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1 | package Text::Tradition::Stemma; |
2 | |
e79c23c7 |
3 | use Encode qw( decode_utf8 ); |
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4 | use File::Temp; |
e05997e2 |
5 | use Graph; |
6 | use Graph::Reader::Dot; |
e79c23c7 |
7 | use IPC::Run qw/ run binary /; |
63778331 |
8 | use Text::Tradition::Error; |
40f19742 |
9 | use Moose; |
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10 | |
027d819c |
11 | =head1 NAME |
12 | |
13 | Text::Tradition::Stemma - a representation of a I<stemma codicum> for a Text::Tradition |
14 | |
15 | =head1 SYNOPSIS |
16 | |
17 | use Text::Tradition; |
18 | my $t = Text::Tradition->new( |
19 | 'name' => 'this is a text', |
20 | 'input' => 'TEI', |
21 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
22 | |
23 | my $s = $tradition->add_stemma( dotfile => '/path/to/stemma.dot' ); |
24 | |
25 | =head1 DESCRIPTION |
26 | |
27 | Text::Tradition is a library for representation and analysis of collated |
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28 | texts, particularly medieval ones. The Stemma is a representation of the |
29 | copying relationships between the witnesses in a Tradition, modelled with |
30 | a connected rooted directed acyclic graph (CRDAG). |
027d819c |
31 | |
32 | =head1 DOT SYNTAX |
33 | |
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34 | The easiest way to define a stemma is to use a special form of the 'dot' |
35 | syntax of GraphViz. |
027d819c |
36 | |
37 | Each stemma opens with the line |
38 | |
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39 | digraph "Name of Stemma" { |
027d819c |
40 | |
41 | and continues with a list of all manuscript witnesses in the stemma, whether |
42 | extant witnesses or missing archetypes or hyparchetypes. Each of these is |
43 | listed by its sigil on its own line, e.g.: |
44 | |
45 | alpha [ class=hypothetical ] |
46 | 1 [ class=hypothetical,label=* ] |
47 | Ms4 [ class=extant ] |
48 | |
49 | Extant witnesses are listed with class=extant; missing or postulated witnesses |
50 | are listed with class=hypothetical. Anonymous hyparchetypes must be given a |
51 | unique name or number, but can be represented as anonymous with the addition |
52 | of 'label=*' to their lines. Greek letters or other special characters may be |
53 | used as names, but they must always be wrapped in double quotes. |
54 | |
55 | Links between manuscripts are then listed with arrow notation, as below. These |
56 | lines show the direction of copying, one step at a time, for the entire stemma. |
57 | |
58 | alpha -> 1 |
59 | 1 -> Ms4 |
60 | |
61 | The final line in the definition should be the closing brace: |
62 | |
63 | } |
64 | |
65 | Thus for a set of extant manuscripts A, B, and C, where A and B were copied |
66 | from the archetype O and C was copied from B, the definition would be: |
67 | |
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68 | digraph "Test stemma 1" { |
027d819c |
69 | O [ class=hypothetical] |
70 | A [ class=extant ] |
71 | B [ class=extant ] |
72 | C [ class=extant ] |
73 | O -> A |
74 | O -> B |
75 | B -> C |
76 | } |
77 | |
78 | =head1 CONSTRUCTOR |
79 | |
80 | =head2 new |
81 | |
82 | The constructor. This should generally be called from Text::Tradition, but |
83 | if called directly it takes the following options: |
84 | |
85 | =over |
86 | |
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87 | =item * dot - A filehandle open to a DOT representation of the stemma graph. |
88 | |
ea45d2a6 |
89 | =item * graph - If no DOT specification is given, you can pass a Graph object |
90 | instead. The vertices of the graph should have an attribute 'class' set to |
91 | either of the values 'extant' or 'hypothetical'. |
92 | |
93 | =item * is_undirected - If the graph specification (or graph object) is for an |
94 | undirected graph (e.g. a phylogenetic tree), this should be set. |
95 | |
027d819c |
96 | =back |
97 | |
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98 | =begin testing |
99 | |
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100 | use TryCatch; |
101 | |
102 | use_ok( 'Text::Tradition::Stemma' ); |
103 | |
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104 | # Try to create a bad graph |
02b6340e |
105 | my $baddotfh; |
106 | open( $baddotfh, 't/data/besoin_bad.dot' ) or die "Could not open test dotfile"; |
107 | try { |
108 | my $stemma = Text::Tradition::Stemma->new( dot => $baddotfh ); |
109 | ok( 0, "Created broken stemma from dotfile with syntax error" ); |
110 | } catch( Text::Tradition::Error $e ) { |
111 | like( $e->message, qr/^Error trying to parse/, "Syntax error in dot threw exception" ); |
64a36834 |
112 | } |
113 | |
114 | # Create a good graph |
115 | my $dotfh; |
116 | open( $dotfh, 't/data/florilegium.dot' ) or die "Could not open test dotfile"; |
117 | binmode( $dotfh, ':utf8' ); |
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118 | my $stemma = Text::Tradition::Stemma->new( dot => $dotfh ); |
64a36834 |
119 | is( ref( $stemma ), 'Text::Tradition::Stemma', "Created stemma from good dotfile" ); |
120 | is( scalar $stemma->witnesses, 13, "Found correct number of extant witnesses" ); |
121 | is( scalar $stemma->hypotheticals, 8, "Found correct number of extant hypotheticals" ); |
f96630e3 |
122 | ok( $stemma->has_identifier, "Stemma identifier was found in dot" ); |
123 | is( $stemma->identifier, 'Coislinianum lineage', "Correct stemma identifier was found in dot" ); |
64a36834 |
124 | my $found_unicode_sigil; |
125 | foreach my $h ( $stemma->hypotheticals ) { |
126 | $found_unicode_sigil = 1 if $h eq "\x{3b1}"; |
127 | } |
128 | ok( $found_unicode_sigil, "Found a correctly encoded Unicode sigil" ); |
129 | |
cb741417 |
130 | # Create an undirected graph |
131 | my $undirdotfh; |
132 | open( $undirdotfh, 't/data/besoin_undirected.dot' ) or die "Could not open test dotfile"; |
133 | binmode( $undirdotfh, ':utf8' ); |
134 | my $udstemma = Text::Tradition::Stemma->new( dot => $undirdotfh ); |
135 | is( ref( $udstemma ), 'Text::Tradition::Stemma', "Created stemma from undirected dotfile" ); |
136 | is( scalar $udstemma->witnesses, 13, "Found correct number of extant witnesses" ); |
137 | is( scalar $udstemma->hypotheticals, 12, "Found correct number of hypotheticals" ); |
138 | ok( $udstemma->is_undirected, "Stemma was recorded as undirected" ); |
6665a327 |
139 | is( $udstemma->identifier, "RHM stemma", "Undirected graph retained its name" ); |
ea45d2a6 |
140 | |
64a36834 |
141 | =end testing |
142 | |
027d819c |
143 | =cut |
144 | |
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145 | has collation => ( |
146 | is => 'ro', |
147 | isa => 'Text::Tradition::Collation', |
ea45d2a6 |
148 | clearer => 'clear_collation', # interim measure to remove refs in DB |
8d9a1cd8 |
149 | weak_ref => 1, |
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150 | ); |
151 | |
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152 | has graph => ( |
153 | is => 'rw', |
154 | isa => 'Graph', |
155 | predicate => 'has_graph', |
156 | ); |
ea45d2a6 |
157 | |
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158 | has identifier => ( |
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159 | is => 'ro', |
98f22390 |
160 | isa => 'Str', |
161 | writer => 'set_identifier', |
162 | predicate => 'has_identifier', |
ea45d2a6 |
163 | ); |
98f22390 |
164 | |
e05997e2 |
165 | sub BUILD { |
166 | my( $self, $args ) = @_; |
167 | # If we have been handed a dotfile, initialize it into a graph. |
168 | if( exists $args->{'dot'} ) { |
027d819c |
169 | $self->_graph_from_dot( $args->{'dot'} ); |
98f22390 |
170 | } |
c0ccdb62 |
171 | } |
172 | |
ea45d2a6 |
173 | before 'graph' => sub { |
174 | my $self = shift; |
175 | if( @_ ) { |
176 | # Make sure all unclassed graph nodes are marked extant. |
177 | my $g = $_[0]; |
178 | throw( "Cannot set graph to a non-Graph object" ) |
cb741417 |
179 | unless $g->isa( 'Graph' ); |
ea45d2a6 |
180 | foreach my $v ( $g->vertices ) { |
181 | unless( $g->has_vertex_attribute( $v, 'class' ) ) { |
182 | $g->set_vertex_attribute( $v, 'class', 'extant' ); |
183 | } |
184 | } |
98f22390 |
185 | } |
186 | }; |
187 | |
027d819c |
188 | sub _graph_from_dot { |
8d9a1cd8 |
189 | my( $self, $dotfh ) = @_; |
8d9a1cd8 |
190 | my $reader = Graph::Reader::Dot->new(); |
64a36834 |
191 | # Redirect STDOUT in order to trap any error messages - syntax errors |
192 | # are evidently not fatal. |
02b6340e |
193 | my $graph; |
194 | my $reader_out; |
cb741417 |
195 | my $reader_err; |
02b6340e |
196 | { |
197 | local(*STDOUT); |
198 | open( STDOUT, ">", \$reader_out ); |
cb741417 |
199 | local(*STDERR); |
200 | open( STDERR, ">", \$reader_err ); |
02b6340e |
201 | $graph = $reader->read_graph( $dotfh ); |
202 | close STDOUT; |
cb741417 |
203 | close STDERR; |
02b6340e |
204 | } |
64a36834 |
205 | if( $reader_out && $reader_out =~ /error/s ) { |
206 | throw( "Error trying to parse dot: $reader_out" ); |
207 | } elsif( !$graph ) { |
208 | throw( "Failed to create graph from dot" ); |
209 | } |
6665a327 |
210 | ## HORRIBLE HACK but there is no API access to graph attributes! |
211 | my $graph_id = exists $graph->[4]->{'name'} ? $graph->[4]->{'name'} : 'stemma'; |
cb741417 |
212 | # Correct for implicit graph -> digraph quirk of reader |
213 | if( $reader_err && $reader_err =~ /graph will be treated as digraph/ ) { |
214 | my $udgraph = $graph->undirected_copy; |
215 | foreach my $v ( $graph->vertices ) { |
216 | $udgraph->set_vertex_attributes( $v, $graph->get_vertex_attributes( $v ) ); |
217 | } |
218 | $graph = $udgraph; |
219 | } |
64a36834 |
220 | $self->graph( $graph ); |
6665a327 |
221 | $self->set_identifier( $graph_id ); |
8d9a1cd8 |
222 | } |
223 | |
98f22390 |
224 | sub is_undirected { |
225 | my( $self ) = @_; |
226 | return undef unless $self->has_graph; |
227 | return $self->graph->is_undirected; |
228 | } |
229 | |
027d819c |
230 | =head1 METHODS |
231 | |
232 | =head2 as_dot( \%options ) |
233 | |
234 | Returns a normal dot representation of the stemma layout, suitable for rendering |
235 | with GraphViz. Options include: |
236 | |
237 | =over |
238 | |
239 | =item * graph - A hashref of global graph options. |
240 | |
241 | =item * node - A hashref of global node options. |
242 | |
243 | =item * edge - A hashref of global edge options. |
244 | |
245 | =back |
246 | |
247 | See the GraphViz documentation for the list of available options. |
248 | |
249 | =cut |
250 | |
8d9a1cd8 |
251 | sub as_dot { |
e367f5c0 |
252 | my( $self, $opts ) = @_; |
7a7c249c |
253 | |
335a62ef |
254 | ## See if we are including any a.c. witnesses in this graph. |
255 | my $graph = $self->graph; |
256 | if( exists $opts->{'layerwits'} ) { |
5c44c598 |
257 | my $extant = {}; |
258 | map { $extant->{$_} = 1 } $self->witnesses; |
259 | $graph = $self->situation_graph( $extant, $opts->{'layerwits'} ); |
335a62ef |
260 | } |
261 | |
7a7c249c |
262 | # Get default and specified options |
e02340f3 |
263 | my %graphopts = ( |
264 | # 'ratio' => 1, |
f05e891c |
265 | 'bgcolor' => 'transparent', |
e02340f3 |
266 | ); |
7a7c249c |
267 | my %nodeopts = ( |
268 | 'fontsize' => 11, |
7a7c249c |
269 | 'style' => 'filled', |
270 | 'fillcolor' => 'white', |
e02340f3 |
271 | 'color' => 'white', |
7a7c249c |
272 | 'shape' => 'ellipse', # Shape for the extant nodes |
273 | ); |
274 | my %edgeopts = ( |
e02340f3 |
275 | 'arrowhead' => 'none', |
7a7c249c |
276 | ); |
277 | @graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}} |
278 | if $opts->{'graph'}; |
279 | @nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}} |
280 | if $opts->{'node'}; |
281 | @edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}} |
282 | if $opts->{'edge'}; |
335a62ef |
283 | |
ea45d2a6 |
284 | my $gdecl = $graph->is_directed ? 'digraph' : 'graph'; |
f96630e3 |
285 | my $gname = $self->has_identifier ? '"' . $self->identifier . '"' |
286 | : 'stemma'; |
7a7c249c |
287 | my @dotlines; |
f96630e3 |
288 | push( @dotlines, "$gdecl $gname {" ); |
7a7c249c |
289 | ## Print out the global attributes |
290 | push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts; |
291 | push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts; |
7a7c249c |
292 | push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts; |
293 | |
294 | # Add each of the nodes. |
335a62ef |
295 | foreach my $n ( $graph->vertices ) { |
c753ea40 |
296 | my %vattr = ( 'id' => $n ); # Set the SVG element ID to the sigil itself |
335a62ef |
297 | if( $graph->has_vertex_attribute( $n, 'label' ) ) { |
c753ea40 |
298 | $vattr{'label'} = $graph->get_vertex_attribute( $n, 'label' ); |
e79c23c7 |
299 | } |
c753ea40 |
300 | push( @dotlines, _make_dotline( $n, %vattr ) ); |
e79c23c7 |
301 | } |
7a7c249c |
302 | # Add each of our edges. |
335a62ef |
303 | foreach my $e ( $graph->edges ) { |
986bbd1b |
304 | my( $from, $to ) = map { _dotquote( $_ ) } @$e; |
ea45d2a6 |
305 | my $connector = $graph->is_directed ? '->' : '--'; |
306 | push( @dotlines, " $from $connector $to;" ); |
7a7c249c |
307 | } |
308 | push( @dotlines, '}' ); |
e79c23c7 |
309 | |
7a7c249c |
310 | return join( "\n", @dotlines ); |
311 | } |
312 | |
0bded693 |
313 | =head2 alter_graph( $dotstring ) |
314 | |
315 | Alters the graph of this stemma according to the definition specified |
316 | in $dotstring. |
317 | |
318 | =cut |
319 | |
320 | sub alter_graph { |
321 | my( $self, $dotstring ) = @_; |
322 | my $dotfh; |
323 | open $dotfh, '<', \$dotstring; |
f90b2bde |
324 | binmode $dotfh, ':utf8'; |
0bded693 |
325 | $self->_graph_from_dot( $dotfh ); |
326 | } |
327 | |
335a62ef |
328 | =head2 editable( $opts ) |
027d819c |
329 | |
5c44c598 |
330 | =head2 editable_graph( $graph, $opts ) |
331 | |
88a6bac5 |
332 | Returns a version of the graph rendered in our definition format. The |
335a62ef |
333 | output separates statements with a newline; set $opts->{'linesep'} to the |
334 | empty string or to a space if the result is to be sent via JSON. |
335 | |
5c44c598 |
336 | If a situational version of the stemma is required, the arguments for |
337 | situation_graph should be passed via $opts->{'extant'} and $opts->{'layerwits'}. |
027d819c |
338 | |
339 | =cut |
7a7c249c |
340 | |
7a7c249c |
341 | sub editable { |
5c44c598 |
342 | my( $self, $opts ) = @_; |
335a62ef |
343 | my $graph = $self->graph; |
f96630e3 |
344 | if( $self->has_identifier ) { |
345 | $opts->{'name'} = $self->identifier; |
346 | } |
5c44c598 |
347 | ## See if we need an editable version of a situational graph. |
348 | if( exists $opts->{'layerwits'} || exists $opts->{'extant'} ) { |
349 | my $extant = delete $opts->{'extant'} || {}; |
350 | my $layerwits = delete $opts->{'layerwits'} || []; |
351 | $graph = $self->situation_graph( $extant, $layerwits ); |
335a62ef |
352 | } |
5c44c598 |
353 | return editable_graph( $graph, $opts ); |
354 | } |
355 | |
356 | sub editable_graph { |
357 | my( $graph, $opts ) = @_; |
335a62ef |
358 | |
359 | # Create the graph |
360 | my $join = ( $opts && exists $opts->{'linesep'} ) ? $opts->{'linesep'} : "\n"; |
ea45d2a6 |
361 | my $gdecl = $graph->is_undirected ? 'graph' : 'digraph'; |
f96630e3 |
362 | my $gname = exists $opts->{'name'} ? '"' . $opts->{'name'} . '"' |
363 | : 'stemma'; |
7a7c249c |
364 | my @dotlines; |
f96630e3 |
365 | push( @dotlines, "$gdecl $gname {" ); |
7a7c249c |
366 | my @real; # A cheap sort |
5c44c598 |
367 | foreach my $n ( sort $graph->vertices ) { |
368 | my $c = $graph->get_vertex_attribute( $n, 'class' ); |
7a7c249c |
369 | $c = 'extant' unless $c; |
370 | if( $c eq 'extant' ) { |
371 | push( @real, $n ); |
372 | } else { |
373 | push( @dotlines, _make_dotline( $n, 'class' => $c ) ); |
374 | } |
e367f5c0 |
375 | } |
7a7c249c |
376 | # Now do the real ones |
377 | foreach my $n ( @real ) { |
378 | push( @dotlines, _make_dotline( $n, 'class' => 'extant' ) ); |
379 | } |
5c44c598 |
380 | foreach my $e ( sort _by_vertex $graph->edges ) { |
986bbd1b |
381 | my( $from, $to ) = map { _dotquote( $_ ) } @$e; |
ea45d2a6 |
382 | my $conn = $graph->is_undirected ? '--' : '->'; |
383 | push( @dotlines, " $from $conn $to;" ); |
7a7c249c |
384 | } |
385 | push( @dotlines, '}' ); |
88a6bac5 |
386 | return join( $join, @dotlines ); |
7a7c249c |
387 | } |
388 | |
389 | sub _make_dotline { |
390 | my( $obj, %attr ) = @_; |
391 | my @pairs; |
392 | foreach my $k ( keys %attr ) { |
986bbd1b |
393 | my $v = _dotquote( $attr{$k} ); |
394 | push( @pairs, "$k=$v" ); |
7a7c249c |
395 | } |
986bbd1b |
396 | return sprintf( " %s [ %s ];", _dotquote( $obj ), join( ', ', @pairs ) ); |
8d9a1cd8 |
397 | } |
398 | |
986bbd1b |
399 | sub _dotquote { |
400 | my( $str ) = @_; |
401 | return $str if $str =~ /^[A-Za-z0-9]+$/; |
402 | $str =~ s/\"/\\\"/g; |
403 | $str = '"' . $str . '"'; |
404 | return $str; |
405 | } |
406 | |
7a7c249c |
407 | sub _by_vertex { |
408 | return $a->[0].$a->[1] cmp $b->[0].$b->[1]; |
409 | } |
8d9a1cd8 |
410 | |
5c44c598 |
411 | =head2 situation_graph( $extant, $layered ) |
335a62ef |
412 | |
ea45d2a6 |
413 | Returns a graph which is the original stemma graph with all witnesses not |
414 | in the %$extant hash marked as hypothetical, and witness layers added to |
415 | the graph according to the list in @$layered. A layered (a.c.) witness is |
416 | added as a parent of its main version, and additionally shares all other |
417 | parents and children with that version. |
335a62ef |
418 | |
419 | =cut |
420 | |
5c44c598 |
421 | sub situation_graph { |
ace5fce5 |
422 | my( $self, $extant, $layerwits, $layerlabel ) = @_; |
5c44c598 |
423 | |
424 | my $graph = $self->graph->copy; |
425 | foreach my $vertex ( $graph->vertices ) { |
426 | # Set as extant any vertex that is extant in the stemma AND |
427 | # exists in the $extant hash. |
428 | my $class = 'hypothetical'; |
429 | $class = 'extant' if exists $extant->{$vertex} && $extant->{$vertex} && |
430 | $self->graph->get_vertex_attribute( $vertex, 'class' ) ne 'hypothetical'; |
431 | $graph->set_vertex_attribute( $vertex, 'class', $class ); |
432 | } |
433 | |
335a62ef |
434 | # For each 'layered' witness in the layerwits array, add it to the graph |
435 | # as an ancestor of the 'main' witness, and otherwise with the same parent/ |
436 | # child links as its main analogue. |
437 | # TOOD Handle case where B is copied from A but corrected from C |
ace5fce5 |
438 | $layerlabel = ' (a.c.)' unless $layerlabel; |
335a62ef |
439 | foreach my $lw ( @$layerwits ) { |
440 | # Add the layered witness and set it with the same attributes as |
441 | # its 'main' analogue |
5c44c598 |
442 | throw( "Cannot add a layer to a hypothetical witness $lw" ) |
443 | unless $graph->get_vertex_attribute( $lw, 'class' ) eq 'extant'; |
ace5fce5 |
444 | my $lwac = $lw . $layerlabel; |
335a62ef |
445 | $graph->add_vertex( $lwac ); |
446 | $graph->set_vertex_attributes( $lwac, |
447 | $graph->get_vertex_attributes( $lw ) ); |
448 | |
449 | # Set it as ancestor to the main witness |
450 | $graph->add_edge( $lwac, $lw ); |
451 | |
452 | # Give it the same ancestors and descendants as the main witness has, |
453 | # bearing in mind that those ancestors and descendants might also just |
454 | # have had a layered witness defined. |
455 | foreach my $v ( $graph->predecessors( $lw ) ) { |
456 | next if $v eq $lwac; # Don't add a loop |
457 | $graph->add_edge( $v, $lwac ); |
ace5fce5 |
458 | $graph->add_edge( $v.$layerlabel, $lwac ) |
459 | if $graph->has_vertex( $v.$layerlabel ); |
335a62ef |
460 | } |
461 | foreach my $v ( $graph->successors( $lw ) ) { |
462 | next if $v eq $lwac; # but this shouldn't occur |
463 | $graph->add_edge( $lwac, $v ); |
ace5fce5 |
464 | $graph->add_edge( $lwac, $v.$layerlabel ) |
465 | if $graph->has_vertex( $v.$layerlabel ); |
335a62ef |
466 | } |
467 | } |
468 | return $graph; |
469 | } |
470 | |
027d819c |
471 | =head2 as_svg |
472 | |
473 | Returns an SVG representation of the graph, calling as_dot first. |
474 | |
475 | =cut |
476 | |
8d9a1cd8 |
477 | sub as_svg { |
478 | my( $self, $opts ) = @_; |
479 | my $dot = $self->as_dot( $opts ); |
ea45d2a6 |
480 | my @cmd = ( '-Tsvg' ); |
481 | unshift( @cmd, $self->is_undirected ? 'neato' : 'dot' ); |
3bf5d6f1 |
482 | my $svg; |
e79c23c7 |
483 | my $dotfile = File::Temp->new(); |
e79c23c7 |
484 | binmode $dotfile, ':utf8'; |
8d9a1cd8 |
485 | print $dotfile $dot; |
459c39b3 |
486 | close $dotfile; |
e79c23c7 |
487 | push( @cmd, $dotfile->filename ); |
488 | run( \@cmd, ">", binary(), \$svg ); |
428bcf0b |
489 | return decode_utf8( $svg ); |
e79c23c7 |
490 | } |
491 | |
027d819c |
492 | =head2 witnesses |
493 | |
494 | Returns a list of the extant witnesses represented in the stemma. |
495 | |
496 | =cut |
497 | |
08e0fb85 |
498 | sub witnesses { |
499 | my $self = shift; |
500 | my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' } |
501 | $self->graph->vertices; |
502 | return @wits; |
503 | } |
504 | |
06e7cbc7 |
505 | =head2 hypotheticals |
506 | |
507 | Returns a list of the hypothetical witnesses represented in the stemma. |
508 | |
509 | =cut |
510 | |
bebec0e9 |
511 | sub hypotheticals { |
512 | my $self = shift; |
513 | my @wits = grep |
514 | { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' } |
515 | $self->graph->vertices; |
516 | return @wits; |
517 | } |
518 | |
37bf09f4 |
519 | =head2 root_graph( $root_vertex ) |
ea45d2a6 |
520 | |
521 | If the stemma graph is undirected, make it directed with $root_vertex at the root. |
522 | If it is directed, re-root it. |
523 | |
524 | =cut |
525 | |
526 | sub root_graph { |
527 | my( $self, $rootvertex ) = @_; |
528 | my $graph; |
907f6671 |
529 | my $ident = $self->identifier; # will have to restore this at the end |
ea45d2a6 |
530 | if( $self->is_undirected ) { |
531 | $graph = $self->graph; |
532 | } else { |
533 | # Make an undirected version of this graph. |
534 | $graph = $self->graph->undirected_copy(); |
535 | } |
1cf6dd32 |
536 | # First, ensure that the requested root is actually a vertex in the graph. |
537 | unless( $graph->has_vertex( $rootvertex ) ) { |
538 | throw( "Cannot orient graph $graph on nonexistent vertex $rootvertex" ); |
539 | } |
540 | |
541 | # Now make a directed version of the graph. |
ea45d2a6 |
542 | my $rooted = Graph->new(); |
543 | $rooted->add_vertex( $rootvertex ); |
544 | my @next = ( $rootvertex ); |
545 | while( @next ) { |
546 | my @children; |
547 | foreach my $v ( @next ) { |
548 | # Place its not-placed neighbors (ergo children) in the tree |
549 | # and connect them |
550 | foreach my $n ( grep { !$rooted->has_vertex( $_ ) } |
551 | $graph->neighbors( $v ) ) { |
552 | $rooted->add_vertex( $n ); |
553 | $rooted->add_edge( $v, $n ); |
554 | push( @children, $n ); |
555 | } |
556 | } |
557 | @next = @children; |
558 | } |
559 | # Set the vertex classes |
560 | map { $rooted->set_vertex_attribute( $_, 'class', 'hypothetical' ) } |
1cf6dd32 |
561 | $self->hypotheticals; |
562 | map { $rooted->set_vertex_attribute( $_, 'class', 'extant' ) } |
563 | $self->witnesses; |
564 | $self->graph( $rooted ); |
907f6671 |
565 | $self->set_identifier( $ident ); |
ea45d2a6 |
566 | } |
567 | |
568 | |
63778331 |
569 | sub throw { |
570 | Text::Tradition::Error->throw( |
571 | 'ident' => 'Stemma error', |
572 | 'message' => $_[0], |
573 | ); |
574 | } |
575 | |
576 | |
9463b0bf |
577 | no Moose; |
578 | __PACKAGE__->meta->make_immutable; |
579 | |
580 | 1; |
027d819c |
581 | |
582 | =head1 LICENSE |
583 | |
584 | This package is free software and is provided "as is" without express |
585 | or implied warranty. You can redistribute it and/or modify it under |
586 | the same terms as Perl itself. |
587 | |
588 | =head1 AUTHOR |
589 | |
590 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |