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d71100ed |
1 | package Text::Tradition::Analysis; |
2 | |
3 | use strict; |
4 | use warnings; |
e4386ba9 |
5 | use Benchmark; |
d1348d38 |
6 | use Exporter 'import'; |
d71100ed |
7 | use Text::Tradition; |
8 | use Text::Tradition::Stemma; |
9 | |
d1348d38 |
10 | use vars qw/ @EXPORT_OK /; |
a2cf85dd |
11 | @EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /; |
d1348d38 |
12 | |
7f52eac8 |
13 | =head1 NAME |
14 | |
15 | Text::Tradition::Analysis - functions for stemma analysis of a tradition |
16 | |
17 | =head1 SYNOPSIS |
18 | |
19 | use Text::Tradition; |
20 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
21 | my $t = Text::Tradition->new( |
22 | 'name' => 'this is a text', |
23 | 'input' => 'TEI', |
24 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
25 | $t->add_stemma( 'dotfile' => $stemmafile ); |
26 | |
27 | my $variant_data = run_analysis( $tradition ); |
28 | # Recalculate rank $n treating all orthographic variants as equivalent |
29 | my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' ); |
30 | |
31 | =head1 DESCRIPTION |
32 | |
33 | Text::Tradition is a library for representation and analysis of collated |
34 | texts, particularly medieval ones. The Collation is the central feature of |
35 | a Tradition, where the text, its sequence of readings, and its relationships |
36 | between readings are actually kept. |
37 | |
38 | =head1 SUBROUTINES |
39 | |
40 | =head2 run_analysis( $tradition, $stemma_id, @merge_relationship_types ) |
41 | |
42 | Runs the analysis described in analyze_variant_location on every location |
43 | in the collation of the given tradition, against the stemma specified in |
44 | $stemma_id. If $stemma_id is not specified, it defaults to 0 (referencing |
45 | the first stemma saved for the tradition.) |
46 | |
47 | The optional @merge_relationship_types contains a list of relationship types |
48 | to treat as equivalent for the analysis. |
49 | |
50 | =begin testing |
51 | |
52 | use Text::Tradition; |
53 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
54 | |
55 | my $datafile = 't/data/florilegium_tei_ps.xml'; |
56 | my $tradition = Text::Tradition->new( 'input' => 'TEI', |
57 | 'name' => 'test0', |
58 | 'file' => $datafile ); |
59 | my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' ); |
60 | is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" ); |
61 | |
62 | my $data = run_analysis( $tradition ); |
5be0cdeb |
63 | # TODO Check genealogical count |
64 | is( $data->{'genealogical_count'}, 13, "Got right genealogical count" ); |
65 | is( $data->{'conflict_count'}, 16, "Got right conflict count" ); |
66 | is( $data->{'variant_count'}, 28, "Got right total variant number" ); |
7f52eac8 |
67 | |
68 | =end testing |
69 | |
70 | =cut |
71 | |
d71100ed |
72 | sub run_analysis { |
7f52eac8 |
73 | my( $tradition, $stemma_id, @collapse ) = @_; |
74 | $stemma_id = 0 unless $stemma_id; |
56cf65bd |
75 | |
7f52eac8 |
76 | # Run the variant analysis on every rank in the graph that doesn't |
77 | # have a common reading. Return the results. |
78 | my @variants; # holds results from analyze_variant_location |
79 | my $genealogical; # counter of 'genealogical' variants |
80 | my $conflicts; # counter of conflicting readings |
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81 | |
7f52eac8 |
82 | # Find and mark 'common' ranks for exclusion. |
83 | my %common_rank; |
84 | foreach my $rdg ( $tradition->collation->common_readings ) { |
85 | $common_rank{$rdg->rank} = 1; |
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86 | } |
7f52eac8 |
87 | |
88 | foreach my $rank ( 1 .. $tradition->collation->end->rank-1 ) { |
89 | next if $common_rank{$rank}; |
90 | my $variant_row = analyze_variant_location( |
91 | $tradition, $rank, $stemma_id, @collapse ); |
5be0cdeb |
92 | next unless $variant_row; |
7f52eac8 |
93 | push( @variants, $variant_row ); |
94 | $genealogical++ if $variant_row->{'genealogical'}; |
95 | $conflicts += grep { $_->{'conflict'} } @{$variant_row->{'readings'}}; |
d71100ed |
96 | } |
97 | |
7f52eac8 |
98 | return { |
99 | 'variants' => \@variants, |
100 | 'variant_count' => scalar @variants, # TODO redundant |
101 | 'conflict_count' => $conflicts, |
102 | 'genealogical_count' => $genealogical, |
103 | }; |
d71100ed |
104 | } |
105 | |
7f52eac8 |
106 | =head2 group_variants( $tradition, $rank, $lacunose, @merge_relationship_types ) |
107 | |
108 | Groups the variants at the given $rank of the collation, treating any |
109 | relationships in @merge_relationship_types as equivalent. $lacunose should |
110 | be a reference to an array, to which the sigla of lacunose witnesses at this |
111 | rank will be appended. |
112 | |
113 | Returns two ordered lists $readings, $groups, where $readings->[$n] is attested |
114 | by the witnesses listed in $groups->[$n]. |
115 | |
116 | =cut |
117 | |
118 | # Return group_readings, groups, lacunose |
d1348d38 |
119 | sub group_variants { |
7f52eac8 |
120 | my( $tradition, $rank, $lacunose, $collapse ) = @_; |
121 | my $c = $tradition->collation; |
122 | # Get the alignment table readings |
123 | my %readings_at_rank; |
124 | my @gap_wits; |
125 | foreach my $tablewit ( @{$tradition->collation->alignment_table->{'alignment'}} ) { |
126 | my $rdg = $tablewit->{'tokens'}->[$rank-1]; |
127 | if( $rdg && $rdg->{'t'}->is_lacuna ) { |
5be0cdeb |
128 | _add_to_witlist( $tablewit->{'witness'}, $lacunose, |
129 | $tradition->collation->ac_label ); |
7f52eac8 |
130 | } elsif( $rdg ) { |
131 | $readings_at_rank{$rdg->{'t'}->text} = $rdg->{'t'}; |
132 | } else { |
5be0cdeb |
133 | _add_to_witlist( $tablewit->{'witness'}, \@gap_wits, |
134 | $tradition->collation->ac_label ); |
7f52eac8 |
135 | } |
136 | } |
d1348d38 |
137 | |
7f52eac8 |
138 | # Group the readings, collapsing groups by relationship if needed |
139 | my %grouped_readings; |
140 | foreach my $rdg ( sort { $b->witnesses <=> $a->witnesses } values %readings_at_rank ) { |
141 | # Skip readings that have been collapsed into others. |
142 | next if exists $grouped_readings{$rdg->text} && !$grouped_readings{$rdg->text}; |
143 | my @wits = $rdg->witnesses; |
144 | if( $collapse ) { |
145 | my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; }; |
146 | foreach my $other ( $rdg->related_readings( $filter ) ) { |
147 | push( @wits, $other->witnesses ); |
148 | $grouped_readings{$other->text} = 0; |
d1348d38 |
149 | } |
150 | } |
7f52eac8 |
151 | $grouped_readings{$rdg->text} = \@wits; |
152 | } |
153 | $grouped_readings{'(omitted)'} = \@gap_wits if @gap_wits; |
154 | # Get rid of our collapsed readings |
155 | map { delete $grouped_readings{$_} unless $grouped_readings{$_} } |
156 | keys %grouped_readings |
157 | if $collapse; |
158 | |
5be0cdeb |
159 | return \%grouped_readings; |
d1348d38 |
160 | } |
161 | |
7f52eac8 |
162 | =head2 analyze_variant_location( $tradition, $rank, $stemma_id, @merge_relationship_types ) |
f6c8ea08 |
163 | |
7f52eac8 |
164 | Runs an analysis of the given tradition, at the location given in $rank, |
165 | against the graph of the stemma specified in $stemma_id. The argument |
166 | @merge_relationship_types is an optional list of relationship types for |
167 | which readings so related should be treated as equivalent. |
f6c8ea08 |
168 | |
7f52eac8 |
169 | Returns a data structure as follows: |
170 | |
171 | { 'id' => $rank, |
172 | 'genealogical' => boolean, |
173 | 'readings => [ { text => $reading_text, |
174 | group => [ witnesses ], |
175 | conflict => [ conflicting ], |
176 | missing => [ excluded ] }, ... ] |
177 | } |
178 | where 'conflicting' is the list of witnesses whose readings conflict with |
179 | this group, and 'excluded' is the list of witnesses either not present in |
180 | the stemma or lacunose at this location. |
181 | |
182 | =cut |
732152b1 |
183 | |
d71100ed |
184 | sub analyze_variant_location { |
7f52eac8 |
185 | my( $tradition, $rank, $sid, @collapse ) = @_; |
7f52eac8 |
186 | # Get the readings in this tradition at this rank |
187 | my @rank_rdgs = grep { $_->rank == $rank } $tradition->collation->readings; |
188 | # Get the applicable stemma |
189 | my $undirected; # TODO Allow undirected distance tree analysis too |
190 | my $stemma = $tradition->stemma( $sid ); |
191 | my $graph = $stemma->graph; |
192 | # Figure out which witnesses we are working with |
bebec0e9 |
193 | my @lacunose = $stemma->hypotheticals; |
194 | push( @lacunose, _symmdiff( [ $stemma->witnesses ], |
195 | [ map { $_->sigil } $tradition->witnesses ] ) ); |
7f52eac8 |
196 | |
197 | # Now group the readings |
5be0cdeb |
198 | my( $readings, $groups ) = _useful_variant( |
199 | group_variants( $tradition, $rank, \@lacunose, \@collapse ), |
200 | $graph, $tradition->collation->ac_label ); |
201 | return unless scalar @$readings; |
7f52eac8 |
202 | my $group_readings = {}; |
203 | # Lookup table group string -> readings |
204 | foreach my $x ( 0 .. $#$groups ) { |
205 | $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x]; |
206 | } |
207 | |
208 | # Now do the work. |
231d71fc |
209 | my $contig = {}; |
210 | my $subgraph = {}; |
c4a4fb1b |
211 | my $is_conflicted; |
d71100ed |
212 | my $conflict = {}; |
bebec0e9 |
213 | my %reading_roots; |
7f52eac8 |
214 | my $variant_row = { 'id' => $rank, 'readings' => [] }; |
94a077d6 |
215 | # Mark each ms as in its own group, first. |
216 | foreach my $g ( @$groups ) { |
217 | my $gst = wit_stringify( $g ); |
231d71fc |
218 | map { $contig->{$_} = $gst } @$g; |
94a077d6 |
219 | } |
c4a4fb1b |
220 | # Now for each unmarked node in the graph, initialize an array |
221 | # for possible group memberships. We will use this later to |
222 | # resolve potential conflicts. |
bebec0e9 |
223 | $DB::single = 1 if $rank == 636; |
231d71fc |
224 | map { $contig->{$_} = [] unless $contig->{$_} } $graph->vertices; |
d71100ed |
225 | foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) { |
c4a4fb1b |
226 | my $gst = wit_stringify( $g ); # This is the group name |
08e0fb85 |
227 | # Copy the graph, and delete all non-members from the new graph. |
c4a4fb1b |
228 | my $part = $graph->copy; |
bebec0e9 |
229 | my @group_roots; |
c4a4fb1b |
230 | $part->delete_vertices( |
231d71fc |
231 | grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices ); |
c4a4fb1b |
232 | |
233 | # Now look to see if our group is connected. |
234 | if( $undirected ) { # For use with distance trees etc. |
235 | # Find all vertices reachable from the first (arbitrary) group |
bebec0e9 |
236 | # member. If we are genealogical this should include them all. |
237 | my $reachable = {}; |
c4a4fb1b |
238 | map { $reachable->{$_} = 1 } $part->all_reachable( $g->[0] ); |
239 | # TODO This is a terrible way to do distance trees, since all |
240 | # non-leaf nodes are included in every graph part now. We may |
241 | # have to go back to SPDP. |
242 | } else { |
243 | if( @$g > 1 ) { |
c4a4fb1b |
244 | # We have to take directionality into account. |
245 | # How many root nodes do we have? |
231d71fc |
246 | my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst } |
bebec0e9 |
247 | $part->predecessorless_vertices; |
c4a4fb1b |
248 | # Assuming that @$g > 1, find the first root node that has at |
249 | # least one successor belonging to our group. If this reading |
250 | # is genealogical, there should be only one, but we will check |
251 | # that implicitly later. |
c4a4fb1b |
252 | foreach my $root ( @roots ) { |
231d71fc |
253 | # Prune the tree to get rid of extraneous hypotheticals. |
7f52eac8 |
254 | $root = _prune_subtree( $part, $root, $contig ); |
bebec0e9 |
255 | next unless $root; |
256 | # Save this root for our group. |
257 | push( @group_roots, $root ); |
c4a4fb1b |
258 | # Get all the successor nodes of our root. |
c4a4fb1b |
259 | } |
bebec0e9 |
260 | } else { |
261 | # Dispense with the trivial case of one reading. |
262 | @group_roots = @$g; |
263 | _prune_subtree( $part, @group_roots, $contig ); |
264 | } |
c4a4fb1b |
265 | } |
266 | |
bebec0e9 |
267 | map { $reading_roots{$_} = 1 } @group_roots; |
268 | if( @group_roots > 1 ) { |
269 | $conflict->{$group_readings->{$gst}} = 1; |
270 | $is_conflicted = 1; |
08e0fb85 |
271 | } |
bebec0e9 |
272 | # Paint the 'hypotheticals' with our group. |
273 | foreach my $wit ( $part->vertices ) { |
274 | if( ref( $contig->{$wit} ) ) { |
275 | push( @{$contig->{$wit}}, $gst ); |
276 | } elsif( $contig->{$wit} ne $gst ) { |
277 | warn "How did we get here?"; |
278 | } |
279 | } |
08e0fb85 |
280 | |
c4a4fb1b |
281 | |
bebec0e9 |
282 | # Start to write the reading, and save the group subgraph. |
732152b1 |
283 | my $reading = { 'text' => $group_readings->{$gst}, |
7f52eac8 |
284 | 'missing' => wit_stringify( \@lacunose ), |
c4a4fb1b |
285 | 'group' => $gst }; # This will change if we find no conflict |
bebec0e9 |
286 | # Save the relevant subgraph. |
287 | $subgraph->{$gst} = $part; |
732152b1 |
288 | push( @{$variant_row->{'readings'}}, $reading ); |
d71100ed |
289 | } |
c4a4fb1b |
290 | |
bebec0e9 |
291 | # For each of our hypothetical readings, flatten its 'contig' array if |
292 | # the array contains zero or one group. If we have any unflattened arrays, |
293 | # we may need to run the resolution process. If the reading is already known |
294 | # to have a conflict, flatten the 'contig' array to nothing; we won't resolve |
295 | # it. |
296 | my @resolve; |
297 | foreach my $wit ( keys %$contig ) { |
298 | next unless ref( $contig->{$wit} ); |
299 | if( @{$contig->{$wit}} > 1 ) { |
300 | if( $is_conflicted ) { |
301 | $contig->{$wit} = ''; # We aren't going to decide. |
302 | } else { |
303 | push( @resolve, $wit ); |
304 | } |
305 | } else { |
306 | my $gst = pop @{$contig->{$wit}}; |
307 | $contig->{$wit} = $gst || ''; |
308 | } |
309 | } |
310 | |
311 | if( @resolve ) { |
231d71fc |
312 | my $still_contig = {}; |
c4a4fb1b |
313 | foreach my $h ( @resolve ) { |
314 | # For each of the hypothetical readings with more than one possibility, |
315 | # try deleting it from each of its member subgraphs in turn, and see |
316 | # if that breaks the contiguous grouping. |
317 | # TODO This can still break in a corner case where group A can use |
318 | # either vertex 1 or 2, and group B can use either vertex 2 or 1. |
319 | # Revisit this if necessary; it could get brute-force nasty. |
231d71fc |
320 | foreach my $gst ( @{$contig->{$h}} ) { |
bebec0e9 |
321 | my $gpart = $subgraph->{$gst}->copy(); |
322 | # If we have come this far, there is only one root and everything |
323 | # is reachable from it. |
324 | my( $root ) = $gpart->predecessorless_vertices; |
325 | my $reachable = {}; |
326 | map { $reachable->{$_} = 1 } $gpart->vertices; |
327 | |
328 | # Try deleting the hypothetical node. |
c4a4fb1b |
329 | $gpart->delete_vertex( $h ); |
bebec0e9 |
330 | if( $h eq $root ) { |
331 | # See if we still have a single root. |
332 | my @roots = $gpart->predecessorless_vertices; |
333 | warn "This shouldn't have happened" unless @roots; |
334 | if( @roots > 1 ) { |
335 | # $h is needed by this group. |
336 | if( exists( $still_contig->{$h} ) ) { |
337 | # Conflict! |
338 | $conflict->{$group_readings->{$gst}} = 1; |
339 | $still_contig->{$h} = ''; |
340 | } else { |
341 | $still_contig->{$h} = $gst; |
342 | } |
343 | } |
344 | } else { |
345 | # $h is somewhere in the middle. See if everything |
346 | # else can still be reached from the root. |
347 | my %still_reachable = ( $root => 1 ); |
348 | map { $still_reachable{$_} = 1 } |
349 | $gpart->all_successors( $root ); |
350 | foreach my $v ( keys %$reachable ) { |
351 | next if $v eq $h; |
352 | if( !$still_reachable{$v} |
353 | && ( $contig->{$v} eq $gst |
354 | || ( exists $still_contig->{$v} |
355 | && $still_contig->{$v} eq $gst ) ) ) { |
356 | # We need $h. |
357 | if( exists $still_contig->{$h} ) { |
358 | # Conflict! |
359 | $conflict->{$group_readings->{$gst}} = 1; |
360 | $still_contig->{$h} = ''; |
361 | } else { |
362 | $still_contig->{$h} = $gst; |
363 | } |
364 | last; |
365 | } # else we don't need $h in this group. |
366 | } # end foreach $v |
367 | } # endif $h eq $root |
368 | } # end foreach $gst |
369 | } # end foreach $h |
c4a4fb1b |
370 | |
bebec0e9 |
371 | # Now we have some hypothetical vertices in $still_contig that are the |
372 | # "real" group memberships. Replace these in $contig. |
373 | foreach my $v ( keys %$contig ) { |
374 | next unless ref $contig->{$v}; |
375 | $contig->{$v} = $still_contig->{$v}; |
376 | } |
377 | } # end if @resolve |
378 | |
379 | # Now that we have all the node group memberships, calculate followed/ |
380 | # non-followed/unknown values for each reading. Also figure out the |
381 | # reading's evident parent(s). |
382 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
383 | my $gst = $rdghash->{'group'}; |
384 | my $part = $subgraph->{$gst}; |
385 | my @roots = $part->predecessorless_vertices; |
386 | $rdghash->{'independent_occurrence'} = scalar @roots; |
387 | $rdghash->{'followed'} = scalar( $part->vertices ) - scalar( @roots ); |
388 | # Find the parent readings, if any, of this reading. |
389 | my @rdgparents; |
390 | foreach my $wit ( @roots ) { |
391 | # Look in the main stemma to find this witness's parent(s), and look |
392 | # up the reading that the parent holds. |
393 | foreach my $wparent( $graph->predecessors( $wit ) ) { |
394 | my $pgroup = $contig->{$wparent}; |
395 | if( $pgroup ) { |
396 | push( @rdgparents, $group_readings->{$pgroup} ); |
397 | } |
398 | } |
399 | } |
400 | $rdghash->{'reading_parents'} = \@rdgparents; |
401 | |
402 | # Find the number of times this reading was altered, and the number of |
403 | # times we're not sure. |
404 | my( %nofollow, %unknownfollow ); |
405 | foreach my $wit ( $part->vertices ) { |
406 | foreach my $wchild ( $graph->successors( $wit ) ) { |
407 | next if $part->has_vertex( $wchild ); |
408 | if( $reading_roots{$wchild} && $contig->{$wchild} ) { |
409 | # It definitely changed here. |
410 | $nofollow{$wchild} = 1; |
411 | } elsif( !($contig->{$wchild}) ) { |
412 | # The child is a hypothetical node not definitely in |
413 | # any group. Answer is unknown. |
414 | $unknownfollow{$wchild} = 1; |
415 | } # else it's a non-root node in a known group, and therefore |
416 | # is presumed to have its reading from its group, not this link. |
417 | } |
418 | } |
419 | $rdghash->{'not_followed'} = keys %nofollow; |
420 | $rdghash->{'follow_unknown'} = keys %unknownfollow; |
c4a4fb1b |
421 | } |
bebec0e9 |
422 | |
c4a4fb1b |
423 | # Now write the group and conflict information into the respective rows. |
bebec0e9 |
424 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
425 | $rdghash->{'conflict'} = $conflict->{$rdghash->{'text'}}; |
426 | my @members = grep { $contig->{$_} eq $rdghash->{'group'} } keys %$contig; |
427 | $rdghash->{'group'} = wit_stringify( \@members ); |
c4a4fb1b |
428 | } |
429 | |
08e0fb85 |
430 | $variant_row->{'genealogical'} = !( keys %$conflict ); |
732152b1 |
431 | return $variant_row; |
d71100ed |
432 | } |
433 | |
7f52eac8 |
434 | sub _prune_subtree { |
231d71fc |
435 | my( $tree, $root, $contighash ) = @_; |
436 | # First, delete hypothetical leaves / orphans until there are none left. |
437 | my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } |
438 | $tree->successorless_vertices; |
439 | while( @orphan_hypotheticals ) { |
440 | $tree->delete_vertices( @orphan_hypotheticals ); |
441 | @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } |
442 | $tree->successorless_vertices; |
443 | } |
444 | # Then delete a hypothetical root with only one successor, moving the |
bebec0e9 |
445 | # root to the first child that has no other predecessors. |
231d71fc |
446 | while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) { |
447 | my @nextroot = $tree->successors( $root ); |
448 | $tree->delete_vertex( $root ); |
bebec0e9 |
449 | ( $root ) = grep { $tree->is_predecessorless_vertex( $_ ) } @nextroot; |
231d71fc |
450 | } |
451 | # The tree has been modified in place, but we need to know the new root. |
bebec0e9 |
452 | $root = undef unless $root && $tree->has_vertex( $root ); |
231d71fc |
453 | return $root; |
454 | } |
d71100ed |
455 | # Add the variant, subject to a.c. representation logic. |
456 | # This assumes that we will see the 'main' version before the a.c. version. |
457 | sub add_variant_wit { |
458 | my( $arr, $wit, $acstr ) = @_; |
459 | my $skip; |
460 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
461 | my $real = $1; |
462 | $skip = grep { $_ =~ /^\Q$real\E$/ } @$arr; |
463 | } |
464 | push( @$arr, $wit ) unless $skip; |
465 | } |
466 | |
5be0cdeb |
467 | sub _useful_variant { |
468 | my( $group_readings, $graph, $acstr ) = @_; |
469 | |
470 | # TODO Decide what to do with AC witnesses |
471 | |
472 | # Sort by group size and return |
473 | my $is_useful = 0; |
474 | my( @readings, @groups ); # The sorted groups for our answer. |
475 | foreach my $rdg ( sort { @{$group_readings->{$b}} <=> @{$group_readings->{$a}} } |
476 | keys %$group_readings ) { |
477 | push( @readings, $rdg ); |
478 | push( @groups, $group_readings->{$rdg} ); |
479 | if( @{$group_readings->{$rdg}} > 1 ) { |
480 | $is_useful++; |
481 | } else { |
482 | my( $wit ) = @{$group_readings->{$rdg}}; |
483 | $wit =~ s/^(.*)\Q$acstr\E$/$1/; |
484 | $is_useful++ unless( $graph->is_sink_vertex( $wit ) ); |
485 | } |
486 | } |
487 | if( $is_useful > 1 ) { |
488 | return( \@readings, \@groups ); |
489 | } else { |
490 | return( [], [] ); |
491 | } |
492 | } |
493 | |
7f52eac8 |
494 | =head2 wit_stringify( $groups ) |
495 | |
496 | Takes an array of witness groupings and produces a string like |
497 | ['A','B'] / ['C','D','E'] / ['F'] |
d71100ed |
498 | |
7f52eac8 |
499 | =cut |
d71100ed |
500 | |
501 | sub wit_stringify { |
502 | my $groups = shift; |
503 | my @gst; |
504 | # If we were passed an array of witnesses instead of an array of |
505 | # groupings, then "group" the witnesses first. |
506 | unless( ref( $groups->[0] ) ) { |
507 | my $mkgrp = [ $groups ]; |
508 | $groups = $mkgrp; |
509 | } |
510 | foreach my $g ( @$groups ) { |
511 | push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' ); |
512 | } |
513 | return join( ' / ', @gst ); |
514 | } |
7f52eac8 |
515 | |
5be0cdeb |
516 | # Helper function to ensure that X and X a.c. never appear in the same list. |
517 | sub _add_to_witlist { |
518 | my( $wit, $list, $acstr ) = @_; |
519 | my %inlist; |
520 | my $idx = 0; |
521 | map { $inlist{$_} = $idx++ } @$list; |
522 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
523 | my $acwit = $1; |
524 | unless( exists $inlist{$acwit} ) { |
525 | push( @$list, $acwit.$acstr ); |
526 | } |
527 | } else { |
528 | if( exists( $inlist{$wit.$acstr} ) ) { |
529 | # Replace the a.c. version with the main witness |
530 | my $i = $inlist{$wit.$acstr}; |
531 | $list->[$i] = $wit; |
532 | } else { |
533 | push( @$list, $wit ); |
534 | } |
535 | } |
536 | } |
537 | |
bebec0e9 |
538 | sub _symmdiff { |
539 | my( $lista, $listb ) = @_; |
7f52eac8 |
540 | my %union; |
541 | my %scalars; |
542 | map { $union{$_} = 1; $scalars{$_} = $_ } @$lista; |
543 | map { $union{$_} += 1; $scalars{$_} = $_ } @$listb; |
bebec0e9 |
544 | my @set = grep { $union{$_} == 1 } keys %union; |
7f52eac8 |
545 | return map { $scalars{$_} } @set; |
546 | } |
547 | |
548 | 1; |
549 | |
550 | =head1 LICENSE |
551 | |
552 | This package is free software and is provided "as is" without express |
553 | or implied warranty. You can redistribute it and/or modify it under |
554 | the same terms as Perl itself. |
555 | |
556 | =head1 AUTHOR |
557 | |
558 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |