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
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:
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 local $TODO = "cannot use stdout redirection trick with FastCGI";
108 open( $baddotfh, 't/data/besoin_bad.dot' ) or die "Could not open test dotfile";
110 my $stemma = Text::Tradition::Stemma->new( dot => $baddotfh );
111 ok( 0, "Created broken stemma from dotfile with syntax error" );
112 } catch( Text::Tradition::Error $e ) {
113 like( $e->message, qr/^Error trying to parse/, "Syntax error in dot threw exception" );
117 # Create a good graph
119 open( $dotfh, 't/data/florilegium.dot' ) or die "Could not open test dotfile";
120 binmode( $dotfh, ':utf8' );
121 my $stemma = Text::Tradition::Stemma->new( dot => $dotfh );
122 is( ref( $stemma ), 'Text::Tradition::Stemma', "Created stemma from good dotfile" );
123 is( scalar $stemma->witnesses, 13, "Found correct number of extant witnesses" );
124 is( scalar $stemma->hypotheticals, 8, "Found correct number of extant hypotheticals" );
125 my $found_unicode_sigil;
126 foreach my $h ( $stemma->hypotheticals ) {
127 $found_unicode_sigil = 1 if $h eq "\x{3b1}";
129 ok( $found_unicode_sigil, "Found a correctly encoded Unicode sigil" );
131 # TODO Create stemma from graph, create stemma from undirected graph,
132 # create stemma from incompletely-specified graph
140 isa => 'Text::Tradition::Collation',
141 clearer => 'clear_collation', # interim measure to remove refs in DB
148 predicate => 'has_graph',
154 writer => 'set_identifier',
155 predicate => 'has_identifier',
159 my( $self, $args ) = @_;
160 # If we have been handed a dotfile, initialize it into a graph.
161 if( exists $args->{'dot'} ) {
162 $self->_graph_from_dot( $args->{'dot'} );
166 before 'graph' => sub {
169 # Make sure all unclassed graph nodes are marked extant.
171 throw( "Cannot set graph to a non-Graph object" )
172 unless ref( $g ) eq 'Graph';
173 foreach my $v ( $g->vertices ) {
174 unless( $g->has_vertex_attribute( $v, 'class' ) ) {
175 $g->set_vertex_attribute( $v, 'class', 'extant' );
181 after 'graph' => sub {
184 unless( $self->has_identifier ) {
185 ## HORRIBLE HACK but there is no API access to graph attributes!
186 if( exists $_[0]->[4]->{'name'} ) {
187 $self->set_identifier( $_[0]->[4]->{'name'} );
192 sub _graph_from_dot {
193 my( $self, $dotfh ) = @_;
194 my $reader = Graph::Reader::Dot->new();
195 # Redirect STDOUT in order to trap any error messages - syntax errors
196 # are evidently not fatal.
197 # TODO This breaks under FastCGI/Apache; reconsider.
200 #open $saved_stderr, ">&STDOUT";
202 #open STDOUT, ">", \$reader_out;
203 my $graph = $reader->read_graph( $dotfh );
205 #open STDOUT, ">", \$saved_stderr;
206 if( $reader_out && $reader_out =~ /error/s ) {
207 throw( "Error trying to parse dot: $reader_out" );
209 throw( "Failed to create graph from dot" );
211 $self->graph( $graph );
216 return undef unless $self->has_graph;
217 return $self->graph->is_undirected;
222 =head2 as_dot( \%options )
224 Returns a normal dot representation of the stemma layout, suitable for rendering
225 with GraphViz. Options include:
229 =item * graph - A hashref of global graph options.
231 =item * node - A hashref of global node options.
233 =item * edge - A hashref of global edge options.
237 See the GraphViz documentation for the list of available options.
242 my( $self, $opts ) = @_;
244 ## See if we are including any a.c. witnesses in this graph.
245 my $graph = $self->graph;
246 if( exists $opts->{'layerwits'} ) {
248 map { $extant->{$_} = 1 } $self->witnesses;
249 $graph = $self->situation_graph( $extant, $opts->{'layerwits'} );
252 # Get default and specified options
255 'bgcolor' => 'transparent',
260 'fillcolor' => 'white',
262 'shape' => 'ellipse', # Shape for the extant nodes
265 'arrowhead' => 'none',
267 @graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}}
269 @nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}}
271 @edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}}
274 my $gdecl = $graph->is_directed ? 'digraph' : 'graph';
276 push( @dotlines, "$gdecl stemma {" );
277 ## Print out the global attributes
278 push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts;
279 push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts;
280 push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts;
282 # Add each of the nodes.
283 foreach my $n ( $graph->vertices ) {
284 my %vattr = ( 'id' => $n ); # Set the SVG element ID to the sigil itself
285 if( $graph->has_vertex_attribute( $n, 'label' ) ) {
286 $vattr{'label'} = $graph->get_vertex_attribute( $n, 'label' );
288 push( @dotlines, _make_dotline( $n, %vattr ) );
290 # Add each of our edges.
291 foreach my $e ( $graph->edges ) {
292 my( $from, $to ) = map { _dotquote( $_ ) } @$e;
293 my $connector = $graph->is_directed ? '->' : '--';
294 push( @dotlines, " $from $connector $to;" );
296 push( @dotlines, '}' );
298 return join( "\n", @dotlines );
301 =head2 alter_graph( $dotstring )
303 Alters the graph of this stemma according to the definition specified
309 my( $self, $dotstring ) = @_;
311 open $dotfh, '<', \$dotstring;
312 binmode $dotfh, ':utf8';
313 $self->_graph_from_dot( $dotfh );
316 =head2 editable( $opts )
318 =head2 editable_graph( $graph, $opts )
320 Returns a version of the graph rendered in our definition format. The
321 output separates statements with a newline; set $opts->{'linesep'} to the
322 empty string or to a space if the result is to be sent via JSON.
324 If a situational version of the stemma is required, the arguments for
325 situation_graph should be passed via $opts->{'extant'} and $opts->{'layerwits'}.
330 my( $self, $opts ) = @_;
331 my $graph = $self->graph;
332 ## See if we need an editable version of a situational graph.
333 if( exists $opts->{'layerwits'} || exists $opts->{'extant'} ) {
334 my $extant = delete $opts->{'extant'} || {};
335 my $layerwits = delete $opts->{'layerwits'} || [];
336 $graph = $self->situation_graph( $extant, $layerwits );
338 return editable_graph( $graph, $opts );
342 my( $graph, $opts ) = @_;
345 my $join = ( $opts && exists $opts->{'linesep'} ) ? $opts->{'linesep'} : "\n";
346 my $gdecl = $graph->is_undirected ? 'graph' : 'digraph';
348 push( @dotlines, "$gdecl stemma {" );
349 my @real; # A cheap sort
350 foreach my $n ( sort $graph->vertices ) {
351 my $c = $graph->get_vertex_attribute( $n, 'class' );
352 $c = 'extant' unless $c;
353 if( $c eq 'extant' ) {
356 push( @dotlines, _make_dotline( $n, 'class' => $c ) );
359 # Now do the real ones
360 foreach my $n ( @real ) {
361 push( @dotlines, _make_dotline( $n, 'class' => 'extant' ) );
363 foreach my $e ( sort _by_vertex $graph->edges ) {
364 my( $from, $to ) = map { _dotquote( $_ ) } @$e;
365 my $conn = $graph->is_undirected ? '--' : '->';
366 push( @dotlines, " $from $conn $to;" );
368 push( @dotlines, '}' );
369 return join( $join, @dotlines );
373 my( $obj, %attr ) = @_;
375 foreach my $k ( keys %attr ) {
376 my $v = _dotquote( $attr{$k} );
377 push( @pairs, "$k=$v" );
379 return sprintf( " %s [ %s ];", _dotquote( $obj ), join( ', ', @pairs ) );
384 return $str if $str =~ /^[A-Za-z0-9]+$/;
386 $str = '"' . $str . '"';
391 return $a->[0].$a->[1] cmp $b->[0].$b->[1];
394 =head2 situation_graph( $extant, $layered )
396 Returns a graph which is the original stemma graph with all witnesses not
397 in the %$extant hash marked as hypothetical, and witness layers added to
398 the graph according to the list in @$layered. A layered (a.c.) witness is
399 added as a parent of its main version, and additionally shares all other
400 parents and children with that version.
404 sub situation_graph {
405 my( $self, $extant, $layerwits, $layerlabel ) = @_;
407 my $graph = $self->graph->copy;
408 foreach my $vertex ( $graph->vertices ) {
409 # Set as extant any vertex that is extant in the stemma AND
410 # exists in the $extant hash.
411 my $class = 'hypothetical';
412 $class = 'extant' if exists $extant->{$vertex} && $extant->{$vertex} &&
413 $self->graph->get_vertex_attribute( $vertex, 'class' ) ne 'hypothetical';
414 $graph->set_vertex_attribute( $vertex, 'class', $class );
417 # For each 'layered' witness in the layerwits array, add it to the graph
418 # as an ancestor of the 'main' witness, and otherwise with the same parent/
419 # child links as its main analogue.
420 # TOOD Handle case where B is copied from A but corrected from C
421 $layerlabel = ' (a.c.)' unless $layerlabel;
422 foreach my $lw ( @$layerwits ) {
423 # Add the layered witness and set it with the same attributes as
424 # its 'main' analogue
425 throw( "Cannot add a layer to a hypothetical witness $lw" )
426 unless $graph->get_vertex_attribute( $lw, 'class' ) eq 'extant';
427 my $lwac = $lw . $layerlabel;
428 $graph->add_vertex( $lwac );
429 $graph->set_vertex_attributes( $lwac,
430 $graph->get_vertex_attributes( $lw ) );
432 # Set it as ancestor to the main witness
433 $graph->add_edge( $lwac, $lw );
435 # Give it the same ancestors and descendants as the main witness has,
436 # bearing in mind that those ancestors and descendants might also just
437 # have had a layered witness defined.
438 foreach my $v ( $graph->predecessors( $lw ) ) {
439 next if $v eq $lwac; # Don't add a loop
440 $graph->add_edge( $v, $lwac );
441 $graph->add_edge( $v.$layerlabel, $lwac )
442 if $graph->has_vertex( $v.$layerlabel );
444 foreach my $v ( $graph->successors( $lw ) ) {
445 next if $v eq $lwac; # but this shouldn't occur
446 $graph->add_edge( $lwac, $v );
447 $graph->add_edge( $lwac, $v.$layerlabel )
448 if $graph->has_vertex( $v.$layerlabel );
456 Returns an SVG representation of the graph, calling as_dot first.
461 my( $self, $opts ) = @_;
462 my $dot = $self->as_dot( $opts );
463 my @cmd = ( '-Tsvg' );
464 unshift( @cmd, $self->is_undirected ? 'neato' : 'dot' );
466 my $dotfile = File::Temp->new();
467 binmode $dotfile, ':utf8';
470 push( @cmd, $dotfile->filename );
471 run( \@cmd, ">", binary(), \$svg );
472 return decode_utf8( $svg );
477 Returns a list of the extant witnesses represented in the stemma.
483 my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' }
484 $self->graph->vertices;
490 Returns a list of the hypothetical witnesses represented in the stemma.
497 { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' }
498 $self->graph->vertices;
502 =head2 root_graph( $root_vertex )
504 If the stemma graph is undirected, make it directed with $root_vertex at the root.
505 If it is directed, re-root it.
510 my( $self, $rootvertex ) = @_;
512 if( $self->is_undirected ) {
513 $graph = $self->graph;
515 # Make an undirected version of this graph.
516 $graph = $self->graph->undirected_copy();
518 my $rooted = Graph->new();
519 $rooted->add_vertex( $rootvertex );
520 my @next = ( $rootvertex );
523 foreach my $v ( @next ) {
524 # Place its not-placed neighbors (ergo children) in the tree
526 foreach my $n ( grep { !$rooted->has_vertex( $_ ) }
527 $graph->neighbors( $v ) ) {
528 $rooted->add_vertex( $n );
529 $rooted->add_edge( $v, $n );
530 push( @children, $n );
535 # Set the vertex classes
536 map { $rooted->set_vertex_attribute( $_, 'class', 'hypothetical' ) }
537 $self->graph->hypotheticals;
538 map { $rooted->set_vertex_class( $_, 'class', 'extant' ) }
539 $self->graph->witnesses;
545 Text::Tradition::Error->throw(
546 'ident' => 'Stemma error',
553 __PACKAGE__->meta->make_immutable;
559 This package is free software and is provided "as is" without express
560 or implied warranty. You can redistribute it and/or modify it under
561 the same terms as Perl itself.
565 Tara L Andrews E<lt>aurum@cpan.orgE<gt>