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1 | package Text::Tradition::Stemma; |
2 | |
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3 | use Bio::Phylo::IO; |
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4 | use Encode qw( decode_utf8 ); |
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5 | use File::Temp; |
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6 | use Graph; |
7 | use Graph::Reader::Dot; |
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8 | use IPC::Run qw/ run binary /; |
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9 | use Text::Tradition::Error; |
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10 | use Text::Tradition::StemmaUtil qw/ character_input phylip_pars 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 | |
41 | digraph Stemma { |
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 | |
70 | digraph Stemma { |
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 | |
89 | =item * collation - The collation with which the stemma is associated. |
90 | |
91 | =item * dot - A filehandle open to a DOT representation of the stemma graph. |
92 | |
93 | =back |
94 | |
95 | =cut |
96 | |
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97 | has collation => ( |
98 | is => 'ro', |
99 | isa => 'Text::Tradition::Collation', |
100 | required => 1, |
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101 | weak_ref => 1, |
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102 | ); |
103 | |
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104 | has graph => ( |
105 | is => 'rw', |
106 | isa => 'Graph', |
107 | predicate => 'has_graph', |
108 | ); |
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109 | |
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110 | sub BUILD { |
111 | my( $self, $args ) = @_; |
112 | # If we have been handed a dotfile, initialize it into a graph. |
113 | if( exists $args->{'dot'} ) { |
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114 | $self->_graph_from_dot( $args->{'dot'} ); |
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115 | } |
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116 | } |
117 | |
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118 | sub _graph_from_dot { |
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119 | my( $self, $dotfh ) = @_; |
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120 | my $reader = Graph::Reader::Dot->new(); |
121 | my $graph = $reader->read_graph( $dotfh ); |
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122 | if( $graph ) { |
123 | $self->graph( $graph ); |
124 | # Go through the nodes and set any non-hypothetical node to extant. |
125 | foreach my $v ( $self->graph->vertices ) { |
126 | $self->graph->set_vertex_attribute( $v, 'class', 'extant' ) |
127 | unless $self->graph->has_vertex_attribute( $v, 'class' ); |
128 | } |
129 | } else { |
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130 | throw( "Failed to parse dot in $dotfh" ); |
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131 | } |
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132 | } |
133 | |
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134 | =head1 METHODS |
135 | |
136 | =head2 as_dot( \%options ) |
137 | |
138 | Returns a normal dot representation of the stemma layout, suitable for rendering |
139 | with GraphViz. Options include: |
140 | |
141 | =over |
142 | |
143 | =item * graph - A hashref of global graph options. |
144 | |
145 | =item * node - A hashref of global node options. |
146 | |
147 | =item * edge - A hashref of global edge options. |
148 | |
149 | =back |
150 | |
151 | See the GraphViz documentation for the list of available options. |
152 | |
153 | =cut |
154 | |
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155 | sub as_dot { |
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156 | my( $self, $opts ) = @_; |
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157 | |
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158 | ## See if we are including any a.c. witnesses in this graph. |
159 | my $graph = $self->graph; |
160 | if( exists $opts->{'layerwits'} ) { |
161 | $graph = $self->extend_graph( $opts->{'layerwits'} ); |
162 | } |
163 | |
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164 | # Get default and specified options |
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165 | my %graphopts = ( |
166 | # 'ratio' => 1, |
167 | ); |
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168 | my %nodeopts = ( |
169 | 'fontsize' => 11, |
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170 | 'style' => 'filled', |
171 | 'fillcolor' => 'white', |
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172 | 'color' => 'white', |
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173 | 'shape' => 'ellipse', # Shape for the extant nodes |
174 | ); |
175 | my %edgeopts = ( |
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176 | 'arrowhead' => 'none', |
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177 | ); |
178 | @graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}} |
179 | if $opts->{'graph'}; |
180 | @nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}} |
181 | if $opts->{'node'}; |
182 | @edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}} |
183 | if $opts->{'edge'}; |
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184 | |
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185 | my @dotlines; |
186 | push( @dotlines, 'digraph stemma {' ); |
187 | ## Print out the global attributes |
188 | push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts; |
189 | push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts; |
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190 | push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts; |
191 | |
192 | # Add each of the nodes. |
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193 | foreach my $n ( $graph->vertices ) { |
194 | if( $graph->has_vertex_attribute( $n, 'label' ) ) { |
195 | my $ltext = $graph->get_vertex_attribute( $n, 'label' ); |
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196 | push( @dotlines, _make_dotline( $n, 'label' => $ltext ) ); |
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197 | } else { |
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198 | # Use the default display settings. |
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199 | $n = _dotquote( $n ); |
7a7c249c |
200 | push( @dotlines, " $n;" ); |
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201 | } |
202 | } |
7a7c249c |
203 | # Add each of our edges. |
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204 | foreach my $e ( $graph->edges ) { |
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205 | my( $from, $to ) = map { _dotquote( $_ ) } @$e; |
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206 | push( @dotlines, " $from -> $to;" ); |
207 | } |
208 | push( @dotlines, '}' ); |
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209 | |
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210 | return join( "\n", @dotlines ); |
211 | } |
212 | |
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213 | =head2 editable( $opts ) |
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214 | |
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215 | Returns a version of the graph rendered in our definition format. The |
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216 | output separates statements with a newline; set $opts->{'linesep'} to the |
217 | empty string or to a space if the result is to be sent via JSON. |
218 | |
219 | Any layer witnesses to be included should be passed via $opts->{'layerwits'}. |
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220 | |
221 | =cut |
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222 | |
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223 | sub editable { |
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224 | my( $self, $opts ) = @_; |
225 | |
226 | ## See if we are including any a.c. witnesses in this graph. |
227 | my $graph = $self->graph; |
228 | if( exists $opts->{'layerwits'} ) { |
229 | $graph = $self->extend_graph( $opts->{'layerwits'} ); |
230 | } |
231 | |
232 | # Create the graph |
233 | my $join = ( $opts && exists $opts->{'linesep'} ) ? $opts->{'linesep'} : "\n"; |
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234 | my @dotlines; |
235 | push( @dotlines, 'digraph stemma {' ); |
236 | my @real; # A cheap sort |
237 | foreach my $n ( sort $self->graph->vertices ) { |
238 | my $c = $self->graph->get_vertex_attribute( $n, 'class' ); |
239 | $c = 'extant' unless $c; |
240 | if( $c eq 'extant' ) { |
241 | push( @real, $n ); |
242 | } else { |
243 | push( @dotlines, _make_dotline( $n, 'class' => $c ) ); |
244 | } |
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245 | } |
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246 | # Now do the real ones |
247 | foreach my $n ( @real ) { |
248 | push( @dotlines, _make_dotline( $n, 'class' => 'extant' ) ); |
249 | } |
250 | foreach my $e ( sort _by_vertex $self->graph->edges ) { |
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251 | my( $from, $to ) = map { _dotquote( $_ ) } @$e; |
7a7c249c |
252 | push( @dotlines, " $from -> $to;" ); |
253 | } |
254 | push( @dotlines, '}' ); |
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255 | return join( $join, @dotlines ); |
7a7c249c |
256 | } |
257 | |
258 | sub _make_dotline { |
259 | my( $obj, %attr ) = @_; |
260 | my @pairs; |
261 | foreach my $k ( keys %attr ) { |
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262 | my $v = _dotquote( $attr{$k} ); |
263 | push( @pairs, "$k=$v" ); |
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264 | } |
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265 | return sprintf( " %s [ %s ];", _dotquote( $obj ), join( ', ', @pairs ) ); |
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266 | } |
267 | |
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268 | sub _dotquote { |
269 | my( $str ) = @_; |
270 | return $str if $str =~ /^[A-Za-z0-9]+$/; |
271 | $str =~ s/\"/\\\"/g; |
272 | $str = '"' . $str . '"'; |
273 | return $str; |
274 | } |
275 | |
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276 | sub _by_vertex { |
277 | return $a->[0].$a->[1] cmp $b->[0].$b->[1]; |
278 | } |
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279 | |
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280 | =head2 extend_graph( $layered_witnesses ) |
281 | |
282 | Returns a graph which is the original stemma with witness layers added for the |
283 | list in @$layered_witnesses. A layered (a.c.) witness is added as a parent |
284 | of its main version, and additionally shares all other parents and children with |
285 | that version. |
286 | |
287 | =cut |
288 | |
289 | sub extend_graph { |
290 | my( $self, $layerwits ) = @_; |
291 | # For each 'layered' witness in the layerwits array, add it to the graph |
292 | # as an ancestor of the 'main' witness, and otherwise with the same parent/ |
293 | # child links as its main analogue. |
294 | # TOOD Handle case where B is copied from A but corrected from C |
295 | |
296 | # Iterate through, adding a.c. witnesses |
297 | my $actag = $self->collation->ac_label; |
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298 | my $graph = $self->graph->deep_copy; |
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299 | foreach my $lw ( @$layerwits ) { |
300 | # Add the layered witness and set it with the same attributes as |
301 | # its 'main' analogue |
302 | my $lwac = $lw . $self->collation->ac_label; |
303 | $graph->add_vertex( $lwac ); |
304 | $graph->set_vertex_attributes( $lwac, |
305 | $graph->get_vertex_attributes( $lw ) ); |
306 | |
307 | # Set it as ancestor to the main witness |
308 | $graph->add_edge( $lwac, $lw ); |
309 | |
310 | # Give it the same ancestors and descendants as the main witness has, |
311 | # bearing in mind that those ancestors and descendants might also just |
312 | # have had a layered witness defined. |
313 | foreach my $v ( $graph->predecessors( $lw ) ) { |
314 | next if $v eq $lwac; # Don't add a loop |
315 | $graph->add_edge( $v, $lwac ); |
316 | $graph->add_edge( $v.$self->collation->ac_label, $lwac ) |
317 | if $graph->has_vertex( $v.$self->collation->ac_label ); |
318 | } |
319 | foreach my $v ( $graph->successors( $lw ) ) { |
320 | next if $v eq $lwac; # but this shouldn't occur |
321 | $graph->add_edge( $lwac, $v ); |
322 | $graph->add_edge( $lwac, $v.$self->collation->ac_label ) |
323 | if $graph->has_vertex( $v.$self->collation->ac_label ); |
324 | } |
325 | } |
326 | return $graph; |
327 | } |
328 | |
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329 | =head2 as_svg |
330 | |
331 | Returns an SVG representation of the graph, calling as_dot first. |
332 | |
333 | =cut |
334 | |
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335 | sub as_svg { |
336 | my( $self, $opts ) = @_; |
337 | my $dot = $self->as_dot( $opts ); |
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338 | my @cmd = qw/dot -Tsvg/; |
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339 | my $svg; |
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340 | my $dotfile = File::Temp->new(); |
341 | ## TODO REMOVE |
342 | # $dotfile->unlink_on_destroy(0); |
343 | binmode $dotfile, ':utf8'; |
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344 | print $dotfile $dot; |
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345 | push( @cmd, $dotfile->filename ); |
346 | run( \@cmd, ">", binary(), \$svg ); |
3bf5d6f1 |
347 | # HACK: Parse the SVG and change the dimensions. |
5a7e26a9 |
348 | # Get rid of width and height attributes to allow scaling. |
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349 | if( $opts->{'size'} ) { |
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350 | require XML::LibXML; |
351 | my $parser = XML::LibXML->new(); |
352 | my $svgdoc = $parser->parse_string( decode_utf8( $svg ) ); |
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353 | my( $ew, $eh ) = @{$opts->{'size'}}; |
354 | # If the graph is wider than it is tall, set width to ew and remove height. |
355 | # Otherwise set height to eh and remove width. |
356 | my $width = $svgdoc->documentElement->getAttribute('width'); |
357 | my $height = $svgdoc->documentElement->getAttribute('height'); |
358 | $width =~ s/\D+//g; |
359 | $height =~ s/\D+//g; |
360 | my( $remove, $keep, $val ); |
361 | if( $width > $height ) { |
362 | $remove = 'height'; |
363 | $keep = 'width'; |
364 | $val = $ew . 'px'; |
365 | } else { |
366 | $remove = 'width'; |
367 | $keep = 'height'; |
368 | $val = $eh . 'px'; |
369 | } |
370 | $svgdoc->documentElement->removeAttribute( $remove ); |
371 | $svgdoc->documentElement->setAttribute( $keep, $val ); |
428bcf0b |
372 | $svg = $svgdoc->toString(); |
c57be097 |
373 | } |
3bf5d6f1 |
374 | # Return the result |
428bcf0b |
375 | return decode_utf8( $svg ); |
e79c23c7 |
376 | } |
377 | |
027d819c |
378 | =head2 witnesses |
379 | |
380 | Returns a list of the extant witnesses represented in the stemma. |
381 | |
382 | =cut |
383 | |
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384 | sub witnesses { |
385 | my $self = shift; |
386 | my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' } |
387 | $self->graph->vertices; |
388 | return @wits; |
389 | } |
390 | |
06e7cbc7 |
391 | =head2 hypotheticals |
392 | |
393 | Returns a list of the hypothetical witnesses represented in the stemma. |
394 | |
395 | =cut |
396 | |
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397 | sub hypotheticals { |
398 | my $self = shift; |
399 | my @wits = grep |
400 | { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' } |
401 | $self->graph->vertices; |
402 | return @wits; |
403 | } |
404 | |
63778331 |
405 | sub throw { |
406 | Text::Tradition::Error->throw( |
407 | 'ident' => 'Stemma error', |
408 | 'message' => $_[0], |
409 | ); |
410 | } |
411 | |
412 | |
9463b0bf |
413 | no Moose; |
414 | __PACKAGE__->meta->make_immutable; |
415 | |
416 | 1; |
027d819c |
417 | |
418 | =head1 LICENSE |
419 | |
420 | This package is free software and is provided "as is" without express |
421 | or implied warranty. You can redistribute it and/or modify it under |
422 | the same terms as Perl itself. |
423 | |
424 | =head1 AUTHOR |
425 | |
426 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |