1 package Text::Tradition::Stemma;
3 use Encode qw( decode_utf8 );
6 use Graph::Reader::Dot;
7 use IPC::Run qw/ run binary /;
8 use Text::Tradition::Error;
13 Text::Tradition::Stemma - a representation of a I<stemma codicum> for a Text::Tradition
18 my $t = Text::Tradition->new(
19 'name' => 'this is a text',
21 'file' => '/path/to/tei_parallel_seg_file.xml' );
23 my $s = $tradition->add_stemma( dotfile => '/path/to/stemma.dot' );
27 Text::Tradition is a library for representation and analysis of collated
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).
34 The easiest way to define a stemma is to use a special form of the 'dot'
37 Each stemma opens with the line
39 digraph "Name of Stemma" {
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.:
45 alpha [ class=hypothetical ]
46 1 [ class=hypothetical,label=* ]
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.
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.
61 The final line in the definition should be the closing brace:
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:
68 digraph "Test stemma 1" {
69 O [ class=hypothetical]
82 The constructor. This should generally be called from Text::Tradition, but
83 if called directly it takes the following options:
87 =item * dot - A filehandle open to a DOT representation of the stemma graph.
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'.
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.
102 use_ok( 'Text::Tradition::Stemma' );
104 # Try to create a bad graph
106 open( $baddotfh, 't/data/besoin_bad.dot' ) or die "Could not open test dotfile";
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" );
114 # Create a good graph
116 open( $dotfh, 't/data/florilegium.dot' ) or die "Could not open test dotfile";
117 binmode( $dotfh, ':utf8' );
118 my $stemma = Text::Tradition::Stemma->new( dot => $dotfh );
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" );
122 ok( $stemma->has_identifier, "Stemma identifier was found in dot" );
123 is( $stemma->identifier, 'Coislinianum lineage', "Correct stemma identifier was found in dot" );
124 my $found_unicode_sigil;
125 foreach my $h ( $stemma->hypotheticals ) {
126 $found_unicode_sigil = 1 if $h eq "\x{3b1}";
128 ok( $found_unicode_sigil, "Found a correctly encoded Unicode sigil" );
130 # Create an undirected graph
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" );
139 is( $udstemma->identifier, "RHM stemma", "Undirected graph retained its name" );
147 isa => 'Text::Tradition::Collation',
148 clearer => 'clear_collation', # interim measure to remove refs in DB
155 predicate => 'has_graph',
161 writer => 'set_identifier',
162 predicate => 'has_identifier',
166 my( $self, $args ) = @_;
167 # If we have been handed a dotfile, initialize it into a graph.
168 if( exists $args->{'dot'} ) {
169 $self->_graph_from_dot( $args->{'dot'} );
173 before 'graph' => sub {
176 # Make sure all unclassed graph nodes are marked extant.
178 throw( "Cannot set graph to a non-Graph object" )
179 unless $g->isa( 'Graph' );
180 foreach my $v ( $g->vertices ) {
181 unless( $g->has_vertex_attribute( $v, 'class' ) ) {
182 $g->set_vertex_attribute( $v, 'class', 'extant' );
188 sub _graph_from_dot {
189 my( $self, $dotfh ) = @_;
190 my $reader = Graph::Reader::Dot->new();
191 # Redirect STDOUT in order to trap any error messages - syntax errors
192 # are evidently not fatal.
198 open( STDOUT, ">", \$reader_out );
200 open( STDERR, ">", \$reader_err );
201 $graph = $reader->read_graph( $dotfh );
205 if( $reader_out && $reader_out =~ /error/s ) {
206 throw( "Error trying to parse dot: $reader_out" );
208 throw( "Failed to create graph from dot" );
210 ## HORRIBLE HACK but there is no API access to graph attributes!
211 my $graph_id = exists $graph->[4]->{'name'} ? $graph->[4]->{'name'} : 'stemma';
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 ) );
220 $self->graph( $graph );
221 $self->set_identifier( $graph_id );
226 return undef unless $self->has_graph;
227 return $self->graph->is_undirected;
232 =head2 as_dot( \%options )
234 Returns a normal dot representation of the stemma layout, suitable for rendering
235 with GraphViz. Options include:
239 =item * graph - A hashref of global graph options.
241 =item * node - A hashref of global node options.
243 =item * edge - A hashref of global edge options.
247 See the GraphViz documentation for the list of available options.
252 my( $self, $opts ) = @_;
254 ## See if we are including any a.c. witnesses in this graph.
255 my $graph = $self->graph;
256 if( exists $opts->{'layerwits'} ) {
258 map { $extant->{$_} = 1 } $self->witnesses;
259 $graph = $self->situation_graph( $extant, $opts->{'layerwits'} );
262 # Get default and specified options
265 'bgcolor' => 'transparent',
270 'fillcolor' => 'white',
272 'shape' => 'ellipse', # Shape for the extant nodes
275 'arrowhead' => 'none',
277 @graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}}
279 @nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}}
281 @edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}}
284 my $gdecl = $graph->is_directed ? 'digraph' : 'graph';
285 my $gname = $self->has_identifier ? '"' . $self->identifier . '"'
288 push( @dotlines, "$gdecl $gname {" );
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;
292 push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts;
294 # Add each of the nodes.
295 foreach my $n ( $graph->vertices ) {
296 my %vattr = ( 'id' => $n ); # Set the SVG element ID to the sigil itself
297 if( $graph->has_vertex_attribute( $n, 'label' ) ) {
298 $vattr{'label'} = $graph->get_vertex_attribute( $n, 'label' );
300 push( @dotlines, _make_dotline( $n, %vattr ) );
302 # Add each of our edges.
303 foreach my $e ( $graph->edges ) {
304 my( $from, $to ) = map { _dotquote( $_ ) } @$e;
305 my $connector = $graph->is_directed ? '->' : '--';
306 push( @dotlines, " $from $connector $to;" );
308 push( @dotlines, '}' );
310 return join( "\n", @dotlines );
313 =head2 alter_graph( $dotstring )
315 Alters the graph of this stemma according to the definition specified
321 my( $self, $dotstring ) = @_;
323 open $dotfh, '<', \$dotstring;
324 binmode $dotfh, ':utf8';
325 $self->_graph_from_dot( $dotfh );
328 =head2 editable( $opts )
330 =head2 editable_graph( $graph, $opts )
332 Returns a version of the graph rendered in our definition format. The
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.
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'}.
342 my( $self, $opts ) = @_;
343 my $graph = $self->graph;
344 if( $self->has_identifier ) {
345 $opts->{'name'} = $self->identifier;
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 );
353 return editable_graph( $graph, $opts );
357 my( $graph, $opts ) = @_;
360 my $join = ( $opts && exists $opts->{'linesep'} ) ? $opts->{'linesep'} : "\n";
361 my $gdecl = $graph->is_undirected ? 'graph' : 'digraph';
362 my $gname = exists $opts->{'name'} ? '"' . $opts->{'name'} . '"'
365 push( @dotlines, "$gdecl $gname {" );
366 my @real; # A cheap sort
367 foreach my $n ( sort $graph->vertices ) {
368 my $c = $graph->get_vertex_attribute( $n, 'class' );
369 $c = 'extant' unless $c;
370 if( $c eq 'extant' ) {
373 push( @dotlines, _make_dotline( $n, 'class' => $c ) );
376 # Now do the real ones
377 foreach my $n ( @real ) {
378 push( @dotlines, _make_dotline( $n, 'class' => 'extant' ) );
380 foreach my $e ( sort _by_vertex $graph->edges ) {
381 my( $from, $to ) = map { _dotquote( $_ ) } @$e;
382 my $conn = $graph->is_undirected ? '--' : '->';
383 push( @dotlines, " $from $conn $to;" );
385 push( @dotlines, '}' );
386 return join( $join, @dotlines );
390 my( $obj, %attr ) = @_;
392 foreach my $k ( keys %attr ) {
393 my $v = _dotquote( $attr{$k} );
394 push( @pairs, "$k=$v" );
396 return sprintf( " %s [ %s ];", _dotquote( $obj ), join( ', ', @pairs ) );
401 return $str if $str =~ /^[A-Za-z0-9]+$/;
403 $str = '"' . $str . '"';
408 return $a->[0].$a->[1] cmp $b->[0].$b->[1];
411 =head2 situation_graph( $extant, $layered )
413 Returns a graph which is the original stemma graph with all witnesses not
414 in the %$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.
421 sub situation_graph {
422 my( $self, $extant, $layerwits, $layerlabel ) = @_;
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 );
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
438 $layerlabel = ' (a.c.)' unless $layerlabel;
439 foreach my $lw ( @$layerwits ) {
440 # Add the layered witness and set it with the same attributes as
441 # its 'main' analogue
442 throw( "Cannot add a layer to a hypothetical witness $lw" )
443 unless $graph->get_vertex_attribute( $lw, 'class' ) eq 'extant';
444 my $lwac = $lw . $layerlabel;
445 $graph->add_vertex( $lwac );
446 $graph->set_vertex_attributes( $lwac,
447 $graph->get_vertex_attributes( $lw ) );
449 # Set it as ancestor to the main witness
450 $graph->add_edge( $lwac, $lw );
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 );
458 $graph->add_edge( $v.$layerlabel, $lwac )
459 if $graph->has_vertex( $v.$layerlabel );
461 foreach my $v ( $graph->successors( $lw ) ) {
462 next if $v eq $lwac; # but this shouldn't occur
463 $graph->add_edge( $lwac, $v );
464 $graph->add_edge( $lwac, $v.$layerlabel )
465 if $graph->has_vertex( $v.$layerlabel );
473 Returns an SVG representation of the graph, calling as_dot first.
478 my( $self, $opts ) = @_;
479 my $dot = $self->as_dot( $opts );
480 my @cmd = ( '-Tsvg' );
481 unshift( @cmd, $self->is_undirected ? 'neato' : 'dot' );
483 my $dotfile = File::Temp->new();
484 binmode $dotfile, ':utf8';
487 push( @cmd, $dotfile->filename );
488 run( \@cmd, ">", binary(), \$svg );
489 return decode_utf8( $svg );
494 Returns a list of the extant witnesses represented in the stemma.
500 my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' }
501 $self->graph->vertices;
507 Returns a list of the hypothetical witnesses represented in the stemma.
514 { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' }
515 $self->graph->vertices;
519 =head2 root_graph( $root_vertex )
521 If the stemma graph is undirected, make it directed with $root_vertex at the root.
522 If it is directed, re-root it.
527 my( $self, $rootvertex ) = @_;
529 my $ident = $self->identifier; # will have to restore this at the end
530 if( $self->is_undirected ) {
531 $graph = $self->graph;
533 # Make an undirected version of this graph.
534 $graph = $self->graph->undirected_copy();
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" );
541 # Now make a directed version of the graph.
542 my $rooted = Graph->new();
543 $rooted->add_vertex( $rootvertex );
544 my @next = ( $rootvertex );
547 foreach my $v ( @next ) {
548 # Place its not-placed neighbors (ergo children) in the tree
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 );
559 # Set the vertex classes
560 map { $rooted->set_vertex_attribute( $_, 'class', 'hypothetical' ) }
561 $self->hypotheticals;
562 map { $rooted->set_vertex_attribute( $_, 'class', 'extant' ) }
564 $self->graph( $rooted );
565 $self->set_identifier( $ident );
570 Text::Tradition::Error->throw(
571 'ident' => 'Stemma error',
578 __PACKAGE__->meta->make_immutable;
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.
590 Tara L Andrews E<lt>aurum@cpan.orgE<gt>