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