |
5c44c598 |
858 | foreach my $wit ( @{$rdghash->{'group'}} ) { |
bebec0e9 |
859 | foreach my $wchild ( $graph->successors( $wit ) ) { |
5c44c598 |
860 | if( $reading_roots->{$wchild} && $contig->{$wchild} |
861 | && $contig->{$wchild} ne $rid ) { |
bebec0e9 |
862 | # It definitely changed here. |
863 | $nofollow{$wchild} = 1; |
864 | } elsif( !($contig->{$wchild}) ) { |
865 | # The child is a hypothetical node not definitely in |
866 | # any group. Answer is unknown. |
867 | $unknownfollow{$wchild} = 1; |
5c44c598 |
868 | } # else it is either in our group, or it is a non-root node in a |
869 | # known group and therefore is presumed to have its reading from |
870 | # its group, not this link. |
bebec0e9 |
871 | } |
872 | } |
873 | $rdghash->{'not_followed'} = keys %nofollow; |
874 | $rdghash->{'follow_unknown'} = keys %unknownfollow; |
fae07016 |
875 | |
876 | # Now say whether this reading represents a conflict. |
877 | unless( $variant_row->{'genealogical'} ) { |
5c44c598 |
878 | my @trueroots; |
c6b011b3 |
879 | if( exists $variant_row->{'reading_types'} ) { |
880 | my $classinfo = delete $variant_row->{'reading_types'}; |
5c44c598 |
881 | # We have tested for reversions. Use the information. |
882 | my @reversions; |
883 | foreach my $rdgroot ( @roots ) { |
c6b011b3 |
884 | if( $classinfo->{$rdgroot} eq 'revert' ) { |
5c44c598 |
885 | push( @reversions, $rdgroot ); |
886 | } else { |
887 | push( @trueroots, $rdgroot ); |
888 | } |
889 | } |
890 | $rdghash->{'independent_occurrence'} = \@trueroots; |
891 | $rdghash->{'reversion'} = \@reversions if @reversions; |
892 | } else { |
893 | @trueroots = @roots; |
894 | } |
895 | $rdghash->{'conflict'} = @trueroots != 1; |
fae07016 |
896 | } |
c4a4fb1b |
897 | } |
d71100ed |
898 | } |
899 | |
428bcf0b |
900 | sub _add_to_hash { |
901 | my( $rel, $phash, $is_transposed ) = @_; |
902 | $phash->{relation} = { type => $rel->type }; |
903 | $phash->{relation}->{transposed} = 1 if $is_transposed; |
904 | $phash->{relation}->{annotation} = $rel->annotation |
905 | if $rel->has_annotation; |
906 | } |
907 | |
908 | =head2 similar( $word1, $word2 ) |
909 | |
910 | Use Algorithm::Diff to get a sense of how close the words are to each other. |
911 | This will hopefully handle substitutions a bit more nicely than Levenshtein. |
912 | |
913 | =cut |
914 | |
915 | #!/usr/bin/env perl |
916 | |
917 | sub similar { |
918 | my( $word1, $word2 ) = sort { length($a) <=> length($b) } @_; |
919 | my @let1 = split( '', lc( $word1 ) ); |
920 | my @let2 = split( '', lc( $word2 ) ); |
921 | my $diff = Algorithm::Diff->new( \@let1, \@let2 ); |
922 | my $mag = 0; |
923 | while( $diff->Next ) { |
924 | if( $diff->Same ) { |
925 | # Take off points for longer strings |
926 | my $cs = $diff->Range(1) - 2; |
927 | $cs = 0 if $cs < 0; |
928 | $mag -= $cs; |
929 | } elsif( !$diff->Items(1) ) { |
930 | $mag += $diff->Range(2); |
931 | } elsif( !$diff->Items(2) ) { |
932 | $mag += $diff->Range(1); |
933 | } else { |
934 | # Split the difference for substitutions |
935 | my $c1 = $diff->Range(1) || 1; |
936 | my $c2 = $diff->Range(2) || 1; |
937 | my $cd = ( $c1 + $c2 ) / 2; |
938 | $mag += $cd; |
939 | } |
940 | } |
941 | return ( $mag <= length( $word1 ) / 2 ); |
942 | } |
943 | |
6d25a3a0 |
944 | sub _prune_group { |
5c44c598 |
945 | my( $group, $graph ) = @_; |
946 | my $relevant = {}; |
947 | # Record the existence of the vertices in the group |
948 | map { $relevant->{$_} = 1 } @$group; |
6d25a3a0 |
949 | # Make our subgraph |
5c44c598 |
950 | my $subgraph = $graph->deep_copy; |
951 | map { $subgraph->delete_vertex( $_ ) unless $relevant->{$_} } |
6d25a3a0 |
952 | $subgraph->vertices; |
6d25a3a0 |
953 | # Now prune and return the remaining vertices. |
5c44c598 |
954 | _prune_subtree( $subgraph ); |
955 | # Return the list of vertices and the list of roots. |
956 | my $pruned_group = [ sort $subgraph->vertices ]; |
957 | my $pruned_roots = [ $subgraph->predecessorless_vertices ]; |
958 | return( $pruned_group, $pruned_roots ); |
6d25a3a0 |
959 | } |
960 | |
7f52eac8 |
961 | sub _prune_subtree { |
5c44c598 |
962 | my( $tree ) = @_; |
94654e27 |
963 | |
964 | # Delete lacunose witnesses that have no successors |
5c44c598 |
965 | my @orphan_hypotheticals; |
966 | my $ctr = 0; |
967 | do { |
968 | die "Infinite loop on leaves" if $ctr > 100; |
969 | @orphan_hypotheticals = |
970 | grep { $tree->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' } |
971 | $tree->successorless_vertices; |
972 | $tree->delete_vertices( @orphan_hypotheticals ); |
973 | $ctr++; |
974 | } while( @orphan_hypotheticals ); |
94654e27 |
975 | |
976 | # Delete lacunose roots that have a single successor |
977 | my @redundant_root; |
978 | $ctr = 0; |
979 | do { |
5c44c598 |
980 | die "Infinite loop on roots" if $ctr > 100; |
981 | @redundant_root = |
982 | grep { $tree->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' |
983 | && $tree->successors( $_ ) == 1 } |
984 | $tree->predecessorless_vertices; |
94654e27 |
985 | $tree->delete_vertices( @redundant_root ); |
986 | $ctr++; |
987 | } while( @redundant_root ); |
988 | } |
989 | |
5be0cdeb |
990 | sub _useful_variant { |
991 | my( $group_readings, $graph, $acstr ) = @_; |
992 | |
993 | # TODO Decide what to do with AC witnesses |
994 | |
995 | # Sort by group size and return |
996 | my $is_useful = 0; |
997 | my( @readings, @groups ); # The sorted groups for our answer. |
998 | foreach my $rdg ( sort { @{$group_readings->{$b}} <=> @{$group_readings->{$a}} } |
999 | keys %$group_readings ) { |
1000 | push( @readings, $rdg ); |
1001 | push( @groups, $group_readings->{$rdg} ); |
1002 | if( @{$group_readings->{$rdg}} > 1 ) { |
1003 | $is_useful++; |
1004 | } else { |
1005 | my( $wit ) = @{$group_readings->{$rdg}}; |
1006 | $wit =~ s/^(.*)\Q$acstr\E$/$1/; |
1007 | $is_useful++ unless( $graph->is_sink_vertex( $wit ) ); |
1008 | } |
1009 | } |
1010 | if( $is_useful > 1 ) { |
1011 | return( \@readings, \@groups ); |
1012 | } else { |
1013 | return( [], [] ); |
1014 | } |
1015 | } |
1016 | |
7f52eac8 |
1017 | =head2 wit_stringify( $groups ) |
1018 | |
1019 | Takes an array of witness groupings and produces a string like |
1020 | ['A','B'] / ['C','D','E'] / ['F'] |
d71100ed |
1021 | |
7f52eac8 |
1022 | =cut |
d71100ed |
1023 | |
1024 | sub wit_stringify { |
1025 | my $groups = shift; |
1026 | my @gst; |
1027 | # If we were passed an array of witnesses instead of an array of |
1028 | # groupings, then "group" the witnesses first. |
1029 | unless( ref( $groups->[0] ) ) { |
1030 | my $mkgrp = [ $groups ]; |
1031 | $groups = $mkgrp; |
1032 | } |
1033 | foreach my $g ( @$groups ) { |
1034 | push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' ); |
1035 | } |
1036 | return join( ' / ', @gst ); |
1037 | } |
7f52eac8 |
1038 | |
bebec0e9 |
1039 | sub _symmdiff { |
1040 | my( $lista, $listb ) = @_; |
7f52eac8 |
1041 | my %union; |
1042 | my %scalars; |
1043 | map { $union{$_} = 1; $scalars{$_} = $_ } @$lista; |
1044 | map { $union{$_} += 1; $scalars{$_} = $_ } @$listb; |
bebec0e9 |
1045 | my @set = grep { $union{$_} == 1 } keys %union; |
7f52eac8 |
1046 | return map { $scalars{$_} } @set; |
1047 | } |
1048 | |
1049 | 1; |
1050 | |
1051 | =head1 LICENSE |
1052 | |
1053 | This package is free software and is provided "as is" without express |
1054 | or implied warranty. You can redistribute it and/or modify it under |
1055 | the same terms as Perl itself. |
1056 | |
1057 | =head1 AUTHOR |
1058 | |
1059 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |