Commit | Line | Data |
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1 | package Text::Tradition::Collation; |
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2 | |
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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 | |
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17 | has 'sequence' => ( |
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18 | is => 'ro', |
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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 | }, |
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24 | ); |
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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', |
22222af9 |
34 | }, |
35 | writer => '_set_relations', |
3a2ebbf4 |
36 | ); |
dd3b58b0 |
37 | |
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38 | has 'tradition' => ( |
39 | is => 'ro', |
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40 | isa => 'Text::Tradition', |
8cfd99c4 |
41 | writer => '_set_tradition', |
8d9a1cd8 |
42 | weak_ref => 1, |
d047cd52 |
43 | ); |
dd3b58b0 |
44 | |
3a2ebbf4 |
45 | has 'readings' => ( |
46 | isa => 'HashRef[Text::Tradition::Collation::Reading]', |
47 | traits => ['Hash'], |
48 | handles => { |
49 | reading => 'get', |
50 | _add_reading => 'set', |
51 | del_reading => 'delete', |
52 | has_reading => 'exists', |
53 | readings => 'values', |
54 | }, |
55 | default => sub { {} }, |
56 | ); |
910a0a6d |
57 | |
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58 | has 'wit_list_separator' => ( |
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59 | is => 'rw', |
60 | isa => 'Str', |
61 | default => ', ', |
62 | ); |
63 | |
64 | has 'baselabel' => ( |
65 | is => 'rw', |
66 | isa => 'Str', |
67 | default => 'base text', |
68 | ); |
4a8828f0 |
69 | |
15d2d3df |
70 | has 'linear' => ( |
71 | is => 'rw', |
72 | isa => 'Bool', |
73 | default => 1, |
74 | ); |
c84275ff |
75 | |
ef9d481f |
76 | has 'ac_label' => ( |
77 | is => 'rw', |
78 | isa => 'Str', |
79 | default => ' (a.c.)', |
80 | ); |
3a2ebbf4 |
81 | |
4e483aa5 |
82 | has 'wordsep' => ( |
83 | is => 'rw', |
84 | isa => 'Str', |
85 | default => ' ', |
86 | ); |
87 | |
3a2ebbf4 |
88 | has 'start' => ( |
89 | is => 'ro', |
90 | isa => 'Text::Tradition::Collation::Reading', |
91 | writer => '_set_start', |
92 | weak_ref => 1, |
93 | ); |
94 | |
95 | has 'end' => ( |
96 | is => 'ro', |
97 | isa => 'Text::Tradition::Collation::Reading', |
98 | writer => '_set_end', |
99 | weak_ref => 1, |
100 | ); |
b365fbae |
101 | |
102 | has 'cached_svg' => ( |
103 | is => 'rw', |
104 | isa => 'Str', |
105 | predicate => 'has_cached_svg', |
106 | clearer => 'wipe_svg', |
107 | ); |
1dd07bda |
108 | |
109 | has 'cached_table' => ( |
110 | is => 'rw', |
111 | isa => 'HashRef', |
112 | predicate => 'has_cached_table', |
113 | clearer => 'wipe_table', |
114 | ); |
c1915ab9 |
115 | |
116 | has '_graphcalc_done' => ( |
117 | is => 'rw', |
118 | isa => 'Bool', |
119 | default => undef, |
120 | ); |
1f563ac3 |
121 | |
4e5a7b2c |
122 | =head1 NAME |
123 | |
124 | Text::Tradition::Collation - a software model for a text collation |
125 | |
126 | =head1 SYNOPSIS |
127 | |
128 | use Text::Tradition; |
129 | my $t = Text::Tradition->new( |
130 | 'name' => 'this is a text', |
131 | 'input' => 'TEI', |
132 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
133 | |
134 | my $c = $t->collation; |
135 | my @readings = $c->readings; |
136 | my @paths = $c->paths; |
137 | my @relationships = $c->relationships; |
138 | |
139 | my $svg_variant_graph = $t->collation->as_svg(); |
140 | |
141 | =head1 DESCRIPTION |
142 | |
143 | Text::Tradition is a library for representation and analysis of collated |
144 | texts, particularly medieval ones. The Collation is the central feature of |
145 | a Tradition, where the text, its sequence of readings, and its relationships |
146 | between readings are actually kept. |
147 | |
148 | =head1 CONSTRUCTOR |
149 | |
150 | =head2 new |
151 | |
152 | The constructor. Takes a hash or hashref of the following arguments: |
153 | |
154 | =over |
155 | |
156 | =item * tradition - The Text::Tradition object to which the collation |
157 | belongs. Required. |
158 | |
159 | =item * linear - Whether the collation should be linear; that is, whether |
160 | transposed readings should be treated as two linked readings rather than one, |
161 | and therefore whether the collation graph is acyclic. Defaults to true. |
162 | |
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163 | =item * baselabel - The default label for the path taken by a base text |
164 | (if any). Defaults to 'base text'. |
165 | |
166 | =item * wit_list_separator - The string to join a list of witnesses for |
167 | purposes of making labels in display graphs. Defaults to ', '. |
168 | |
169 | =item * ac_label - The extra label to tack onto a witness sigil when |
170 | representing another layer of path for the given witness - that is, when |
171 | a text has more than one possible reading due to scribal corrections or |
172 | the like. Defaults to ' (a.c.)'. |
173 | |
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174 | =item * wordsep - The string used to separate words in the original text. |
175 | Defaults to ' '. |
176 | |
4e5a7b2c |
177 | =back |
178 | |
179 | =head1 ACCESSORS |
180 | |
181 | =head2 tradition |
182 | |
183 | =head2 linear |
184 | |
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185 | =head2 wit_list_separator |
186 | |
187 | =head2 baselabel |
188 | |
189 | =head2 ac_label |
190 | |
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191 | =head2 wordsep |
192 | |
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193 | Simple accessors for collation attributes. |
194 | |
195 | =head2 start |
196 | |
197 | The meta-reading at the start of every witness path. |
198 | |
199 | =head2 end |
200 | |
201 | The meta-reading at the end of every witness path. |
202 | |
203 | =head2 readings |
204 | |
205 | Returns all Reading objects in the graph. |
206 | |
207 | =head2 reading( $id ) |
208 | |
209 | Returns the Reading object corresponding to the given ID. |
210 | |
211 | =head2 add_reading( $reading_args ) |
212 | |
213 | Adds a new reading object to the collation. |
214 | See L<Text::Tradition::Collation::Reading> for the available arguments. |
215 | |
216 | =head2 del_reading( $object_or_id ) |
217 | |
218 | Removes the given reading from the collation, implicitly removing its |
219 | paths and relationships. |
220 | |
4e483aa5 |
221 | =head2 merge_readings( $main, $second, $concatenate, $with_str ) |
222 | |
223 | Merges the $second reading into the $main one. If $concatenate is true, then |
224 | the merged node will carry the text of both readings, concatenated with either |
225 | $with_str (if specified) or a sensible default (the empty string if the |
226 | appropriate 'join_*' flag is set on either reading, or else $self->wordsep.) |
4e5a7b2c |
227 | |
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228 | The first two arguments may be either readings or reading IDs. |
4e5a7b2c |
229 | |
230 | =head2 has_reading( $id ) |
231 | |
232 | Predicate to see whether a given reading ID is in the graph. |
233 | |
234 | =head2 reading_witnesses( $object_or_id ) |
235 | |
236 | Returns a list of sigils whose witnesses contain the reading. |
237 | |
238 | =head2 paths |
239 | |
240 | Returns all reading paths within the document - that is, all edges in the |
241 | collation graph. Each path is an arrayref of [ $source, $target ] reading IDs. |
242 | |
243 | =head2 add_path( $source, $target, $sigil ) |
244 | |
245 | Links the given readings in the collation in sequence, under the given witness |
246 | sigil. The readings may be specified by object or ID. |
247 | |
248 | =head2 del_path( $source, $target, $sigil ) |
249 | |
250 | Links the given readings in the collation in sequence, under the given witness |
251 | sigil. The readings may be specified by object or ID. |
252 | |
253 | =head2 has_path( $source, $target ); |
254 | |
255 | Returns true if the two readings are linked in sequence in any witness. |
256 | The readings may be specified by object or ID. |
257 | |
258 | =head2 relationships |
259 | |
260 | Returns all Relationship objects in the collation. |
261 | |
262 | =head2 add_relationship( $reading, $other_reading, $options ) |
263 | |
264 | Adds a new relationship of the type given in $options between the two readings, |
265 | which may be specified by object or ID. Returns a value of ( $status, @vectors) |
266 | where $status is true on success, and @vectors is a list of relationship edges |
267 | that were ultimately added. |
268 | See L<Text::Tradition::Collation::Relationship> for the available options. |
269 | |
270 | =cut |
dd3b58b0 |
271 | |
d047cd52 |
272 | sub BUILD { |
3a2ebbf4 |
273 | my $self = shift; |
22222af9 |
274 | $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) ); |
3a2ebbf4 |
275 | $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) ); |
276 | $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) ); |
d047cd52 |
277 | } |
784877d9 |
278 | |
3a2ebbf4 |
279 | ### Reading construct/destruct functions |
280 | |
281 | sub add_reading { |
282 | my( $self, $reading ) = @_; |
283 | unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) { |
284 | my %args = %$reading; |
285 | $reading = Text::Tradition::Collation::Reading->new( |
286 | 'collation' => $self, |
287 | %args ); |
288 | } |
289 | # First check to see if a reading with this ID exists. |
290 | if( $self->reading( $reading->id ) ) { |
63778331 |
291 | throw( "Collation already has a reading with id " . $reading->id ); |
3a2ebbf4 |
292 | } |
c1915ab9 |
293 | $self->_graphcalc_done(0); |
3a2ebbf4 |
294 | $self->_add_reading( $reading->id => $reading ); |
295 | # Once the reading has been added, put it in both graphs. |
296 | $self->sequence->add_vertex( $reading->id ); |
22222af9 |
297 | $self->relations->add_reading( $reading->id ); |
3a2ebbf4 |
298 | return $reading; |
eca16057 |
299 | }; |
300 | |
3a2ebbf4 |
301 | around del_reading => sub { |
302 | my $orig = shift; |
303 | my $self = shift; |
304 | my $arg = shift; |
305 | |
306 | if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) { |
307 | $arg = $arg->id; |
308 | } |
3a2ebbf4 |
309 | # Remove the reading from the graphs. |
c1915ab9 |
310 | $self->_graphcalc_done(0); |
4e483aa5 |
311 | $self->_clear_cache; # Explicitly clear caches to GC the reading |
3a2ebbf4 |
312 | $self->sequence->delete_vertex( $arg ); |
22222af9 |
313 | $self->relations->delete_reading( $arg ); |
3a2ebbf4 |
314 | |
315 | # Carry on. |
316 | $self->$orig( $arg ); |
317 | }; |
7854e12e |
318 | |
4e483aa5 |
319 | =begin testing |
320 | |
321 | use Text::Tradition; |
322 | |
323 | my $cxfile = 't/data/Collatex-16.xml'; |
324 | my $t = Text::Tradition->new( |
325 | 'name' => 'inline', |
326 | 'input' => 'CollateX', |
327 | 'file' => $cxfile, |
328 | ); |
329 | my $c = $t->collation; |
330 | |
331 | my $rno = scalar $c->readings; |
332 | # Split n21 for testing purposes |
333 | my $new_r = $c->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } ); |
334 | my $old_r = $c->reading( 'n21' ); |
335 | $old_r->alter_text( 'to' ); |
336 | $c->del_path( 'n20', 'n21', 'A' ); |
337 | $c->add_path( 'n20', 'n21p0', 'A' ); |
338 | $c->add_path( 'n21p0', 'n21', 'A' ); |
339 | $c->flatten_ranks(); |
340 | ok( $c->reading( 'n21p0' ), "New reading exists" ); |
341 | is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" ); |
342 | |
679f17e1 |
343 | # Combine n3 and n4 ( with his ) |
4e483aa5 |
344 | $c->merge_readings( 'n3', 'n4', 1 ); |
345 | ok( !$c->reading('n4'), "Reading n4 is gone" ); |
346 | is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" ); |
347 | |
679f17e1 |
348 | # Collapse n9 and n10 ( rood / root ) |
349 | $c->merge_readings( 'n9', 'n10' ); |
350 | ok( !$c->reading('n10'), "Reading n10 is gone" ); |
351 | is( $c->reading('n9')->text, 'rood', "Reading n9 has an unchanged word" ); |
4e483aa5 |
352 | |
353 | # Combine n21 and n21p0 |
354 | my $remaining = $c->reading('n21'); |
355 | $remaining ||= $c->reading('n22'); # one of these should still exist |
356 | $c->merge_readings( 'n21p0', $remaining, 1 ); |
357 | ok( !$c->reading('n21'), "Reading $remaining is gone" ); |
358 | is( $c->reading('n21p0')->text, 'unto', "Reading n21p0 merged correctly" ); |
359 | |
360 | =end testing |
361 | |
362 | =cut |
7854e12e |
363 | |
3a2ebbf4 |
364 | sub merge_readings { |
365 | my $self = shift; |
366 | |
367 | # We only need the IDs for adding paths to the graph, not the reading |
368 | # objects themselves. |
4e483aa5 |
369 | my( $kept, $deleted, $combine, $combine_char ) = $self->_stringify_args( @_ ); |
c1915ab9 |
370 | $self->_graphcalc_done(0); |
3a2ebbf4 |
371 | |
372 | # The kept reading should inherit the paths and the relationships |
373 | # of the deleted reading. |
374 | foreach my $path ( $self->sequence->edges_at( $deleted ) ) { |
375 | my @vector = ( $kept ); |
376 | push( @vector, $path->[1] ) if $path->[0] eq $deleted; |
377 | unshift( @vector, $path->[0] ) if $path->[1] eq $deleted; |
49d4f2ac |
378 | next if $vector[0] eq $vector[1]; # Don't add a self loop |
3a2ebbf4 |
379 | my %wits = %{$self->sequence->get_edge_attributes( @$path )}; |
380 | $self->sequence->add_edge( @vector ); |
381 | my $fwits = $self->sequence->get_edge_attributes( @vector ); |
382 | @wits{keys %$fwits} = values %$fwits; |
383 | $self->sequence->set_edge_attributes( @vector, \%wits ); |
384 | } |
22222af9 |
385 | $self->relations->merge_readings( $kept, $deleted, $combine_char ); |
3a2ebbf4 |
386 | |
387 | # Do the deletion deed. |
4e483aa5 |
388 | if( $combine ) { |
49d4f2ac |
389 | my $kept_obj = $self->reading( $kept ); |
4e483aa5 |
390 | my $del_obj = $self->reading( $deleted ); |
391 | my $joinstr = $combine_char; |
392 | unless( defined $joinstr ) { |
393 | $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior; |
394 | $joinstr = $self->wordsep unless defined $joinstr; |
395 | } |
396 | $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) ); |
49d4f2ac |
397 | } |
3a2ebbf4 |
398 | $self->del_reading( $deleted ); |
399 | } |
7854e12e |
400 | |
3265b0ce |
401 | |
3a2ebbf4 |
402 | # Helper function for manipulating the graph. |
403 | sub _stringify_args { |
4e483aa5 |
404 | my( $self, $first, $second, @args ) = @_; |
3a2ebbf4 |
405 | $first = $first->id |
406 | if ref( $first ) eq 'Text::Tradition::Collation::Reading'; |
407 | $second = $second->id |
408 | if ref( $second ) eq 'Text::Tradition::Collation::Reading'; |
4e483aa5 |
409 | return( $first, $second, @args ); |
3a2ebbf4 |
410 | } |
df6d9812 |
411 | |
4e5a7b2c |
412 | # Helper function for manipulating the graph. |
413 | sub _objectify_args { |
414 | my( $self, $first, $second, $arg ) = @_; |
415 | $first = $self->reading( $first ) |
416 | unless ref( $first ) eq 'Text::Tradition::Collation::Reading'; |
417 | $second = $self->reading( $second ) |
418 | unless ref( $second ) eq 'Text::Tradition::Collation::Reading'; |
419 | return( $first, $second, $arg ); |
420 | } |
3a2ebbf4 |
421 | ### Path logic |
422 | |
423 | sub add_path { |
424 | my $self = shift; |
425 | |
426 | # We only need the IDs for adding paths to the graph, not the reading |
427 | # objects themselves. |
428 | my( $source, $target, $wit ) = $self->_stringify_args( @_ ); |
429 | |
c1915ab9 |
430 | $self->_graphcalc_done(0); |
3a2ebbf4 |
431 | # Connect the readings |
432 | $self->sequence->add_edge( $source, $target ); |
433 | # Note the witness in question |
434 | $self->sequence->set_edge_attribute( $source, $target, $wit, 1 ); |
b15511bf |
435 | }; |
436 | |
3a2ebbf4 |
437 | sub del_path { |
438 | my $self = shift; |
49d4f2ac |
439 | my @args; |
440 | if( ref( $_[0] ) eq 'ARRAY' ) { |
441 | my $e = shift @_; |
442 | @args = ( @$e, @_ ); |
443 | } else { |
444 | @args = @_; |
445 | } |
3a2ebbf4 |
446 | |
447 | # We only need the IDs for adding paths to the graph, not the reading |
448 | # objects themselves. |
49d4f2ac |
449 | my( $source, $target, $wit ) = $self->_stringify_args( @args ); |
3a2ebbf4 |
450 | |
c1915ab9 |
451 | $self->_graphcalc_done(0); |
3a2ebbf4 |
452 | if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) { |
49d4f2ac |
453 | $self->sequence->delete_edge_attribute( $source, $target, $wit ); |
3a2ebbf4 |
454 | } |
455 | unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) { |
456 | $self->sequence->delete_edge( $source, $target ); |
457 | } |
784877d9 |
458 | } |
459 | |
3a2ebbf4 |
460 | |
15d2d3df |
461 | # Extra graph-alike utility |
462 | sub has_path { |
3a2ebbf4 |
463 | my $self = shift; |
464 | my( $source, $target, $wit ) = $self->_stringify_args( @_ ); |
465 | return undef unless $self->sequence->has_edge( $source, $target ); |
466 | return $self->sequence->has_edge_attribute( $source, $target, $wit ); |
b15511bf |
467 | } |
468 | |
4e5a7b2c |
469 | =head2 clear_witness( @sigil_list ) |
3a2ebbf4 |
470 | |
4e5a7b2c |
471 | Clear the given witnesses out of the collation entirely, removing references |
472 | to them in paths, and removing readings that belong only to them. Should only |
473 | be called via $tradition->del_witness. |
3a2ebbf4 |
474 | |
475 | =cut |
476 | |
4e5a7b2c |
477 | sub clear_witness { |
478 | my( $self, @sigils ) = @_; |
479 | |
c1915ab9 |
480 | $self->_graphcalc_done(0); |
4e5a7b2c |
481 | # Clear the witness(es) out of the paths |
482 | foreach my $e ( $self->paths ) { |
483 | foreach my $sig ( @sigils ) { |
484 | $self->del_path( $e, $sig ); |
485 | } |
486 | } |
487 | |
488 | # Clear out the newly unused readings |
489 | foreach my $r ( $self->readings ) { |
490 | unless( $self->reading_witnesses( $r ) ) { |
491 | $self->del_reading( $r ); |
492 | } |
493 | } |
494 | } |
3a2ebbf4 |
495 | |
496 | sub add_relationship { |
497 | my $self = shift; |
22222af9 |
498 | my( $source, $target, $opts ) = $self->_stringify_args( @_ ); |
414cc046 |
499 | my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts ); |
c1915ab9 |
500 | $self->_graphcalc_done(0); |
63778331 |
501 | return @vectors; |
22222af9 |
502 | } |
ef9d481f |
503 | |
ca6e6095 |
504 | around qw/ get_relationship del_relationship / => sub { |
505 | my $orig = shift; |
506 | my $self = shift; |
507 | my @args = @_; |
508 | if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) { |
509 | @args = @{$_[0]}; |
510 | } |
511 | my( $source, $target ) = $self->_stringify_args( @args ); |
512 | $self->$orig( $source, $target ); |
513 | }; |
514 | |
22222af9 |
515 | =head2 reading_witnesses( $reading ) |
910a0a6d |
516 | |
22222af9 |
517 | Return a list of sigils corresponding to the witnesses in which the reading appears. |
3265b0ce |
518 | |
22222af9 |
519 | =cut |
1d310495 |
520 | |
1d310495 |
521 | sub reading_witnesses { |
522 | my( $self, $reading ) = @_; |
523 | # We need only check either the incoming or the outgoing edges; I have |
96dc90ec |
524 | # arbitrarily chosen "incoming". Thus, special-case the start node. |
525 | if( $reading eq $self->start ) { |
526 | return map { $_->sigil } $self->tradition->witnesses; |
527 | } |
1d310495 |
528 | my %all_witnesses; |
529 | foreach my $e ( $self->sequence->edges_to( $reading ) ) { |
530 | my $wits = $self->sequence->get_edge_attributes( @$e ); |
531 | @all_witnesses{ keys %$wits } = 1; |
532 | } |
c12bb878 |
533 | my $acstr = $self->ac_label; |
534 | foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) { |
535 | delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit}; |
536 | } |
1d310495 |
537 | return keys %all_witnesses; |
910a0a6d |
538 | } |
539 | |
4e5a7b2c |
540 | =head1 OUTPUT METHODS |
8e1394aa |
541 | |
0ecb975c |
542 | =head2 as_svg( \%options ) |
8e1394aa |
543 | |
0068967c |
544 | Returns an SVG string that represents the graph, via as_dot and graphviz. |
bfcbcecb |
545 | See as_dot for a list of options. Must have GraphViz (dot) installed to run. |
8e1394aa |
546 | |
547 | =cut |
548 | |
549 | sub as_svg { |
0ecb975c |
550 | my( $self, $opts ) = @_; |
bfcbcecb |
551 | throw( "Need GraphViz installed to output SVG" ) |
552 | unless File::Which::which( 'dot' ); |
e247aad1 |
553 | my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'}; |
5f082716 |
554 | $self->calculate_ranks() unless( $self->_graphcalc_done || $opts->{'nocalc'} ); |
e247aad1 |
555 | if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) { |
b365fbae |
556 | my @cmd = qw/dot -Tsvg/; |
557 | my( $svg, $err ); |
558 | my $dotfile = File::Temp->new(); |
559 | ## USE FOR DEBUGGING |
560 | # $dotfile->unlink_on_destroy(0); |
561 | binmode $dotfile, ':utf8'; |
562 | print $dotfile $self->as_dot( $opts ); |
563 | push( @cmd, $dotfile->filename ); |
564 | run( \@cmd, ">", binary(), \$svg ); |
e247aad1 |
565 | $svg = decode_utf8( $svg ); |
566 | $self->cached_svg( $svg ) unless $want_subgraph; |
567 | return $svg; |
568 | } else { |
569 | return $self->cached_svg; |
b365fbae |
570 | } |
8e1394aa |
571 | } |
572 | |
b22576c6 |
573 | |
0ecb975c |
574 | =head2 as_dot( \%options ) |
b22576c6 |
575 | |
0ecb975c |
576 | Returns a string that is the collation graph expressed in dot |
577 | (i.e. GraphViz) format. Options include: |
b22576c6 |
578 | |
0ecb975c |
579 | =over 4 |
b22576c6 |
580 | |
0ecb975c |
581 | =item * from |
b22576c6 |
582 | |
0ecb975c |
583 | =item * to |
df6d9812 |
584 | |
0ecb975c |
585 | =item * color_common |
586 | |
587 | =back |
df6d9812 |
588 | |
589 | =cut |
590 | |
591 | sub as_dot { |
0ecb975c |
592 | my( $self, $opts ) = @_; |
593 | my $startrank = $opts->{'from'} if $opts; |
594 | my $endrank = $opts->{'to'} if $opts; |
595 | my $color_common = $opts->{'color_common'} if $opts; |
b365fbae |
596 | my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank |
597 | && $self->end->rank > 100; |
6648ee3d |
598 | $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs |
b365fbae |
599 | |
b22576c6 |
600 | # Check the arguments |
601 | if( $startrank ) { |
602 | return if $endrank && $startrank > $endrank; |
603 | return if $startrank > $self->end->rank; |
604 | } |
605 | if( defined $endrank ) { |
606 | return if $endrank < 0; |
f1b3b33a |
607 | $endrank = undef if $endrank == $self->end->rank; |
b22576c6 |
608 | } |
609 | |
67da8d6c |
610 | my $graph_name = $self->tradition->name; |
611 | $graph_name =~ s/[^\w\s]//g; |
612 | $graph_name = join( '_', split( /\s+/, $graph_name ) ); |
f13b5582 |
613 | |
614 | my %graph_attrs = ( |
615 | 'rankdir' => 'LR', |
616 | 'bgcolor' => 'none', |
617 | ); |
618 | my %node_attrs = ( |
b8990398 |
619 | 'fontsize' => 14, |
f13b5582 |
620 | 'fillcolor' => 'white', |
621 | 'style' => 'filled', |
622 | 'shape' => 'ellipse' |
623 | ); |
624 | my %edge_attrs = ( |
625 | 'arrowhead' => 'open', |
626 | 'color' => '#000000', |
627 | 'fontcolor' => '#000000', |
628 | ); |
629 | |
67da8d6c |
630 | my $dot = sprintf( "digraph %s {\n", $graph_name ); |
f13b5582 |
631 | $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n"; |
632 | $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n"; |
df6d9812 |
633 | |
b22576c6 |
634 | # Output substitute start/end readings if necessary |
635 | if( $startrank ) { |
636 | $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n"; |
637 | } |
638 | if( $endrank ) { |
639 | $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n"; |
640 | } |
b365fbae |
641 | if( $STRAIGHTENHACK ) { |
642 | ## HACK part 1 |
6648ee3d |
643 | my $startlabel = $startrank ? 'SUBSTART' : 'START'; |
644 | $dot .= "\tsubgraph { rank=same \"#$startlabel#\" \"#SILENT#\" }\n"; |
b365fbae |
645 | $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];" |
646 | } |
b22576c6 |
647 | my %used; # Keep track of the readings that actually appear in the graph |
30ddc24c |
648 | # Sort the readings by rank if we have ranks; this speeds layout. |
649 | my @all_readings = $self->end->has_rank |
650 | ? sort { $a->rank <=> $b->rank } $self->readings |
651 | : $self->readings; |
4633f9e4 |
652 | # TODO Refrain from outputting lacuna nodes - just grey out the edges. |
30ddc24c |
653 | foreach my $reading ( @all_readings ) { |
b22576c6 |
654 | # Only output readings within our rank range. |
655 | next if $startrank && $reading->rank < $startrank; |
656 | next if $endrank && $reading->rank > $endrank; |
657 | $used{$reading->id} = 1; |
910a0a6d |
658 | # Need not output nodes without separate labels |
3a2ebbf4 |
659 | next if $reading->id eq $reading->text; |
d4b75f44 |
660 | my $rattrs; |
30f0df34 |
661 | my $label = $reading->text; |
629e27b0 |
662 | $label .= '-' if $reading->join_next; |
663 | $label = "-$label" if $reading->join_prior; |
8f9cab7b |
664 | $label =~ s/\"/\\\"/g; |
d4b75f44 |
665 | $rattrs->{'label'} = $label; |
0ecb975c |
666 | $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common; |
d4b75f44 |
667 | $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) ); |
df6d9812 |
668 | } |
3a2ebbf4 |
669 | |
30ddc24c |
670 | # Add the real edges. Need to weight one edge per rank jump, in a |
671 | # continuous line. |
b365fbae |
672 | # my $weighted = $self->_add_edge_weights; |
b22576c6 |
673 | my @edges = $self->paths; |
3bdec618 |
674 | my( %substart, %subend ); |
b22576c6 |
675 | foreach my $edge ( @edges ) { |
676 | # Do we need to output this edge? |
508fd430 |
677 | if( $used{$edge->[0]} && $used{$edge->[1]} ) { |
027d819c |
678 | my $label = $self->_path_display_label( $self->path_witnesses( $edge ) ); |
f13b5582 |
679 | my $variables = { %edge_attrs, 'label' => $label }; |
30ddc24c |
680 | |
b22576c6 |
681 | # Account for the rank gap if necessary |
30ddc24c |
682 | my $rank0 = $self->reading( $edge->[0] )->rank |
683 | if $self->reading( $edge->[0] )->has_rank; |
684 | my $rank1 = $self->reading( $edge->[1] )->rank |
685 | if $self->reading( $edge->[1] )->has_rank; |
686 | if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) { |
687 | $variables->{'minlen'} = $rank1 - $rank0; |
688 | } |
689 | |
690 | # Add the calculated edge weights |
b365fbae |
691 | # if( exists $weighted->{$edge->[0]} |
e247aad1 |
692 | # && $weighted->{$edge->[0]} eq $edge->[1] ) { |
693 | # # $variables->{'color'} = 'red'; |
694 | # $variables->{'weight'} = 3.0; |
695 | # } |
30ddc24c |
696 | |
508fd430 |
697 | # EXPERIMENTAL: make edge width reflect no. of witnesses |
698 | my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2; |
699 | $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit |
700 | |
f13b5582 |
701 | my $varopts = _dot_attr_string( $variables ); |
702 | $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n", |
703 | $edge->[0], $edge->[1], $varopts ); |
3bdec618 |
704 | } elsif( $used{$edge->[0]} ) { |
705 | $subend{$edge->[0]} = 1; |
706 | } elsif( $used{$edge->[1]} ) { |
707 | $substart{$edge->[1]} = 1; |
b22576c6 |
708 | } |
df6d9812 |
709 | } |
3bdec618 |
710 | # Add substitute start and end edges if necessary |
711 | foreach my $node ( keys %substart ) { |
027d819c |
712 | my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) ); |
f13b5582 |
713 | my $variables = { %edge_attrs, 'label' => $witstr }; |
714 | my $varopts = _dot_attr_string( $variables ); |
715 | $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;"; |
3bdec618 |
716 | } |
717 | foreach my $node ( keys %subend ) { |
027d819c |
718 | my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) ); |
f13b5582 |
719 | my $variables = { %edge_attrs, 'label' => $witstr }; |
720 | my $varopts = _dot_attr_string( $variables ); |
721 | $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;"; |
3bdec618 |
722 | } |
b365fbae |
723 | # HACK part 2 |
724 | if( $STRAIGHTENHACK ) { |
6648ee3d |
725 | my $endlabel = $endrank ? 'SUBEND' : 'END'; |
726 | $dot .= "\t\"#$endlabel#\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n"; |
b365fbae |
727 | } |
30ddc24c |
728 | |
df6d9812 |
729 | $dot .= "}\n"; |
730 | return $dot; |
731 | } |
732 | |
f13b5582 |
733 | sub _dot_attr_string { |
734 | my( $hash ) = @_; |
735 | my @attrs; |
736 | foreach my $k ( sort keys %$hash ) { |
737 | my $v = $hash->{$k}; |
738 | push( @attrs, $k.'="'.$v.'"' ); |
739 | } |
740 | return( '[ ' . join( ', ', @attrs ) . ' ]' ); |
741 | } |
742 | |
30ddc24c |
743 | sub _add_edge_weights { |
744 | my $self = shift; |
745 | # Walk the graph from START to END, choosing the successor node with |
746 | # the largest number of witness paths each time. |
747 | my $weighted = {}; |
748 | my $curr = $self->start->id; |
008fc8a6 |
749 | my $ranked = $self->end->has_rank; |
30ddc24c |
750 | while( $curr ne $self->end->id ) { |
008fc8a6 |
751 | my $rank = $ranked ? $self->reading( $curr )->rank : 0; |
30ddc24c |
752 | my @succ = sort { $self->path_witnesses( $curr, $a ) |
753 | <=> $self->path_witnesses( $curr, $b ) } |
754 | $self->sequence->successors( $curr ); |
755 | my $next = pop @succ; |
008fc8a6 |
756 | my $nextrank = $ranked ? $self->reading( $next )->rank : 0; |
30ddc24c |
757 | # Try to avoid lacunae in the weighted path. |
008fc8a6 |
758 | while( @succ && |
759 | ( $self->reading( $next )->is_lacuna || |
760 | $nextrank - $rank > 1 ) ){ |
30ddc24c |
761 | $next = pop @succ; |
762 | } |
763 | $weighted->{$curr} = $next; |
764 | $curr = $next; |
765 | } |
766 | return $weighted; |
767 | } |
768 | |
027d819c |
769 | =head2 path_witnesses( $edge ) |
770 | |
771 | Returns the list of sigils whose witnesses are associated with the given edge. |
772 | The edge can be passed as either an array or an arrayref of ( $source, $target ). |
773 | |
774 | =cut |
775 | |
3a2ebbf4 |
776 | sub path_witnesses { |
777 | my( $self, @edge ) = @_; |
778 | # If edge is an arrayref, cope. |
779 | if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) { |
780 | my $e = shift @edge; |
781 | @edge = @$e; |
782 | } |
783 | my @wits = keys %{$self->sequence->get_edge_attributes( @edge )}; |
508fd430 |
784 | return @wits; |
3a2ebbf4 |
785 | } |
786 | |
7f9f05e8 |
787 | # Helper function. Make a display label for the given witnesses, showing a.c. |
788 | # witnesses only where the main witness is not also in the list. |
027d819c |
789 | sub _path_display_label { |
508fd430 |
790 | my $self = shift; |
7f9f05e8 |
791 | my %wits; |
792 | map { $wits{$_} = 1 } @_; |
793 | |
794 | # If an a.c. wit is listed, remove it if the main wit is also listed. |
795 | # Otherwise keep it for explicit listing. |
796 | my $aclabel = $self->ac_label; |
797 | my @disp_ac; |
798 | foreach my $w ( sort keys %wits ) { |
799 | if( $w =~ /^(.*)\Q$aclabel\E$/ ) { |
800 | if( exists $wits{$1} ) { |
801 | delete $wits{$w}; |
802 | } else { |
803 | push( @disp_ac, $w ); |
804 | } |
805 | } |
806 | } |
807 | |
808 | # See if we are in a majority situation. |
8f9cab7b |
809 | my $maj = scalar( $self->tradition->witnesses ) * 0.6; |
7f9f05e8 |
810 | if( scalar keys %wits > $maj ) { |
811 | unshift( @disp_ac, 'majority' ); |
812 | return join( ', ', @disp_ac ); |
8f9cab7b |
813 | } else { |
7f9f05e8 |
814 | return join( ', ', sort keys %wits ); |
8f9cab7b |
815 | } |
816 | } |
1dd07bda |
817 | |
bf6e338d |
818 | =head2 readings_at_rank( $rank ) |
1dd07bda |
819 | |
bf6e338d |
820 | Returns a list of readings at a given rank, taken from the alignment table. |
1dd07bda |
821 | |
822 | =cut |
823 | |
bf6e338d |
824 | sub readings_at_rank { |
1dd07bda |
825 | my( $self, $rank ) = @_; |
bf6e338d |
826 | my $table = $self->alignment_table; |
827 | # Table rank is real rank - 1. |
828 | my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}}; |
829 | my %readings; |
830 | foreach my $e ( @elements ) { |
831 | next unless ref( $e ) eq 'HASH'; |
832 | next unless exists $e->{'t'}; |
833 | $readings{$e->{'t'}->id} = $e->{'t'}; |
834 | } |
835 | return values %readings; |
1dd07bda |
836 | } |
8f9cab7b |
837 | |
4e5a7b2c |
838 | =head2 as_graphml |
8e1394aa |
839 | |
4e5a7b2c |
840 | Returns a GraphML representation of the collation. The GraphML will contain |
841 | two graphs. The first expresses the attributes of the readings and the witness |
842 | paths that link them; the second expresses the relationships that link the |
843 | readings. This is the native transfer format for a tradition. |
8e1394aa |
844 | |
56eefa04 |
845 | =begin testing |
846 | |
847 | use Text::Tradition; |
848 | |
849 | my $READINGS = 311; |
850 | my $PATHS = 361; |
851 | |
852 | my $datafile = 't/data/florilegium_tei_ps.xml'; |
853 | my $tradition = Text::Tradition->new( 'input' => 'TEI', |
854 | 'name' => 'test0', |
855 | 'file' => $datafile, |
856 | 'linear' => 1 ); |
857 | |
858 | ok( $tradition, "Got a tradition object" ); |
859 | is( scalar $tradition->witnesses, 13, "Found all witnesses" ); |
860 | ok( $tradition->collation, "Tradition has a collation" ); |
861 | |
862 | my $c = $tradition->collation; |
863 | is( scalar $c->readings, $READINGS, "Collation has all readings" ); |
864 | is( scalar $c->paths, $PATHS, "Collation has all paths" ); |
865 | is( scalar $c->relationships, 0, "Collation has all relationships" ); |
866 | |
867 | # Add a few relationships |
868 | $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } ); |
869 | $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } ); |
870 | $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } ); |
871 | |
872 | # Now write it to GraphML and parse it again. |
873 | |
874 | my $graphml = $c->as_graphml; |
875 | my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml ); |
876 | is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" ); |
877 | is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" ); |
878 | is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" ); |
879 | |
880 | =end testing |
881 | |
8e1394aa |
882 | =cut |
883 | |
884 | sub as_graphml { |
a30ca502 |
885 | my( $self, $options ) = @_; |
3d14b48e |
886 | $self->calculate_ranks unless $self->_graphcalc_done; |
887 | |
a30ca502 |
888 | my $start = $options->{'from'} |
889 | ? $self->reading( $options->{'from'} ) : $self->start; |
890 | my $end = $options->{'to'} |
891 | ? $self->reading( $options->{'to'} ) : $self->end; |
892 | if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) { |
893 | throw( 'Start node must be before end node' ); |
894 | } |
895 | # The readings need to be ranked for this to work. |
896 | $start = $self->start unless $start->has_rank; |
897 | $end = $self->end unless $end->has_rank; |
414cc046 |
898 | my $rankoffset = 0; |
899 | unless( $start eq $self->start ) { |
900 | $rankoffset = $start->rank - 1; |
901 | } |
a30ca502 |
902 | my %use_readings; |
903 | |
8e1394aa |
904 | # Some namespaces |
905 | my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns'; |
906 | my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance'; |
907 | my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' . |
910a0a6d |
908 | 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd'; |
8e1394aa |
909 | |
910 | # Create the document and root node |
911 | my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" ); |
912 | my $root = $graphml->createElementNS( $graphml_ns, 'graphml' ); |
913 | $graphml->setDocumentElement( $root ); |
914 | $root->setNamespace( $xsi_ns, 'xsi', 0 ); |
915 | $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema ); |
bbd064a9 |
916 | |
917 | # List of attribute types to save on our objects and their corresponding |
918 | # GraphML types |
919 | my %save_types = ( |
920 | 'Str' => 'string', |
921 | 'Int' => 'int', |
922 | 'Bool' => 'boolean', |
923 | 'RelationshipType' => 'string', |
924 | 'RelationshipScope' => 'string', |
925 | ); |
926 | |
927 | # List of attribute names *not* to save on our objects. |
928 | # We will also not save any attribute beginning with _. |
929 | my %skipsave; |
930 | map { $skipsave{$_} = 1 } qw/ cached_svg /; |
8e1394aa |
931 | |
bbd064a9 |
932 | # Add the data keys for the graph. Include an extra key 'version' for the |
933 | # GraphML output version. |
e309421a |
934 | my %graph_data_keys; |
935 | my $gdi = 0; |
bbd064a9 |
936 | my %graph_attributes = ( 'version' => 'string' ); |
937 | # Graph attributes include those of Tradition and those of Collation. |
938 | my %gattr_from; |
939 | my $tmeta = $self->tradition->meta; |
940 | my $cmeta = $self->meta; |
941 | map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes; |
942 | map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes; |
943 | foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) { |
944 | next if $attr->name =~ /^_/; |
945 | next if $skipsave{$attr->name}; |
946 | next unless $save_types{$attr->type_constraint->name}; |
947 | $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; |
948 | } |
949 | |
950 | foreach my $datum ( sort keys %graph_attributes ) { |
e309421a |
951 | $graph_data_keys{$datum} = 'dg'.$gdi++; |
952 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
953 | $key->setAttribute( 'attr.name', $datum ); |
bbd064a9 |
954 | $key->setAttribute( 'attr.type', $graph_attributes{$datum} ); |
e309421a |
955 | $key->setAttribute( 'for', 'graph' ); |
956 | $key->setAttribute( 'id', $graph_data_keys{$datum} ); |
957 | } |
f6066bac |
958 | |
bbd064a9 |
959 | # Add the data keys for reading nodes |
960 | my %reading_attributes; |
961 | my $rmeta = Text::Tradition::Collation::Reading->meta; |
962 | foreach my $attr( $rmeta->get_all_attributes ) { |
963 | next if $attr->name =~ /^_/; |
964 | next if $skipsave{$attr->name}; |
965 | next unless $save_types{$attr->type_constraint->name}; |
966 | $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; |
967 | } |
ef9d481f |
968 | my %node_data_keys; |
969 | my $ndi = 0; |
bbd064a9 |
970 | foreach my $datum ( sort keys %reading_attributes ) { |
910a0a6d |
971 | $node_data_keys{$datum} = 'dn'.$ndi++; |
972 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
973 | $key->setAttribute( 'attr.name', $datum ); |
bbd064a9 |
974 | $key->setAttribute( 'attr.type', $reading_attributes{$datum} ); |
910a0a6d |
975 | $key->setAttribute( 'for', 'node' ); |
976 | $key->setAttribute( 'id', $node_data_keys{$datum} ); |
8e1394aa |
977 | } |
978 | |
bbd064a9 |
979 | # Add the data keys for edges, that is, paths and relationships. Path |
980 | # data does not come from a Moose class so is here manually. |
ef9d481f |
981 | my $edi = 0; |
982 | my %edge_data_keys; |
bbd064a9 |
983 | my %edge_attributes = ( |
3a2ebbf4 |
984 | witness => 'string', # ID/label for a path |
3a2ebbf4 |
985 | extra => 'boolean', # Path key |
3a2ebbf4 |
986 | ); |
bbd064a9 |
987 | my @path_attributes = keys %edge_attributes; # track our manual additions |
988 | my $pmeta = Text::Tradition::Collation::Relationship->meta; |
989 | foreach my $attr( $pmeta->get_all_attributes ) { |
990 | next if $attr->name =~ /^_/; |
991 | next if $skipsave{$attr->name}; |
992 | next unless $save_types{$attr->type_constraint->name}; |
993 | $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; |
994 | } |
995 | foreach my $datum ( sort keys %edge_attributes ) { |
3a2ebbf4 |
996 | $edge_data_keys{$datum} = 'de'.$edi++; |
910a0a6d |
997 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
3a2ebbf4 |
998 | $key->setAttribute( 'attr.name', $datum ); |
bbd064a9 |
999 | $key->setAttribute( 'attr.type', $edge_attributes{$datum} ); |
910a0a6d |
1000 | $key->setAttribute( 'for', 'edge' ); |
3a2ebbf4 |
1001 | $key->setAttribute( 'id', $edge_data_keys{$datum} ); |
8e1394aa |
1002 | } |
3a2ebbf4 |
1003 | |
cc31ebaa |
1004 | # Add the collation graph itself. First, sanitize the name to a valid XML ID. |
1005 | my $xmlidname = $self->tradition->name; |
1006 | $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g; |
1007 | if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) { |
1008 | $xmlidname = '_'.$xmlidname; |
1009 | } |
2c669bca |
1010 | my $sgraph = $root->addNewChild( $graphml_ns, 'graph' ); |
1011 | $sgraph->setAttribute( 'edgedefault', 'directed' ); |
cc31ebaa |
1012 | $sgraph->setAttribute( 'id', $xmlidname ); |
2c669bca |
1013 | $sgraph->setAttribute( 'parse.edgeids', 'canonical' ); |
cc31ebaa |
1014 | $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later |
2c669bca |
1015 | $sgraph->setAttribute( 'parse.nodeids', 'canonical' ); |
cc31ebaa |
1016 | $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later |
2c669bca |
1017 | $sgraph->setAttribute( 'parse.order', 'nodesfirst' ); |
22222af9 |
1018 | |
e309421a |
1019 | # Collation attribute data |
bbd064a9 |
1020 | foreach my $datum ( keys %graph_attributes ) { |
1021 | my $value; |
1022 | if( $datum eq 'version' ) { |
1023 | $value = '3.1'; |
1024 | } elsif( $gattr_from{$datum} eq 'Tradition' ) { |
1025 | $value = $self->tradition->$datum; |
1026 | } else { |
1027 | $value = $self->$datum; |
1028 | } |
2c669bca |
1029 | _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value ); |
e309421a |
1030 | } |
8e1394aa |
1031 | |
1032 | my $node_ctr = 0; |
1033 | my %node_hash; |
22222af9 |
1034 | # Add our readings to the graph |
3a2ebbf4 |
1035 | foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) { |
a30ca502 |
1036 | next if $n->has_rank && $n ne $self->start && $n ne $self->end && |
1037 | ( $n->rank < $start->rank || $n->rank > $end->rank ); |
1038 | $use_readings{$n->id} = 1; |
2c669bca |
1039 | # Add to the main graph |
1040 | my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' ); |
910a0a6d |
1041 | my $node_xmlid = 'n' . $node_ctr++; |
3a2ebbf4 |
1042 | $node_hash{ $n->id } = $node_xmlid; |
910a0a6d |
1043 | $node_el->setAttribute( 'id', $node_xmlid ); |
bbd064a9 |
1044 | foreach my $d ( keys %reading_attributes ) { |
255875b8 |
1045 | my $nval = $n->$d; |
cc31ebaa |
1046 | if( $rankoffset && $d eq 'rank' && $n ne $self->start ) { |
414cc046 |
1047 | # Adjust the ranks within the subgraph. |
cc31ebaa |
1048 | $nval = $n eq $self->end ? $end->rank - $rankoffset + 1 |
1049 | : $nval - $rankoffset; |
414cc046 |
1050 | } |
255875b8 |
1051 | _add_graphml_data( $node_el, $node_data_keys{$d}, $nval ) |
1052 | if defined $nval; |
1053 | } |
b15511bf |
1054 | } |
1055 | |
2c669bca |
1056 | # Add the path edges to the sequence graph |
df6d9812 |
1057 | my $edge_ctr = 0; |
cc31ebaa |
1058 | $DB::single = 1; |
3a2ebbf4 |
1059 | foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) { |
1060 | # We add an edge in the graphml for every witness in $e. |
a30ca502 |
1061 | next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} ); |
1062 | my @edge_wits = sort $self->path_witnesses( $e ); |
cc31ebaa |
1063 | $e->[0] = $self->start->id unless $use_readings{$e->[0]}; |
1064 | $e->[1] = $self->end->id unless $use_readings{$e->[1]}; |
1065 | # Skip any path from start to end; that witness is not in the subgraph. |
1066 | next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id ); |
a30ca502 |
1067 | foreach my $wit ( @edge_wits ) { |
3a2ebbf4 |
1068 | my( $id, $from, $to ) = ( 'e'.$edge_ctr++, |
1069 | $node_hash{ $e->[0] }, |
1070 | $node_hash{ $e->[1] } ); |
2c669bca |
1071 | my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' ); |
3a2ebbf4 |
1072 | $edge_el->setAttribute( 'source', $from ); |
1073 | $edge_el->setAttribute( 'target', $to ); |
1074 | $edge_el->setAttribute( 'id', $id ); |
3a2ebbf4 |
1075 | |
1076 | # It's a witness path, so add the witness |
1077 | my $base = $wit; |
1078 | my $key = $edge_data_keys{'witness'}; |
1079 | # Is this an ante-corr witness? |
1080 | my $aclabel = $self->ac_label; |
1081 | if( $wit =~ /^(.*)\Q$aclabel\E$/ ) { |
1082 | # Keep the base witness |
1083 | $base = $1; |
1084 | # ...and record that this is an 'extra' reading path |
1085 | _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel ); |
1086 | } |
1087 | _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base ); |
1088 | } |
1089 | } |
1090 | |
cc31ebaa |
1091 | # Report the actual number of nodes and edges that went in |
1092 | $sgraph->setAttribute( 'parse.edges', $edge_ctr ); |
1093 | $sgraph->setAttribute( 'parse.nodes', $node_ctr ); |
1094 | |
22222af9 |
1095 | # Add the relationship graph to the XML |
bbd064a9 |
1096 | map { delete $edge_data_keys{$_} } @path_attributes; |
826d8773 |
1097 | $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash, |
1098 | $node_data_keys{'id'}, \%edge_data_keys ); |
8e1394aa |
1099 | |
94c00c71 |
1100 | # Save and return the thing |
1101 | my $result = decode_utf8( $graphml->toString(1) ); |
94c00c71 |
1102 | return $result; |
df6d9812 |
1103 | } |
1104 | |
b15511bf |
1105 | sub _add_graphml_data { |
1106 | my( $el, $key, $value ) = @_; |
b15511bf |
1107 | return unless defined $value; |
c9bf3dbf |
1108 | my $data_el = $el->addNewChild( $el->namespaceURI, 'data' ); |
b15511bf |
1109 | $data_el->setAttribute( 'key', $key ); |
1110 | $data_el->appendText( $value ); |
8e1394aa |
1111 | } |
1112 | |
4e5a7b2c |
1113 | =head2 as_csv |
910a0a6d |
1114 | |
1115 | Returns a CSV alignment table representation of the collation graph, one |
2c669bca |
1116 | row per witness (or witness uncorrected.) |
910a0a6d |
1117 | |
1118 | =cut |
1119 | |
1120 | sub as_csv { |
3a2ebbf4 |
1121 | my( $self ) = @_; |
1dd07bda |
1122 | my $table = $self->alignment_table; |
82fa4d57 |
1123 | my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } ); |
910a0a6d |
1124 | my @result; |
2c669bca |
1125 | # Make the header row |
1126 | $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} ); |
1127 | push( @result, decode_utf8( $csv->string ) ); |
1128 | # Make the rest of the rows |
1129 | foreach my $idx ( 0 .. $table->{'length'} - 1 ) { |
566f4595 |
1130 | my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}}; |
1dd07bda |
1131 | my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs; |
2c669bca |
1132 | $csv->combine( @row ); |
910a0a6d |
1133 | push( @result, decode_utf8( $csv->string ) ); |
1134 | } |
3a2ebbf4 |
1135 | return join( "\n", @result ); |
910a0a6d |
1136 | } |
1137 | |
1dd07bda |
1138 | =head2 alignment_table( $use_refs, $include_witnesses ) |
2c669bca |
1139 | |
566f4595 |
1140 | Return a reference to an alignment table, in a slightly enhanced CollateX |
1141 | format which looks like this: |
1142 | |
1143 | $table = { alignment => [ { witness => "SIGIL", |
4e5a7b2c |
1144 | tokens => [ { t => "TEXT" }, ... ] }, |
566f4595 |
1145 | { witness => "SIG2", |
4e5a7b2c |
1146 | tokens => [ { t => "TEXT" }, ... ] }, |
566f4595 |
1147 | ... ], |
1148 | length => TEXTLEN }; |
1149 | |
1150 | If $use_refs is set to 1, the reading object is returned in the table |
1151 | instead of READINGTEXT; if not, the text of the reading is returned. |
4e5a7b2c |
1152 | |
1153 | If $include_witnesses is set to a hashref, only the witnesses whose sigil |
566f4595 |
1154 | keys have a true hash value will be included. |
2c669bca |
1155 | |
1156 | =cut |
9f3ba6f7 |
1157 | |
1dd07bda |
1158 | sub alignment_table { |
1159 | my( $self ) = @_; |
c1915ab9 |
1160 | $self->calculate_ranks() unless $self->_graphcalc_done; |
1dd07bda |
1161 | return $self->cached_table if $self->has_cached_table; |
1162 | |
0ecb975c |
1163 | # Make sure we can do this |
1164 | throw( "Need a linear graph in order to make an alignment table" ) |
1165 | unless $self->linear; |
1166 | $self->calculate_ranks unless $self->end->has_rank; |
1167 | |
2c669bca |
1168 | my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 }; |
3a2ebbf4 |
1169 | my @all_pos = ( 1 .. $self->end->rank - 1 ); |
68454b71 |
1170 | foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) { |
eca16057 |
1171 | # print STDERR "Making witness row(s) for " . $wit->sigil . "\n"; |
1f7aa795 |
1172 | my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil ); |
1dd07bda |
1173 | my @row = _make_witness_row( \@wit_path, \@all_pos ); |
2c669bca |
1174 | push( @{$table->{'alignment'}}, |
1175 | { 'witness' => $wit->sigil, 'tokens' => \@row } ); |
1f7aa795 |
1176 | if( $wit->is_layered ) { |
1177 | my @wit_ac_path = $self->reading_sequence( $self->start, $self->end, |
861c3e27 |
1178 | $wit->sigil.$self->ac_label ); |
1dd07bda |
1179 | my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos ); |
2c669bca |
1180 | push( @{$table->{'alignment'}}, |
1181 | { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } ); |
910a0a6d |
1182 | } |
1183 | } |
1dd07bda |
1184 | $self->cached_table( $table ); |
1185 | return $table; |
910a0a6d |
1186 | } |
1187 | |
1188 | sub _make_witness_row { |
1dd07bda |
1189 | my( $path, $positions ) = @_; |
910a0a6d |
1190 | my %char_hash; |
1191 | map { $char_hash{$_} = undef } @$positions; |
2c669bca |
1192 | my $debug = 0; |
910a0a6d |
1193 | foreach my $rdg ( @$path ) { |
eca16057 |
1194 | my $rtext = $rdg->text; |
1195 | $rtext = '#LACUNA#' if $rdg->is_lacuna; |
2c669bca |
1196 | print STDERR "rank " . $rdg->rank . "\n" if $debug; |
3a2ebbf4 |
1197 | # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank; |
1dd07bda |
1198 | $char_hash{$rdg->rank} = { 't' => $rdg }; |
910a0a6d |
1199 | } |
1200 | my @row = map { $char_hash{$_} } @$positions; |
eca16057 |
1201 | # Fill in lacuna markers for undef spots in the row |
1202 | my $last_el = shift @row; |
1203 | my @filled_row = ( $last_el ); |
1204 | foreach my $el ( @row ) { |
0e476982 |
1205 | # If we are using node reference, make the lacuna node appear many times |
1206 | # in the table. If not, use the lacuna tag. |
1dd07bda |
1207 | if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) { |
1208 | $el = $last_el; |
eca16057 |
1209 | } |
1210 | push( @filled_row, $el ); |
1211 | $last_el = $el; |
1212 | } |
1213 | return @filled_row; |
910a0a6d |
1214 | } |
1215 | |
4e5a7b2c |
1216 | =head1 NAVIGATION METHODS |
910a0a6d |
1217 | |
4e5a7b2c |
1218 | =head2 reading_sequence( $first, $last, $sigil, $backup ) |
e2902068 |
1219 | |
1220 | Returns the ordered list of readings, starting with $first and ending |
4e5a7b2c |
1221 | with $last, for the witness given in $sigil. If a $backup sigil is |
1222 | specified (e.g. when walking a layered witness), it will be used wherever |
1223 | no $sigil path exists. If there is a base text reading, that will be |
1224 | used wherever no path exists for $sigil or $backup. |
e2902068 |
1225 | |
1226 | =cut |
1227 | |
910a0a6d |
1228 | # TODO Think about returning some lazy-eval iterator. |
b0b4421a |
1229 | # TODO Get rid of backup; we should know from what witness is whether we need it. |
910a0a6d |
1230 | |
e2902068 |
1231 | sub reading_sequence { |
861c3e27 |
1232 | my( $self, $start, $end, $witness ) = @_; |
e2902068 |
1233 | |
930ff666 |
1234 | $witness = $self->baselabel unless $witness; |
e2902068 |
1235 | my @readings = ( $start ); |
1236 | my %seen; |
1237 | my $n = $start; |
3a2ebbf4 |
1238 | while( $n && $n->id ne $end->id ) { |
1239 | if( exists( $seen{$n->id} ) ) { |
63778331 |
1240 | throw( "Detected loop for $witness at " . $n->id ); |
910a0a6d |
1241 | } |
3a2ebbf4 |
1242 | $seen{$n->id} = 1; |
910a0a6d |
1243 | |
861c3e27 |
1244 | my $next = $self->next_reading( $n, $witness ); |
44771cf2 |
1245 | unless( $next ) { |
63778331 |
1246 | throw( "Did not find any path for $witness from reading " . $n->id ); |
44771cf2 |
1247 | } |
910a0a6d |
1248 | push( @readings, $next ); |
1249 | $n = $next; |
e2902068 |
1250 | } |
1251 | # Check that the last reading is our end reading. |
1252 | my $last = $readings[$#readings]; |
63778331 |
1253 | throw( "Last reading found from " . $start->text . |
1254 | " for witness $witness is not the end!" ) # TODO do we get this far? |
3a2ebbf4 |
1255 | unless $last->id eq $end->id; |
e2902068 |
1256 | |
1257 | return @readings; |
1258 | } |
1259 | |
4e5a7b2c |
1260 | =head2 next_reading( $reading, $sigil ); |
8e1394aa |
1261 | |
4a8828f0 |
1262 | Returns the reading that follows the given reading along the given witness |
930ff666 |
1263 | path. |
8e1394aa |
1264 | |
1265 | =cut |
1266 | |
4a8828f0 |
1267 | sub next_reading { |
e2902068 |
1268 | # Return the successor via the corresponding path. |
8e1394aa |
1269 | my $self = shift; |
3a2ebbf4 |
1270 | my $answer = $self->_find_linked_reading( 'next', @_ ); |
2c669bca |
1271 | return undef unless $answer; |
3a2ebbf4 |
1272 | return $self->reading( $answer ); |
8e1394aa |
1273 | } |
1274 | |
4e5a7b2c |
1275 | =head2 prior_reading( $reading, $sigil ) |
8e1394aa |
1276 | |
4a8828f0 |
1277 | Returns the reading that precedes the given reading along the given witness |
930ff666 |
1278 | path. |
8e1394aa |
1279 | |
1280 | =cut |
1281 | |
4a8828f0 |
1282 | sub prior_reading { |
e2902068 |
1283 | # Return the predecessor via the corresponding path. |
8e1394aa |
1284 | my $self = shift; |
3a2ebbf4 |
1285 | my $answer = $self->_find_linked_reading( 'prior', @_ ); |
1286 | return $self->reading( $answer ); |
8e1394aa |
1287 | } |
1288 | |
4a8828f0 |
1289 | sub _find_linked_reading { |
861c3e27 |
1290 | my( $self, $direction, $node, $path ) = @_; |
1291 | |
1292 | # Get a backup if we are dealing with a layered witness |
1293 | my $alt_path; |
1294 | my $aclabel = $self->ac_label; |
1295 | if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) { |
1296 | $alt_path = $1; |
1297 | } |
1298 | |
e2902068 |
1299 | my @linked_paths = $direction eq 'next' |
3a2ebbf4 |
1300 | ? $self->sequence->edges_from( $node ) |
1301 | : $self->sequence->edges_to( $node ); |
e2902068 |
1302 | return undef unless scalar( @linked_paths ); |
8e1394aa |
1303 | |
e2902068 |
1304 | # We have to find the linked path that contains all of the |
1305 | # witnesses supplied in $path. |
1306 | my( @path_wits, @alt_path_wits ); |
4e5a7b2c |
1307 | @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path; |
1308 | @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path; |
e2902068 |
1309 | my $base_le; |
1310 | my $alt_le; |
1311 | foreach my $le ( @linked_paths ) { |
3a2ebbf4 |
1312 | if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) { |
910a0a6d |
1313 | $base_le = $le; |
910a0a6d |
1314 | } |
508fd430 |
1315 | my @le_wits = sort $self->path_witnesses( $le ); |
3a2ebbf4 |
1316 | if( _is_within( \@path_wits, \@le_wits ) ) { |
1317 | # This is the right path. |
1318 | return $direction eq 'next' ? $le->[1] : $le->[0]; |
1319 | } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) { |
1320 | $alt_le = $le; |
1321 | } |
8e1394aa |
1322 | } |
e2902068 |
1323 | # Got this far? Return the alternate path if it exists. |
3a2ebbf4 |
1324 | return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0] |
910a0a6d |
1325 | if $alt_le; |
e2902068 |
1326 | |
1327 | # Got this far? Return the base path if it exists. |
3a2ebbf4 |
1328 | return $direction eq 'next' ? $base_le->[1] : $base_le->[0] |
910a0a6d |
1329 | if $base_le; |
e2902068 |
1330 | |
1331 | # Got this far? We have no appropriate path. |
2c669bca |
1332 | warn "Could not find $direction node from " . $node->id |
910a0a6d |
1333 | . " along path $path"; |
8e1394aa |
1334 | return undef; |
1335 | } |
1336 | |
4a8828f0 |
1337 | # Some set logic. |
1338 | sub _is_within { |
1339 | my( $set1, $set2 ) = @_; |
7854e12e |
1340 | my $ret = @$set1; # will be 0, i.e. false, if set1 is empty |
4a8828f0 |
1341 | foreach my $el ( @$set1 ) { |
910a0a6d |
1342 | $ret = 0 unless grep { /^\Q$el\E$/ } @$set2; |
4a8828f0 |
1343 | } |
1344 | return $ret; |
1345 | } |
1346 | |
4e5a7b2c |
1347 | # Return the string that joins together a list of witnesses for |
1348 | # display on a single path. |
1349 | sub _witnesses_of_label { |
1350 | my( $self, $label ) = @_; |
1351 | my $regex = $self->wit_list_separator; |
1352 | my @answer = split( /\Q$regex\E/, $label ); |
1353 | return @answer; |
b0b4421a |
1354 | } |
1355 | |
d4b75f44 |
1356 | =head2 common_readings |
1357 | |
1358 | Returns the list of common readings in the graph (i.e. those readings that are |
1359 | shared by all non-lacunose witnesses.) |
1360 | |
1361 | =cut |
1362 | |
1363 | sub common_readings { |
1364 | my $self = shift; |
1365 | my @common = grep { $_->is_common } $self->readings; |
1366 | return @common; |
1367 | } |
1368 | |
fae52efd |
1369 | =head2 path_text( $sigil, [, $start, $end ] ) |
b0b4421a |
1370 | |
1371 | Returns the text of a witness (plus its backup, if we are using a layer) |
1372 | as stored in the collation. The text is returned as a string, where the |
1373 | individual readings are joined with spaces and the meta-readings (e.g. |
1374 | lacunae) are omitted. Optional specification of $start and $end allows |
1375 | the generation of a subset of the witness text. |
4e5a7b2c |
1376 | |
b0b4421a |
1377 | =cut |
1378 | |
1379 | sub path_text { |
861c3e27 |
1380 | my( $self, $wit, $start, $end ) = @_; |
b0b4421a |
1381 | $start = $self->start unless $start; |
1382 | $end = $self->end unless $end; |
861c3e27 |
1383 | my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit ); |
629e27b0 |
1384 | my $pathtext = ''; |
1385 | my $last; |
1386 | foreach my $r ( @path ) { |
1387 | if( $r->join_prior || !$last || $last->join_next ) { |
1388 | $pathtext .= $r->text; |
1389 | } else { |
1390 | $pathtext .= ' ' . $r->text; |
1391 | } |
1392 | $last = $r; |
1393 | } |
1394 | return $pathtext; |
b0b4421a |
1395 | } |
4e5a7b2c |
1396 | |
1397 | =head1 INITIALIZATION METHODS |
1398 | |
1399 | These are mostly for use by parsers. |
1400 | |
1401 | =head2 make_witness_path( $witness ) |
1402 | |
1403 | Link the array of readings contained in $witness->path (and in |
1404 | $witness->uncorrected_path if it exists) into collation paths. |
1405 | Clear out the arrays when finished. |
de51424a |
1406 | |
4e5a7b2c |
1407 | =head2 make_witness_paths |
1408 | |
1409 | Call make_witness_path for all witnesses in the tradition. |
1410 | |
1411 | =cut |
930ff666 |
1412 | |
7e450e44 |
1413 | # For use when a collation is constructed from a base text and an apparatus. |
1414 | # We have the sequences of readings and just need to add path edges. |
1f7aa795 |
1415 | # When we are done, clear out the witness path attributes, as they are no |
1416 | # longer needed. |
1417 | # TODO Find a way to replace the witness path attributes with encapsulated functions? |
e2902068 |
1418 | |
6a222840 |
1419 | sub make_witness_paths { |
1420 | my( $self ) = @_; |
910a0a6d |
1421 | foreach my $wit ( $self->tradition->witnesses ) { |
0068967c |
1422 | # print STDERR "Making path for " . $wit->sigil . "\n"; |
910a0a6d |
1423 | $self->make_witness_path( $wit ); |
7854e12e |
1424 | } |
7854e12e |
1425 | } |
1426 | |
6a222840 |
1427 | sub make_witness_path { |
7854e12e |
1428 | my( $self, $wit ) = @_; |
1429 | my @chain = @{$wit->path}; |
15d2d3df |
1430 | my $sig = $wit->sigil; |
fae52efd |
1431 | # Add start and end if necessary |
1432 | unshift( @chain, $self->start ) unless $chain[0] eq $self->start; |
1433 | push( @chain, $self->end ) unless $chain[-1] eq $self->end; |
7854e12e |
1434 | foreach my $idx ( 0 .. $#chain-1 ) { |
910a0a6d |
1435 | $self->add_path( $chain[$idx], $chain[$idx+1], $sig ); |
7854e12e |
1436 | } |
1f7aa795 |
1437 | if( $wit->is_layered ) { |
d9e873d0 |
1438 | @chain = @{$wit->uncorrected_path}; |
fae52efd |
1439 | unshift( @chain, $self->start ) unless $chain[0] eq $self->start; |
1440 | push( @chain, $self->end ) unless $chain[-1] eq $self->end; |
d9e873d0 |
1441 | foreach my $idx( 0 .. $#chain-1 ) { |
1442 | my $source = $chain[$idx]; |
1443 | my $target = $chain[$idx+1]; |
1444 | $self->add_path( $source, $target, $sig.$self->ac_label ) |
1445 | unless $self->has_path( $source, $target, $sig ); |
1446 | } |
15d2d3df |
1447 | } |
1f7aa795 |
1448 | $wit->clear_path; |
1449 | $wit->clear_uncorrected_path; |
e2902068 |
1450 | } |
1451 | |
414cc046 |
1452 | =head2 equivalence_graph( \%readingmap, $startrank, $endrank, @testvector ) |
ac4d7ac2 |
1453 | |
1454 | Returns an equivalence graph of the collation, in which all readings |
1455 | related via a 'colocated' relationship are transformed into a single |
1456 | vertex. Can be used to determine the validity of a new relationship. The |
1457 | mapping between equivalence vertices and reading IDs will be stored in the |
1458 | hash whose reference is passed as readingmap. For a subset of the graph, |
1459 | pass in a start and/or an ending rank (this only works if L<calculate_ranks> |
1460 | has been called at least once.) |
1461 | |
414cc046 |
1462 | It is also possible to pass in a test relationship in @testvector, and get |
1463 | the resulting equivalence graph before the relationship has been made. |
1464 | |
ac4d7ac2 |
1465 | =cut |
1466 | |
1467 | sub equivalence_graph { |
414cc046 |
1468 | my( $self, $map, $start, $end, @newvector ) = @_; |
ac4d7ac2 |
1469 | $start = undef unless $self->end->has_rank; |
1470 | $end = undef unless $self->end->has_rank; |
ac4d7ac2 |
1471 | my $eqgraph = Graph->new(); |
1472 | my $rel_ctr = 0; |
1473 | # Add the nodes |
1474 | foreach my $r ( $self->readings ) { |
1475 | unless( $r eq $self->start || $r eq $self->end ) { |
1476 | next if $start && $r->rank < $start; |
1477 | next if $end && $r->rank > $end; |
1478 | } |
1479 | next if exists $map->{$r->id}; |
414cc046 |
1480 | my @rels = $self->related_readings( $r->id, 'colocated' ); |
1481 | push( @rels, $r->id ); |
1482 | # Make an equivalence vertex |
1483 | my $rn = 'equivalence_' . $rel_ctr++; |
1484 | $eqgraph->add_vertex( $rn ); |
1485 | # Note which readings belong to this vertex. |
1486 | push( @rels, $r->id ); |
1487 | foreach( @rels ) { |
1488 | $map->{$_} = $rn; |
1489 | } |
ac4d7ac2 |
1490 | } |
1491 | |
1492 | # Add the edges. |
1493 | foreach my $p ( $self->paths ) { |
1494 | my $efrom = exists $map->{$p->[0]} ? $map->{$p->[0]} |
1495 | : $map->{$self->start->id}; |
1496 | my $eto = exists $map->{$p->[1]} ? $map->{$p->[1]} |
1497 | : $map->{$self->end->id}; |
1498 | $eqgraph->add_edge( $efrom, $eto ); |
1499 | } |
414cc046 |
1500 | |
1501 | # Collapse the vertices in @newvector if applicable. |
1502 | if( @newvector ) { |
1503 | my( $eqs, $eqt ) = map { $map->{$_} } @newvector; |
1504 | $DB::single = 1 unless $eqs && $eqt; |
1505 | unless( $eqs eq $eqt ) { |
1506 | # Combine the vertices. |
1507 | map { $eqgraph->add_edge( $eqs, $_ ) } $eqgraph->successors( $eqt ); |
1508 | map { $eqgraph->add_edge( $_, $eqs ) } $eqgraph->predecessors( $eqt ); |
1509 | $eqgraph->delete_vertex( $eqt ); |
1510 | } |
1511 | } |
ac4d7ac2 |
1512 | return $eqgraph; |
1513 | } |
1514 | |
4e5a7b2c |
1515 | =head2 calculate_ranks |
1516 | |
1517 | Calculate the reading ranks (that is, their aligned positions relative |
1518 | to each other) for the graph. This can only be called on linear collations. |
1519 | |
b365fbae |
1520 | =begin testing |
1521 | |
1522 | use Text::Tradition; |
1523 | |
1524 | my $cxfile = 't/data/Collatex-16.xml'; |
1525 | my $t = Text::Tradition->new( |
1526 | 'name' => 'inline', |
1527 | 'input' => 'CollateX', |
1528 | 'file' => $cxfile, |
1529 | ); |
1530 | my $c = $t->collation; |
1531 | |
1532 | # Make an svg |
bfcbcecb |
1533 | my $table = $c->alignment_table; |
1534 | ok( $c->has_cached_table, "Alignment table was cached" ); |
1535 | is( $c->alignment_table, $table, "Cached table returned upon second call" ); |
b365fbae |
1536 | $c->calculate_ranks; |
bfcbcecb |
1537 | is( $c->alignment_table, $table, "Cached table retained with no rank change" ); |
679f17e1 |
1538 | $c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } ); |
bfcbcecb |
1539 | isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" ); |
b365fbae |
1540 | |
1541 | =end testing |
1542 | |
4e5a7b2c |
1543 | =cut |
1544 | |
910a0a6d |
1545 | sub calculate_ranks { |
1546 | my $self = shift; |
b365fbae |
1547 | # Save the existing ranks, in case we need to invalidate the cached SVG. |
1548 | my %existing_ranks; |
ac4d7ac2 |
1549 | map { $existing_ranks{$_} = $_->rank } $self->readings; |
910a0a6d |
1550 | # Walk a version of the graph where every node linked by a relationship |
1551 | # edge is fundamentally the same node, and do a topological ranking on |
1552 | # the nodes in this graph. |
910a0a6d |
1553 | my %rel_containers; |
ac4d7ac2 |
1554 | my $topo_graph = $self->equivalence_graph( \%rel_containers ); |
910a0a6d |
1555 | |
1556 | # Now do the rankings, starting with the start node. |
3a2ebbf4 |
1557 | my $topo_start = $rel_containers{$self->start->id}; |
c9bf3dbf |
1558 | my $node_ranks = { $topo_start => 0 }; |
910a0a6d |
1559 | my @curr_origin = ( $topo_start ); |
1560 | # A little iterative function. |
1561 | while( @curr_origin ) { |
c9bf3dbf |
1562 | @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin ); |
910a0a6d |
1563 | } |
1564 | # Transfer our rankings from the topological graph to the real one. |
1565 | foreach my $r ( $self->readings ) { |
3a2ebbf4 |
1566 | if( defined $node_ranks->{$rel_containers{$r->id}} ) { |
1567 | $r->rank( $node_ranks->{$rel_containers{$r->id}} ); |
67da8d6c |
1568 | } else { |
63778331 |
1569 | # Die. Find the last rank we calculated. |
7ec89b0e |
1570 | my @all_defined = sort { ( $node_ranks->{$rel_containers{$a->id}}||-1 ) |
1571 | <=> ( $node_ranks->{$rel_containers{$b->id}}||-1 ) } |
63778331 |
1572 | $self->readings; |
1573 | my $last = pop @all_defined; |
1574 | throw( "Ranks not calculated after $last - do you have a cycle in the graph?" ); |
67da8d6c |
1575 | } |
de51424a |
1576 | } |
bfcbcecb |
1577 | # Do we need to invalidate the cached data? |
1578 | if( $self->has_cached_svg || $self->has_cached_table ) { |
b365fbae |
1579 | foreach my $r ( $self->readings ) { |
7c293912 |
1580 | next if defined( $existing_ranks{$r} ) |
1581 | && $existing_ranks{$r} == $r->rank; |
c1915ab9 |
1582 | # Something has changed, so clear the cache |
bfcbcecb |
1583 | $self->_clear_cache; |
c1915ab9 |
1584 | # ...and recalculate the common readings. |
1585 | $self->calculate_common_readings(); |
b365fbae |
1586 | last; |
1587 | } |
1588 | } |
c1915ab9 |
1589 | # The graph calculation information is now up to date. |
1590 | $self->_graphcalc_done(1); |
8e1394aa |
1591 | } |
3a1f2523 |
1592 | |
910a0a6d |
1593 | sub _assign_rank { |
c9bf3dbf |
1594 | my( $graph, $node_ranks, @current_nodes ) = @_; |
910a0a6d |
1595 | # Look at each of the children of @current_nodes. If all the child's |
1596 | # parents have a rank, assign it the highest rank + 1 and add it to |
c9bf3dbf |
1597 | # @next_nodes. Otherwise skip it; we will return when the highest-ranked |
1598 | # parent gets a rank. |
910a0a6d |
1599 | my @next_nodes; |
1600 | foreach my $c ( @current_nodes ) { |
c9bf3dbf |
1601 | warn "Current reading $c has no rank!" |
1602 | unless exists $node_ranks->{$c}; |
1603 | # print STDERR "Looking at child of node $c, rank " |
1604 | # . $node_ranks->{$c} . "\n"; |
1605 | foreach my $child ( $graph->successors( $c ) ) { |
1606 | next if exists $node_ranks->{$child}; |
910a0a6d |
1607 | my $highest_rank = -1; |
1608 | my $skip = 0; |
c9bf3dbf |
1609 | foreach my $parent ( $graph->predecessors( $child ) ) { |
1610 | if( exists $node_ranks->{$parent} ) { |
1611 | $highest_rank = $node_ranks->{$parent} |
1612 | if $highest_rank <= $node_ranks->{$parent}; |
910a0a6d |
1613 | } else { |
1614 | $skip = 1; |
1615 | last; |
1616 | } |
1617 | } |
1618 | next if $skip; |
c9bf3dbf |
1619 | my $c_rank = $highest_rank + 1; |
1620 | # print STDERR "Assigning rank $c_rank to node $child \n"; |
1621 | $node_ranks->{$child} = $c_rank; |
910a0a6d |
1622 | push( @next_nodes, $child ); |
1623 | } |
1624 | } |
1625 | return @next_nodes; |
4cdd82f1 |
1626 | } |
910a0a6d |
1627 | |
c1915ab9 |
1628 | sub _clear_cache { |
1629 | my $self = shift; |
1630 | $self->wipe_svg if $self->has_cached_svg; |
1631 | $self->wipe_table if $self->has_cached_table; |
1632 | } |
1633 | |
1634 | |
4e5a7b2c |
1635 | =head2 flatten_ranks |
1636 | |
1637 | A convenience method for parsing collation data. Searches the graph for readings |
1638 | with the same text at the same rank, and merges any that are found. |
1639 | |
1640 | =cut |
1641 | |
0e476982 |
1642 | sub flatten_ranks { |
1643 | my $self = shift; |
1644 | my %unique_rank_rdg; |
bf6e338d |
1645 | my $changed; |
0e476982 |
1646 | foreach my $rdg ( $self->readings ) { |
1647 | next unless $rdg->has_rank; |
1648 | my $key = $rdg->rank . "||" . $rdg->text; |
1649 | if( exists $unique_rank_rdg{$key} ) { |
1650 | # Combine! |
56eefa04 |
1651 | # print STDERR "Combining readings at same rank: $key\n"; |
bf6e338d |
1652 | $changed = 1; |
0e476982 |
1653 | $self->merge_readings( $unique_rank_rdg{$key}, $rdg ); |
0ecb975c |
1654 | # TODO see if this now makes a common point. |
0e476982 |
1655 | } else { |
1656 | $unique_rank_rdg{$key} = $rdg; |
1657 | } |
1658 | } |
bf6e338d |
1659 | # If we merged readings, the ranks are still fine but the alignment |
1660 | # table is wrong. Wipe it. |
1661 | $self->wipe_table() if $changed; |
0e476982 |
1662 | } |
4633f9e4 |
1663 | |
1664 | |
d4b75f44 |
1665 | =head2 calculate_common_readings |
1666 | |
1667 | Goes through the graph identifying the readings that appear in every witness |
1668 | (apart from those with lacunae at that spot.) Marks them as common and returns |
1669 | the list. |
1670 | |
1671 | =begin testing |
1672 | |
1673 | use Text::Tradition; |
1674 | |
1675 | my $cxfile = 't/data/Collatex-16.xml'; |
1676 | my $t = Text::Tradition->new( |
1677 | 'name' => 'inline', |
1678 | 'input' => 'CollateX', |
1679 | 'file' => $cxfile, |
1680 | ); |
1681 | my $c = $t->collation; |
1682 | |
1683 | my @common = $c->calculate_common_readings(); |
1684 | is( scalar @common, 8, "Found correct number of common readings" ); |
1685 | my @marked = sort $c->common_readings(); |
1686 | is( scalar @common, 8, "All common readings got marked as such" ); |
679f17e1 |
1687 | my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /; |
d4b75f44 |
1688 | is_deeply( \@marked, \@expected, "Found correct list of common readings" ); |
1689 | |
1690 | =end testing |
1691 | |
1692 | =cut |
1693 | |
1694 | sub calculate_common_readings { |
1695 | my $self = shift; |
1696 | my @common; |
c1915ab9 |
1697 | map { $_->is_common( 0 ) } $self->readings; |
1698 | # Implicitly calls calculate_ranks |
1dd07bda |
1699 | my $table = $self->alignment_table; |
d4b75f44 |
1700 | foreach my $idx ( 0 .. $table->{'length'} - 1 ) { |
7f52eac8 |
1701 | my @row = map { $_->{'tokens'}->[$idx] |
1702 | ? $_->{'tokens'}->[$idx]->{'t'} : '' } |
1703 | @{$table->{'alignment'}}; |
d4b75f44 |
1704 | my %hash; |
1705 | foreach my $r ( @row ) { |
1706 | if( $r ) { |
1707 | $hash{$r->id} = $r unless $r->is_meta; |
1708 | } else { |
1709 | $hash{'UNDEF'} = $r; |
1710 | } |
1711 | } |
1712 | if( keys %hash == 1 && !exists $hash{'UNDEF'} ) { |
1713 | my( $r ) = values %hash; |
1714 | $r->is_common( 1 ); |
1715 | push( @common, $r ); |
1716 | } |
1717 | } |
1718 | return @common; |
1719 | } |
1720 | |
861c3e27 |
1721 | =head2 text_from_paths |
1722 | |
1723 | Calculate the text array for all witnesses from the path, for later consistency |
1724 | checking. Only to be used if there is no non-graph-based way to know the |
1725 | original texts. |
1726 | |
1727 | =cut |
1728 | |
1729 | sub text_from_paths { |
1730 | my $self = shift; |
1731 | foreach my $wit ( $self->tradition->witnesses ) { |
5164a6f0 |
1732 | my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil ); |
1733 | my @text; |
1734 | foreach my $r ( @readings ) { |
1735 | next if $r->is_meta; |
1736 | push( @text, $r->text ); |
1737 | } |
861c3e27 |
1738 | $wit->text( \@text ); |
1739 | if( $wit->is_layered ) { |
5164a6f0 |
1740 | my @ucrdgs = $self->reading_sequence( $self->start, $self->end, |
1741 | $wit->sigil.$self->ac_label ); |
1742 | my @uctext; |
1743 | foreach my $r ( @ucrdgs ) { |
1744 | next if $r->is_meta; |
1745 | push( @uctext, $r->text ); |
1746 | } |
1747 | $wit->layertext( \@uctext ); |
861c3e27 |
1748 | } |
1749 | } |
1750 | } |
0e476982 |
1751 | |
4e5a7b2c |
1752 | =head1 UTILITY FUNCTIONS |
1753 | |
1754 | =head2 common_predecessor( $reading_a, $reading_b ) |
8e1394aa |
1755 | |
4e5a7b2c |
1756 | Find the last reading that occurs in sequence before both the given readings. |
414cc046 |
1757 | At the very least this should be $self->start. |
4e5a7b2c |
1758 | |
1759 | =head2 common_successor( $reading_a, $reading_b ) |
1760 | |
1761 | Find the first reading that occurs in sequence after both the given readings. |
414cc046 |
1762 | At the very least this should be $self->end. |
4e5a7b2c |
1763 | |
22222af9 |
1764 | =begin testing |
1765 | |
1766 | use Text::Tradition; |
1767 | |
1768 | my $cxfile = 't/data/Collatex-16.xml'; |
1769 | my $t = Text::Tradition->new( |
1770 | 'name' => 'inline', |
1771 | 'input' => 'CollateX', |
1772 | 'file' => $cxfile, |
1773 | ); |
1774 | my $c = $t->collation; |
1775 | |
679f17e1 |
1776 | is( $c->common_predecessor( 'n24', 'n23' )->id, |
22222af9 |
1777 | 'n20', "Found correct common predecessor" ); |
679f17e1 |
1778 | is( $c->common_successor( 'n24', 'n23' )->id, |
22222af9 |
1779 | '#END#', "Found correct common successor" ); |
1780 | |
4e5a7b2c |
1781 | is( $c->common_predecessor( 'n19', 'n17' )->id, |
22222af9 |
1782 | 'n16', "Found correct common predecessor for readings on same path" ); |
679f17e1 |
1783 | is( $c->common_successor( 'n21', 'n10' )->id, |
22222af9 |
1784 | '#END#', "Found correct common successor for readings on same path" ); |
1785 | |
1786 | =end testing |
1787 | |
1788 | =cut |
1789 | |
1790 | ## Return the closest reading that is a predecessor of both the given readings. |
1791 | sub common_predecessor { |
1792 | my $self = shift; |
4e5a7b2c |
1793 | my( $r1, $r2 ) = $self->_objectify_args( @_ ); |
027d819c |
1794 | return $self->_common_in_path( $r1, $r2, 'predecessors' ); |
22222af9 |
1795 | } |
1796 | |
1797 | sub common_successor { |
1798 | my $self = shift; |
4e5a7b2c |
1799 | my( $r1, $r2 ) = $self->_objectify_args( @_ ); |
027d819c |
1800 | return $self->_common_in_path( $r1, $r2, 'successors' ); |
22222af9 |
1801 | } |
1802 | |
414cc046 |
1803 | |
1804 | # TODO think about how to do this without ranks... |
027d819c |
1805 | sub _common_in_path { |
22222af9 |
1806 | my( $self, $r1, $r2, $dir ) = @_; |
414cc046 |
1807 | my $iter = $self->end->rank; |
22222af9 |
1808 | my @candidates; |
414cc046 |
1809 | my @last_r1 = ( $r1 ); |
1810 | my @last_r2 = ( $r2 ); |
1811 | # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' ); |
22222af9 |
1812 | my %all_seen; |
414cc046 |
1813 | # print STDERR "Finding common $dir for $r1, $r2\n"; |
22222af9 |
1814 | while( !@candidates ) { |
414cc046 |
1815 | last unless $iter--; # Avoid looping infinitely |
1816 | # Iterate separately down the graph from r1 and r2 |
1817 | my( @new_lc1, @new_lc2 ); |
1818 | foreach my $lc ( @last_r1 ) { |
1819 | foreach my $p ( $lc->$dir ) { |
1820 | if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) { |
1821 | # print STDERR "Path candidate $p from $lc\n"; |
1822 | push( @candidates, $p ); |
002e3600 |
1823 | } elsif( !$all_seen{$p->id} ) { |
414cc046 |
1824 | $all_seen{$p->id} = 'r1'; |
1825 | push( @new_lc1, $p ); |
1826 | } |
1827 | } |
1828 | } |
1829 | foreach my $lc ( @last_r2 ) { |
22222af9 |
1830 | foreach my $p ( $lc->$dir ) { |
414cc046 |
1831 | if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) { |
1832 | # print STDERR "Path candidate $p from $lc\n"; |
22222af9 |
1833 | push( @candidates, $p ); |
002e3600 |
1834 | } elsif( !$all_seen{$p->id} ) { |
414cc046 |
1835 | $all_seen{$p->id} = 'r2'; |
1836 | push( @new_lc2, $p ); |
22222af9 |
1837 | } |
1838 | } |
1839 | } |
414cc046 |
1840 | @last_r1 = @new_lc1; |
1841 | @last_r2 = @new_lc2; |
22222af9 |
1842 | } |
1843 | my @answer = sort { $a->rank <=> $b->rank } @candidates; |
1844 | return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer ); |
1845 | } |
1846 | |
63778331 |
1847 | sub throw { |
1848 | Text::Tradition::Error->throw( |
1849 | 'ident' => 'Collation error', |
1850 | 'message' => $_[0], |
1851 | ); |
1852 | } |
1853 | |
dd3b58b0 |
1854 | no Moose; |
1855 | __PACKAGE__->meta->make_immutable; |
e867486f |
1856 | |
027d819c |
1857 | =head1 LICENSE |
e867486f |
1858 | |
027d819c |
1859 | This package is free software and is provided "as is" without express |
1860 | or implied warranty. You can redistribute it and/or modify it under |
1861 | the same terms as Perl itself. |
e867486f |
1862 | |
027d819c |
1863 | =head1 AUTHOR |
e867486f |
1864 | |
027d819c |
1865 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |