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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 XML::LibXML; |
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12 | use Moose; |
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13 | |
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14 | =head1 NAME |
15 | |
16 | Text::Tradition::Stemma - a representation of a I<stemma codicum> for a Text::Tradition |
17 | |
18 | =head1 SYNOPSIS |
19 | |
20 | use Text::Tradition; |
21 | my $t = Text::Tradition->new( |
22 | 'name' => 'this is a text', |
23 | 'input' => 'TEI', |
24 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
25 | |
26 | my $s = $tradition->add_stemma( dotfile => '/path/to/stemma.dot' ); |
27 | |
28 | =head1 DESCRIPTION |
29 | |
30 | Text::Tradition is a library for representation and analysis of collated |
31 | texts, particularly medieval ones. The Collation is the central feature of |
32 | a Tradition, where the text, its sequence of readings, and its relationships |
33 | between readings are actually kept. |
34 | |
35 | =head1 DOT SYNTAX |
36 | |
37 | The easiest way to define a stemma (which is a directed acyclic graph, denoting |
38 | the scholar's hypothesis concerning which text(s) were copied from which other(s)) |
39 | is to use a special form of the 'dot' syntax of GraphViz. |
40 | |
41 | Each stemma opens with the line |
42 | |
43 | digraph Stemma { |
44 | |
45 | and continues with a list of all manuscript witnesses in the stemma, whether |
46 | extant witnesses or missing archetypes or hyparchetypes. Each of these is |
47 | listed by its sigil on its own line, e.g.: |
48 | |
49 | alpha [ class=hypothetical ] |
50 | 1 [ class=hypothetical,label=* ] |
51 | Ms4 [ class=extant ] |
52 | |
53 | Extant witnesses are listed with class=extant; missing or postulated witnesses |
54 | are listed with class=hypothetical. Anonymous hyparchetypes must be given a |
55 | unique name or number, but can be represented as anonymous with the addition |
56 | of 'label=*' to their lines. Greek letters or other special characters may be |
57 | used as names, but they must always be wrapped in double quotes. |
58 | |
59 | Links between manuscripts are then listed with arrow notation, as below. These |
60 | lines show the direction of copying, one step at a time, for the entire stemma. |
61 | |
62 | alpha -> 1 |
63 | 1 -> Ms4 |
64 | |
65 | The final line in the definition should be the closing brace: |
66 | |
67 | } |
68 | |
69 | Thus for a set of extant manuscripts A, B, and C, where A and B were copied |
70 | from the archetype O and C was copied from B, the definition would be: |
71 | |
72 | digraph Stemma { |
73 | O [ class=hypothetical] |
74 | A [ class=extant ] |
75 | B [ class=extant ] |
76 | C [ class=extant ] |
77 | O -> A |
78 | O -> B |
79 | B -> C |
80 | } |
81 | |
82 | =head1 CONSTRUCTOR |
83 | |
84 | =head2 new |
85 | |
86 | The constructor. This should generally be called from Text::Tradition, but |
87 | if called directly it takes the following options: |
88 | |
89 | =over |
90 | |
91 | =item * collation - The collation with which the stemma is associated. |
92 | |
93 | =item * dot - A filehandle open to a DOT representation of the stemma graph. |
94 | |
95 | =back |
96 | |
97 | =cut |
98 | |
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99 | has collation => ( |
100 | is => 'ro', |
101 | isa => 'Text::Tradition::Collation', |
102 | required => 1, |
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103 | weak_ref => 1, |
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104 | ); |
105 | |
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106 | has graph => ( |
107 | is => 'rw', |
108 | isa => 'Graph', |
109 | predicate => 'has_graph', |
110 | ); |
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111 | |
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112 | sub BUILD { |
113 | my( $self, $args ) = @_; |
114 | # If we have been handed a dotfile, initialize it into a graph. |
115 | if( exists $args->{'dot'} ) { |
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116 | $self->_graph_from_dot( $args->{'dot'} ); |
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117 | } |
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118 | } |
119 | |
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120 | sub _graph_from_dot { |
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121 | my( $self, $dotfh ) = @_; |
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122 | my $reader = Graph::Reader::Dot->new(); |
123 | my $graph = $reader->read_graph( $dotfh ); |
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124 | if( $graph ) { |
125 | $self->graph( $graph ); |
126 | # Go through the nodes and set any non-hypothetical node to extant. |
127 | foreach my $v ( $self->graph->vertices ) { |
128 | $self->graph->set_vertex_attribute( $v, 'class', 'extant' ) |
129 | unless $self->graph->has_vertex_attribute( $v, 'class' ); |
130 | } |
131 | } else { |
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132 | throw( "Failed to parse dot in $dotfh" ); |
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133 | } |
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134 | } |
135 | |
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136 | =head1 METHODS |
137 | |
138 | =head2 as_dot( \%options ) |
139 | |
140 | Returns a normal dot representation of the stemma layout, suitable for rendering |
141 | with GraphViz. Options include: |
142 | |
143 | =over |
144 | |
145 | =item * graph - A hashref of global graph options. |
146 | |
147 | =item * node - A hashref of global node options. |
148 | |
149 | =item * edge - A hashref of global edge options. |
150 | |
151 | =back |
152 | |
153 | See the GraphViz documentation for the list of available options. |
154 | |
155 | =cut |
156 | |
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157 | sub as_dot { |
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158 | my( $self, $opts ) = @_; |
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159 | |
160 | # Get default and specified options |
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161 | my %graphopts = ( |
162 | # 'ratio' => 1, |
163 | ); |
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164 | my %nodeopts = ( |
165 | 'fontsize' => 11, |
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166 | 'style' => 'filled', |
167 | 'fillcolor' => 'white', |
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168 | 'color' => 'white', |
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169 | 'shape' => 'ellipse', # Shape for the extant nodes |
170 | ); |
171 | my %edgeopts = ( |
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172 | 'arrowhead' => 'none', |
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173 | ); |
174 | @graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}} |
175 | if $opts->{'graph'}; |
176 | @nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}} |
177 | if $opts->{'node'}; |
178 | @edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}} |
179 | if $opts->{'edge'}; |
180 | |
181 | my @dotlines; |
182 | push( @dotlines, 'digraph stemma {' ); |
183 | ## Print out the global attributes |
184 | push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts; |
185 | push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts; |
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186 | push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts; |
187 | |
188 | # Add each of the nodes. |
189 | foreach my $n ( $self->graph->vertices ) { |
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190 | if( $self->graph->has_vertex_attribute( $n, 'label' ) ) { |
191 | my $ltext = $self->graph->get_vertex_attribute( $n, 'label' ); |
192 | push( @dotlines, _make_dotline( $n, 'label' => $ltext ) ); |
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193 | } else { |
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194 | # Use the default display settings. |
195 | push( @dotlines, " $n;" ); |
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196 | } |
197 | } |
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198 | # Add each of our edges. |
199 | foreach my $e ( $self->graph->edges ) { |
200 | my( $from, $to ) = @$e; |
201 | push( @dotlines, " $from -> $to;" ); |
202 | } |
203 | push( @dotlines, '}' ); |
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204 | |
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205 | return join( "\n", @dotlines ); |
206 | } |
207 | |
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208 | =head2 editable( $linesep ) |
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209 | |
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210 | Returns a version of the graph rendered in our definition format. The |
211 | $linesep argument defaults to newline; set it to the empty string or to |
212 | a space if the result is to be sent via JSON. |
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213 | |
214 | =cut |
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215 | |
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216 | sub editable { |
217 | my $self = shift; |
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218 | my $join = shift || "\n"; |
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219 | my @dotlines; |
220 | push( @dotlines, 'digraph stemma {' ); |
221 | my @real; # A cheap sort |
222 | foreach my $n ( sort $self->graph->vertices ) { |
223 | my $c = $self->graph->get_vertex_attribute( $n, 'class' ); |
224 | $c = 'extant' unless $c; |
225 | if( $c eq 'extant' ) { |
226 | push( @real, $n ); |
227 | } else { |
228 | push( @dotlines, _make_dotline( $n, 'class' => $c ) ); |
229 | } |
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230 | } |
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231 | # Now do the real ones |
232 | foreach my $n ( @real ) { |
233 | push( @dotlines, _make_dotline( $n, 'class' => 'extant' ) ); |
234 | } |
235 | foreach my $e ( sort _by_vertex $self->graph->edges ) { |
236 | my( $from, $to ) = @$e; |
237 | push( @dotlines, " $from -> $to;" ); |
238 | } |
239 | push( @dotlines, '}' ); |
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240 | return join( $join, @dotlines ); |
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241 | } |
242 | |
243 | sub _make_dotline { |
244 | my( $obj, %attr ) = @_; |
245 | my @pairs; |
246 | foreach my $k ( keys %attr ) { |
247 | my $v = $attr{$k}; |
248 | $v =~ s/\"/\\\"/g; |
249 | push( @pairs, "$k=\"$v\"" ); |
250 | } |
251 | return sprintf( " %s [ %s ];", $obj, join( ', ', @pairs ) ); |
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252 | } |
253 | |
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254 | sub _by_vertex { |
255 | return $a->[0].$a->[1] cmp $b->[0].$b->[1]; |
256 | } |
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257 | |
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258 | =head2 as_svg |
259 | |
260 | Returns an SVG representation of the graph, calling as_dot first. |
261 | |
262 | =cut |
263 | |
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264 | sub as_svg { |
265 | my( $self, $opts ) = @_; |
266 | my $dot = $self->as_dot( $opts ); |
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267 | my @cmd = qw/dot -Tsvg/; |
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268 | my $svg; |
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269 | my $dotfile = File::Temp->new(); |
270 | ## TODO REMOVE |
271 | # $dotfile->unlink_on_destroy(0); |
272 | binmode $dotfile, ':utf8'; |
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273 | print $dotfile $dot; |
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274 | push( @cmd, $dotfile->filename ); |
275 | run( \@cmd, ">", binary(), \$svg ); |
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276 | # HACK: Parse the SVG and change the dimensions. |
277 | # Convert width from pt to px, and remove height to allow scaling. |
278 | my $parser = XML::LibXML->new(); |
279 | my $svgdoc = $parser->parse_string( decode_utf8( $svg ) ); |
280 | my $dval = $svgdoc->documentElement->getAttribute('width'); |
281 | $dval =~ s/pt/px/; |
282 | $svgdoc->documentElement->setAttribute( 'width', $dval ); |
283 | $svgdoc->documentElement->removeAttribute('height'); |
284 | # Return the result |
285 | return decode_utf8( $svgdoc->toString ); |
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286 | } |
287 | |
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288 | =head2 witnesses |
289 | |
290 | Returns a list of the extant witnesses represented in the stemma. |
291 | |
292 | =cut |
293 | |
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294 | sub witnesses { |
295 | my $self = shift; |
296 | my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' } |
297 | $self->graph->vertices; |
298 | return @wits; |
299 | } |
300 | |
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301 | sub hypotheticals { |
302 | my $self = shift; |
303 | my @wits = grep |
304 | { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' } |
305 | $self->graph->vertices; |
306 | return @wits; |
307 | } |
308 | |
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309 | sub throw { |
310 | Text::Tradition::Error->throw( |
311 | 'ident' => 'Stemma error', |
312 | 'message' => $_[0], |
313 | ); |
314 | } |
315 | |
316 | |
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317 | no Moose; |
318 | __PACKAGE__->meta->make_immutable; |
319 | |
320 | 1; |
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321 | |
322 | =head1 LICENSE |
323 | |
324 | This package is free software and is provided "as is" without express |
325 | or implied warranty. You can redistribute it and/or modify it under |
326 | the same terms as Perl itself. |
327 | |
328 | =head1 AUTHOR |
329 | |
330 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |