1 package Text::Tradition::Collation;
3 use Encode qw( decode_utf8 );
7 use IPC::Run qw( run binary );
9 use Text::Tradition::Collation::Reading;
10 use Text::Tradition::Collation::RelationshipStore;
11 use Text::Tradition::Error;
12 use XML::Easy::Syntax qw( $xml10_namestartchar_rx $xml10_namechar_rx );
14 use XML::LibXML::XPathContext;
20 default => sub { Graph->new() },
28 isa => 'Text::Tradition::Collation::RelationshipStore',
30 relationships => 'relationships',
31 related_readings => 'related_readings',
32 get_relationship => 'get_relationship',
33 del_relationship => 'del_relationship',
34 equivalence => 'equivalence',
35 equivalence_graph => 'equivalence_graph',
37 writer => '_set_relations',
42 isa => 'Text::Tradition',
43 writer => '_set_tradition',
48 isa => 'HashRef[Text::Tradition::Collation::Reading]',
52 _add_reading => 'set',
53 del_reading => 'delete',
54 has_reading => 'exists',
57 default => sub { {} },
60 has 'wit_list_separator' => (
69 default => 'base text',
92 isa => 'Text::Tradition::Collation::Reading',
93 writer => '_set_start',
99 isa => 'Text::Tradition::Collation::Reading',
100 writer => '_set_end',
104 has 'cached_svg' => (
107 predicate => 'has_cached_svg',
108 clearer => 'wipe_svg',
111 has 'cached_table' => (
114 predicate => 'has_cached_table',
115 clearer => 'wipe_table',
118 has '_graphcalc_done' => (
126 Text::Tradition::Collation - a software model for a text collation
131 my $t = Text::Tradition->new(
132 'name' => 'this is a text',
134 'file' => '/path/to/tei_parallel_seg_file.xml' );
136 my $c = $t->collation;
137 my @readings = $c->readings;
138 my @paths = $c->paths;
139 my @relationships = $c->relationships;
141 my $svg_variant_graph = $t->collation->as_svg();
145 Text::Tradition is a library for representation and analysis of collated
146 texts, particularly medieval ones. The Collation is the central feature of
147 a Tradition, where the text, its sequence of readings, and its relationships
148 between readings are actually kept.
154 The constructor. Takes a hash or hashref of the following arguments:
158 =item * tradition - The Text::Tradition object to which the collation
161 =item * linear - Whether the collation should be linear; that is, whether
162 transposed readings should be treated as two linked readings rather than one,
163 and therefore whether the collation graph is acyclic. Defaults to true.
165 =item * baselabel - The default label for the path taken by a base text
166 (if any). Defaults to 'base text'.
168 =item * wit_list_separator - The string to join a list of witnesses for
169 purposes of making labels in display graphs. Defaults to ', '.
171 =item * ac_label - The extra label to tack onto a witness sigil when
172 representing another layer of path for the given witness - that is, when
173 a text has more than one possible reading due to scribal corrections or
174 the like. Defaults to ' (a.c.)'.
176 =item * wordsep - The string used to separate words in the original text.
187 =head2 wit_list_separator
195 Simple accessors for collation attributes.
199 The meta-reading at the start of every witness path.
203 The meta-reading at the end of every witness path.
207 Returns all Reading objects in the graph.
209 =head2 reading( $id )
211 Returns the Reading object corresponding to the given ID.
213 =head2 add_reading( $reading_args )
215 Adds a new reading object to the collation.
216 See L<Text::Tradition::Collation::Reading> for the available arguments.
218 =head2 del_reading( $object_or_id )
220 Removes the given reading from the collation, implicitly removing its
221 paths and relationships.
223 =head2 merge_readings( $main, $second, $concatenate, $with_str )
225 Merges the $second reading into the $main one. If $concatenate is true, then
226 the merged node will carry the text of both readings, concatenated with either
227 $with_str (if specified) or a sensible default (the empty string if the
228 appropriate 'join_*' flag is set on either reading, or else $self->wordsep.)
230 The first two arguments may be either readings or reading IDs.
232 =head2 has_reading( $id )
234 Predicate to see whether a given reading ID is in the graph.
236 =head2 reading_witnesses( $object_or_id )
238 Returns a list of sigils whose witnesses contain the reading.
242 Returns all reading paths within the document - that is, all edges in the
243 collation graph. Each path is an arrayref of [ $source, $target ] reading IDs.
245 =head2 add_path( $source, $target, $sigil )
247 Links the given readings in the collation in sequence, under the given witness
248 sigil. The readings may be specified by object or ID.
250 =head2 del_path( $source, $target, $sigil )
252 Links the given readings in the collation in sequence, under the given witness
253 sigil. The readings may be specified by object or ID.
255 =head2 has_path( $source, $target );
257 Returns true if the two readings are linked in sequence in any witness.
258 The readings may be specified by object or ID.
262 Returns all Relationship objects in the collation.
264 =head2 add_relationship( $reading, $other_reading, $options )
266 Adds a new relationship of the type given in $options between the two readings,
267 which may be specified by object or ID. Returns a value of ( $status, @vectors)
268 where $status is true on success, and @vectors is a list of relationship edges
269 that were ultimately added.
270 See L<Text::Tradition::Collation::Relationship> for the available options.
276 $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
277 $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
278 $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
281 ### Reading construct/destruct functions
284 my( $self, $reading ) = @_;
285 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
286 my %args = %$reading;
287 if( $self->tradition->has_language && !exists $args{'language'} ) {
288 $args{'language'} = $self->tradition->language;
290 $reading = Text::Tradition::Collation::Reading->new(
291 'collation' => $self,
294 # First check to see if a reading with this ID exists.
295 if( $self->reading( $reading->id ) ) {
296 throw( "Collation already has a reading with id " . $reading->id );
298 $self->_graphcalc_done(0);
299 $self->_add_reading( $reading->id => $reading );
300 # Once the reading has been added, put it in both graphs.
301 $self->sequence->add_vertex( $reading->id );
302 $self->relations->add_reading( $reading->id );
306 around del_reading => sub {
311 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
314 # Remove the reading from the graphs.
315 $self->_graphcalc_done(0);
316 $self->_clear_cache; # Explicitly clear caches to GC the reading
317 $self->sequence->delete_vertex( $arg );
318 $self->relations->delete_reading( $arg );
321 $self->$orig( $arg );
328 my $cxfile = 't/data/Collatex-16.xml';
329 my $t = Text::Tradition->new(
331 'input' => 'CollateX',
334 my $c = $t->collation;
336 my $rno = scalar $c->readings;
337 # Split n21 for testing purposes
338 my $new_r = $c->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } );
339 my $old_r = $c->reading( 'n21' );
340 $old_r->alter_text( 'to' );
341 $c->del_path( 'n20', 'n21', 'A' );
342 $c->add_path( 'n20', 'n21p0', 'A' );
343 $c->add_path( 'n21p0', 'n21', 'A' );
345 ok( $c->reading( 'n21p0' ), "New reading exists" );
346 is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" );
348 # Combine n3 and n4 ( with his )
349 $c->merge_readings( 'n3', 'n4', 1 );
350 ok( !$c->reading('n4'), "Reading n4 is gone" );
351 is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" );
353 # Collapse n9 and n10 ( rood / root )
354 $c->merge_readings( 'n9', 'n10' );
355 ok( !$c->reading('n10'), "Reading n10 is gone" );
356 is( $c->reading('n9')->text, 'rood', "Reading n9 has an unchanged word" );
358 # Combine n21 and n21p0
359 my $remaining = $c->reading('n21');
360 $remaining ||= $c->reading('n22'); # one of these should still exist
361 $c->merge_readings( 'n21p0', $remaining, 1 );
362 ok( !$c->reading('n21'), "Reading $remaining is gone" );
363 is( $c->reading('n21p0')->text, 'unto', "Reading n21p0 merged correctly" );
372 # We only need the IDs for adding paths to the graph, not the reading
373 # objects themselves.
374 my( $kept, $deleted, $combine, $combine_char ) = $self->_stringify_args( @_ );
375 $self->_graphcalc_done(0);
377 # The kept reading should inherit the paths and the relationships
378 # of the deleted reading.
379 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
380 my @vector = ( $kept );
381 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
382 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
383 next if $vector[0] eq $vector[1]; # Don't add a self loop
384 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
385 $self->sequence->add_edge( @vector );
386 my $fwits = $self->sequence->get_edge_attributes( @vector );
387 @wits{keys %$fwits} = values %$fwits;
388 $self->sequence->set_edge_attributes( @vector, \%wits );
390 $self->relations->merge_readings( $kept, $deleted, $combine );
392 # Do the deletion deed.
394 my $kept_obj = $self->reading( $kept );
395 my $del_obj = $self->reading( $deleted );
396 my $joinstr = $combine_char;
397 unless( defined $joinstr ) {
398 $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior;
399 $joinstr = $self->wordsep unless defined $joinstr;
401 $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) );
403 $self->del_reading( $deleted );
407 # Helper function for manipulating the graph.
408 sub _stringify_args {
409 my( $self, $first, $second, @args ) = @_;
411 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
412 $second = $second->id
413 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
414 return( $first, $second, @args );
417 # Helper function for manipulating the graph.
418 sub _objectify_args {
419 my( $self, $first, $second, $arg ) = @_;
420 $first = $self->reading( $first )
421 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
422 $second = $self->reading( $second )
423 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
424 return( $first, $second, $arg );
431 # We only need the IDs for adding paths to the graph, not the reading
432 # objects themselves.
433 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
435 $self->_graphcalc_done(0);
436 # Connect the readings
437 unless( $self->sequence->has_edge( $source, $target ) ) {
438 $self->sequence->add_edge( $source, $target );
439 $self->relations->add_equivalence_edge( $source, $target );
441 # Note the witness in question
442 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
448 if( ref( $_[0] ) eq 'ARRAY' ) {
455 # We only need the IDs for adding paths to the graph, not the reading
456 # objects themselves.
457 my( $source, $target, $wit ) = $self->_stringify_args( @args );
459 $self->_graphcalc_done(0);
460 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
461 $self->sequence->delete_edge_attribute( $source, $target, $wit );
463 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
464 $self->sequence->delete_edge( $source, $target );
465 $self->relations->delete_equivalence_edge( $source, $target );
470 # Extra graph-alike utility
473 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
474 return undef unless $self->sequence->has_edge( $source, $target );
475 return $self->sequence->has_edge_attribute( $source, $target, $wit );
478 =head2 clear_witness( @sigil_list )
480 Clear the given witnesses out of the collation entirely, removing references
481 to them in paths, and removing readings that belong only to them. Should only
482 be called via $tradition->del_witness.
487 my( $self, @sigils ) = @_;
489 $self->_graphcalc_done(0);
490 # Clear the witness(es) out of the paths
491 foreach my $e ( $self->paths ) {
492 foreach my $sig ( @sigils ) {
493 $self->del_path( $e, $sig );
497 # Clear out the newly unused readings
498 foreach my $r ( $self->readings ) {
499 unless( $self->reading_witnesses( $r ) ) {
500 $self->del_reading( $r );
505 sub add_relationship {
507 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
508 my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts );
509 $self->_graphcalc_done(0);
513 around qw/ get_relationship del_relationship / => sub {
517 if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) {
520 my( $source, $target ) = $self->_stringify_args( @args );
521 $self->$orig( $source, $target );
524 =head2 reading_witnesses( $reading )
526 Return a list of sigils corresponding to the witnesses in which the reading appears.
530 sub reading_witnesses {
531 my( $self, $reading ) = @_;
532 # We need only check either the incoming or the outgoing edges; I have
533 # arbitrarily chosen "incoming". Thus, special-case the start node.
534 if( $reading eq $self->start ) {
535 return map { $_->sigil } $self->tradition->witnesses;
538 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
539 my $wits = $self->sequence->get_edge_attributes( @$e );
540 @all_witnesses{ keys %$wits } = 1;
542 my $acstr = $self->ac_label;
543 foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) {
544 delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit};
546 return keys %all_witnesses;
549 =head1 OUTPUT METHODS
551 =head2 as_svg( \%options )
553 Returns an SVG string that represents the graph, via as_dot and graphviz.
554 See as_dot for a list of options. Must have GraphViz (dot) installed to run.
559 my( $self, $opts ) = @_;
560 throw( "Need GraphViz installed to output SVG" )
561 unless File::Which::which( 'dot' );
562 my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'};
563 $self->calculate_ranks()
564 unless( $self->_graphcalc_done || $opts->{'nocalc'} || !$self->linear );
565 if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) {
566 my @cmd = qw/dot -Tsvg/;
568 my $dotfile = File::Temp->new();
570 # $dotfile->unlink_on_destroy(0);
571 binmode $dotfile, ':utf8';
572 print $dotfile $self->as_dot( $opts );
573 push( @cmd, $dotfile->filename );
574 run( \@cmd, ">", binary(), \$svg );
575 $svg = decode_utf8( $svg );
576 $self->cached_svg( $svg ) unless $want_subgraph;
579 return $self->cached_svg;
584 =head2 as_dot( \%options )
586 Returns a string that is the collation graph expressed in dot
587 (i.e. GraphViz) format. Options include:
602 my( $self, $opts ) = @_;
603 my $startrank = $opts->{'from'} if $opts;
604 my $endrank = $opts->{'to'} if $opts;
605 my $color_common = $opts->{'color_common'} if $opts;
606 my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank
607 && $self->end->rank > 100;
608 $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs
610 # Check the arguments
612 return if $endrank && $startrank > $endrank;
613 return if $startrank > $self->end->rank;
615 if( defined $endrank ) {
616 return if $endrank < 0;
617 $endrank = undef if $endrank == $self->end->rank;
620 my $graph_name = $self->tradition->name;
621 $graph_name =~ s/[^\w\s]//g;
622 $graph_name = join( '_', split( /\s+/, $graph_name ) );
630 'fillcolor' => 'white',
635 'arrowhead' => 'open',
636 'color' => '#000000',
637 'fontcolor' => '#000000',
640 my $dot = sprintf( "digraph %s {\n", $graph_name );
641 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
642 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
644 # Output substitute start/end readings if necessary
646 $dot .= "\t\"__SUBSTART__\" [ label=\"...\",id=\"__START__\" ];\n";
649 $dot .= "\t\"__SUBEND__\" [ label=\"...\",id=\"__END__\" ];\n";
651 if( $STRAIGHTENHACK ) {
653 my $startlabel = $startrank ? '__SUBSTART__' : '__START__';
654 $dot .= "\tsubgraph { rank=same \"$startlabel\" \"#SILENT#\" }\n";
655 $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];"
657 my %used; # Keep track of the readings that actually appear in the graph
658 # Sort the readings by rank if we have ranks; this speeds layout.
659 my @all_readings = $self->end->has_rank
660 ? sort { $a->rank <=> $b->rank } $self->readings
662 # TODO Refrain from outputting lacuna nodes - just grey out the edges.
663 foreach my $reading ( @all_readings ) {
664 # Only output readings within our rank range.
665 next if $startrank && $reading->rank < $startrank;
666 next if $endrank && $reading->rank > $endrank;
667 $used{$reading->id} = 1;
668 # Need not output nodes without separate labels
669 next if $reading->id eq $reading->text;
671 my $label = $reading->text;
672 $label .= '-' if $reading->join_next;
673 $label = "-$label" if $reading->join_prior;
674 $label =~ s/\"/\\\"/g;
675 $rattrs->{'label'} = $label;
676 $rattrs->{'id'} = $reading->id;
677 $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
678 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
681 # Add the real edges. Need to weight one edge per rank jump, in a
683 # my $weighted = $self->_add_edge_weights;
684 my @edges = $self->paths;
685 my( %substart, %subend );
686 foreach my $edge ( @edges ) {
687 # Do we need to output this edge?
688 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
689 my $label = $self->_path_display_label( $self->path_witnesses( $edge ) );
690 my $variables = { %edge_attrs, 'label' => $label };
692 # Account for the rank gap if necessary
693 my $rank0 = $self->reading( $edge->[0] )->rank
694 if $self->reading( $edge->[0] )->has_rank;
695 my $rank1 = $self->reading( $edge->[1] )->rank
696 if $self->reading( $edge->[1] )->has_rank;
697 if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) {
698 $variables->{'minlen'} = $rank1 - $rank0;
701 # Add the calculated edge weights
702 # if( exists $weighted->{$edge->[0]}
703 # && $weighted->{$edge->[0]} eq $edge->[1] ) {
704 # # $variables->{'color'} = 'red';
705 # $variables->{'weight'} = 3.0;
708 # EXPERIMENTAL: make edge width reflect no. of witnesses
709 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
710 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
712 my $varopts = _dot_attr_string( $variables );
713 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
714 $edge->[0], $edge->[1], $varopts );
715 } elsif( $used{$edge->[0]} ) {
716 $subend{$edge->[0]} = 1;
717 } elsif( $used{$edge->[1]} ) {
718 $substart{$edge->[1]} = 1;
721 # Add substitute start and end edges if necessary
722 foreach my $node ( keys %substart ) {
723 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
724 my $variables = { %edge_attrs, 'label' => $witstr };
725 my $varopts = _dot_attr_string( $variables );
726 $dot .= "\t\"__SUBSTART__\" -> \"$node\" $varopts;";
728 foreach my $node ( keys %subend ) {
729 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
730 my $variables = { %edge_attrs, 'label' => $witstr };
731 my $varopts = _dot_attr_string( $variables );
732 $dot .= "\t\"$node\" -> \"__SUBEND__\" $varopts;";
735 if( $STRAIGHTENHACK ) {
736 my $endlabel = $endrank ? '__SUBEND__' : '__END__';
737 $dot .= "\t\"$endlabel\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
744 sub _dot_attr_string {
747 foreach my $k ( sort keys %$hash ) {
749 push( @attrs, $k.'="'.$v.'"' );
751 return( '[ ' . join( ', ', @attrs ) . ' ]' );
754 sub _add_edge_weights {
756 # Walk the graph from START to END, choosing the successor node with
757 # the largest number of witness paths each time.
759 my $curr = $self->start->id;
760 my $ranked = $self->end->has_rank;
761 while( $curr ne $self->end->id ) {
762 my $rank = $ranked ? $self->reading( $curr )->rank : 0;
763 my @succ = sort { $self->path_witnesses( $curr, $a )
764 <=> $self->path_witnesses( $curr, $b ) }
765 $self->sequence->successors( $curr );
766 my $next = pop @succ;
767 my $nextrank = $ranked ? $self->reading( $next )->rank : 0;
768 # Try to avoid lacunae in the weighted path.
770 ( $self->reading( $next )->is_lacuna ||
771 $nextrank - $rank > 1 ) ){
774 $weighted->{$curr} = $next;
780 =head2 path_witnesses( $edge )
782 Returns the list of sigils whose witnesses are associated with the given edge.
783 The edge can be passed as either an array or an arrayref of ( $source, $target ).
788 my( $self, @edge ) = @_;
789 # If edge is an arrayref, cope.
790 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
794 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
798 # Helper function. Make a display label for the given witnesses, showing a.c.
799 # witnesses only where the main witness is not also in the list.
800 sub _path_display_label {
803 map { $wits{$_} = 1 } @_;
805 # If an a.c. wit is listed, remove it if the main wit is also listed.
806 # Otherwise keep it for explicit listing.
807 my $aclabel = $self->ac_label;
809 foreach my $w ( sort keys %wits ) {
810 if( $w =~ /^(.*)\Q$aclabel\E$/ ) {
811 if( exists $wits{$1} ) {
814 push( @disp_ac, $w );
819 # See if we are in a majority situation.
820 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
821 $maj = $maj > 5 ? $maj : 5;
822 if( scalar keys %wits > $maj ) {
823 unshift( @disp_ac, 'majority' );
824 return join( ', ', @disp_ac );
826 return join( ', ', sort keys %wits );
830 =head2 readings_at_rank( $rank )
832 Returns a list of readings at a given rank, taken from the alignment table.
836 sub readings_at_rank {
837 my( $self, $rank ) = @_;
838 my $table = $self->alignment_table;
839 # Table rank is real rank - 1.
840 my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}};
842 foreach my $e ( @elements ) {
843 next unless ref( $e ) eq 'HASH';
844 next unless exists $e->{'t'};
845 $readings{$e->{'t'}->id} = $e->{'t'};
847 return values %readings;
852 Returns a GraphML representation of the collation. The GraphML will contain
853 two graphs. The first expresses the attributes of the readings and the witness
854 paths that link them; the second expresses the relationships that link the
855 readings. This is the native transfer format for a tradition.
864 my $datafile = 't/data/florilegium_tei_ps.xml';
865 my $tradition = Text::Tradition->new( 'input' => 'TEI',
870 ok( $tradition, "Got a tradition object" );
871 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
872 ok( $tradition->collation, "Tradition has a collation" );
874 my $c = $tradition->collation;
875 is( scalar $c->readings, $READINGS, "Collation has all readings" );
876 is( scalar $c->paths, $PATHS, "Collation has all paths" );
877 is( scalar $c->relationships, 0, "Collation has all relationships" );
879 # Add a few relationships
880 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
881 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
882 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
884 # Now write it to GraphML and parse it again.
886 my $graphml = $c->as_graphml;
887 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
888 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
889 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
890 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
892 # Now add a stemma, write to GraphML, and parse again.
893 my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
894 is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" );
895 is( $tradition->stemmata, 1, "Tradition now has the stemma" );
896 $graphml = $c->as_graphml;
897 like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" );
904 my( $self, $options ) = @_;
905 $self->calculate_ranks unless $self->_graphcalc_done;
907 my $start = $options->{'from'}
908 ? $self->reading( $options->{'from'} ) : $self->start;
909 my $end = $options->{'to'}
910 ? $self->reading( $options->{'to'} ) : $self->end;
911 if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) {
912 throw( 'Start node must be before end node' );
914 # The readings need to be ranked for this to work.
915 $start = $self->start unless $start->has_rank;
916 $end = $self->end unless $end->has_rank;
918 unless( $start eq $self->start ) {
919 $rankoffset = $start->rank - 1;
924 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
925 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
926 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
927 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
929 # Create the document and root node
930 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
931 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
932 $graphml->setDocumentElement( $root );
933 $root->setNamespace( $xsi_ns, 'xsi', 0 );
934 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
936 # List of attribute types to save on our objects and their corresponding
942 'ReadingID' => 'string',
943 'RelationshipType' => 'string',
944 'RelationshipScope' => 'string',
947 # List of attribute names *not* to save on our objects.
948 # We will also not save any attribute beginning with _.
950 map { $skipsave{$_} = 1 } qw/ cached_svg /;
952 # Add the data keys for the graph. Include an extra key 'version' for the
953 # GraphML output version.
956 my %graph_attributes = ( 'version' => 'string' );
957 # Graph attributes include those of Tradition and those of Collation.
959 my $tmeta = $self->tradition->meta;
960 my $cmeta = $self->meta;
961 map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes;
962 map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes;
963 foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) {
964 next if $attr->name =~ /^_/;
965 next if $skipsave{$attr->name};
966 next unless $save_types{$attr->type_constraint->name};
967 $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
969 # Extra custom key for the tradition stemma(ta)
970 $graph_attributes{'stemmata'} = 'string';
972 foreach my $datum ( sort keys %graph_attributes ) {
973 $graph_data_keys{$datum} = 'dg'.$gdi++;
974 my $key = $root->addNewChild( $graphml_ns, 'key' );
975 $key->setAttribute( 'attr.name', $datum );
976 $key->setAttribute( 'attr.type', $graph_attributes{$datum} );
977 $key->setAttribute( 'for', 'graph' );
978 $key->setAttribute( 'id', $graph_data_keys{$datum} );
981 # Add the data keys for reading nodes
982 my %reading_attributes;
983 my $rmeta = Text::Tradition::Collation::Reading->meta;
984 foreach my $attr( $rmeta->get_all_attributes ) {
985 next if $attr->name =~ /^_/;
986 next if $skipsave{$attr->name};
987 next unless $save_types{$attr->type_constraint->name};
988 $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
990 # Extra custom key for the reading morphology
991 $reading_attributes{'lexemes'} = 'string';
995 foreach my $datum ( sort keys %reading_attributes ) {
996 $node_data_keys{$datum} = 'dn'.$ndi++;
997 my $key = $root->addNewChild( $graphml_ns, 'key' );
998 $key->setAttribute( 'attr.name', $datum );
999 $key->setAttribute( 'attr.type', $reading_attributes{$datum} );
1000 $key->setAttribute( 'for', 'node' );
1001 $key->setAttribute( 'id', $node_data_keys{$datum} );
1004 # Add the data keys for edges, that is, paths and relationships. Path
1005 # data does not come from a Moose class so is here manually.
1008 my %edge_attributes = (
1009 witness => 'string', # ID/label for a path
1010 extra => 'boolean', # Path key
1012 my @path_attributes = keys %edge_attributes; # track our manual additions
1013 my $pmeta = Text::Tradition::Collation::Relationship->meta;
1014 foreach my $attr( $pmeta->get_all_attributes ) {
1015 next if $attr->name =~ /^_/;
1016 next if $skipsave{$attr->name};
1017 next unless $save_types{$attr->type_constraint->name};
1018 $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
1020 foreach my $datum ( sort keys %edge_attributes ) {
1021 $edge_data_keys{$datum} = 'de'.$edi++;
1022 my $key = $root->addNewChild( $graphml_ns, 'key' );
1023 $key->setAttribute( 'attr.name', $datum );
1024 $key->setAttribute( 'attr.type', $edge_attributes{$datum} );
1025 $key->setAttribute( 'for', 'edge' );
1026 $key->setAttribute( 'id', $edge_data_keys{$datum} );
1029 # Add the collation graph itself. First, sanitize the name to a valid XML ID.
1030 my $xmlidname = $self->tradition->name;
1031 $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g;
1032 if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) {
1033 $xmlidname = '_'.$xmlidname;
1035 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
1036 $sgraph->setAttribute( 'edgedefault', 'directed' );
1037 $sgraph->setAttribute( 'id', $xmlidname );
1038 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
1039 $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later
1040 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
1041 $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later
1042 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
1044 # Tradition/collation attribute data
1045 foreach my $datum ( keys %graph_attributes ) {
1047 if( $datum eq 'version' ) {
1049 } elsif( $datum eq 'stemmata' ) {
1051 map { push( @stemstrs, $_->editable( {linesep => ''} ) ) }
1052 $self->tradition->stemmata;
1053 $value = join( "\n", @stemstrs );
1054 } elsif( $gattr_from{$datum} eq 'Tradition' ) {
1055 $value = $self->tradition->$datum;
1057 $value = $self->$datum;
1059 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
1064 # Add our readings to the graph
1065 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
1066 next if $n->has_rank && $n ne $self->start && $n ne $self->end &&
1067 ( $n->rank < $start->rank || $n->rank > $end->rank );
1068 $use_readings{$n->id} = 1;
1069 # Add to the main graph
1070 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
1071 my $node_xmlid = 'n' . $node_ctr++;
1072 $node_hash{ $n->id } = $node_xmlid;
1073 $node_el->setAttribute( 'id', $node_xmlid );
1074 foreach my $d ( keys %reading_attributes ) {
1076 # Custom serialization
1077 if( $d eq 'lexemes' ) {
1078 # If nval is a true value, we have lexemes so we need to
1079 # serialize them. Otherwise set nval to undef so that the
1080 # key is excluded from this reading.
1081 $nval = $nval ? $n->_serialize_lexemes : undef;
1083 if( $rankoffset && $d eq 'rank' && $n ne $self->start ) {
1084 # Adjust the ranks within the subgraph.
1085 $nval = $n eq $self->end ? $end->rank - $rankoffset + 1
1086 : $nval - $rankoffset;
1088 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
1093 # Add the path edges to the sequence graph
1095 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
1096 # We add an edge in the graphml for every witness in $e.
1097 next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} );
1098 my @edge_wits = sort $self->path_witnesses( $e );
1099 $e->[0] = $self->start->id unless $use_readings{$e->[0]};
1100 $e->[1] = $self->end->id unless $use_readings{$e->[1]};
1101 # Skip any path from start to end; that witness is not in the subgraph.
1102 next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id );
1103 foreach my $wit ( @edge_wits ) {
1104 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
1105 $node_hash{ $e->[0] },
1106 $node_hash{ $e->[1] } );
1107 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
1108 $edge_el->setAttribute( 'source', $from );
1109 $edge_el->setAttribute( 'target', $to );
1110 $edge_el->setAttribute( 'id', $id );
1112 # It's a witness path, so add the witness
1114 my $key = $edge_data_keys{'witness'};
1115 # Is this an ante-corr witness?
1116 my $aclabel = $self->ac_label;
1117 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
1118 # Keep the base witness
1120 # ...and record that this is an 'extra' reading path
1121 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
1123 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
1127 # Report the actual number of nodes and edges that went in
1128 $sgraph->setAttribute( 'parse.edges', $edge_ctr );
1129 $sgraph->setAttribute( 'parse.nodes', $node_ctr );
1131 # Add the relationship graph to the XML
1132 map { delete $edge_data_keys{$_} } @path_attributes;
1133 $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
1134 $node_data_keys{'id'}, \%edge_data_keys );
1136 # Save and return the thing
1137 my $result = decode_utf8( $graphml->toString(1) );
1141 sub _add_graphml_data {
1142 my( $el, $key, $value ) = @_;
1143 return unless defined $value;
1144 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
1145 $data_el->setAttribute( 'key', $key );
1146 $data_el->appendText( $value );
1151 Returns a CSV alignment table representation of the collation graph, one
1152 row per witness (or witness uncorrected.)
1158 my $table = $self->alignment_table;
1159 my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } );
1161 # Make the header row
1162 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
1163 push( @result, decode_utf8( $csv->string ) );
1164 # Make the rest of the rows
1165 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1166 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
1167 my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs;
1168 $csv->combine( @row );
1169 push( @result, decode_utf8( $csv->string ) );
1171 return join( "\n", @result );
1174 =head2 alignment_table( $use_refs, $include_witnesses )
1176 Return a reference to an alignment table, in a slightly enhanced CollateX
1177 format which looks like this:
1179 $table = { alignment => [ { witness => "SIGIL",
1180 tokens => [ { t => "TEXT" }, ... ] },
1181 { witness => "SIG2",
1182 tokens => [ { t => "TEXT" }, ... ] },
1184 length => TEXTLEN };
1186 If $use_refs is set to 1, the reading object is returned in the table
1187 instead of READINGTEXT; if not, the text of the reading is returned.
1189 If $include_witnesses is set to a hashref, only the witnesses whose sigil
1190 keys have a true hash value will be included.
1194 sub alignment_table {
1196 $self->calculate_ranks() unless $self->_graphcalc_done;
1197 return $self->cached_table if $self->has_cached_table;
1199 # Make sure we can do this
1200 throw( "Need a linear graph in order to make an alignment table" )
1201 unless $self->linear;
1202 $self->calculate_ranks unless $self->end->has_rank;
1204 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
1205 my @all_pos = ( 1 .. $self->end->rank - 1 );
1206 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
1207 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
1208 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1209 my @row = _make_witness_row( \@wit_path, \@all_pos );
1210 push( @{$table->{'alignment'}},
1211 { 'witness' => $wit->sigil, 'tokens' => \@row } );
1212 if( $wit->is_layered ) {
1213 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
1214 $wit->sigil.$self->ac_label );
1215 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
1216 push( @{$table->{'alignment'}},
1217 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
1220 $self->cached_table( $table );
1224 sub _make_witness_row {
1225 my( $path, $positions ) = @_;
1227 map { $char_hash{$_} = undef } @$positions;
1229 foreach my $rdg ( @$path ) {
1230 my $rtext = $rdg->text;
1231 $rtext = '#LACUNA#' if $rdg->is_lacuna;
1232 print STDERR "rank " . $rdg->rank . "\n" if $debug;
1233 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
1234 $char_hash{$rdg->rank} = { 't' => $rdg };
1236 my @row = map { $char_hash{$_} } @$positions;
1237 # Fill in lacuna markers for undef spots in the row
1238 my $last_el = shift @row;
1239 my @filled_row = ( $last_el );
1240 foreach my $el ( @row ) {
1241 # If we are using node reference, make the lacuna node appear many times
1242 # in the table. If not, use the lacuna tag.
1243 if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) {
1246 push( @filled_row, $el );
1252 =head1 NAVIGATION METHODS
1254 =head2 reading_sequence( $first, $last, $sigil, $backup )
1256 Returns the ordered list of readings, starting with $first and ending
1257 with $last, for the witness given in $sigil. If a $backup sigil is
1258 specified (e.g. when walking a layered witness), it will be used wherever
1259 no $sigil path exists. If there is a base text reading, that will be
1260 used wherever no path exists for $sigil or $backup.
1264 # TODO Think about returning some lazy-eval iterator.
1265 # TODO Get rid of backup; we should know from what witness is whether we need it.
1267 sub reading_sequence {
1268 my( $self, $start, $end, $witness ) = @_;
1270 $witness = $self->baselabel unless $witness;
1271 my @readings = ( $start );
1274 while( $n && $n->id ne $end->id ) {
1275 if( exists( $seen{$n->id} ) ) {
1276 throw( "Detected loop for $witness at " . $n->id );
1280 my $next = $self->next_reading( $n, $witness );
1282 throw( "Did not find any path for $witness from reading " . $n->id );
1284 push( @readings, $next );
1287 # Check that the last reading is our end reading.
1288 my $last = $readings[$#readings];
1289 throw( "Last reading found from " . $start->text .
1290 " for witness $witness is not the end!" ) # TODO do we get this far?
1291 unless $last->id eq $end->id;
1296 =head2 next_reading( $reading, $sigil );
1298 Returns the reading that follows the given reading along the given witness
1304 # Return the successor via the corresponding path.
1306 my $answer = $self->_find_linked_reading( 'next', @_ );
1307 return undef unless $answer;
1308 return $self->reading( $answer );
1311 =head2 prior_reading( $reading, $sigil )
1313 Returns the reading that precedes the given reading along the given witness
1319 # Return the predecessor via the corresponding path.
1321 my $answer = $self->_find_linked_reading( 'prior', @_ );
1322 return $self->reading( $answer );
1325 sub _find_linked_reading {
1326 my( $self, $direction, $node, $path ) = @_;
1328 # Get a backup if we are dealing with a layered witness
1330 my $aclabel = $self->ac_label;
1331 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1335 my @linked_paths = $direction eq 'next'
1336 ? $self->sequence->edges_from( $node )
1337 : $self->sequence->edges_to( $node );
1338 return undef unless scalar( @linked_paths );
1340 # We have to find the linked path that contains all of the
1341 # witnesses supplied in $path.
1342 my( @path_wits, @alt_path_wits );
1343 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1344 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1347 foreach my $le ( @linked_paths ) {
1348 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1351 my @le_wits = sort $self->path_witnesses( $le );
1352 if( _is_within( \@path_wits, \@le_wits ) ) {
1353 # This is the right path.
1354 return $direction eq 'next' ? $le->[1] : $le->[0];
1355 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1359 # Got this far? Return the alternate path if it exists.
1360 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1363 # Got this far? Return the base path if it exists.
1364 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1367 # Got this far? We have no appropriate path.
1368 warn "Could not find $direction node from " . $node->id
1369 . " along path $path";
1375 my( $set1, $set2 ) = @_;
1376 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1377 foreach my $el ( @$set1 ) {
1378 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1383 # Return the string that joins together a list of witnesses for
1384 # display on a single path.
1385 sub _witnesses_of_label {
1386 my( $self, $label ) = @_;
1387 my $regex = $self->wit_list_separator;
1388 my @answer = split( /\Q$regex\E/, $label );
1392 =head2 common_readings
1394 Returns the list of common readings in the graph (i.e. those readings that are
1395 shared by all non-lacunose witnesses.)
1399 sub common_readings {
1401 my @common = grep { $_->is_common } $self->readings;
1405 =head2 path_text( $sigil, [, $start, $end ] )
1407 Returns the text of a witness (plus its backup, if we are using a layer)
1408 as stored in the collation. The text is returned as a string, where the
1409 individual readings are joined with spaces and the meta-readings (e.g.
1410 lacunae) are omitted. Optional specification of $start and $end allows
1411 the generation of a subset of the witness text.
1416 my( $self, $wit, $start, $end ) = @_;
1417 $start = $self->start unless $start;
1418 $end = $self->end unless $end;
1419 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1422 foreach my $r ( @path ) {
1423 unless ( $r->join_prior || !$last || $last->join_next ) {
1426 $pathtext .= $r->text;
1432 =head1 INITIALIZATION METHODS
1434 These are mostly for use by parsers.
1436 =head2 make_witness_path( $witness )
1438 Link the array of readings contained in $witness->path (and in
1439 $witness->uncorrected_path if it exists) into collation paths.
1440 Clear out the arrays when finished.
1442 =head2 make_witness_paths
1444 Call make_witness_path for all witnesses in the tradition.
1448 # For use when a collation is constructed from a base text and an apparatus.
1449 # We have the sequences of readings and just need to add path edges.
1450 # When we are done, clear out the witness path attributes, as they are no
1452 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1454 sub make_witness_paths {
1456 foreach my $wit ( $self->tradition->witnesses ) {
1457 # print STDERR "Making path for " . $wit->sigil . "\n";
1458 $self->make_witness_path( $wit );
1462 sub make_witness_path {
1463 my( $self, $wit ) = @_;
1464 my @chain = @{$wit->path};
1465 my $sig = $wit->sigil;
1466 # Add start and end if necessary
1467 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1468 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1469 foreach my $idx ( 0 .. $#chain-1 ) {
1470 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1472 if( $wit->is_layered ) {
1473 @chain = @{$wit->uncorrected_path};
1474 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1475 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1476 foreach my $idx( 0 .. $#chain-1 ) {
1477 my $source = $chain[$idx];
1478 my $target = $chain[$idx+1];
1479 $self->add_path( $source, $target, $sig.$self->ac_label )
1480 unless $self->has_path( $source, $target, $sig );
1484 $wit->clear_uncorrected_path;
1487 =head2 calculate_ranks
1489 Calculate the reading ranks (that is, their aligned positions relative
1490 to each other) for the graph. This can only be called on linear collations.
1494 use Text::Tradition;
1496 my $cxfile = 't/data/Collatex-16.xml';
1497 my $t = Text::Tradition->new(
1499 'input' => 'CollateX',
1502 my $c = $t->collation;
1505 my $table = $c->alignment_table;
1506 ok( $c->has_cached_table, "Alignment table was cached" );
1507 is( $c->alignment_table, $table, "Cached table returned upon second call" );
1508 $c->calculate_ranks;
1509 is( $c->alignment_table, $table, "Cached table retained with no rank change" );
1510 $c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } );
1511 isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" );
1517 sub calculate_ranks {
1519 # Save the existing ranks, in case we need to invalidate the cached SVG.
1521 map { $existing_ranks{$_} = $_->rank } $self->readings;
1523 # Do the rankings based on the relationship equivalence graph, starting
1524 # with the start node.
1525 my $topo_start = $self->equivalence( $self->start->id );
1526 my $node_ranks = { $topo_start => 0 };
1527 my @curr_origin = ( $topo_start );
1528 # A little iterative function.
1529 while( @curr_origin ) {
1530 @curr_origin = _assign_rank( $self->equivalence_graph,
1531 $node_ranks, @curr_origin );
1533 # Transfer our rankings from the topological graph to the real one.
1534 foreach my $r ( $self->readings ) {
1535 if( defined $node_ranks->{$self->equivalence( $r->id )} ) {
1536 $r->rank( $node_ranks->{$self->equivalence( $r->id )} );
1538 # Die. Find the last rank we calculated.
1539 my @all_defined = sort { ( $node_ranks->{$self->equivalence( $a->id )}||-1 )
1540 <=> ( $node_ranks->{$self->equivalence( $b->id )}||-1 ) }
1542 my $last = pop @all_defined;
1543 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1546 # Do we need to invalidate the cached data?
1547 if( $self->has_cached_svg || $self->has_cached_table ) {
1548 foreach my $r ( $self->readings ) {
1549 next if defined( $existing_ranks{$r} )
1550 && $existing_ranks{$r} == $r->rank;
1551 # Something has changed, so clear the cache
1552 $self->_clear_cache;
1553 # ...and recalculate the common readings.
1554 $self->calculate_common_readings();
1558 # The graph calculation information is now up to date.
1559 $self->_graphcalc_done(1);
1563 my( $graph, $node_ranks, @current_nodes ) = @_;
1564 # Look at each of the children of @current_nodes. If all the child's
1565 # parents have a rank, assign it the highest rank + 1 and add it to
1566 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1567 # parent gets a rank.
1569 foreach my $c ( @current_nodes ) {
1570 warn "Current reading $c has no rank!"
1571 unless exists $node_ranks->{$c};
1572 # print STDERR "Looking at child of node $c, rank "
1573 # . $node_ranks->{$c} . "\n";
1574 foreach my $child ( $graph->successors( $c ) ) {
1575 next if exists $node_ranks->{$child};
1576 my $highest_rank = -1;
1578 foreach my $parent ( $graph->predecessors( $child ) ) {
1579 if( exists $node_ranks->{$parent} ) {
1580 $highest_rank = $node_ranks->{$parent}
1581 if $highest_rank <= $node_ranks->{$parent};
1588 my $c_rank = $highest_rank + 1;
1589 # print STDERR "Assigning rank $c_rank to node $child \n";
1590 $node_ranks->{$child} = $c_rank;
1591 push( @next_nodes, $child );
1599 $self->wipe_svg if $self->has_cached_svg;
1600 $self->wipe_table if $self->has_cached_table;
1604 =head2 flatten_ranks
1606 A convenience method for parsing collation data. Searches the graph for readings
1607 with the same text at the same rank, and merges any that are found.
1613 my %unique_rank_rdg;
1615 foreach my $rdg ( $self->readings ) {
1616 next unless $rdg->has_rank;
1617 my $key = $rdg->rank . "||" . $rdg->text;
1618 if( exists $unique_rank_rdg{$key} ) {
1620 # print STDERR "Combining readings at same rank: $key\n";
1622 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1623 # TODO see if this now makes a common point.
1625 $unique_rank_rdg{$key} = $rdg;
1628 # If we merged readings, the ranks are still fine but the alignment
1629 # table is wrong. Wipe it.
1630 $self->wipe_table() if $changed;
1634 =head2 calculate_common_readings
1636 Goes through the graph identifying the readings that appear in every witness
1637 (apart from those with lacunae at that spot.) Marks them as common and returns
1642 use Text::Tradition;
1644 my $cxfile = 't/data/Collatex-16.xml';
1645 my $t = Text::Tradition->new(
1647 'input' => 'CollateX',
1650 my $c = $t->collation;
1652 my @common = $c->calculate_common_readings();
1653 is( scalar @common, 8, "Found correct number of common readings" );
1654 my @marked = sort $c->common_readings();
1655 is( scalar @common, 8, "All common readings got marked as such" );
1656 my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /;
1657 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1663 sub calculate_common_readings {
1666 map { $_->is_common( 0 ) } $self->readings;
1667 # Implicitly calls calculate_ranks
1668 my $table = $self->alignment_table;
1669 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1670 my @row = map { $_->{'tokens'}->[$idx]
1671 ? $_->{'tokens'}->[$idx]->{'t'} : '' }
1672 @{$table->{'alignment'}};
1674 foreach my $r ( @row ) {
1676 $hash{$r->id} = $r unless $r->is_meta;
1678 $hash{'UNDEF'} = $r;
1681 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1682 my( $r ) = values %hash;
1684 push( @common, $r );
1690 =head2 text_from_paths
1692 Calculate the text array for all witnesses from the path, for later consistency
1693 checking. Only to be used if there is no non-graph-based way to know the
1698 sub text_from_paths {
1700 foreach my $wit ( $self->tradition->witnesses ) {
1701 my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1703 foreach my $r ( @readings ) {
1704 next if $r->is_meta;
1705 push( @text, $r->text );
1707 $wit->text( \@text );
1708 if( $wit->is_layered ) {
1709 my @ucrdgs = $self->reading_sequence( $self->start, $self->end,
1710 $wit->sigil.$self->ac_label );
1712 foreach my $r ( @ucrdgs ) {
1713 next if $r->is_meta;
1714 push( @uctext, $r->text );
1716 $wit->layertext( \@uctext );
1721 =head1 UTILITY FUNCTIONS
1723 =head2 common_predecessor( $reading_a, $reading_b )
1725 Find the last reading that occurs in sequence before both the given readings.
1726 At the very least this should be $self->start.
1728 =head2 common_successor( $reading_a, $reading_b )
1730 Find the first reading that occurs in sequence after both the given readings.
1731 At the very least this should be $self->end.
1735 use Text::Tradition;
1737 my $cxfile = 't/data/Collatex-16.xml';
1738 my $t = Text::Tradition->new(
1740 'input' => 'CollateX',
1743 my $c = $t->collation;
1745 is( $c->common_predecessor( 'n24', 'n23' )->id,
1746 'n20', "Found correct common predecessor" );
1747 is( $c->common_successor( 'n24', 'n23' )->id,
1748 '__END__', "Found correct common successor" );
1750 is( $c->common_predecessor( 'n19', 'n17' )->id,
1751 'n16', "Found correct common predecessor for readings on same path" );
1752 is( $c->common_successor( 'n21', 'n10' )->id,
1753 '__END__', "Found correct common successor for readings on same path" );
1759 ## Return the closest reading that is a predecessor of both the given readings.
1760 sub common_predecessor {
1762 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1763 return $self->_common_in_path( $r1, $r2, 'predecessors' );
1766 sub common_successor {
1768 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1769 return $self->_common_in_path( $r1, $r2, 'successors' );
1773 # TODO think about how to do this without ranks...
1774 sub _common_in_path {
1775 my( $self, $r1, $r2, $dir ) = @_;
1776 my $iter = $self->end->rank;
1778 my @last_r1 = ( $r1 );
1779 my @last_r2 = ( $r2 );
1780 # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' );
1782 # print STDERR "Finding common $dir for $r1, $r2\n";
1783 while( !@candidates ) {
1784 last unless $iter--; # Avoid looping infinitely
1785 # Iterate separately down the graph from r1 and r2
1786 my( @new_lc1, @new_lc2 );
1787 foreach my $lc ( @last_r1 ) {
1788 foreach my $p ( $lc->$dir ) {
1789 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) {
1790 # print STDERR "Path candidate $p from $lc\n";
1791 push( @candidates, $p );
1792 } elsif( !$all_seen{$p->id} ) {
1793 $all_seen{$p->id} = 'r1';
1794 push( @new_lc1, $p );
1798 foreach my $lc ( @last_r2 ) {
1799 foreach my $p ( $lc->$dir ) {
1800 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) {
1801 # print STDERR "Path candidate $p from $lc\n";
1802 push( @candidates, $p );
1803 } elsif( !$all_seen{$p->id} ) {
1804 $all_seen{$p->id} = 'r2';
1805 push( @new_lc2, $p );
1809 @last_r1 = @new_lc1;
1810 @last_r2 = @new_lc2;
1812 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1813 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1817 Text::Tradition::Error->throw(
1818 'ident' => 'Collation error',
1824 __PACKAGE__->meta->make_immutable;
1828 This package is free software and is provided "as is" without express
1829 or implied warranty. You can redistribute it and/or modify it under
1830 the same terms as Perl itself.
1834 Tara L Andrews E<lt>aurum@cpan.orgE<gt>