Commit | Line | Data |
dd3b58b0 |
1 | package Text::Tradition::Collation; |
d047cd52 |
2 | |
910a0a6d |
3 | use Encode qw( decode_utf8 ); |
4 | use File::Temp; |
bfcbcecb |
5 | use File::Which; |
c9bf3dbf |
6 | use Graph; |
8e1394aa |
7 | use IPC::Run qw( run binary ); |
82fa4d57 |
8 | use Text::CSV; |
b15511bf |
9 | use Text::Tradition::Collation::Reading; |
22222af9 |
10 | use Text::Tradition::Collation::RelationshipStore; |
63778331 |
11 | use Text::Tradition::Error; |
cc31ebaa |
12 | use XML::Easy::Syntax qw( $xml10_namestartchar_rx $xml10_namechar_rx ); |
df6d9812 |
13 | use XML::LibXML; |
a344ffcf |
14 | use XML::LibXML::XPathContext; |
dd3b58b0 |
15 | use Moose; |
16 | |
3a2ebbf4 |
17 | has 'sequence' => ( |
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18 | is => 'ro', |
3a2ebbf4 |
19 | isa => 'Graph', |
20 | default => sub { Graph->new() }, |
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21 | handles => { |
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22 | paths => 'edges', |
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23 | }, |
d047cd52 |
24 | ); |
3a2ebbf4 |
25 | |
26 | has 'relations' => ( |
27 | is => 'ro', |
22222af9 |
28 | isa => 'Text::Tradition::Collation::RelationshipStore', |
29 | handles => { |
30 | relationships => 'relationships', |
31 | related_readings => 'related_readings', |
202ccb18 |
32 | get_relationship => 'get_relationship', |
ee801e17 |
33 | del_relationship => 'del_relationship', |
359944f7 |
34 | equivalence => 'equivalence', |
35 | equivalence_graph => 'equivalence_graph', |
22222af9 |
36 | }, |
37 | writer => '_set_relations', |
3a2ebbf4 |
38 | ); |
dd3b58b0 |
39 | |
3a2ebbf4 |
40 | has 'tradition' => ( |
41 | is => 'ro', |
d047cd52 |
42 | isa => 'Text::Tradition', |
8cfd99c4 |
43 | writer => '_set_tradition', |
8d9a1cd8 |
44 | weak_ref => 1, |
d047cd52 |
45 | ); |
dd3b58b0 |
46 | |
3a2ebbf4 |
47 | has 'readings' => ( |
48 | isa => 'HashRef[Text::Tradition::Collation::Reading]', |
49 | traits => ['Hash'], |
50 | handles => { |
51 | reading => 'get', |
52 | _add_reading => 'set', |
53 | del_reading => 'delete', |
54 | has_reading => 'exists', |
55 | readings => 'values', |
56 | }, |
57 | default => sub { {} }, |
58 | ); |
910a0a6d |
59 | |
4a8828f0 |
60 | has 'wit_list_separator' => ( |
7854e12e |
61 | is => 'rw', |
62 | isa => 'Str', |
63 | default => ', ', |
64 | ); |
65 | |
66 | has 'baselabel' => ( |
67 | is => 'rw', |
68 | isa => 'Str', |
69 | default => 'base text', |
70 | ); |
4a8828f0 |
71 | |
15d2d3df |
72 | has 'linear' => ( |
73 | is => 'rw', |
74 | isa => 'Bool', |
75 | default => 1, |
76 | ); |
c84275ff |
77 | |
ef9d481f |
78 | has 'ac_label' => ( |
79 | is => 'rw', |
80 | isa => 'Str', |
81 | default => ' (a.c.)', |
82 | ); |
3a2ebbf4 |
83 | |
4e483aa5 |
84 | has 'wordsep' => ( |
85 | is => 'rw', |
86 | isa => 'Str', |
87 | default => ' ', |
88 | ); |
89 | |
3a2ebbf4 |
90 | has 'start' => ( |
91 | is => 'ro', |
92 | isa => 'Text::Tradition::Collation::Reading', |
93 | writer => '_set_start', |
94 | weak_ref => 1, |
95 | ); |
96 | |
97 | has 'end' => ( |
98 | is => 'ro', |
99 | isa => 'Text::Tradition::Collation::Reading', |
100 | writer => '_set_end', |
101 | weak_ref => 1, |
102 | ); |
b365fbae |
103 | |
104 | has 'cached_svg' => ( |
105 | is => 'rw', |
106 | isa => 'Str', |
107 | predicate => 'has_cached_svg', |
108 | clearer => 'wipe_svg', |
109 | ); |
1dd07bda |
110 | |
111 | has 'cached_table' => ( |
112 | is => 'rw', |
113 | isa => 'HashRef', |
114 | predicate => 'has_cached_table', |
115 | clearer => 'wipe_table', |
116 | ); |
c1915ab9 |
117 | |
118 | has '_graphcalc_done' => ( |
119 | is => 'rw', |
120 | isa => 'Bool', |
121 | default => undef, |
122 | ); |
1f563ac3 |
123 | |
4e5a7b2c |
124 | =head1 NAME |
125 | |
126 | Text::Tradition::Collation - a software model for a text collation |
127 | |
128 | =head1 SYNOPSIS |
129 | |
130 | use Text::Tradition; |
131 | my $t = Text::Tradition->new( |
132 | 'name' => 'this is a text', |
133 | 'input' => 'TEI', |
134 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
135 | |
136 | my $c = $t->collation; |
137 | my @readings = $c->readings; |
138 | my @paths = $c->paths; |
139 | my @relationships = $c->relationships; |
140 | |
141 | my $svg_variant_graph = $t->collation->as_svg(); |
142 | |
143 | =head1 DESCRIPTION |
144 | |
145 | Text::Tradition is a library for representation and analysis of collated |
146 | texts, particularly medieval ones. The Collation is the central feature of |
147 | a Tradition, where the text, its sequence of readings, and its relationships |
148 | between readings are actually kept. |
149 | |
150 | =head1 CONSTRUCTOR |
151 | |
152 | =head2 new |
153 | |
154 | The constructor. Takes a hash or hashref of the following arguments: |
155 | |
156 | =over |
157 | |
158 | =item * tradition - The Text::Tradition object to which the collation |
159 | belongs. Required. |
160 | |
161 | =item * linear - Whether the collation should be linear; that is, whether |
162 | transposed readings should be treated as two linked readings rather than one, |
163 | and therefore whether the collation graph is acyclic. Defaults to true. |
164 | |
4e5a7b2c |
165 | =item * baselabel - The default label for the path taken by a base text |
166 | (if any). Defaults to 'base text'. |
167 | |
168 | =item * wit_list_separator - The string to join a list of witnesses for |
169 | purposes of making labels in display graphs. Defaults to ', '. |
170 | |
171 | =item * ac_label - The extra label to tack onto a witness sigil when |
172 | representing another layer of path for the given witness - that is, when |
173 | a text has more than one possible reading due to scribal corrections or |
174 | the like. Defaults to ' (a.c.)'. |
175 | |
4e483aa5 |
176 | =item * wordsep - The string used to separate words in the original text. |
177 | Defaults to ' '. |
178 | |
4e5a7b2c |
179 | =back |
180 | |
181 | =head1 ACCESSORS |
182 | |
183 | =head2 tradition |
184 | |
185 | =head2 linear |
186 | |
4e5a7b2c |
187 | =head2 wit_list_separator |
188 | |
189 | =head2 baselabel |
190 | |
191 | =head2 ac_label |
192 | |
4e483aa5 |
193 | =head2 wordsep |
194 | |
4e5a7b2c |
195 | Simple accessors for collation attributes. |
196 | |
197 | =head2 start |
198 | |
199 | The meta-reading at the start of every witness path. |
200 | |
201 | =head2 end |
202 | |
203 | The meta-reading at the end of every witness path. |
204 | |
205 | =head2 readings |
206 | |
207 | Returns all Reading objects in the graph. |
208 | |
209 | =head2 reading( $id ) |
210 | |
211 | Returns the Reading object corresponding to the given ID. |
212 | |
213 | =head2 add_reading( $reading_args ) |
214 | |
215 | Adds a new reading object to the collation. |
216 | See L<Text::Tradition::Collation::Reading> for the available arguments. |
217 | |
218 | =head2 del_reading( $object_or_id ) |
219 | |
220 | Removes the given reading from the collation, implicitly removing its |
221 | paths and relationships. |
222 | |
4e483aa5 |
223 | =head2 merge_readings( $main, $second, $concatenate, $with_str ) |
224 | |
225 | Merges the $second reading into the $main one. If $concatenate is true, then |
226 | the merged node will carry the text of both readings, concatenated with either |
227 | $with_str (if specified) or a sensible default (the empty string if the |
228 | appropriate 'join_*' flag is set on either reading, or else $self->wordsep.) |
4e5a7b2c |
229 | |
4e483aa5 |
230 | The first two arguments may be either readings or reading IDs. |
4e5a7b2c |
231 | |
232 | =head2 has_reading( $id ) |
233 | |
234 | Predicate to see whether a given reading ID is in the graph. |
235 | |
236 | =head2 reading_witnesses( $object_or_id ) |
237 | |
238 | Returns a list of sigils whose witnesses contain the reading. |
239 | |
240 | =head2 paths |
241 | |
242 | Returns all reading paths within the document - that is, all edges in the |
243 | collation graph. Each path is an arrayref of [ $source, $target ] reading IDs. |
244 | |
245 | =head2 add_path( $source, $target, $sigil ) |
246 | |
247 | Links the given readings in the collation in sequence, under the given witness |
248 | sigil. The readings may be specified by object or ID. |
249 | |
250 | =head2 del_path( $source, $target, $sigil ) |
251 | |
252 | Links the given readings in the collation in sequence, under the given witness |
253 | sigil. The readings may be specified by object or ID. |
254 | |
255 | =head2 has_path( $source, $target ); |
256 | |
257 | Returns true if the two readings are linked in sequence in any witness. |
258 | The readings may be specified by object or ID. |
259 | |
260 | =head2 relationships |
261 | |
262 | Returns all Relationship objects in the collation. |
263 | |
264 | =head2 add_relationship( $reading, $other_reading, $options ) |
265 | |
266 | Adds a new relationship of the type given in $options between the two readings, |
267 | which may be specified by object or ID. Returns a value of ( $status, @vectors) |
268 | where $status is true on success, and @vectors is a list of relationship edges |
269 | that were ultimately added. |
270 | See L<Text::Tradition::Collation::Relationship> for the available options. |
271 | |
272 | =cut |
dd3b58b0 |
273 | |
d047cd52 |
274 | sub BUILD { |
3a2ebbf4 |
275 | my $self = shift; |
22222af9 |
276 | $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) ); |
3a2ebbf4 |
277 | $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) ); |
278 | $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) ); |
d047cd52 |
279 | } |
784877d9 |
280 | |
3a2ebbf4 |
281 | ### Reading construct/destruct functions |
282 | |
283 | sub add_reading { |
284 | my( $self, $reading ) = @_; |
285 | unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) { |
286 | my %args = %$reading; |
6ad2ce78 |
287 | if( $self->tradition->has_language && !exists $args{'language'} ) { |
288 | $args{'language'} = $self->tradition->language; |
289 | } |
3a2ebbf4 |
290 | $reading = Text::Tradition::Collation::Reading->new( |
291 | 'collation' => $self, |
292 | %args ); |
293 | } |
294 | # First check to see if a reading with this ID exists. |
295 | if( $self->reading( $reading->id ) ) { |
63778331 |
296 | throw( "Collation already has a reading with id " . $reading->id ); |
3a2ebbf4 |
297 | } |
c1915ab9 |
298 | $self->_graphcalc_done(0); |
3a2ebbf4 |
299 | $self->_add_reading( $reading->id => $reading ); |
300 | # Once the reading has been added, put it in both graphs. |
301 | $self->sequence->add_vertex( $reading->id ); |
22222af9 |
302 | $self->relations->add_reading( $reading->id ); |
3a2ebbf4 |
303 | return $reading; |
eca16057 |
304 | }; |
305 | |
3a2ebbf4 |
306 | around del_reading => sub { |
307 | my $orig = shift; |
308 | my $self = shift; |
309 | my $arg = shift; |
310 | |
311 | if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) { |
312 | $arg = $arg->id; |
313 | } |
3a2ebbf4 |
314 | # Remove the reading from the graphs. |
c1915ab9 |
315 | $self->_graphcalc_done(0); |
4e483aa5 |
316 | $self->_clear_cache; # Explicitly clear caches to GC the reading |
3a2ebbf4 |
317 | $self->sequence->delete_vertex( $arg ); |
22222af9 |
318 | $self->relations->delete_reading( $arg ); |
3a2ebbf4 |
319 | |
320 | # Carry on. |
321 | $self->$orig( $arg ); |
322 | }; |
7854e12e |
323 | |
4e483aa5 |
324 | =begin testing |
325 | |
326 | use Text::Tradition; |
327 | |
328 | my $cxfile = 't/data/Collatex-16.xml'; |
329 | my $t = Text::Tradition->new( |
330 | 'name' => 'inline', |
331 | 'input' => 'CollateX', |
332 | 'file' => $cxfile, |
333 | ); |
334 | my $c = $t->collation; |
335 | |
336 | my $rno = scalar $c->readings; |
337 | # Split n21 for testing purposes |
338 | my $new_r = $c->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } ); |
339 | my $old_r = $c->reading( 'n21' ); |
340 | $old_r->alter_text( 'to' ); |
341 | $c->del_path( 'n20', 'n21', 'A' ); |
342 | $c->add_path( 'n20', 'n21p0', 'A' ); |
343 | $c->add_path( 'n21p0', 'n21', 'A' ); |
344 | $c->flatten_ranks(); |
345 | ok( $c->reading( 'n21p0' ), "New reading exists" ); |
346 | is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" ); |
347 | |
679f17e1 |
348 | # Combine n3 and n4 ( with his ) |
4e483aa5 |
349 | $c->merge_readings( 'n3', 'n4', 1 ); |
350 | ok( !$c->reading('n4'), "Reading n4 is gone" ); |
351 | is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" ); |
352 | |
679f17e1 |
353 | # Collapse n9 and n10 ( rood / root ) |
354 | $c->merge_readings( 'n9', 'n10' ); |
355 | ok( !$c->reading('n10'), "Reading n10 is gone" ); |
356 | is( $c->reading('n9')->text, 'rood', "Reading n9 has an unchanged word" ); |
4e483aa5 |
357 | |
358 | # Combine n21 and n21p0 |
359 | my $remaining = $c->reading('n21'); |
360 | $remaining ||= $c->reading('n22'); # one of these should still exist |
361 | $c->merge_readings( 'n21p0', $remaining, 1 ); |
362 | ok( !$c->reading('n21'), "Reading $remaining is gone" ); |
363 | is( $c->reading('n21p0')->text, 'unto', "Reading n21p0 merged correctly" ); |
364 | |
365 | =end testing |
366 | |
367 | =cut |
7854e12e |
368 | |
3a2ebbf4 |
369 | sub merge_readings { |
370 | my $self = shift; |
371 | |
372 | # We only need the IDs for adding paths to the graph, not the reading |
373 | # objects themselves. |
4e483aa5 |
374 | my( $kept, $deleted, $combine, $combine_char ) = $self->_stringify_args( @_ ); |
c1915ab9 |
375 | $self->_graphcalc_done(0); |
3a2ebbf4 |
376 | |
377 | # The kept reading should inherit the paths and the relationships |
378 | # of the deleted reading. |
379 | foreach my $path ( $self->sequence->edges_at( $deleted ) ) { |
380 | my @vector = ( $kept ); |
381 | push( @vector, $path->[1] ) if $path->[0] eq $deleted; |
382 | unshift( @vector, $path->[0] ) if $path->[1] eq $deleted; |
49d4f2ac |
383 | next if $vector[0] eq $vector[1]; # Don't add a self loop |
3a2ebbf4 |
384 | my %wits = %{$self->sequence->get_edge_attributes( @$path )}; |
385 | $self->sequence->add_edge( @vector ); |
386 | my $fwits = $self->sequence->get_edge_attributes( @vector ); |
387 | @wits{keys %$fwits} = values %$fwits; |
388 | $self->sequence->set_edge_attributes( @vector, \%wits ); |
389 | } |
22222af9 |
390 | $self->relations->merge_readings( $kept, $deleted, $combine_char ); |
3a2ebbf4 |
391 | |
392 | # Do the deletion deed. |
4e483aa5 |
393 | if( $combine ) { |
49d4f2ac |
394 | my $kept_obj = $self->reading( $kept ); |
4e483aa5 |
395 | my $del_obj = $self->reading( $deleted ); |
396 | my $joinstr = $combine_char; |
397 | unless( defined $joinstr ) { |
398 | $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior; |
399 | $joinstr = $self->wordsep unless defined $joinstr; |
400 | } |
401 | $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) ); |
49d4f2ac |
402 | } |
3a2ebbf4 |
403 | $self->del_reading( $deleted ); |
404 | } |
7854e12e |
405 | |
3265b0ce |
406 | |
3a2ebbf4 |
407 | # Helper function for manipulating the graph. |
408 | sub _stringify_args { |
4e483aa5 |
409 | my( $self, $first, $second, @args ) = @_; |
3a2ebbf4 |
410 | $first = $first->id |
411 | if ref( $first ) eq 'Text::Tradition::Collation::Reading'; |
412 | $second = $second->id |
413 | if ref( $second ) eq 'Text::Tradition::Collation::Reading'; |
4e483aa5 |
414 | return( $first, $second, @args ); |
3a2ebbf4 |
415 | } |
df6d9812 |
416 | |
4e5a7b2c |
417 | # Helper function for manipulating the graph. |
418 | sub _objectify_args { |
419 | my( $self, $first, $second, $arg ) = @_; |
420 | $first = $self->reading( $first ) |
421 | unless ref( $first ) eq 'Text::Tradition::Collation::Reading'; |
422 | $second = $self->reading( $second ) |
423 | unless ref( $second ) eq 'Text::Tradition::Collation::Reading'; |
424 | return( $first, $second, $arg ); |
425 | } |
3a2ebbf4 |
426 | ### Path logic |
427 | |
428 | sub add_path { |
429 | my $self = shift; |
430 | |
431 | # We only need the IDs for adding paths to the graph, not the reading |
432 | # objects themselves. |
433 | my( $source, $target, $wit ) = $self->_stringify_args( @_ ); |
434 | |
c1915ab9 |
435 | $self->_graphcalc_done(0); |
3a2ebbf4 |
436 | # Connect the readings |
359944f7 |
437 | unless( $self->sequence->has_edge( $source, $target ) ) { |
438 | $self->sequence->add_edge( $source, $target ); |
439 | $self->relations->add_equivalence_edge( $source, $target ); |
440 | } |
3a2ebbf4 |
441 | # Note the witness in question |
442 | $self->sequence->set_edge_attribute( $source, $target, $wit, 1 ); |
359944f7 |
443 | } |
b15511bf |
444 | |
3a2ebbf4 |
445 | sub del_path { |
446 | my $self = shift; |
49d4f2ac |
447 | my @args; |
448 | if( ref( $_[0] ) eq 'ARRAY' ) { |
449 | my $e = shift @_; |
450 | @args = ( @$e, @_ ); |
451 | } else { |
452 | @args = @_; |
453 | } |
3a2ebbf4 |
454 | |
455 | # We only need the IDs for adding paths to the graph, not the reading |
456 | # objects themselves. |
49d4f2ac |
457 | my( $source, $target, $wit ) = $self->_stringify_args( @args ); |
3a2ebbf4 |
458 | |
c1915ab9 |
459 | $self->_graphcalc_done(0); |
3a2ebbf4 |
460 | if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) { |
49d4f2ac |
461 | $self->sequence->delete_edge_attribute( $source, $target, $wit ); |
3a2ebbf4 |
462 | } |
463 | unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) { |
464 | $self->sequence->delete_edge( $source, $target ); |
359944f7 |
465 | $self->relations->delete_equivalence_edge( $source, $target ); |
3a2ebbf4 |
466 | } |
784877d9 |
467 | } |
468 | |
3a2ebbf4 |
469 | |
15d2d3df |
470 | # Extra graph-alike utility |
471 | sub has_path { |
3a2ebbf4 |
472 | my $self = shift; |
473 | my( $source, $target, $wit ) = $self->_stringify_args( @_ ); |
474 | return undef unless $self->sequence->has_edge( $source, $target ); |
475 | return $self->sequence->has_edge_attribute( $source, $target, $wit ); |
b15511bf |
476 | } |
477 | |
4e5a7b2c |
478 | =head2 clear_witness( @sigil_list ) |
3a2ebbf4 |
479 | |
4e5a7b2c |
480 | Clear the given witnesses out of the collation entirely, removing references |
481 | to them in paths, and removing readings that belong only to them. Should only |
482 | be called via $tradition->del_witness. |
3a2ebbf4 |
483 | |
484 | =cut |
485 | |
4e5a7b2c |
486 | sub clear_witness { |
487 | my( $self, @sigils ) = @_; |
488 | |
c1915ab9 |
489 | $self->_graphcalc_done(0); |
4e5a7b2c |
490 | # Clear the witness(es) out of the paths |
491 | foreach my $e ( $self->paths ) { |
492 | foreach my $sig ( @sigils ) { |
493 | $self->del_path( $e, $sig ); |
494 | } |
495 | } |
496 | |
497 | # Clear out the newly unused readings |
498 | foreach my $r ( $self->readings ) { |
499 | unless( $self->reading_witnesses( $r ) ) { |
500 | $self->del_reading( $r ); |
501 | } |
502 | } |
503 | } |
3a2ebbf4 |
504 | |
505 | sub add_relationship { |
506 | my $self = shift; |
22222af9 |
507 | my( $source, $target, $opts ) = $self->_stringify_args( @_ ); |
414cc046 |
508 | my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts ); |
c1915ab9 |
509 | $self->_graphcalc_done(0); |
63778331 |
510 | return @vectors; |
22222af9 |
511 | } |
ef9d481f |
512 | |
ca6e6095 |
513 | around qw/ get_relationship del_relationship / => sub { |
514 | my $orig = shift; |
515 | my $self = shift; |
516 | my @args = @_; |
517 | if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) { |
518 | @args = @{$_[0]}; |
519 | } |
520 | my( $source, $target ) = $self->_stringify_args( @args ); |
521 | $self->$orig( $source, $target ); |
522 | }; |
523 | |
22222af9 |
524 | =head2 reading_witnesses( $reading ) |
910a0a6d |
525 | |
22222af9 |
526 | Return a list of sigils corresponding to the witnesses in which the reading appears. |
3265b0ce |
527 | |
22222af9 |
528 | =cut |
1d310495 |
529 | |
1d310495 |
530 | sub reading_witnesses { |
531 | my( $self, $reading ) = @_; |
532 | # We need only check either the incoming or the outgoing edges; I have |
96dc90ec |
533 | # arbitrarily chosen "incoming". Thus, special-case the start node. |
534 | if( $reading eq $self->start ) { |
535 | return map { $_->sigil } $self->tradition->witnesses; |
536 | } |
1d310495 |
537 | my %all_witnesses; |
538 | foreach my $e ( $self->sequence->edges_to( $reading ) ) { |
539 | my $wits = $self->sequence->get_edge_attributes( @$e ); |
540 | @all_witnesses{ keys %$wits } = 1; |
541 | } |
c12bb878 |
542 | my $acstr = $self->ac_label; |
543 | foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) { |
544 | delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit}; |
545 | } |
1d310495 |
546 | return keys %all_witnesses; |
910a0a6d |
547 | } |
548 | |
4e5a7b2c |
549 | =head1 OUTPUT METHODS |
8e1394aa |
550 | |
0ecb975c |
551 | =head2 as_svg( \%options ) |
8e1394aa |
552 | |
0068967c |
553 | Returns an SVG string that represents the graph, via as_dot and graphviz. |
bfcbcecb |
554 | See as_dot for a list of options. Must have GraphViz (dot) installed to run. |
8e1394aa |
555 | |
556 | =cut |
557 | |
558 | sub as_svg { |
0ecb975c |
559 | my( $self, $opts ) = @_; |
bfcbcecb |
560 | throw( "Need GraphViz installed to output SVG" ) |
561 | unless File::Which::which( 'dot' ); |
e247aad1 |
562 | my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'}; |
5f082716 |
563 | $self->calculate_ranks() unless( $self->_graphcalc_done || $opts->{'nocalc'} ); |
e247aad1 |
564 | if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) { |
b365fbae |
565 | my @cmd = qw/dot -Tsvg/; |
566 | my( $svg, $err ); |
567 | my $dotfile = File::Temp->new(); |
568 | ## USE FOR DEBUGGING |
569 | # $dotfile->unlink_on_destroy(0); |
570 | binmode $dotfile, ':utf8'; |
571 | print $dotfile $self->as_dot( $opts ); |
572 | push( @cmd, $dotfile->filename ); |
573 | run( \@cmd, ">", binary(), \$svg ); |
e247aad1 |
574 | $svg = decode_utf8( $svg ); |
575 | $self->cached_svg( $svg ) unless $want_subgraph; |
576 | return $svg; |
577 | } else { |
578 | return $self->cached_svg; |
b365fbae |
579 | } |
8e1394aa |
580 | } |
581 | |
b22576c6 |
582 | |
0ecb975c |
583 | =head2 as_dot( \%options ) |
b22576c6 |
584 | |
0ecb975c |
585 | Returns a string that is the collation graph expressed in dot |
586 | (i.e. GraphViz) format. Options include: |
b22576c6 |
587 | |
0ecb975c |
588 | =over 4 |
b22576c6 |
589 | |
0ecb975c |
590 | =item * from |
b22576c6 |
591 | |
0ecb975c |
592 | =item * to |
df6d9812 |
593 | |
0ecb975c |
594 | =item * color_common |
595 | |
596 | =back |
df6d9812 |
597 | |
598 | =cut |
599 | |
600 | sub as_dot { |
0ecb975c |
601 | my( $self, $opts ) = @_; |
602 | my $startrank = $opts->{'from'} if $opts; |
603 | my $endrank = $opts->{'to'} if $opts; |
604 | my $color_common = $opts->{'color_common'} if $opts; |
b365fbae |
605 | my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank |
606 | && $self->end->rank > 100; |
6648ee3d |
607 | $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs |
b365fbae |
608 | |
b22576c6 |
609 | # Check the arguments |
610 | if( $startrank ) { |
611 | return if $endrank && $startrank > $endrank; |
612 | return if $startrank > $self->end->rank; |
613 | } |
614 | if( defined $endrank ) { |
615 | return if $endrank < 0; |
f1b3b33a |
616 | $endrank = undef if $endrank == $self->end->rank; |
b22576c6 |
617 | } |
618 | |
67da8d6c |
619 | my $graph_name = $self->tradition->name; |
620 | $graph_name =~ s/[^\w\s]//g; |
621 | $graph_name = join( '_', split( /\s+/, $graph_name ) ); |
f13b5582 |
622 | |
623 | my %graph_attrs = ( |
624 | 'rankdir' => 'LR', |
625 | 'bgcolor' => 'none', |
626 | ); |
627 | my %node_attrs = ( |
b8990398 |
628 | 'fontsize' => 14, |
f13b5582 |
629 | 'fillcolor' => 'white', |
630 | 'style' => 'filled', |
631 | 'shape' => 'ellipse' |
632 | ); |
633 | my %edge_attrs = ( |
634 | 'arrowhead' => 'open', |
635 | 'color' => '#000000', |
636 | 'fontcolor' => '#000000', |
637 | ); |
638 | |
67da8d6c |
639 | my $dot = sprintf( "digraph %s {\n", $graph_name ); |
f13b5582 |
640 | $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n"; |
641 | $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n"; |
df6d9812 |
642 | |
b22576c6 |
643 | # Output substitute start/end readings if necessary |
644 | if( $startrank ) { |
10e4b1ac |
645 | $dot .= "\t\"#SUBSTART#\" [ label=\"...\",id=\"__SUBSTART__\" ];\n"; |
b22576c6 |
646 | } |
647 | if( $endrank ) { |
10e4b1ac |
648 | $dot .= "\t\"#SUBEND#\" [ label=\"...\",id=\"__SUBEND__\" ];\n"; |
b22576c6 |
649 | } |
b365fbae |
650 | if( $STRAIGHTENHACK ) { |
651 | ## HACK part 1 |
6648ee3d |
652 | my $startlabel = $startrank ? 'SUBSTART' : 'START'; |
653 | $dot .= "\tsubgraph { rank=same \"#$startlabel#\" \"#SILENT#\" }\n"; |
b365fbae |
654 | $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];" |
655 | } |
b22576c6 |
656 | my %used; # Keep track of the readings that actually appear in the graph |
30ddc24c |
657 | # Sort the readings by rank if we have ranks; this speeds layout. |
658 | my @all_readings = $self->end->has_rank |
659 | ? sort { $a->rank <=> $b->rank } $self->readings |
660 | : $self->readings; |
4633f9e4 |
661 | # TODO Refrain from outputting lacuna nodes - just grey out the edges. |
30ddc24c |
662 | foreach my $reading ( @all_readings ) { |
b22576c6 |
663 | # Only output readings within our rank range. |
664 | next if $startrank && $reading->rank < $startrank; |
665 | next if $endrank && $reading->rank > $endrank; |
666 | $used{$reading->id} = 1; |
910a0a6d |
667 | # Need not output nodes without separate labels |
3a2ebbf4 |
668 | next if $reading->id eq $reading->text; |
d4b75f44 |
669 | my $rattrs; |
30f0df34 |
670 | my $label = $reading->text; |
629e27b0 |
671 | $label .= '-' if $reading->join_next; |
672 | $label = "-$label" if $reading->join_prior; |
8f9cab7b |
673 | $label =~ s/\"/\\\"/g; |
d4b75f44 |
674 | $rattrs->{'label'} = $label; |
10e4b1ac |
675 | $rattrs->{'id'} = $reading->id; |
0ecb975c |
676 | $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common; |
d4b75f44 |
677 | $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) ); |
df6d9812 |
678 | } |
3a2ebbf4 |
679 | |
30ddc24c |
680 | # Add the real edges. Need to weight one edge per rank jump, in a |
681 | # continuous line. |
b365fbae |
682 | # my $weighted = $self->_add_edge_weights; |
b22576c6 |
683 | my @edges = $self->paths; |
3bdec618 |
684 | my( %substart, %subend ); |
b22576c6 |
685 | foreach my $edge ( @edges ) { |
686 | # Do we need to output this edge? |
508fd430 |
687 | if( $used{$edge->[0]} && $used{$edge->[1]} ) { |
027d819c |
688 | my $label = $self->_path_display_label( $self->path_witnesses( $edge ) ); |
f13b5582 |
689 | my $variables = { %edge_attrs, 'label' => $label }; |
30ddc24c |
690 | |
b22576c6 |
691 | # Account for the rank gap if necessary |
30ddc24c |
692 | my $rank0 = $self->reading( $edge->[0] )->rank |
693 | if $self->reading( $edge->[0] )->has_rank; |
694 | my $rank1 = $self->reading( $edge->[1] )->rank |
695 | if $self->reading( $edge->[1] )->has_rank; |
696 | if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) { |
697 | $variables->{'minlen'} = $rank1 - $rank0; |
698 | } |
699 | |
700 | # Add the calculated edge weights |
b365fbae |
701 | # if( exists $weighted->{$edge->[0]} |
e247aad1 |
702 | # && $weighted->{$edge->[0]} eq $edge->[1] ) { |
703 | # # $variables->{'color'} = 'red'; |
704 | # $variables->{'weight'} = 3.0; |
705 | # } |
30ddc24c |
706 | |
508fd430 |
707 | # EXPERIMENTAL: make edge width reflect no. of witnesses |
708 | my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2; |
709 | $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit |
710 | |
f13b5582 |
711 | my $varopts = _dot_attr_string( $variables ); |
712 | $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n", |
713 | $edge->[0], $edge->[1], $varopts ); |
3bdec618 |
714 | } elsif( $used{$edge->[0]} ) { |
715 | $subend{$edge->[0]} = 1; |
716 | } elsif( $used{$edge->[1]} ) { |
717 | $substart{$edge->[1]} = 1; |
b22576c6 |
718 | } |
df6d9812 |
719 | } |
3bdec618 |
720 | # Add substitute start and end edges if necessary |
721 | foreach my $node ( keys %substart ) { |
027d819c |
722 | my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) ); |
f13b5582 |
723 | my $variables = { %edge_attrs, 'label' => $witstr }; |
724 | my $varopts = _dot_attr_string( $variables ); |
725 | $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;"; |
3bdec618 |
726 | } |
727 | foreach my $node ( keys %subend ) { |
027d819c |
728 | my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) ); |
f13b5582 |
729 | my $variables = { %edge_attrs, 'label' => $witstr }; |
730 | my $varopts = _dot_attr_string( $variables ); |
731 | $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;"; |
3bdec618 |
732 | } |
b365fbae |
733 | # HACK part 2 |
734 | if( $STRAIGHTENHACK ) { |
6648ee3d |
735 | my $endlabel = $endrank ? 'SUBEND' : 'END'; |
736 | $dot .= "\t\"#$endlabel#\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n"; |
b365fbae |
737 | } |
30ddc24c |
738 | |
df6d9812 |
739 | $dot .= "}\n"; |
740 | return $dot; |
741 | } |
742 | |
f13b5582 |
743 | sub _dot_attr_string { |
744 | my( $hash ) = @_; |
745 | my @attrs; |
746 | foreach my $k ( sort keys %$hash ) { |
747 | my $v = $hash->{$k}; |
748 | push( @attrs, $k.'="'.$v.'"' ); |
749 | } |
750 | return( '[ ' . join( ', ', @attrs ) . ' ]' ); |
751 | } |
752 | |
30ddc24c |
753 | sub _add_edge_weights { |
754 | my $self = shift; |
755 | # Walk the graph from START to END, choosing the successor node with |
756 | # the largest number of witness paths each time. |
757 | my $weighted = {}; |
758 | my $curr = $self->start->id; |
008fc8a6 |
759 | my $ranked = $self->end->has_rank; |
30ddc24c |
760 | while( $curr ne $self->end->id ) { |
008fc8a6 |
761 | my $rank = $ranked ? $self->reading( $curr )->rank : 0; |
30ddc24c |
762 | my @succ = sort { $self->path_witnesses( $curr, $a ) |
763 | <=> $self->path_witnesses( $curr, $b ) } |
764 | $self->sequence->successors( $curr ); |
765 | my $next = pop @succ; |
008fc8a6 |
766 | my $nextrank = $ranked ? $self->reading( $next )->rank : 0; |
30ddc24c |
767 | # Try to avoid lacunae in the weighted path. |
008fc8a6 |
768 | while( @succ && |
769 | ( $self->reading( $next )->is_lacuna || |
770 | $nextrank - $rank > 1 ) ){ |
30ddc24c |
771 | $next = pop @succ; |
772 | } |
773 | $weighted->{$curr} = $next; |
774 | $curr = $next; |
775 | } |
776 | return $weighted; |
777 | } |
778 | |
027d819c |
779 | =head2 path_witnesses( $edge ) |
780 | |
781 | Returns the list of sigils whose witnesses are associated with the given edge. |
782 | The edge can be passed as either an array or an arrayref of ( $source, $target ). |
783 | |
784 | =cut |
785 | |
3a2ebbf4 |
786 | sub path_witnesses { |
787 | my( $self, @edge ) = @_; |
788 | # If edge is an arrayref, cope. |
789 | if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) { |
790 | my $e = shift @edge; |
791 | @edge = @$e; |
792 | } |
793 | my @wits = keys %{$self->sequence->get_edge_attributes( @edge )}; |
508fd430 |
794 | return @wits; |
3a2ebbf4 |
795 | } |
796 | |
7f9f05e8 |
797 | # Helper function. Make a display label for the given witnesses, showing a.c. |
798 | # witnesses only where the main witness is not also in the list. |
027d819c |
799 | sub _path_display_label { |
508fd430 |
800 | my $self = shift; |
7f9f05e8 |
801 | my %wits; |
802 | map { $wits{$_} = 1 } @_; |
803 | |
804 | # If an a.c. wit is listed, remove it if the main wit is also listed. |
805 | # Otherwise keep it for explicit listing. |
806 | my $aclabel = $self->ac_label; |
807 | my @disp_ac; |
808 | foreach my $w ( sort keys %wits ) { |
809 | if( $w =~ /^(.*)\Q$aclabel\E$/ ) { |
810 | if( exists $wits{$1} ) { |
811 | delete $wits{$w}; |
812 | } else { |
813 | push( @disp_ac, $w ); |
814 | } |
815 | } |
816 | } |
817 | |
818 | # See if we are in a majority situation. |
8f9cab7b |
819 | my $maj = scalar( $self->tradition->witnesses ) * 0.6; |
7f9f05e8 |
820 | if( scalar keys %wits > $maj ) { |
821 | unshift( @disp_ac, 'majority' ); |
822 | return join( ', ', @disp_ac ); |
8f9cab7b |
823 | } else { |
7f9f05e8 |
824 | return join( ', ', sort keys %wits ); |
8f9cab7b |
825 | } |
826 | } |
1dd07bda |
827 | |
bf6e338d |
828 | =head2 readings_at_rank( $rank ) |
1dd07bda |
829 | |
bf6e338d |
830 | Returns a list of readings at a given rank, taken from the alignment table. |
1dd07bda |
831 | |
832 | =cut |
833 | |
bf6e338d |
834 | sub readings_at_rank { |
1dd07bda |
835 | my( $self, $rank ) = @_; |
bf6e338d |
836 | my $table = $self->alignment_table; |
837 | # Table rank is real rank - 1. |
838 | my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}}; |
839 | my %readings; |
840 | foreach my $e ( @elements ) { |
841 | next unless ref( $e ) eq 'HASH'; |
842 | next unless exists $e->{'t'}; |
843 | $readings{$e->{'t'}->id} = $e->{'t'}; |
844 | } |
845 | return values %readings; |
1dd07bda |
846 | } |
8f9cab7b |
847 | |
4e5a7b2c |
848 | =head2 as_graphml |
8e1394aa |
849 | |
4e5a7b2c |
850 | Returns a GraphML representation of the collation. The GraphML will contain |
851 | two graphs. The first expresses the attributes of the readings and the witness |
852 | paths that link them; the second expresses the relationships that link the |
853 | readings. This is the native transfer format for a tradition. |
8e1394aa |
854 | |
56eefa04 |
855 | =begin testing |
856 | |
857 | use Text::Tradition; |
858 | |
859 | my $READINGS = 311; |
860 | my $PATHS = 361; |
861 | |
862 | my $datafile = 't/data/florilegium_tei_ps.xml'; |
863 | my $tradition = Text::Tradition->new( 'input' => 'TEI', |
864 | 'name' => 'test0', |
865 | 'file' => $datafile, |
866 | 'linear' => 1 ); |
867 | |
868 | ok( $tradition, "Got a tradition object" ); |
869 | is( scalar $tradition->witnesses, 13, "Found all witnesses" ); |
870 | ok( $tradition->collation, "Tradition has a collation" ); |
871 | |
872 | my $c = $tradition->collation; |
873 | is( scalar $c->readings, $READINGS, "Collation has all readings" ); |
874 | is( scalar $c->paths, $PATHS, "Collation has all paths" ); |
875 | is( scalar $c->relationships, 0, "Collation has all relationships" ); |
876 | |
877 | # Add a few relationships |
878 | $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } ); |
879 | $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } ); |
880 | $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } ); |
881 | |
882 | # Now write it to GraphML and parse it again. |
883 | |
884 | my $graphml = $c->as_graphml; |
885 | my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml ); |
886 | is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" ); |
887 | is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" ); |
888 | is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" ); |
889 | |
890 | =end testing |
891 | |
8e1394aa |
892 | =cut |
893 | |
894 | sub as_graphml { |
a30ca502 |
895 | my( $self, $options ) = @_; |
3d14b48e |
896 | $self->calculate_ranks unless $self->_graphcalc_done; |
897 | |
a30ca502 |
898 | my $start = $options->{'from'} |
899 | ? $self->reading( $options->{'from'} ) : $self->start; |
900 | my $end = $options->{'to'} |
901 | ? $self->reading( $options->{'to'} ) : $self->end; |
902 | if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) { |
903 | throw( 'Start node must be before end node' ); |
904 | } |
905 | # The readings need to be ranked for this to work. |
906 | $start = $self->start unless $start->has_rank; |
907 | $end = $self->end unless $end->has_rank; |
414cc046 |
908 | my $rankoffset = 0; |
909 | unless( $start eq $self->start ) { |
910 | $rankoffset = $start->rank - 1; |
911 | } |
a30ca502 |
912 | my %use_readings; |
913 | |
8e1394aa |
914 | # Some namespaces |
915 | my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns'; |
916 | my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance'; |
917 | my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' . |
910a0a6d |
918 | 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd'; |
8e1394aa |
919 | |
920 | # Create the document and root node |
921 | my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" ); |
922 | my $root = $graphml->createElementNS( $graphml_ns, 'graphml' ); |
923 | $graphml->setDocumentElement( $root ); |
924 | $root->setNamespace( $xsi_ns, 'xsi', 0 ); |
925 | $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema ); |
bbd064a9 |
926 | |
927 | # List of attribute types to save on our objects and their corresponding |
928 | # GraphML types |
929 | my %save_types = ( |
930 | 'Str' => 'string', |
931 | 'Int' => 'int', |
932 | 'Bool' => 'boolean', |
10e4b1ac |
933 | 'ReadingID' => 'string', |
bbd064a9 |
934 | 'RelationshipType' => 'string', |
935 | 'RelationshipScope' => 'string', |
936 | ); |
937 | |
938 | # List of attribute names *not* to save on our objects. |
939 | # We will also not save any attribute beginning with _. |
940 | my %skipsave; |
941 | map { $skipsave{$_} = 1 } qw/ cached_svg /; |
8e1394aa |
942 | |
bbd064a9 |
943 | # Add the data keys for the graph. Include an extra key 'version' for the |
944 | # GraphML output version. |
e309421a |
945 | my %graph_data_keys; |
946 | my $gdi = 0; |
bbd064a9 |
947 | my %graph_attributes = ( 'version' => 'string' ); |
948 | # Graph attributes include those of Tradition and those of Collation. |
949 | my %gattr_from; |
950 | my $tmeta = $self->tradition->meta; |
951 | my $cmeta = $self->meta; |
952 | map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes; |
953 | map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes; |
954 | foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) { |
955 | next if $attr->name =~ /^_/; |
956 | next if $skipsave{$attr->name}; |
957 | next unless $save_types{$attr->type_constraint->name}; |
958 | $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; |
959 | } |
960 | |
961 | foreach my $datum ( sort keys %graph_attributes ) { |
e309421a |
962 | $graph_data_keys{$datum} = 'dg'.$gdi++; |
963 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
964 | $key->setAttribute( 'attr.name', $datum ); |
bbd064a9 |
965 | $key->setAttribute( 'attr.type', $graph_attributes{$datum} ); |
e309421a |
966 | $key->setAttribute( 'for', 'graph' ); |
967 | $key->setAttribute( 'id', $graph_data_keys{$datum} ); |
968 | } |
f6066bac |
969 | |
bbd064a9 |
970 | # Add the data keys for reading nodes |
971 | my %reading_attributes; |
972 | my $rmeta = Text::Tradition::Collation::Reading->meta; |
973 | foreach my $attr( $rmeta->get_all_attributes ) { |
974 | next if $attr->name =~ /^_/; |
975 | next if $skipsave{$attr->name}; |
976 | next unless $save_types{$attr->type_constraint->name}; |
977 | $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; |
978 | } |
7cd9f181 |
979 | # Extra custom key for the reading morphology |
980 | $reading_attributes{'lexemes'} = 'string'; |
981 | |
ef9d481f |
982 | my %node_data_keys; |
983 | my $ndi = 0; |
bbd064a9 |
984 | foreach my $datum ( sort keys %reading_attributes ) { |
910a0a6d |
985 | $node_data_keys{$datum} = 'dn'.$ndi++; |
986 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
987 | $key->setAttribute( 'attr.name', $datum ); |
bbd064a9 |
988 | $key->setAttribute( 'attr.type', $reading_attributes{$datum} ); |
910a0a6d |
989 | $key->setAttribute( 'for', 'node' ); |
990 | $key->setAttribute( 'id', $node_data_keys{$datum} ); |
8e1394aa |
991 | } |
992 | |
bbd064a9 |
993 | # Add the data keys for edges, that is, paths and relationships. Path |
994 | # data does not come from a Moose class so is here manually. |
ef9d481f |
995 | my $edi = 0; |
996 | my %edge_data_keys; |
bbd064a9 |
997 | my %edge_attributes = ( |
3a2ebbf4 |
998 | witness => 'string', # ID/label for a path |
3a2ebbf4 |
999 | extra => 'boolean', # Path key |
3a2ebbf4 |
1000 | ); |
bbd064a9 |
1001 | my @path_attributes = keys %edge_attributes; # track our manual additions |
1002 | my $pmeta = Text::Tradition::Collation::Relationship->meta; |
1003 | foreach my $attr( $pmeta->get_all_attributes ) { |
1004 | next if $attr->name =~ /^_/; |
1005 | next if $skipsave{$attr->name}; |
1006 | next unless $save_types{$attr->type_constraint->name}; |
1007 | $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; |
1008 | } |
1009 | foreach my $datum ( sort keys %edge_attributes ) { |
3a2ebbf4 |
1010 | $edge_data_keys{$datum} = 'de'.$edi++; |
910a0a6d |
1011 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
3a2ebbf4 |
1012 | $key->setAttribute( 'attr.name', $datum ); |
bbd064a9 |
1013 | $key->setAttribute( 'attr.type', $edge_attributes{$datum} ); |
910a0a6d |
1014 | $key->setAttribute( 'for', 'edge' ); |
3a2ebbf4 |
1015 | $key->setAttribute( 'id', $edge_data_keys{$datum} ); |
8e1394aa |
1016 | } |
3a2ebbf4 |
1017 | |
cc31ebaa |
1018 | # Add the collation graph itself. First, sanitize the name to a valid XML ID. |
1019 | my $xmlidname = $self->tradition->name; |
1020 | $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g; |
1021 | if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) { |
1022 | $xmlidname = '_'.$xmlidname; |
1023 | } |
2c669bca |
1024 | my $sgraph = $root->addNewChild( $graphml_ns, 'graph' ); |
1025 | $sgraph->setAttribute( 'edgedefault', 'directed' ); |
cc31ebaa |
1026 | $sgraph->setAttribute( 'id', $xmlidname ); |
2c669bca |
1027 | $sgraph->setAttribute( 'parse.edgeids', 'canonical' ); |
cc31ebaa |
1028 | $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later |
2c669bca |
1029 | $sgraph->setAttribute( 'parse.nodeids', 'canonical' ); |
cc31ebaa |
1030 | $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later |
2c669bca |
1031 | $sgraph->setAttribute( 'parse.order', 'nodesfirst' ); |
22222af9 |
1032 | |
e309421a |
1033 | # Collation attribute data |
bbd064a9 |
1034 | foreach my $datum ( keys %graph_attributes ) { |
1035 | my $value; |
1036 | if( $datum eq 'version' ) { |
1037 | $value = '3.1'; |
1038 | } elsif( $gattr_from{$datum} eq 'Tradition' ) { |
1039 | $value = $self->tradition->$datum; |
1040 | } else { |
1041 | $value = $self->$datum; |
1042 | } |
2c669bca |
1043 | _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value ); |
e309421a |
1044 | } |
8e1394aa |
1045 | |
1046 | my $node_ctr = 0; |
1047 | my %node_hash; |
22222af9 |
1048 | # Add our readings to the graph |
3a2ebbf4 |
1049 | foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) { |
a30ca502 |
1050 | next if $n->has_rank && $n ne $self->start && $n ne $self->end && |
1051 | ( $n->rank < $start->rank || $n->rank > $end->rank ); |
1052 | $use_readings{$n->id} = 1; |
2c669bca |
1053 | # Add to the main graph |
1054 | my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' ); |
910a0a6d |
1055 | my $node_xmlid = 'n' . $node_ctr++; |
3a2ebbf4 |
1056 | $node_hash{ $n->id } = $node_xmlid; |
910a0a6d |
1057 | $node_el->setAttribute( 'id', $node_xmlid ); |
bbd064a9 |
1058 | foreach my $d ( keys %reading_attributes ) { |
255875b8 |
1059 | my $nval = $n->$d; |
7cd9f181 |
1060 | # Custom serialization |
1061 | if( $d eq 'lexemes' ) { |
1062 | # If nval is a true value, we have lexemes so we need to |
1063 | # serialize them. Otherwise set nval to undef so that the |
1064 | # key is excluded from this reading. |
1065 | $nval = $nval ? $n->_serialize_lexemes : undef; |
1066 | } |
cc31ebaa |
1067 | if( $rankoffset && $d eq 'rank' && $n ne $self->start ) { |
414cc046 |
1068 | # Adjust the ranks within the subgraph. |
cc31ebaa |
1069 | $nval = $n eq $self->end ? $end->rank - $rankoffset + 1 |
1070 | : $nval - $rankoffset; |
414cc046 |
1071 | } |
255875b8 |
1072 | _add_graphml_data( $node_el, $node_data_keys{$d}, $nval ) |
1073 | if defined $nval; |
1074 | } |
b15511bf |
1075 | } |
1076 | |
2c669bca |
1077 | # Add the path edges to the sequence graph |
df6d9812 |
1078 | my $edge_ctr = 0; |
3a2ebbf4 |
1079 | foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) { |
1080 | # We add an edge in the graphml for every witness in $e. |
a30ca502 |
1081 | next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} ); |
1082 | my @edge_wits = sort $self->path_witnesses( $e ); |
cc31ebaa |
1083 | $e->[0] = $self->start->id unless $use_readings{$e->[0]}; |
1084 | $e->[1] = $self->end->id unless $use_readings{$e->[1]}; |
1085 | # Skip any path from start to end; that witness is not in the subgraph. |
1086 | next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id ); |
a30ca502 |
1087 | foreach my $wit ( @edge_wits ) { |
3a2ebbf4 |
1088 | my( $id, $from, $to ) = ( 'e'.$edge_ctr++, |
1089 | $node_hash{ $e->[0] }, |
1090 | $node_hash{ $e->[1] } ); |
2c669bca |
1091 | my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' ); |
3a2ebbf4 |
1092 | $edge_el->setAttribute( 'source', $from ); |
1093 | $edge_el->setAttribute( 'target', $to ); |
1094 | $edge_el->setAttribute( 'id', $id ); |
3a2ebbf4 |
1095 | |
1096 | # It's a witness path, so add the witness |
1097 | my $base = $wit; |
1098 | my $key = $edge_data_keys{'witness'}; |
1099 | # Is this an ante-corr witness? |
1100 | my $aclabel = $self->ac_label; |
1101 | if( $wit =~ /^(.*)\Q$aclabel\E$/ ) { |
1102 | # Keep the base witness |
1103 | $base = $1; |
1104 | # ...and record that this is an 'extra' reading path |
1105 | _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel ); |
1106 | } |
1107 | _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base ); |
1108 | } |
1109 | } |
1110 | |
cc31ebaa |
1111 | # Report the actual number of nodes and edges that went in |
1112 | $sgraph->setAttribute( 'parse.edges', $edge_ctr ); |
1113 | $sgraph->setAttribute( 'parse.nodes', $node_ctr ); |
1114 | |
22222af9 |
1115 | # Add the relationship graph to the XML |
bbd064a9 |
1116 | map { delete $edge_data_keys{$_} } @path_attributes; |
826d8773 |
1117 | $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash, |
1118 | $node_data_keys{'id'}, \%edge_data_keys ); |
8e1394aa |
1119 | |
94c00c71 |
1120 | # Save and return the thing |
1121 | my $result = decode_utf8( $graphml->toString(1) ); |
94c00c71 |
1122 | return $result; |
df6d9812 |
1123 | } |
1124 | |
b15511bf |
1125 | sub _add_graphml_data { |
1126 | my( $el, $key, $value ) = @_; |
b15511bf |
1127 | return unless defined $value; |
c9bf3dbf |
1128 | my $data_el = $el->addNewChild( $el->namespaceURI, 'data' ); |
b15511bf |
1129 | $data_el->setAttribute( 'key', $key ); |
1130 | $data_el->appendText( $value ); |
8e1394aa |
1131 | } |
1132 | |
4e5a7b2c |
1133 | =head2 as_csv |
910a0a6d |
1134 | |
1135 | Returns a CSV alignment table representation of the collation graph, one |
2c669bca |
1136 | row per witness (or witness uncorrected.) |
910a0a6d |
1137 | |
1138 | =cut |
1139 | |
1140 | sub as_csv { |
3a2ebbf4 |
1141 | my( $self ) = @_; |
1dd07bda |
1142 | my $table = $self->alignment_table; |
82fa4d57 |
1143 | my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } ); |
910a0a6d |
1144 | my @result; |
2c669bca |
1145 | # Make the header row |
1146 | $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} ); |
1147 | push( @result, decode_utf8( $csv->string ) ); |
1148 | # Make the rest of the rows |
1149 | foreach my $idx ( 0 .. $table->{'length'} - 1 ) { |
566f4595 |
1150 | my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}}; |
1dd07bda |
1151 | my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs; |
2c669bca |
1152 | $csv->combine( @row ); |
910a0a6d |
1153 | push( @result, decode_utf8( $csv->string ) ); |
1154 | } |
3a2ebbf4 |
1155 | return join( "\n", @result ); |
910a0a6d |
1156 | } |
1157 | |
1dd07bda |
1158 | =head2 alignment_table( $use_refs, $include_witnesses ) |
2c669bca |
1159 | |
566f4595 |
1160 | Return a reference to an alignment table, in a slightly enhanced CollateX |
1161 | format which looks like this: |
1162 | |
1163 | $table = { alignment => [ { witness => "SIGIL", |
4e5a7b2c |
1164 | tokens => [ { t => "TEXT" }, ... ] }, |
566f4595 |
1165 | { witness => "SIG2", |
4e5a7b2c |
1166 | tokens => [ { t => "TEXT" }, ... ] }, |
566f4595 |
1167 | ... ], |
1168 | length => TEXTLEN }; |
1169 | |
1170 | If $use_refs is set to 1, the reading object is returned in the table |
1171 | instead of READINGTEXT; if not, the text of the reading is returned. |
4e5a7b2c |
1172 | |
1173 | If $include_witnesses is set to a hashref, only the witnesses whose sigil |
566f4595 |
1174 | keys have a true hash value will be included. |
2c669bca |
1175 | |
1176 | =cut |
9f3ba6f7 |
1177 | |
1dd07bda |
1178 | sub alignment_table { |
1179 | my( $self ) = @_; |
c1915ab9 |
1180 | $self->calculate_ranks() unless $self->_graphcalc_done; |
1dd07bda |
1181 | return $self->cached_table if $self->has_cached_table; |
1182 | |
0ecb975c |
1183 | # Make sure we can do this |
1184 | throw( "Need a linear graph in order to make an alignment table" ) |
1185 | unless $self->linear; |
1186 | $self->calculate_ranks unless $self->end->has_rank; |
1187 | |
2c669bca |
1188 | my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 }; |
3a2ebbf4 |
1189 | my @all_pos = ( 1 .. $self->end->rank - 1 ); |
68454b71 |
1190 | foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) { |
eca16057 |
1191 | # print STDERR "Making witness row(s) for " . $wit->sigil . "\n"; |
1f7aa795 |
1192 | my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil ); |
1dd07bda |
1193 | my @row = _make_witness_row( \@wit_path, \@all_pos ); |
2c669bca |
1194 | push( @{$table->{'alignment'}}, |
1195 | { 'witness' => $wit->sigil, 'tokens' => \@row } ); |
1f7aa795 |
1196 | if( $wit->is_layered ) { |
1197 | my @wit_ac_path = $self->reading_sequence( $self->start, $self->end, |
861c3e27 |
1198 | $wit->sigil.$self->ac_label ); |
1dd07bda |
1199 | my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos ); |
2c669bca |
1200 | push( @{$table->{'alignment'}}, |
1201 | { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } ); |
910a0a6d |
1202 | } |
1203 | } |
1dd07bda |
1204 | $self->cached_table( $table ); |
1205 | return $table; |
910a0a6d |
1206 | } |
1207 | |
1208 | sub _make_witness_row { |
1dd07bda |
1209 | my( $path, $positions ) = @_; |
910a0a6d |
1210 | my %char_hash; |
1211 | map { $char_hash{$_} = undef } @$positions; |
2c669bca |
1212 | my $debug = 0; |
910a0a6d |
1213 | foreach my $rdg ( @$path ) { |
eca16057 |
1214 | my $rtext = $rdg->text; |
1215 | $rtext = '#LACUNA#' if $rdg->is_lacuna; |
2c669bca |
1216 | print STDERR "rank " . $rdg->rank . "\n" if $debug; |
3a2ebbf4 |
1217 | # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank; |
1dd07bda |
1218 | $char_hash{$rdg->rank} = { 't' => $rdg }; |
910a0a6d |
1219 | } |
1220 | my @row = map { $char_hash{$_} } @$positions; |
eca16057 |
1221 | # Fill in lacuna markers for undef spots in the row |
1222 | my $last_el = shift @row; |
1223 | my @filled_row = ( $last_el ); |
1224 | foreach my $el ( @row ) { |
0e476982 |
1225 | # If we are using node reference, make the lacuna node appear many times |
1226 | # in the table. If not, use the lacuna tag. |
1dd07bda |
1227 | if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) { |
1228 | $el = $last_el; |
eca16057 |
1229 | } |
1230 | push( @filled_row, $el ); |
1231 | $last_el = $el; |
1232 | } |
1233 | return @filled_row; |
910a0a6d |
1234 | } |
1235 | |
4e5a7b2c |
1236 | =head1 NAVIGATION METHODS |
910a0a6d |
1237 | |
4e5a7b2c |
1238 | =head2 reading_sequence( $first, $last, $sigil, $backup ) |
e2902068 |
1239 | |
1240 | Returns the ordered list of readings, starting with $first and ending |
4e5a7b2c |
1241 | with $last, for the witness given in $sigil. If a $backup sigil is |
1242 | specified (e.g. when walking a layered witness), it will be used wherever |
1243 | no $sigil path exists. If there is a base text reading, that will be |
1244 | used wherever no path exists for $sigil or $backup. |
e2902068 |
1245 | |
1246 | =cut |
1247 | |
910a0a6d |
1248 | # TODO Think about returning some lazy-eval iterator. |
b0b4421a |
1249 | # TODO Get rid of backup; we should know from what witness is whether we need it. |
910a0a6d |
1250 | |
e2902068 |
1251 | sub reading_sequence { |
861c3e27 |
1252 | my( $self, $start, $end, $witness ) = @_; |
e2902068 |
1253 | |
930ff666 |
1254 | $witness = $self->baselabel unless $witness; |
e2902068 |
1255 | my @readings = ( $start ); |
1256 | my %seen; |
1257 | my $n = $start; |
3a2ebbf4 |
1258 | while( $n && $n->id ne $end->id ) { |
1259 | if( exists( $seen{$n->id} ) ) { |
63778331 |
1260 | throw( "Detected loop for $witness at " . $n->id ); |
910a0a6d |
1261 | } |
3a2ebbf4 |
1262 | $seen{$n->id} = 1; |
910a0a6d |
1263 | |
861c3e27 |
1264 | my $next = $self->next_reading( $n, $witness ); |
44771cf2 |
1265 | unless( $next ) { |
63778331 |
1266 | throw( "Did not find any path for $witness from reading " . $n->id ); |
44771cf2 |
1267 | } |
910a0a6d |
1268 | push( @readings, $next ); |
1269 | $n = $next; |
e2902068 |
1270 | } |
1271 | # Check that the last reading is our end reading. |
1272 | my $last = $readings[$#readings]; |
63778331 |
1273 | throw( "Last reading found from " . $start->text . |
1274 | " for witness $witness is not the end!" ) # TODO do we get this far? |
3a2ebbf4 |
1275 | unless $last->id eq $end->id; |
e2902068 |
1276 | |
1277 | return @readings; |
1278 | } |
1279 | |
4e5a7b2c |
1280 | =head2 next_reading( $reading, $sigil ); |
8e1394aa |
1281 | |
4a8828f0 |
1282 | Returns the reading that follows the given reading along the given witness |
930ff666 |
1283 | path. |
8e1394aa |
1284 | |
1285 | =cut |
1286 | |
4a8828f0 |
1287 | sub next_reading { |
e2902068 |
1288 | # Return the successor via the corresponding path. |
8e1394aa |
1289 | my $self = shift; |
3a2ebbf4 |
1290 | my $answer = $self->_find_linked_reading( 'next', @_ ); |
2c669bca |
1291 | return undef unless $answer; |
3a2ebbf4 |
1292 | return $self->reading( $answer ); |
8e1394aa |
1293 | } |
1294 | |
4e5a7b2c |
1295 | =head2 prior_reading( $reading, $sigil ) |
8e1394aa |
1296 | |
4a8828f0 |
1297 | Returns the reading that precedes the given reading along the given witness |
930ff666 |
1298 | path. |
8e1394aa |
1299 | |
1300 | =cut |
1301 | |
4a8828f0 |
1302 | sub prior_reading { |
e2902068 |
1303 | # Return the predecessor via the corresponding path. |
8e1394aa |
1304 | my $self = shift; |
3a2ebbf4 |
1305 | my $answer = $self->_find_linked_reading( 'prior', @_ ); |
1306 | return $self->reading( $answer ); |
8e1394aa |
1307 | } |
1308 | |
4a8828f0 |
1309 | sub _find_linked_reading { |
861c3e27 |
1310 | my( $self, $direction, $node, $path ) = @_; |
1311 | |
1312 | # Get a backup if we are dealing with a layered witness |
1313 | my $alt_path; |
1314 | my $aclabel = $self->ac_label; |
1315 | if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) { |
1316 | $alt_path = $1; |
1317 | } |
1318 | |
e2902068 |
1319 | my @linked_paths = $direction eq 'next' |
3a2ebbf4 |
1320 | ? $self->sequence->edges_from( $node ) |
1321 | : $self->sequence->edges_to( $node ); |
e2902068 |
1322 | return undef unless scalar( @linked_paths ); |
8e1394aa |
1323 | |
e2902068 |
1324 | # We have to find the linked path that contains all of the |
1325 | # witnesses supplied in $path. |
1326 | my( @path_wits, @alt_path_wits ); |
4e5a7b2c |
1327 | @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path; |
1328 | @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path; |
e2902068 |
1329 | my $base_le; |
1330 | my $alt_le; |
1331 | foreach my $le ( @linked_paths ) { |
3a2ebbf4 |
1332 | if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) { |
910a0a6d |
1333 | $base_le = $le; |
910a0a6d |
1334 | } |
508fd430 |
1335 | my @le_wits = sort $self->path_witnesses( $le ); |
3a2ebbf4 |
1336 | if( _is_within( \@path_wits, \@le_wits ) ) { |
1337 | # This is the right path. |
1338 | return $direction eq 'next' ? $le->[1] : $le->[0]; |
1339 | } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) { |
1340 | $alt_le = $le; |
1341 | } |
8e1394aa |
1342 | } |
e2902068 |
1343 | # Got this far? Return the alternate path if it exists. |
3a2ebbf4 |
1344 | return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0] |
910a0a6d |
1345 | if $alt_le; |
e2902068 |
1346 | |
1347 | # Got this far? Return the base path if it exists. |
3a2ebbf4 |
1348 | return $direction eq 'next' ? $base_le->[1] : $base_le->[0] |
910a0a6d |
1349 | if $base_le; |
e2902068 |
1350 | |
1351 | # Got this far? We have no appropriate path. |
2c669bca |
1352 | warn "Could not find $direction node from " . $node->id |
910a0a6d |
1353 | . " along path $path"; |
8e1394aa |
1354 | return undef; |
1355 | } |
1356 | |
4a8828f0 |
1357 | # Some set logic. |
1358 | sub _is_within { |
1359 | my( $set1, $set2 ) = @_; |
7854e12e |
1360 | my $ret = @$set1; # will be 0, i.e. false, if set1 is empty |
4a8828f0 |
1361 | foreach my $el ( @$set1 ) { |
910a0a6d |
1362 | $ret = 0 unless grep { /^\Q$el\E$/ } @$set2; |
4a8828f0 |
1363 | } |
1364 | return $ret; |
1365 | } |
1366 | |
4e5a7b2c |
1367 | # Return the string that joins together a list of witnesses for |
1368 | # display on a single path. |
1369 | sub _witnesses_of_label { |
1370 | my( $self, $label ) = @_; |
1371 | my $regex = $self->wit_list_separator; |
1372 | my @answer = split( /\Q$regex\E/, $label ); |
1373 | return @answer; |
b0b4421a |
1374 | } |
1375 | |
d4b75f44 |
1376 | =head2 common_readings |
1377 | |
1378 | Returns the list of common readings in the graph (i.e. those readings that are |
1379 | shared by all non-lacunose witnesses.) |
1380 | |
1381 | =cut |
1382 | |
1383 | sub common_readings { |
1384 | my $self = shift; |
1385 | my @common = grep { $_->is_common } $self->readings; |
1386 | return @common; |
1387 | } |
1388 | |
fae52efd |
1389 | =head2 path_text( $sigil, [, $start, $end ] ) |
b0b4421a |
1390 | |
1391 | Returns the text of a witness (plus its backup, if we are using a layer) |
1392 | as stored in the collation. The text is returned as a string, where the |
1393 | individual readings are joined with spaces and the meta-readings (e.g. |
1394 | lacunae) are omitted. Optional specification of $start and $end allows |
1395 | the generation of a subset of the witness text. |
4e5a7b2c |
1396 | |
b0b4421a |
1397 | =cut |
1398 | |
1399 | sub path_text { |
861c3e27 |
1400 | my( $self, $wit, $start, $end ) = @_; |
b0b4421a |
1401 | $start = $self->start unless $start; |
1402 | $end = $self->end unless $end; |
861c3e27 |
1403 | my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit ); |
629e27b0 |
1404 | my $pathtext = ''; |
1405 | my $last; |
1406 | foreach my $r ( @path ) { |
6ad2ce78 |
1407 | unless ( $r->join_prior || !$last || $last->join_next ) { |
1408 | $pathtext .= ' '; |
1409 | } |
1410 | $pathtext .= $r->text; |
629e27b0 |
1411 | $last = $r; |
1412 | } |
1413 | return $pathtext; |
b0b4421a |
1414 | } |
4e5a7b2c |
1415 | |
1416 | =head1 INITIALIZATION METHODS |
1417 | |
1418 | These are mostly for use by parsers. |
1419 | |
1420 | =head2 make_witness_path( $witness ) |
1421 | |
1422 | Link the array of readings contained in $witness->path (and in |
1423 | $witness->uncorrected_path if it exists) into collation paths. |
1424 | Clear out the arrays when finished. |
de51424a |
1425 | |
4e5a7b2c |
1426 | =head2 make_witness_paths |
1427 | |
1428 | Call make_witness_path for all witnesses in the tradition. |
1429 | |
1430 | =cut |
930ff666 |
1431 | |
7e450e44 |
1432 | # For use when a collation is constructed from a base text and an apparatus. |
1433 | # We have the sequences of readings and just need to add path edges. |
1f7aa795 |
1434 | # When we are done, clear out the witness path attributes, as they are no |
1435 | # longer needed. |
1436 | # TODO Find a way to replace the witness path attributes with encapsulated functions? |
e2902068 |
1437 | |
6a222840 |
1438 | sub make_witness_paths { |
1439 | my( $self ) = @_; |
910a0a6d |
1440 | foreach my $wit ( $self->tradition->witnesses ) { |
0068967c |
1441 | # print STDERR "Making path for " . $wit->sigil . "\n"; |
910a0a6d |
1442 | $self->make_witness_path( $wit ); |
7854e12e |
1443 | } |
7854e12e |
1444 | } |
1445 | |
6a222840 |
1446 | sub make_witness_path { |
7854e12e |
1447 | my( $self, $wit ) = @_; |
1448 | my @chain = @{$wit->path}; |
15d2d3df |
1449 | my $sig = $wit->sigil; |
fae52efd |
1450 | # Add start and end if necessary |
1451 | unshift( @chain, $self->start ) unless $chain[0] eq $self->start; |
1452 | push( @chain, $self->end ) unless $chain[-1] eq $self->end; |
7854e12e |
1453 | foreach my $idx ( 0 .. $#chain-1 ) { |
910a0a6d |
1454 | $self->add_path( $chain[$idx], $chain[$idx+1], $sig ); |
7854e12e |
1455 | } |
1f7aa795 |
1456 | if( $wit->is_layered ) { |
d9e873d0 |
1457 | @chain = @{$wit->uncorrected_path}; |
fae52efd |
1458 | unshift( @chain, $self->start ) unless $chain[0] eq $self->start; |
1459 | push( @chain, $self->end ) unless $chain[-1] eq $self->end; |
d9e873d0 |
1460 | foreach my $idx( 0 .. $#chain-1 ) { |
1461 | my $source = $chain[$idx]; |
1462 | my $target = $chain[$idx+1]; |
1463 | $self->add_path( $source, $target, $sig.$self->ac_label ) |
1464 | unless $self->has_path( $source, $target, $sig ); |
1465 | } |
15d2d3df |
1466 | } |
1f7aa795 |
1467 | $wit->clear_path; |
1468 | $wit->clear_uncorrected_path; |
e2902068 |
1469 | } |
1470 | |
4e5a7b2c |
1471 | =head2 calculate_ranks |
1472 | |
1473 | Calculate the reading ranks (that is, their aligned positions relative |
1474 | to each other) for the graph. This can only be called on linear collations. |
1475 | |
b365fbae |
1476 | =begin testing |
1477 | |
1478 | use Text::Tradition; |
1479 | |
1480 | my $cxfile = 't/data/Collatex-16.xml'; |
1481 | my $t = Text::Tradition->new( |
1482 | 'name' => 'inline', |
1483 | 'input' => 'CollateX', |
1484 | 'file' => $cxfile, |
1485 | ); |
1486 | my $c = $t->collation; |
1487 | |
1488 | # Make an svg |
bfcbcecb |
1489 | my $table = $c->alignment_table; |
1490 | ok( $c->has_cached_table, "Alignment table was cached" ); |
1491 | is( $c->alignment_table, $table, "Cached table returned upon second call" ); |
b365fbae |
1492 | $c->calculate_ranks; |
bfcbcecb |
1493 | is( $c->alignment_table, $table, "Cached table retained with no rank change" ); |
679f17e1 |
1494 | $c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } ); |
bfcbcecb |
1495 | isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" ); |
b365fbae |
1496 | |
1497 | =end testing |
1498 | |
4e5a7b2c |
1499 | =cut |
1500 | |
910a0a6d |
1501 | sub calculate_ranks { |
1502 | my $self = shift; |
b365fbae |
1503 | # Save the existing ranks, in case we need to invalidate the cached SVG. |
1504 | my %existing_ranks; |
ac4d7ac2 |
1505 | map { $existing_ranks{$_} = $_->rank } $self->readings; |
359944f7 |
1506 | |
1507 | # Do the rankings based on the relationship equivalence graph, starting |
1508 | # with the start node. |
1509 | my $topo_start = $self->equivalence( $self->start->id ); |
c9bf3dbf |
1510 | my $node_ranks = { $topo_start => 0 }; |
910a0a6d |
1511 | my @curr_origin = ( $topo_start ); |
1512 | # A little iterative function. |
1513 | while( @curr_origin ) { |
359944f7 |
1514 | @curr_origin = _assign_rank( $self->equivalence_graph, |
1515 | $node_ranks, @curr_origin ); |
910a0a6d |
1516 | } |
1517 | # Transfer our rankings from the topological graph to the real one. |
1518 | foreach my $r ( $self->readings ) { |
359944f7 |
1519 | if( defined $node_ranks->{$self->equivalence( $r->id )} ) { |
1520 | $r->rank( $node_ranks->{$self->equivalence( $r->id )} ); |
67da8d6c |
1521 | } else { |
63778331 |
1522 | # Die. Find the last rank we calculated. |
359944f7 |
1523 | my @all_defined = sort { ( $node_ranks->{$self->equivalence( $a->id )}||-1 ) |
1524 | <=> ( $node_ranks->{$self->equivalence( $b->id )}||-1 ) } |
63778331 |
1525 | $self->readings; |
1526 | my $last = pop @all_defined; |
1527 | throw( "Ranks not calculated after $last - do you have a cycle in the graph?" ); |
67da8d6c |
1528 | } |
de51424a |
1529 | } |
bfcbcecb |
1530 | # Do we need to invalidate the cached data? |
1531 | if( $self->has_cached_svg || $self->has_cached_table ) { |
b365fbae |
1532 | foreach my $r ( $self->readings ) { |
7c293912 |
1533 | next if defined( $existing_ranks{$r} ) |
1534 | && $existing_ranks{$r} == $r->rank; |
c1915ab9 |
1535 | # Something has changed, so clear the cache |
bfcbcecb |
1536 | $self->_clear_cache; |
c1915ab9 |
1537 | # ...and recalculate the common readings. |
1538 | $self->calculate_common_readings(); |
b365fbae |
1539 | last; |
1540 | } |
1541 | } |
c1915ab9 |
1542 | # The graph calculation information is now up to date. |
1543 | $self->_graphcalc_done(1); |
8e1394aa |
1544 | } |
3a1f2523 |
1545 | |
910a0a6d |
1546 | sub _assign_rank { |
c9bf3dbf |
1547 | my( $graph, $node_ranks, @current_nodes ) = @_; |
910a0a6d |
1548 | # Look at each of the children of @current_nodes. If all the child's |
1549 | # parents have a rank, assign it the highest rank + 1 and add it to |
c9bf3dbf |
1550 | # @next_nodes. Otherwise skip it; we will return when the highest-ranked |
1551 | # parent gets a rank. |
910a0a6d |
1552 | my @next_nodes; |
1553 | foreach my $c ( @current_nodes ) { |
c9bf3dbf |
1554 | warn "Current reading $c has no rank!" |
1555 | unless exists $node_ranks->{$c}; |
1556 | # print STDERR "Looking at child of node $c, rank " |
1557 | # . $node_ranks->{$c} . "\n"; |
1558 | foreach my $child ( $graph->successors( $c ) ) { |
1559 | next if exists $node_ranks->{$child}; |
910a0a6d |
1560 | my $highest_rank = -1; |
1561 | my $skip = 0; |
c9bf3dbf |
1562 | foreach my $parent ( $graph->predecessors( $child ) ) { |
1563 | if( exists $node_ranks->{$parent} ) { |
1564 | $highest_rank = $node_ranks->{$parent} |
1565 | if $highest_rank <= $node_ranks->{$parent}; |
910a0a6d |
1566 | } else { |
1567 | $skip = 1; |
1568 | last; |
1569 | } |
1570 | } |
1571 | next if $skip; |
c9bf3dbf |
1572 | my $c_rank = $highest_rank + 1; |
1573 | # print STDERR "Assigning rank $c_rank to node $child \n"; |
1574 | $node_ranks->{$child} = $c_rank; |
910a0a6d |
1575 | push( @next_nodes, $child ); |
1576 | } |
1577 | } |
1578 | return @next_nodes; |
4cdd82f1 |
1579 | } |
910a0a6d |
1580 | |
c1915ab9 |
1581 | sub _clear_cache { |
1582 | my $self = shift; |
1583 | $self->wipe_svg if $self->has_cached_svg; |
1584 | $self->wipe_table if $self->has_cached_table; |
1585 | } |
1586 | |
1587 | |
4e5a7b2c |
1588 | =head2 flatten_ranks |
1589 | |
1590 | A convenience method for parsing collation data. Searches the graph for readings |
1591 | with the same text at the same rank, and merges any that are found. |
1592 | |
1593 | =cut |
1594 | |
0e476982 |
1595 | sub flatten_ranks { |
1596 | my $self = shift; |
1597 | my %unique_rank_rdg; |
bf6e338d |
1598 | my $changed; |
0e476982 |
1599 | foreach my $rdg ( $self->readings ) { |
1600 | next unless $rdg->has_rank; |
1601 | my $key = $rdg->rank . "||" . $rdg->text; |
1602 | if( exists $unique_rank_rdg{$key} ) { |
1603 | # Combine! |
56eefa04 |
1604 | # print STDERR "Combining readings at same rank: $key\n"; |
bf6e338d |
1605 | $changed = 1; |
0e476982 |
1606 | $self->merge_readings( $unique_rank_rdg{$key}, $rdg ); |
0ecb975c |
1607 | # TODO see if this now makes a common point. |
0e476982 |
1608 | } else { |
1609 | $unique_rank_rdg{$key} = $rdg; |
1610 | } |
1611 | } |
bf6e338d |
1612 | # If we merged readings, the ranks are still fine but the alignment |
1613 | # table is wrong. Wipe it. |
1614 | $self->wipe_table() if $changed; |
0e476982 |
1615 | } |
4633f9e4 |
1616 | |
1617 | |
d4b75f44 |
1618 | =head2 calculate_common_readings |
1619 | |
1620 | Goes through the graph identifying the readings that appear in every witness |
1621 | (apart from those with lacunae at that spot.) Marks them as common and returns |
1622 | the list. |
1623 | |
1624 | =begin testing |
1625 | |
1626 | use Text::Tradition; |
1627 | |
1628 | my $cxfile = 't/data/Collatex-16.xml'; |
1629 | my $t = Text::Tradition->new( |
1630 | 'name' => 'inline', |
1631 | 'input' => 'CollateX', |
1632 | 'file' => $cxfile, |
1633 | ); |
1634 | my $c = $t->collation; |
1635 | |
1636 | my @common = $c->calculate_common_readings(); |
1637 | is( scalar @common, 8, "Found correct number of common readings" ); |
1638 | my @marked = sort $c->common_readings(); |
1639 | is( scalar @common, 8, "All common readings got marked as such" ); |
679f17e1 |
1640 | my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /; |
d4b75f44 |
1641 | is_deeply( \@marked, \@expected, "Found correct list of common readings" ); |
1642 | |
1643 | =end testing |
1644 | |
1645 | =cut |
1646 | |
1647 | sub calculate_common_readings { |
1648 | my $self = shift; |
1649 | my @common; |
c1915ab9 |
1650 | map { $_->is_common( 0 ) } $self->readings; |
1651 | # Implicitly calls calculate_ranks |
1dd07bda |
1652 | my $table = $self->alignment_table; |
d4b75f44 |
1653 | foreach my $idx ( 0 .. $table->{'length'} - 1 ) { |
7f52eac8 |
1654 | my @row = map { $_->{'tokens'}->[$idx] |
1655 | ? $_->{'tokens'}->[$idx]->{'t'} : '' } |
1656 | @{$table->{'alignment'}}; |
d4b75f44 |
1657 | my %hash; |
1658 | foreach my $r ( @row ) { |
1659 | if( $r ) { |
1660 | $hash{$r->id} = $r unless $r->is_meta; |
1661 | } else { |
1662 | $hash{'UNDEF'} = $r; |
1663 | } |
1664 | } |
1665 | if( keys %hash == 1 && !exists $hash{'UNDEF'} ) { |
1666 | my( $r ) = values %hash; |
1667 | $r->is_common( 1 ); |
1668 | push( @common, $r ); |
1669 | } |
1670 | } |
1671 | return @common; |
1672 | } |
1673 | |
861c3e27 |
1674 | =head2 text_from_paths |
1675 | |
1676 | Calculate the text array for all witnesses from the path, for later consistency |
1677 | checking. Only to be used if there is no non-graph-based way to know the |
1678 | original texts. |
1679 | |
1680 | =cut |
1681 | |
1682 | sub text_from_paths { |
1683 | my $self = shift; |
1684 | foreach my $wit ( $self->tradition->witnesses ) { |
5164a6f0 |
1685 | my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil ); |
1686 | my @text; |
1687 | foreach my $r ( @readings ) { |
1688 | next if $r->is_meta; |
1689 | push( @text, $r->text ); |
1690 | } |
861c3e27 |
1691 | $wit->text( \@text ); |
1692 | if( $wit->is_layered ) { |
5164a6f0 |
1693 | my @ucrdgs = $self->reading_sequence( $self->start, $self->end, |
1694 | $wit->sigil.$self->ac_label ); |
1695 | my @uctext; |
1696 | foreach my $r ( @ucrdgs ) { |
1697 | next if $r->is_meta; |
1698 | push( @uctext, $r->text ); |
1699 | } |
1700 | $wit->layertext( \@uctext ); |
861c3e27 |
1701 | } |
1702 | } |
1703 | } |
0e476982 |
1704 | |
4e5a7b2c |
1705 | =head1 UTILITY FUNCTIONS |
1706 | |
1707 | =head2 common_predecessor( $reading_a, $reading_b ) |
8e1394aa |
1708 | |
4e5a7b2c |
1709 | Find the last reading that occurs in sequence before both the given readings. |
414cc046 |
1710 | At the very least this should be $self->start. |
4e5a7b2c |
1711 | |
1712 | =head2 common_successor( $reading_a, $reading_b ) |
1713 | |
1714 | Find the first reading that occurs in sequence after both the given readings. |
414cc046 |
1715 | At the very least this should be $self->end. |
4e5a7b2c |
1716 | |
22222af9 |
1717 | =begin testing |
1718 | |
1719 | use Text::Tradition; |
1720 | |
1721 | my $cxfile = 't/data/Collatex-16.xml'; |
1722 | my $t = Text::Tradition->new( |
1723 | 'name' => 'inline', |
1724 | 'input' => 'CollateX', |
1725 | 'file' => $cxfile, |
1726 | ); |
1727 | my $c = $t->collation; |
1728 | |
679f17e1 |
1729 | is( $c->common_predecessor( 'n24', 'n23' )->id, |
22222af9 |
1730 | 'n20', "Found correct common predecessor" ); |
679f17e1 |
1731 | is( $c->common_successor( 'n24', 'n23' )->id, |
10e4b1ac |
1732 | '__END__', "Found correct common successor" ); |
22222af9 |
1733 | |
4e5a7b2c |
1734 | is( $c->common_predecessor( 'n19', 'n17' )->id, |
22222af9 |
1735 | 'n16', "Found correct common predecessor for readings on same path" ); |
679f17e1 |
1736 | is( $c->common_successor( 'n21', 'n10' )->id, |
10e4b1ac |
1737 | '__END__', "Found correct common successor for readings on same path" ); |
22222af9 |
1738 | |
1739 | =end testing |
1740 | |
1741 | =cut |
1742 | |
1743 | ## Return the closest reading that is a predecessor of both the given readings. |
1744 | sub common_predecessor { |
1745 | my $self = shift; |
4e5a7b2c |
1746 | my( $r1, $r2 ) = $self->_objectify_args( @_ ); |
027d819c |
1747 | return $self->_common_in_path( $r1, $r2, 'predecessors' ); |
22222af9 |
1748 | } |
1749 | |
1750 | sub common_successor { |
1751 | my $self = shift; |
4e5a7b2c |
1752 | my( $r1, $r2 ) = $self->_objectify_args( @_ ); |
027d819c |
1753 | return $self->_common_in_path( $r1, $r2, 'successors' ); |
22222af9 |
1754 | } |
1755 | |
414cc046 |
1756 | |
1757 | # TODO think about how to do this without ranks... |
027d819c |
1758 | sub _common_in_path { |
22222af9 |
1759 | my( $self, $r1, $r2, $dir ) = @_; |
414cc046 |
1760 | my $iter = $self->end->rank; |
22222af9 |
1761 | my @candidates; |
414cc046 |
1762 | my @last_r1 = ( $r1 ); |
1763 | my @last_r2 = ( $r2 ); |
1764 | # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' ); |
22222af9 |
1765 | my %all_seen; |
414cc046 |
1766 | # print STDERR "Finding common $dir for $r1, $r2\n"; |
22222af9 |
1767 | while( !@candidates ) { |
414cc046 |
1768 | last unless $iter--; # Avoid looping infinitely |
1769 | # Iterate separately down the graph from r1 and r2 |
1770 | my( @new_lc1, @new_lc2 ); |
1771 | foreach my $lc ( @last_r1 ) { |
1772 | foreach my $p ( $lc->$dir ) { |
1773 | if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) { |
1774 | # print STDERR "Path candidate $p from $lc\n"; |
1775 | push( @candidates, $p ); |
002e3600 |
1776 | } elsif( !$all_seen{$p->id} ) { |
414cc046 |
1777 | $all_seen{$p->id} = 'r1'; |
1778 | push( @new_lc1, $p ); |
1779 | } |
1780 | } |
1781 | } |
1782 | foreach my $lc ( @last_r2 ) { |
22222af9 |
1783 | foreach my $p ( $lc->$dir ) { |
414cc046 |
1784 | if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) { |
1785 | # print STDERR "Path candidate $p from $lc\n"; |
22222af9 |
1786 | push( @candidates, $p ); |
002e3600 |
1787 | } elsif( !$all_seen{$p->id} ) { |
414cc046 |
1788 | $all_seen{$p->id} = 'r2'; |
1789 | push( @new_lc2, $p ); |
22222af9 |
1790 | } |
1791 | } |
1792 | } |
414cc046 |
1793 | @last_r1 = @new_lc1; |
1794 | @last_r2 = @new_lc2; |
22222af9 |
1795 | } |
1796 | my @answer = sort { $a->rank <=> $b->rank } @candidates; |
1797 | return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer ); |
1798 | } |
1799 | |
63778331 |
1800 | sub throw { |
1801 | Text::Tradition::Error->throw( |
1802 | 'ident' => 'Collation error', |
1803 | 'message' => $_[0], |
1804 | ); |
1805 | } |
1806 | |
dd3b58b0 |
1807 | no Moose; |
1808 | __PACKAGE__->meta->make_immutable; |
e867486f |
1809 | |
027d819c |
1810 | =head1 LICENSE |
e867486f |
1811 | |
027d819c |
1812 | This package is free software and is provided "as is" without express |
1813 | or implied warranty. You can redistribute it and/or modify it under |
1814 | the same terms as Perl itself. |
e867486f |
1815 | |
027d819c |
1816 | =head1 AUTHOR |
e867486f |
1817 | |
027d819c |
1818 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |