1 package Text::Tradition::Stemma;
4 use Encode qw( decode_utf8 );
7 use Graph::Reader::Dot;
8 use IPC::Run qw/ run binary /;
9 use Text::Tradition::Error;
10 use Text::Tradition::StemmaUtil qw/ character_input phylip_pars parse_newick /;
15 Text::Tradition::Stemma - a representation of a I<stemma codicum> for a Text::Tradition
20 my $t = Text::Tradition->new(
21 'name' => 'this is a text',
23 'file' => '/path/to/tei_parallel_seg_file.xml' );
25 my $s = $tradition->add_stemma( dotfile => '/path/to/stemma.dot' );
29 Text::Tradition is a library for representation and analysis of collated
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).
36 The easiest way to define a stemma is to use a special form of the 'dot'
39 Each stemma opens with the line
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.:
47 alpha [ class=hypothetical ]
48 1 [ class=hypothetical,label=* ]
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.
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.
63 The final line in the definition should be the closing brace:
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:
71 O [ class=hypothetical]
84 The constructor. This should generally be called from Text::Tradition, but
85 if called directly it takes the following options:
89 =item * collation - The collation with which the stemma is associated.
91 =item * dot - A filehandle open to a DOT representation of the stemma graph.
99 isa => 'Text::Tradition::Collation',
107 predicate => 'has_graph',
111 my( $self, $args ) = @_;
112 # If we have been handed a dotfile, initialize it into a graph.
113 if( exists $args->{'dot'} ) {
114 $self->_graph_from_dot( $args->{'dot'} );
118 sub _graph_from_dot {
119 my( $self, $dotfh ) = @_;
120 my $reader = Graph::Reader::Dot->new();
121 my $graph = $reader->read_graph( $dotfh );
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' );
130 throw( "Failed to parse dot in $dotfh" );
136 =head2 as_dot( \%options )
138 Returns a normal dot representation of the stemma layout, suitable for rendering
139 with GraphViz. Options include:
143 =item * graph - A hashref of global graph options.
145 =item * node - A hashref of global node options.
147 =item * edge - A hashref of global edge options.
151 See the GraphViz documentation for the list of available options.
156 my( $self, $opts ) = @_;
158 ## See if we are including any a.c. witnesses in this graph.
159 my $graph = $self->graph;
160 if( exists $opts->{'layerwits'} ) {
162 map { $extant->{$_} = 1 } $self->witnesses;
163 $graph = $self->situation_graph( $extant, $opts->{'layerwits'} );
166 # Get default and specified options
173 'fillcolor' => 'white',
175 'shape' => 'ellipse', # Shape for the extant nodes
178 'arrowhead' => 'none',
180 @graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}}
182 @nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}}
184 @edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}}
188 push( @dotlines, 'digraph stemma {' );
189 ## Print out the global attributes
190 push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts;
191 push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts;
192 push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts;
194 # Add each of the nodes.
195 foreach my $n ( $graph->vertices ) {
196 if( $graph->has_vertex_attribute( $n, 'label' ) ) {
197 my $ltext = $graph->get_vertex_attribute( $n, 'label' );
198 push( @dotlines, _make_dotline( $n, 'label' => $ltext ) );
200 # Use the default display settings.
201 $n = _dotquote( $n );
202 push( @dotlines, " $n;" );
205 # Add each of our edges.
206 foreach my $e ( $graph->edges ) {
207 my( $from, $to ) = map { _dotquote( $_ ) } @$e;
208 push( @dotlines, " $from -> $to;" );
210 push( @dotlines, '}' );
212 return join( "\n", @dotlines );
215 =head2 editable( $opts )
217 =head2 editable_graph( $graph, $opts )
219 Returns a version of the graph rendered in our definition format. The
220 output separates statements with a newline; set $opts->{'linesep'} to the
221 empty string or to a space if the result is to be sent via JSON.
223 If a situational version of the stemma is required, the arguments for
224 situation_graph should be passed via $opts->{'extant'} and $opts->{'layerwits'}.
229 my( $self, $opts ) = @_;
230 my $graph = $self->graph;
231 ## See if we need an editable version of a situational graph.
232 if( exists $opts->{'layerwits'} || exists $opts->{'extant'} ) {
233 my $extant = delete $opts->{'extant'} || {};
234 my $layerwits = delete $opts->{'layerwits'} || [];
235 $graph = $self->situation_graph( $extant, $layerwits );
237 return editable_graph( $graph, $opts );
241 my( $graph, $opts ) = @_;
244 my $join = ( $opts && exists $opts->{'linesep'} ) ? $opts->{'linesep'} : "\n";
246 push( @dotlines, 'digraph stemma {' );
247 my @real; # A cheap sort
248 foreach my $n ( sort $graph->vertices ) {
249 my $c = $graph->get_vertex_attribute( $n, 'class' );
250 $c = 'extant' unless $c;
251 if( $c eq 'extant' ) {
254 push( @dotlines, _make_dotline( $n, 'class' => $c ) );
257 # Now do the real ones
258 foreach my $n ( @real ) {
259 push( @dotlines, _make_dotline( $n, 'class' => 'extant' ) );
261 foreach my $e ( sort _by_vertex $graph->edges ) {
262 my( $from, $to ) = map { _dotquote( $_ ) } @$e;
263 push( @dotlines, " $from -> $to;" );
265 push( @dotlines, '}' );
266 return join( $join, @dotlines );
270 my( $obj, %attr ) = @_;
272 foreach my $k ( keys %attr ) {
273 my $v = _dotquote( $attr{$k} );
274 push( @pairs, "$k=$v" );
276 return sprintf( " %s [ %s ];", _dotquote( $obj ), join( ', ', @pairs ) );
281 return $str if $str =~ /^[A-Za-z0-9]+$/;
283 $str = '"' . $str . '"';
288 return $a->[0].$a->[1] cmp $b->[0].$b->[1];
291 =head2 situation_graph( $extant, $layered )
293 Returns a graph which is the original stemma with all witnesses not in the
294 %$extant hash marked as hypothetical, and witness layers added to the graph
295 according to the list in @$layered. A layered (a.c.) witness is added as a
296 parent of its main version, and additionally shares all other parents and
297 children with that version.
301 sub situation_graph {
302 my( $self, $extant, $layerwits ) = @_;
304 my $graph = $self->graph->copy;
305 foreach my $vertex ( $graph->vertices ) {
306 # Set as extant any vertex that is extant in the stemma AND
307 # exists in the $extant hash.
308 my $class = 'hypothetical';
309 $class = 'extant' if exists $extant->{$vertex} && $extant->{$vertex} &&
310 $self->graph->get_vertex_attribute( $vertex, 'class' ) ne 'hypothetical';
311 $graph->set_vertex_attribute( $vertex, 'class', $class );
314 # For each 'layered' witness in the layerwits array, add it to the graph
315 # as an ancestor of the 'main' witness, and otherwise with the same parent/
316 # child links as its main analogue.
317 # TOOD Handle case where B is copied from A but corrected from C
318 my $aclabel = $self->collation->ac_label;
319 foreach my $lw ( @$layerwits ) {
320 # Add the layered witness and set it with the same attributes as
321 # its 'main' analogue
322 throw( "Cannot add a layer to a hypothetical witness $lw" )
323 unless $graph->get_vertex_attribute( $lw, 'class' ) eq 'extant';
324 my $lwac = $lw . $aclabel;
325 $graph->add_vertex( $lwac );
326 $graph->set_vertex_attributes( $lwac,
327 $graph->get_vertex_attributes( $lw ) );
329 # Set it as ancestor to the main witness
330 $graph->add_edge( $lwac, $lw );
332 # Give it the same ancestors and descendants as the main witness has,
333 # bearing in mind that those ancestors and descendants might also just
334 # have had a layered witness defined.
335 foreach my $v ( $graph->predecessors( $lw ) ) {
336 next if $v eq $lwac; # Don't add a loop
337 $graph->add_edge( $v, $lwac );
338 $graph->add_edge( $v.$aclabel, $lwac )
339 if $graph->has_vertex( $v.$aclabel );
341 foreach my $v ( $graph->successors( $lw ) ) {
342 next if $v eq $lwac; # but this shouldn't occur
343 $graph->add_edge( $lwac, $v );
344 $graph->add_edge( $lwac, $v.$aclabel )
345 if $graph->has_vertex( $v.$aclabel );
353 Returns an SVG representation of the graph, calling as_dot first.
358 my( $self, $opts ) = @_;
359 my $dot = $self->as_dot( $opts );
360 my @cmd = qw/dot -Tsvg/;
362 my $dotfile = File::Temp->new();
364 # $dotfile->unlink_on_destroy(0);
365 binmode $dotfile, ':utf8';
367 push( @cmd, $dotfile->filename );
368 run( \@cmd, ">", binary(), \$svg );
369 # HACK: Parse the SVG and change the dimensions.
370 # Get rid of width and height attributes to allow scaling.
371 if( $opts->{'size'} ) {
373 my $parser = XML::LibXML->new();
374 my $svgdoc = $parser->parse_string( decode_utf8( $svg ) );
375 my( $ew, $eh ) = @{$opts->{'size'}};
376 # If the graph is wider than it is tall, set width to ew and remove height.
377 # Otherwise set height to eh and remove width.
378 my $width = $svgdoc->documentElement->getAttribute('width');
379 my $height = $svgdoc->documentElement->getAttribute('height');
382 my( $remove, $keep, $val );
383 if( $width > $height ) {
392 $svgdoc->documentElement->removeAttribute( $remove );
393 $svgdoc->documentElement->setAttribute( $keep, $val );
394 $svg = $svgdoc->toString();
397 return decode_utf8( $svg );
402 Returns a list of the extant witnesses represented in the stemma.
408 my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' }
409 $self->graph->vertices;
415 Returns a list of the hypothetical witnesses represented in the stemma.
422 { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' }
423 $self->graph->vertices;
428 Text::Tradition::Error->throw(
429 'ident' => 'Stemma error',
436 __PACKAGE__->meta->make_immutable;
442 This package is free software and is provided "as is" without express
443 or implied warranty. You can redistribute it and/or modify it under
444 the same terms as Perl itself.
448 Tara L Andrews E<lt>aurum@cpan.orgE<gt>