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d71100ed |
1 | package Text::Tradition::Analysis; |
2 | |
3 | use strict; |
4 | use warnings; |
d1348d38 |
5 | use Exporter 'import'; |
d71100ed |
6 | use Text::Tradition; |
7 | use Text::Tradition::Stemma; |
8 | |
d1348d38 |
9 | use vars qw/ @EXPORT_OK /; |
10 | @EXPORT_OK = qw/ run_analysis group_variants wit_stringify /; |
11 | |
d71100ed |
12 | sub new { |
13 | my( $class, $args ) = @_; |
14 | my $self = {}; |
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15 | bless( $self, $class ); |
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16 | $self->{'data'} = []; |
17 | foreach my $t ( @{$args->{'traditions'}} ) { |
18 | $self->run_analysis( $t->{'file'}, $t->{'stemmadot'} ); |
19 | } |
d71100ed |
20 | return $self; |
21 | } |
22 | |
23 | sub run_analysis { |
732152b1 |
24 | my( $self, $file, $stemmadot ) = @_; |
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25 | # What we will return |
26 | my $svg; |
27 | my $variants = []; |
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28 | my $data = {}; |
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29 | |
3d79e248 |
30 | # Read in the file and stemma |
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31 | my $tradition = Text::Tradition->new( |
3d79e248 |
32 | 'input' => 'Self', |
33 | 'file' => $file, |
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34 | 'linear' => 1, |
35 | ); |
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36 | $data->{'title'} = $tradition->name; |
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37 | |
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38 | my $stemma = Text::Tradition::Stemma->new( |
39 | 'collation' => $tradition->collation, |
40 | 'dot' => $stemmadot, |
41 | ); |
42 | # We will return the stemma picture |
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43 | $svg = $stemma->as_svg( { size => "8,7.5" } );; |
44 | $data->{'svg'} = $svg; |
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45 | |
46 | # We have the collation, so get the alignment table with witnesses in rows. |
47 | # Also return the reading objects in the table, rather than just the words. |
08e0fb85 |
48 | my $wits = {}; |
49 | map { $wits->{$_} = 1 } $stemma->witnesses; |
50 | my $all_wits_table = $tradition->collation->make_alignment_table( 'refs', $wits ); |
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51 | |
52 | # For each column in the alignment table, we want to see if the existing |
53 | # groupings of witnesses match our stemma hypothesis. We also want, at the |
54 | # end, to produce an HTML table with all the variants. |
55 | my $html_columns = 0; |
732152b1 |
56 | my ( $total, $genealogical, $conflicts ) = ( 0, 0, 0 ); |
d71100ed |
57 | |
58 | # Strip the list of sigla and save it for correlation to the readings. |
59 | my $col_wits = shift @$all_wits_table; |
4f343ec0 |
60 | # Any witness in the stemma that has no row should be noted. |
61 | foreach ( @$col_wits ) { |
fa954f4c |
62 | $wits->{$_}++; # Witnesses present in table and stemma now have value 2. |
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63 | } |
64 | my @not_collated = grep { $wits->{$_} == 1 } keys %$wits; |
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65 | |
66 | # We will return a data structure, an array for each row that looks like: |
67 | # { id = X, genealogical = Y, readings = [ text = X, group = Y], empty = N } |
68 | foreach my $i ( 0 .. $#$all_wits_table ) { |
69 | # For each column in the table, group the readings by witness. |
70 | my $rdg_wits = {}; |
71 | my $col_rdgs = shift @$all_wits_table; |
72 | my $rank; |
4f343ec0 |
73 | my $lacunose = [ @not_collated ]; |
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74 | foreach my $j ( 0 .. $#{$col_rdgs} ) { |
75 | my $rdg = $col_rdgs->[$j]; |
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76 | my $rdg_text = '(omitted)'; # Initialize in case of empty reading |
77 | if( $rdg ) { |
c4e11e3f |
78 | if( $rdg->is_lacuna ) { |
79 | $rdg_text = undef; # Don't count lacunae |
80 | push( @$lacunose, $col_wits->[$j] ); |
81 | } else { |
82 | $rdg_text = $rdg->text; |
83 | # Get the rank from any real reading; they should be identical. |
84 | $rank = $rdg->rank; |
85 | } |
d71100ed |
86 | } |
87 | if( defined $rdg_text ) { |
88 | # Initialize the witness array if we haven't got one yet |
89 | $rdg_wits->{$rdg_text} = [] unless $rdg_wits->{$rdg_text}; |
90 | # Add the relevant witness, subject to a.c. logic |
91 | add_variant_wit( $rdg_wits->{$rdg_text}, $col_wits->[$j], |
92 | $tradition->collation->ac_label ); |
93 | } |
94 | } |
95 | |
96 | # See if this column has any potentially genealogical variants. |
97 | # If not, skip to the next. |
98 | $total++ unless scalar keys %$rdg_wits == 1; |
99 | my( $groups, $readings ) = useful_variant( $rdg_wits ); |
100 | next unless $groups && $readings; |
101 | |
d71100ed |
102 | # Keep track of our widest row |
103 | $html_columns = scalar @$groups if scalar @$groups > $html_columns; |
104 | |
105 | # We can already look up witnesses for a reading; we also want to look |
106 | # up readings for a given witness. |
107 | my $group_readings = {}; |
108 | foreach my $x ( 0 .. $#$groups ) { |
109 | $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x]; |
110 | } |
111 | |
112 | # For all the groups with more than one member, collect the list of all |
113 | # contiguous vertices needed to connect them. |
732152b1 |
114 | my $variant_row = analyze_variant_location( $group_readings, $groups, |
08e0fb85 |
115 | $stemma->graph, $lacunose ); |
732152b1 |
116 | $variant_row->{'id'} = $rank; |
117 | $genealogical++ if $variant_row->{'genealogical'}; |
118 | $conflicts += grep { $_->{'conflict'} } @{$variant_row->{'readings'}}; |
119 | |
d71100ed |
120 | # Now run the same analysis given the calculated distance tree(s). |
732152b1 |
121 | # my @trees = @{$stemma->distance_trees}; |
122 | # if( @trees ) { |
123 | # foreach my $tree ( 0 .. $#trees ) { |
c4a4fb1b |
124 | # my $dc = analyze_variant_location( $group_readings, $groups, $tree, $lacunose, 'undirected' ); |
732152b1 |
125 | # foreach my $rdg ( keys %$dc ) { |
126 | # my $var = $dc->{$rdg}; |
127 | # # TODO Do something with this |
128 | # } |
129 | # } |
130 | # } |
131 | |
d71100ed |
132 | # Record that we used this variant in an analysis |
133 | push( @$variants, $variant_row ); |
134 | } |
135 | |
732152b1 |
136 | # Go through our variant rows, after we have seen all of them once, |
137 | # and add the number of empty columns needed by each. |
d71100ed |
138 | foreach my $row ( @$variants ) { |
139 | my $empty = $html_columns - scalar @{$row->{'readings'}}; |
140 | $row->{'empty'} = $empty; |
141 | } |
142 | |
732152b1 |
143 | # Populate self with our analysis data. |
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144 | $data->{'variants'} = $variants; |
145 | $data->{'variant_count'} = $total; |
146 | $data->{'conflict_count'} = $conflicts; |
147 | $data->{'genealogical_count'} = $genealogical; |
148 | push( @{$self->{'data'}}, $data ); |
d71100ed |
149 | } |
150 | |
d1348d38 |
151 | sub group_variants { |
152 | my( $c, $wits ) = @_; |
153 | my $variant_groups = []; |
154 | |
155 | my $all_wits_table = $c->make_alignment_table( 'refs', $wits ); |
156 | # Strip the list of sigla and save it for correlation to the readings. |
157 | my $col_wits = shift @$all_wits_table; |
158 | # Any witness in the stemma that has no row should be noted. |
159 | foreach ( @$col_wits ) { |
160 | $wits->{$_}++; # Witnesses present in table and stemma now have value 2. |
161 | } |
162 | my @not_collated = grep { $wits->{$_} == 1 } keys %$wits; |
163 | foreach my $i ( 0 .. $#$all_wits_table ) { |
164 | # For each column in the table, group the readings by witness. |
165 | my $rdg_wits = {}; |
166 | my $col_rdgs = shift @$all_wits_table; |
167 | my $rank; |
168 | my $lacunose = [ @not_collated ]; |
169 | foreach my $j ( 0 .. $#{$col_rdgs} ) { |
170 | my $rdg = $col_rdgs->[$j]; |
171 | my $rdg_text = '(omitted)'; # Initialize in case of empty reading |
172 | if( $rdg ) { |
173 | if( $rdg->is_lacuna ) { |
174 | $rdg_text = undef; # Don't count lacunae |
175 | push( @$lacunose, $col_wits->[$j] ); |
176 | } else { |
177 | $rdg_text = $rdg->text; |
178 | # Get the rank from any real reading; they should be identical. |
179 | $rank = $rdg->rank; |
180 | } |
181 | } |
182 | if( defined $rdg_text ) { |
183 | # Initialize the witness array if we haven't got one yet |
184 | $rdg_wits->{$rdg_text} = [] unless $rdg_wits->{$rdg_text}; |
185 | # Add the relevant witness, subject to a.c. logic |
186 | add_variant_wit( $rdg_wits->{$rdg_text}, $col_wits->[$j], |
187 | $c->ac_label ); |
188 | } |
189 | } |
190 | |
191 | # See if this column has any potentially genealogical variants. |
192 | # If not, skip to the next. |
193 | my( $groups, $readings ) = useful_variant( $rdg_wits ); |
194 | next unless $groups && $readings; |
195 | |
196 | push( @$variant_groups, $groups ); |
197 | } |
198 | return $variant_groups; |
199 | } |
200 | |
732152b1 |
201 | # variant_row -> genealogical |
202 | # -> readings [ { text, group, conflict, missing } ] |
203 | |
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204 | sub analyze_variant_location { |
c4a4fb1b |
205 | my( $group_readings, $groups, $graph, $lacunose, $undirected ) = @_; |
231d71fc |
206 | my $contig = {}; |
207 | my $subgraph = {}; |
c4a4fb1b |
208 | my $is_conflicted; |
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209 | my $conflict = {}; |
231d71fc |
210 | my $missing = {}; |
211 | map { $missing->{$_} = 1 } @$lacunose; |
732152b1 |
212 | my $variant_row = { 'readings' => [] }; |
94a077d6 |
213 | # Mark each ms as in its own group, first. |
214 | foreach my $g ( @$groups ) { |
215 | my $gst = wit_stringify( $g ); |
231d71fc |
216 | map { $contig->{$_} = $gst } @$g; |
94a077d6 |
217 | } |
c4a4fb1b |
218 | # Now for each unmarked node in the graph, initialize an array |
219 | # for possible group memberships. We will use this later to |
220 | # resolve potential conflicts. |
231d71fc |
221 | map { $contig->{$_} = [] unless $contig->{$_} } $graph->vertices; |
d71100ed |
222 | foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) { |
c4a4fb1b |
223 | my $gst = wit_stringify( $g ); # This is the group name |
224 | my $reachable = { $g->[0] => 1 }; |
08e0fb85 |
225 | # Copy the graph, and delete all non-members from the new graph. |
c4a4fb1b |
226 | my $part = $graph->copy; |
227 | my $group_root; |
228 | $part->delete_vertices( |
231d71fc |
229 | grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices ); |
c4a4fb1b |
230 | |
231 | # Now look to see if our group is connected. |
232 | if( $undirected ) { # For use with distance trees etc. |
233 | # Find all vertices reachable from the first (arbitrary) group |
234 | # member. If we are genealogical this should include them all. |
235 | map { $reachable->{$_} = 1 } $part->all_reachable( $g->[0] ); |
236 | # TODO This is a terrible way to do distance trees, since all |
237 | # non-leaf nodes are included in every graph part now. We may |
238 | # have to go back to SPDP. |
239 | } else { |
240 | if( @$g > 1 ) { |
241 | # Dispense with the trivial case of one reading. |
242 | # We have to take directionality into account. |
243 | # How many root nodes do we have? |
231d71fc |
244 | my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst } |
c4a4fb1b |
245 | $part->source_vertices; |
246 | # Assuming that @$g > 1, find the first root node that has at |
247 | # least one successor belonging to our group. If this reading |
248 | # is genealogical, there should be only one, but we will check |
249 | # that implicitly later. |
250 | my $nodes_in_subtree = 0; |
251 | foreach my $root ( @roots ) { |
231d71fc |
252 | # Prune the tree to get rid of extraneous hypotheticals. |
253 | $root = prune_subtree( $part, $root, $contig ); |
c4a4fb1b |
254 | # Get all the successor nodes of our root. |
255 | my $tmp_reach = { $root => 1 }; |
256 | map { $tmp_reach->{$_} = 1 } $part->all_successors( $root ); |
257 | # Skip this root if none of our successors are in our group |
258 | # (e.g. isolated 'hypothetical' witnesses with no group) |
231d71fc |
259 | next unless grep { $contig->{$_} } keys %$tmp_reach; |
c4a4fb1b |
260 | if( keys %$tmp_reach > $nodes_in_subtree ) { |
261 | $nodes_in_subtree = keys %$tmp_reach; |
262 | $reachable = $tmp_reach; |
263 | $group_root = $root; |
264 | } |
265 | } |
266 | } # else it is a single-node group, nothing to calculate. |
267 | } |
268 | |
269 | # None of the 'reachable' nodes should be marked as being in another |
270 | # group. Paint the 'hypotheticals' with our group while we are at it, |
271 | # unless there is a conflict present. |
272 | foreach ( keys %$reachable ) { |
231d71fc |
273 | if( ref $contig->{$_} ) { |
274 | push( @{$contig->{$_}}, $gst ); |
275 | } elsif( $contig->{$_} ne $gst ) { |
276 | $conflict->{$group_readings->{$gst}} = $group_readings->{$contig->{$_}}; |
c4a4fb1b |
277 | } # else it is an 'extant' node marked with our group already. |
d71100ed |
278 | } |
08e0fb85 |
279 | # None of the unreachable nodes should be in our group either. |
280 | foreach ( $part->vertices ) { |
c4a4fb1b |
281 | next if $reachable->{$_}; |
231d71fc |
282 | if( $contig->{$_} eq $gst ) { |
c4a4fb1b |
283 | $conflict->{$group_readings->{$gst}} = $group_readings->{$gst}; |
284 | last; |
285 | } |
08e0fb85 |
286 | } |
287 | |
c4a4fb1b |
288 | # Now, if we have a conflict, we can write the reading in full. If not, |
289 | # we have to save the subgraph so that we can resolve possible conflicts |
290 | # on hypothetical nodes. |
291 | $is_conflicted = 1 if exists $conflict->{$group_readings->{$gst}}; |
292 | |
732152b1 |
293 | # Write the reading. |
294 | my $reading = { 'text' => $group_readings->{$gst}, |
295 | 'missing' => wit_stringify( $lacunose ), |
c4a4fb1b |
296 | 'group' => $gst }; # This will change if we find no conflict |
297 | if( $is_conflicted ) { |
298 | $reading->{'conflict'} = $conflict->{$group_readings->{$gst}} |
732152b1 |
299 | } else { |
c4a4fb1b |
300 | # Save the relevant subgraph. |
231d71fc |
301 | $subgraph->{$gst} = { 'graph' => $part, |
c4a4fb1b |
302 | 'root' => $group_root, |
303 | 'reachable' => $reachable }; |
732152b1 |
304 | } |
305 | push( @{$variant_row->{'readings'}}, $reading ); |
d71100ed |
306 | } |
c4a4fb1b |
307 | |
308 | # Now that we have gone through all the rows, check the hypothetical |
309 | # readings for conflict if we haven't found one yet. |
231d71fc |
310 | if( keys %$subgraph && !keys %$conflict ) { |
c4a4fb1b |
311 | my @resolve; |
231d71fc |
312 | foreach ( keys %$contig ) { |
313 | next unless ref $contig->{$_}; |
314 | if( scalar @{$contig->{$_}} > 1 ) { |
c4a4fb1b |
315 | push( @resolve, $_ ); |
316 | } else { |
231d71fc |
317 | $contig->{$_} = scalar @{$contig->{$_}} ? $contig->{$_}->[0] : ''; |
c4a4fb1b |
318 | } |
319 | } |
320 | # Do we still have a possible conflict? |
231d71fc |
321 | my $still_contig = {}; |
c4a4fb1b |
322 | foreach my $h ( @resolve ) { |
323 | # For each of the hypothetical readings with more than one possibility, |
324 | # try deleting it from each of its member subgraphs in turn, and see |
325 | # if that breaks the contiguous grouping. |
326 | # TODO This can still break in a corner case where group A can use |
327 | # either vertex 1 or 2, and group B can use either vertex 2 or 1. |
328 | # Revisit this if necessary; it could get brute-force nasty. |
231d71fc |
329 | foreach my $gst ( @{$contig->{$h}} ) { |
330 | my $gpart = $subgraph->{$gst}->{'graph'}->copy; |
331 | my $reachable = $subgraph->{$gst}->{'reachable'}; |
c4a4fb1b |
332 | $gpart->delete_vertex( $h ); |
333 | # Is everything else still reachable from the root? |
334 | # TODO If $h was the root, see if we still have a single root. |
231d71fc |
335 | my %still_reachable = ( $subgraph->{$gst}->{'root'} => 1 ); |
c4a4fb1b |
336 | map { $still_reachable{$_} = 1 } |
231d71fc |
337 | $gpart->all_successors( $subgraph->{$gst}->{'root'} ); |
c4a4fb1b |
338 | foreach my $v ( keys %$reachable ) { |
339 | next if $v eq $h; |
340 | if( !$still_reachable{$v} |
231d71fc |
341 | && ( $contig->{$v} eq $gst |
342 | || ( exists $still_contig->{$v} |
343 | && $still_contig->{$v} eq $gst ) ) ) { |
c4a4fb1b |
344 | # We need $h. |
231d71fc |
345 | if( exists $still_contig->{$h} ) { |
c4a4fb1b |
346 | # Conflict! |
347 | $conflict->{$group_readings->{$gst}} = |
231d71fc |
348 | $group_readings->{$still_contig->{$h}}; |
c4a4fb1b |
349 | } else { |
231d71fc |
350 | $still_contig->{$h} = $gst; |
c4a4fb1b |
351 | } |
352 | last; |
353 | } # else we don't need $h in this group. |
354 | } |
355 | } |
356 | } |
357 | |
358 | # Now, assuming no conflict, we have some hypothetical vertices in |
359 | # $still_contig that are the "real" group memberships. Replace these |
360 | # in $contig. |
361 | unless ( keys %$conflict ) { |
231d71fc |
362 | foreach my $v ( keys %$contig ) { |
363 | next unless ref $contig->{$v}; |
364 | $contig->{$v} = $still_contig->{$v}; |
c4a4fb1b |
365 | } |
366 | } |
367 | } |
368 | |
369 | # Now write the group and conflict information into the respective rows. |
370 | foreach my $rdg ( @{$variant_row->{'readings'}} ) { |
371 | $rdg->{'conflict'} = $conflict->{$rdg->{'text'}}; |
372 | next if $rdg->{'conflict'}; |
231d71fc |
373 | my @members = grep { $contig->{$_} eq $rdg->{'group'} && !$missing->{$_} } |
374 | keys %$contig; |
c4a4fb1b |
375 | $rdg->{'group'} = wit_stringify( \@members ); |
376 | } |
377 | |
08e0fb85 |
378 | $variant_row->{'genealogical'} = !( keys %$conflict ); |
732152b1 |
379 | return $variant_row; |
d71100ed |
380 | } |
381 | |
231d71fc |
382 | sub prune_subtree { |
383 | my( $tree, $root, $contighash ) = @_; |
384 | # First, delete hypothetical leaves / orphans until there are none left. |
385 | my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } |
386 | $tree->successorless_vertices; |
387 | while( @orphan_hypotheticals ) { |
388 | $tree->delete_vertices( @orphan_hypotheticals ); |
389 | @orphan_hypotheticals = grep { ref( $contighash->{$_} ) } |
390 | $tree->successorless_vertices; |
391 | } |
392 | # Then delete a hypothetical root with only one successor, moving the |
393 | # root to the child. |
394 | while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) { |
395 | my @nextroot = $tree->successors( $root ); |
396 | $tree->delete_vertex( $root ); |
397 | $root = $nextroot[0]; |
398 | } |
399 | # The tree has been modified in place, but we need to know the new root. |
400 | return $root; |
401 | } |
d71100ed |
402 | # Add the variant, subject to a.c. representation logic. |
403 | # This assumes that we will see the 'main' version before the a.c. version. |
404 | sub add_variant_wit { |
405 | my( $arr, $wit, $acstr ) = @_; |
406 | my $skip; |
407 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
408 | my $real = $1; |
409 | $skip = grep { $_ =~ /^\Q$real\E$/ } @$arr; |
410 | } |
411 | push( @$arr, $wit ) unless $skip; |
412 | } |
413 | |
414 | # Return an answer if the variant is useful, i.e. if there are at least 2 variants |
415 | # with at least 2 witnesses each. |
416 | sub useful_variant { |
417 | my( $readings ) = @_; |
418 | my $total = keys %$readings; |
419 | foreach my $var ( keys %$readings ) { |
420 | $total-- if @{$readings->{$var}} == 1; |
421 | } |
422 | return( undef, undef ) if $total <= 1; |
423 | my( $groups, $text ); |
424 | foreach my $var ( keys %$readings ) { |
425 | push( @$groups, $readings->{$var} ); |
426 | push( @$text, $var ); |
427 | } |
428 | return( $groups, $text ); |
429 | } |
430 | |
431 | # Take an array of witness groupings and produce a string like |
432 | # ['A','B'] / ['C','D','E'] / ['F'] |
433 | |
434 | sub wit_stringify { |
435 | my $groups = shift; |
436 | my @gst; |
437 | # If we were passed an array of witnesses instead of an array of |
438 | # groupings, then "group" the witnesses first. |
439 | unless( ref( $groups->[0] ) ) { |
440 | my $mkgrp = [ $groups ]; |
441 | $groups = $mkgrp; |
442 | } |
443 | foreach my $g ( @$groups ) { |
444 | push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' ); |
445 | } |
446 | return join( ' / ', @gst ); |
447 | } |
448 | |
449 | 1; |