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(
278 { 'collation' => $self, 'is_start' => 1, 'init' => 1 } ) );
279 $self->_set_end( $self->add_reading(
280 { 'collation' => $self, 'is_end' => 1, 'init' => 1 } ) );
283 ### Reading construct/destruct functions
286 my( $self, $reading ) = @_;
287 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
288 my %args = %$reading;
289 if( $args{'init'} ) {
290 # If we are initializing an empty collation, don't assume that we
291 # have set a tradition.
292 delete $args{'init'};
293 } elsif( $self->tradition->has_language && !exists $args{'language'} ) {
294 $args{'language'} = $self->tradition->language;
296 $reading = Text::Tradition::Collation::Reading->new(
297 'collation' => $self,
300 # First check to see if a reading with this ID exists.
301 if( $self->reading( $reading->id ) ) {
302 throw( "Collation already has a reading with id " . $reading->id );
304 $self->_graphcalc_done(0);
305 $self->_add_reading( $reading->id => $reading );
306 # Once the reading has been added, put it in both graphs.
307 $self->sequence->add_vertex( $reading->id );
308 $self->relations->add_reading( $reading->id );
312 around del_reading => sub {
317 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
320 # Remove the reading from the graphs.
321 $self->_graphcalc_done(0);
322 $self->_clear_cache; # Explicitly clear caches to GC the reading
323 $self->sequence->delete_vertex( $arg );
324 $self->relations->delete_reading( $arg );
327 $self->$orig( $arg );
334 my $cxfile = 't/data/Collatex-16.xml';
335 my $t = Text::Tradition->new(
337 'input' => 'CollateX',
340 my $c = $t->collation;
342 my $rno = scalar $c->readings;
343 # Split n21 for testing purposes
344 my $new_r = $c->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } );
345 my $old_r = $c->reading( 'n21' );
346 $old_r->alter_text( 'to' );
347 $c->del_path( 'n20', 'n21', 'A' );
348 $c->add_path( 'n20', 'n21p0', 'A' );
349 $c->add_path( 'n21p0', 'n21', 'A' );
351 ok( $c->reading( 'n21p0' ), "New reading exists" );
352 is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" );
354 # Combine n3 and n4 ( with his )
355 $c->merge_readings( 'n3', 'n4', 1 );
356 ok( !$c->reading('n4'), "Reading n4 is gone" );
357 is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" );
359 # Collapse n9 and n10 ( rood / root )
360 $c->merge_readings( 'n9', 'n10' );
361 ok( !$c->reading('n10'), "Reading n10 is gone" );
362 is( $c->reading('n9')->text, 'rood', "Reading n9 has an unchanged word" );
364 # Combine n21 and n21p0
365 my $remaining = $c->reading('n21');
366 $remaining ||= $c->reading('n22'); # one of these should still exist
367 $c->merge_readings( 'n21p0', $remaining, 1 );
368 ok( !$c->reading('n21'), "Reading $remaining is gone" );
369 is( $c->reading('n21p0')->text, 'unto', "Reading n21p0 merged correctly" );
379 my( $kept_obj, $del_obj, $combine, $combine_char ) = $self->_objectify_args( @_ );
380 my $mergemeta = $kept_obj->is_meta;
381 throw( "Cannot merge meta and non-meta reading" )
382 unless ( $mergemeta && $del_obj->is_meta )
383 || ( !$mergemeta && !$del_obj->is_meta );
385 throw( "Cannot merge with start or end node" )
386 if( $kept_obj eq $self->start || $kept_obj eq $self->end
387 || $del_obj eq $self->start || $del_obj eq $self->end );
389 # We only need the IDs for adding paths to the graph, not the reading
390 # objects themselves.
391 my $kept = $kept_obj->id;
392 my $deleted = $del_obj->id;
393 $self->_graphcalc_done(0);
395 # The kept reading should inherit the paths and the relationships
396 # of the deleted reading.
397 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
398 my @vector = ( $kept );
399 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
400 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
401 next if $vector[0] eq $vector[1]; # Don't add a self loop
402 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
403 $self->sequence->add_edge( @vector );
404 my $fwits = $self->sequence->get_edge_attributes( @vector );
405 @wits{keys %$fwits} = values %$fwits;
406 $self->sequence->set_edge_attributes( @vector, \%wits );
408 $self->relations->merge_readings( $kept, $deleted, $combine );
410 # Do the deletion deed.
412 my $joinstr = $combine_char;
413 unless( defined $joinstr ) {
414 $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior;
415 $joinstr = $self->wordsep unless defined $joinstr;
417 $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) );
419 $self->del_reading( $deleted );
423 # Helper function for manipulating the graph.
424 sub _stringify_args {
425 my( $self, $first, $second, @args ) = @_;
427 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
428 $second = $second->id
429 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
430 return( $first, $second, @args );
433 # Helper function for manipulating the graph.
434 sub _objectify_args {
435 my( $self, $first, $second, $arg ) = @_;
436 $first = $self->reading( $first )
437 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
438 $second = $self->reading( $second )
439 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
440 return( $first, $second, $arg );
447 # We only need the IDs for adding paths to the graph, not the reading
448 # objects themselves.
449 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
451 $self->_graphcalc_done(0);
452 # Connect the readings
453 unless( $self->sequence->has_edge( $source, $target ) ) {
454 $self->sequence->add_edge( $source, $target );
455 $self->relations->add_equivalence_edge( $source, $target );
457 # Note the witness in question
458 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
464 if( ref( $_[0] ) eq 'ARRAY' ) {
471 # We only need the IDs for adding paths to the graph, not the reading
472 # objects themselves.
473 my( $source, $target, $wit ) = $self->_stringify_args( @args );
475 $self->_graphcalc_done(0);
476 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
477 $self->sequence->delete_edge_attribute( $source, $target, $wit );
479 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
480 $self->sequence->delete_edge( $source, $target );
481 $self->relations->delete_equivalence_edge( $source, $target );
486 # Extra graph-alike utility
489 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
490 return undef unless $self->sequence->has_edge( $source, $target );
491 return $self->sequence->has_edge_attribute( $source, $target, $wit );
494 =head2 clear_witness( @sigil_list )
496 Clear the given witnesses out of the collation entirely, removing references
497 to them in paths, and removing readings that belong only to them. Should only
498 be called via $tradition->del_witness.
503 my( $self, @sigils ) = @_;
505 $self->_graphcalc_done(0);
506 # Clear the witness(es) out of the paths
507 foreach my $e ( $self->paths ) {
508 foreach my $sig ( @sigils ) {
509 $self->del_path( $e, $sig );
513 # Clear out the newly unused readings
514 foreach my $r ( $self->readings ) {
515 unless( $self->reading_witnesses( $r ) ) {
516 $self->del_reading( $r );
521 sub add_relationship {
523 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
524 my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts );
525 $self->_graphcalc_done(0);
529 around qw/ get_relationship del_relationship / => sub {
533 if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) {
536 my( $source, $target ) = $self->_stringify_args( @args );
537 $self->$orig( $source, $target );
540 =head2 reading_witnesses( $reading )
542 Return a list of sigils corresponding to the witnesses in which the reading appears.
546 sub reading_witnesses {
547 my( $self, $reading ) = @_;
548 # We need only check either the incoming or the outgoing edges; I have
549 # arbitrarily chosen "incoming". Thus, special-case the start node.
550 if( $reading eq $self->start ) {
551 return map { $_->sigil } $self->tradition->witnesses;
554 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
555 my $wits = $self->sequence->get_edge_attributes( @$e );
556 @all_witnesses{ keys %$wits } = 1;
558 my $acstr = $self->ac_label;
559 foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) {
560 delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit};
562 return keys %all_witnesses;
565 =head1 OUTPUT METHODS
567 =head2 as_svg( \%options )
569 Returns an SVG string that represents the graph, via as_dot and graphviz.
570 See as_dot for a list of options. Must have GraphViz (dot) installed to run.
575 my( $self, $opts ) = @_;
576 throw( "Need GraphViz installed to output SVG" )
577 unless File::Which::which( 'dot' );
578 my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'};
579 $self->calculate_ranks()
580 unless( $self->_graphcalc_done || $opts->{'nocalc'} || !$self->linear );
581 if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) {
582 my @cmd = qw/dot -Tsvg/;
584 my $dotfile = File::Temp->new();
586 # $dotfile->unlink_on_destroy(0);
587 binmode $dotfile, ':utf8';
588 print $dotfile $self->as_dot( $opts );
589 push( @cmd, $dotfile->filename );
590 run( \@cmd, ">", binary(), \$svg );
591 $svg = decode_utf8( $svg );
592 $self->cached_svg( $svg ) unless $want_subgraph;
595 return $self->cached_svg;
600 =head2 as_dot( \%options )
602 Returns a string that is the collation graph expressed in dot
603 (i.e. GraphViz) format. Options include:
618 my( $self, $opts ) = @_;
619 my $startrank = $opts->{'from'} if $opts;
620 my $endrank = $opts->{'to'} if $opts;
621 my $color_common = $opts->{'color_common'} if $opts;
622 my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank
623 && $self->end->rank > 100;
624 $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs
626 # Check the arguments
628 return if $endrank && $startrank > $endrank;
629 return if $startrank > $self->end->rank;
631 if( defined $endrank ) {
632 return if $endrank < 0;
633 $endrank = undef if $endrank == $self->end->rank;
636 my $graph_name = $self->tradition->name;
637 $graph_name =~ s/[^\w\s]//g;
638 $graph_name = join( '_', split( /\s+/, $graph_name ) );
646 'fillcolor' => 'white',
651 'arrowhead' => 'open',
652 'color' => '#000000',
653 'fontcolor' => '#000000',
656 my $dot = sprintf( "digraph %s {\n", $graph_name );
657 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
658 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
660 # Output substitute start/end readings if necessary
662 $dot .= "\t\"__SUBSTART__\" [ label=\"...\",id=\"__START__\" ];\n";
665 $dot .= "\t\"__SUBEND__\" [ label=\"...\",id=\"__END__\" ];\n";
667 if( $STRAIGHTENHACK ) {
669 my $startlabel = $startrank ? '__SUBSTART__' : '__START__';
670 $dot .= "\tsubgraph { rank=same \"$startlabel\" \"#SILENT#\" }\n";
671 $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];"
673 my %used; # Keep track of the readings that actually appear in the graph
674 # Sort the readings by rank if we have ranks; this speeds layout.
675 my @all_readings = $self->end->has_rank
676 ? sort { $a->rank <=> $b->rank } $self->readings
678 # TODO Refrain from outputting lacuna nodes - just grey out the edges.
679 foreach my $reading ( @all_readings ) {
680 # Only output readings within our rank range.
681 next if $startrank && $reading->rank < $startrank;
682 next if $endrank && $reading->rank > $endrank;
683 $used{$reading->id} = 1;
684 # Need not output nodes without separate labels
685 next if $reading->id eq $reading->text;
687 my $label = $reading->text;
688 $label .= '-' if $reading->join_next;
689 $label = "-$label" if $reading->join_prior;
690 $label =~ s/\"/\\\"/g;
691 $rattrs->{'label'} = $label;
692 $rattrs->{'id'} = $reading->id;
693 $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
694 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
697 # Add the real edges. Need to weight one edge per rank jump, in a
699 # my $weighted = $self->_add_edge_weights;
700 my @edges = $self->paths;
701 my( %substart, %subend );
702 foreach my $edge ( @edges ) {
703 # Do we need to output this edge?
704 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
705 my $label = $self->_path_display_label( $self->path_witnesses( $edge ) );
706 my $variables = { %edge_attrs, 'label' => $label };
708 # Account for the rank gap if necessary
709 my $rank0 = $self->reading( $edge->[0] )->rank
710 if $self->reading( $edge->[0] )->has_rank;
711 my $rank1 = $self->reading( $edge->[1] )->rank
712 if $self->reading( $edge->[1] )->has_rank;
713 if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) {
714 $variables->{'minlen'} = $rank1 - $rank0;
717 # Add the calculated edge weights
718 # if( exists $weighted->{$edge->[0]}
719 # && $weighted->{$edge->[0]} eq $edge->[1] ) {
720 # # $variables->{'color'} = 'red';
721 # $variables->{'weight'} = 3.0;
724 # EXPERIMENTAL: make edge width reflect no. of witnesses
725 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
726 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
728 my $varopts = _dot_attr_string( $variables );
729 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
730 $edge->[0], $edge->[1], $varopts );
731 } elsif( $used{$edge->[0]} ) {
732 $subend{$edge->[0]} = $edge->[1];
733 } elsif( $used{$edge->[1]} ) {
734 $substart{$edge->[1]} = $edge->[0];
737 # Add substitute start and end edges if necessary
738 foreach my $node ( keys %substart ) {
739 my $witstr = $self->_path_display_label ( $self->path_witnesses( $substart{$node}, $node ) );
740 my $variables = { %edge_attrs, 'label' => $witstr };
741 my $nrdg = $self->reading( $node );
742 if( $nrdg->has_rank && $nrdg->rank > $startrank ) {
743 # Substart is actually one lower than $startrank
744 $variables->{'minlen'} = $nrdg->rank - ( $startrank - 1 );
746 my $varopts = _dot_attr_string( $variables );
747 $dot .= "\t\"__SUBSTART__\" -> \"$node\" $varopts;\n";
749 foreach my $node ( keys %subend ) {
750 my $witstr = $self->_path_display_label ( $self->path_witnesses( $node, $subend{$node} ) );
751 my $variables = { %edge_attrs, 'label' => $witstr };
752 my $varopts = _dot_attr_string( $variables );
753 $dot .= "\t\"$node\" -> \"__SUBEND__\" $varopts;\n";
756 if( $STRAIGHTENHACK ) {
757 my $endlabel = $endrank ? '__SUBEND__' : '__END__';
758 $dot .= "\t\"$endlabel\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
765 sub _dot_attr_string {
768 foreach my $k ( sort keys %$hash ) {
770 push( @attrs, $k.'="'.$v.'"' );
772 return( '[ ' . join( ', ', @attrs ) . ' ]' );
775 sub _add_edge_weights {
777 # Walk the graph from START to END, choosing the successor node with
778 # the largest number of witness paths each time.
780 my $curr = $self->start->id;
781 my $ranked = $self->end->has_rank;
782 while( $curr ne $self->end->id ) {
783 my $rank = $ranked ? $self->reading( $curr )->rank : 0;
784 my @succ = sort { $self->path_witnesses( $curr, $a )
785 <=> $self->path_witnesses( $curr, $b ) }
786 $self->sequence->successors( $curr );
787 my $next = pop @succ;
788 my $nextrank = $ranked ? $self->reading( $next )->rank : 0;
789 # Try to avoid lacunae in the weighted path.
791 ( $self->reading( $next )->is_lacuna ||
792 $nextrank - $rank > 1 ) ){
795 $weighted->{$curr} = $next;
801 =head2 path_witnesses( $edge )
803 Returns the list of sigils whose witnesses are associated with the given edge.
804 The edge can be passed as either an array or an arrayref of ( $source, $target ).
809 my( $self, @edge ) = @_;
810 # If edge is an arrayref, cope.
811 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
815 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
819 # Helper function. Make a display label for the given witnesses, showing a.c.
820 # witnesses only where the main witness is not also in the list.
821 sub _path_display_label {
824 map { $wits{$_} = 1 } @_;
826 # If an a.c. wit is listed, remove it if the main wit is also listed.
827 # Otherwise keep it for explicit listing.
828 my $aclabel = $self->ac_label;
830 foreach my $w ( sort keys %wits ) {
831 if( $w =~ /^(.*)\Q$aclabel\E$/ ) {
832 if( exists $wits{$1} ) {
835 push( @disp_ac, $w );
840 # See if we are in a majority situation.
841 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
842 $maj = $maj > 5 ? $maj : 5;
843 if( scalar keys %wits > $maj ) {
844 unshift( @disp_ac, 'majority' );
845 return join( ', ', @disp_ac );
847 return join( ', ', sort keys %wits );
851 =head2 readings_at_rank( $rank )
853 Returns a list of readings at a given rank, taken from the alignment table.
857 sub readings_at_rank {
858 my( $self, $rank ) = @_;
859 my $table = $self->alignment_table;
860 # Table rank is real rank - 1.
861 my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}};
863 foreach my $e ( @elements ) {
864 next unless ref( $e ) eq 'HASH';
865 next unless exists $e->{'t'};
866 $readings{$e->{'t'}->id} = $e->{'t'};
868 return values %readings;
873 Returns a GraphML representation of the collation. The GraphML will contain
874 two graphs. The first expresses the attributes of the readings and the witness
875 paths that link them; the second expresses the relationships that link the
876 readings. This is the native transfer format for a tradition.
885 my $datafile = 't/data/florilegium_tei_ps.xml';
886 my $tradition = Text::Tradition->new( 'input' => 'TEI',
891 ok( $tradition, "Got a tradition object" );
892 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
893 ok( $tradition->collation, "Tradition has a collation" );
895 my $c = $tradition->collation;
896 is( scalar $c->readings, $READINGS, "Collation has all readings" );
897 is( scalar $c->paths, $PATHS, "Collation has all paths" );
898 is( scalar $c->relationships, 0, "Collation has all relationships" );
900 # Add a few relationships
901 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
902 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
903 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
905 # Now write it to GraphML and parse it again.
907 my $graphml = $c->as_graphml;
908 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
909 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
910 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
911 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
913 # Now add a stemma, write to GraphML, and parse again.
914 my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
915 is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" );
916 is( $tradition->stemmata, 1, "Tradition now has the stemma" );
917 $graphml = $c->as_graphml;
918 like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" );
925 my( $self, $options ) = @_;
926 $self->calculate_ranks unless $self->_graphcalc_done;
928 my $start = $options->{'from'}
929 ? $self->reading( $options->{'from'} ) : $self->start;
930 my $end = $options->{'to'}
931 ? $self->reading( $options->{'to'} ) : $self->end;
932 if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) {
933 throw( 'Start node must be before end node' );
935 # The readings need to be ranked for this to work.
936 $start = $self->start unless $start->has_rank;
937 $end = $self->end unless $end->has_rank;
939 unless( $start eq $self->start ) {
940 $rankoffset = $start->rank - 1;
945 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
946 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
947 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
948 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
950 # Create the document and root node
951 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
952 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
953 $graphml->setDocumentElement( $root );
954 $root->setNamespace( $xsi_ns, 'xsi', 0 );
955 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
957 # List of attribute types to save on our objects and their corresponding
963 'ReadingID' => 'string',
964 'RelationshipType' => 'string',
965 'RelationshipScope' => 'string',
968 # List of attribute names *not* to save on our objects.
969 # We will also not save any attribute beginning with _.
971 map { $skipsave{$_} = 1 } qw/ cached_svg /;
973 # Add the data keys for the graph. Include an extra key 'version' for the
974 # GraphML output version.
977 my %graph_attributes = ( 'version' => 'string' );
978 # Graph attributes include those of Tradition and those of Collation.
980 my $tmeta = $self->tradition->meta;
981 my $cmeta = $self->meta;
982 map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes;
983 map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes;
984 foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) {
985 next if $attr->name =~ /^_/;
986 next if $skipsave{$attr->name};
987 next unless $save_types{$attr->type_constraint->name};
988 $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
990 # Extra custom key for the tradition stemma(ta)
991 $graph_attributes{'stemmata'} = 'string';
993 foreach my $datum ( sort keys %graph_attributes ) {
994 $graph_data_keys{$datum} = 'dg'.$gdi++;
995 my $key = $root->addNewChild( $graphml_ns, 'key' );
996 $key->setAttribute( 'attr.name', $datum );
997 $key->setAttribute( 'attr.type', $graph_attributes{$datum} );
998 $key->setAttribute( 'for', 'graph' );
999 $key->setAttribute( 'id', $graph_data_keys{$datum} );
1002 # Add the data keys for reading nodes
1003 my %reading_attributes;
1004 my $rmeta = Text::Tradition::Collation::Reading->meta;
1005 foreach my $attr( $rmeta->get_all_attributes ) {
1006 next if $attr->name =~ /^_/;
1007 next if $skipsave{$attr->name};
1008 next unless $save_types{$attr->type_constraint->name};
1009 $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
1011 # Extra custom key for the reading morphology
1012 $reading_attributes{'lexemes'} = 'string';
1016 foreach my $datum ( sort keys %reading_attributes ) {
1017 $node_data_keys{$datum} = 'dn'.$ndi++;
1018 my $key = $root->addNewChild( $graphml_ns, 'key' );
1019 $key->setAttribute( 'attr.name', $datum );
1020 $key->setAttribute( 'attr.type', $reading_attributes{$datum} );
1021 $key->setAttribute( 'for', 'node' );
1022 $key->setAttribute( 'id', $node_data_keys{$datum} );
1025 # Add the data keys for edges, that is, paths and relationships. Path
1026 # data does not come from a Moose class so is here manually.
1029 my %edge_attributes = (
1030 witness => 'string', # ID/label for a path
1031 extra => 'boolean', # Path key
1033 my @path_attributes = keys %edge_attributes; # track our manual additions
1034 my $pmeta = Text::Tradition::Collation::Relationship->meta;
1035 foreach my $attr( $pmeta->get_all_attributes ) {
1036 next if $attr->name =~ /^_/;
1037 next if $skipsave{$attr->name};
1038 next unless $save_types{$attr->type_constraint->name};
1039 $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
1041 foreach my $datum ( sort keys %edge_attributes ) {
1042 $edge_data_keys{$datum} = 'de'.$edi++;
1043 my $key = $root->addNewChild( $graphml_ns, 'key' );
1044 $key->setAttribute( 'attr.name', $datum );
1045 $key->setAttribute( 'attr.type', $edge_attributes{$datum} );
1046 $key->setAttribute( 'for', 'edge' );
1047 $key->setAttribute( 'id', $edge_data_keys{$datum} );
1050 # Add the collation graph itself. First, sanitize the name to a valid XML ID.
1051 my $xmlidname = $self->tradition->name;
1052 $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g;
1053 if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) {
1054 $xmlidname = '_'.$xmlidname;
1056 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
1057 $sgraph->setAttribute( 'edgedefault', 'directed' );
1058 $sgraph->setAttribute( 'id', $xmlidname );
1059 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
1060 $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later
1061 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
1062 $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later
1063 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
1065 # Tradition/collation attribute data
1066 foreach my $datum ( keys %graph_attributes ) {
1068 if( $datum eq 'version' ) {
1070 } elsif( $datum eq 'stemmata' ) {
1072 map { push( @stemstrs, $_->editable( {linesep => ''} ) ) }
1073 $self->tradition->stemmata;
1074 $value = join( "\n", @stemstrs );
1075 } elsif( $gattr_from{$datum} eq 'Tradition' ) {
1076 $value = $self->tradition->$datum;
1078 $value = $self->$datum;
1080 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
1085 # Add our readings to the graph
1086 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
1087 next if $n->has_rank && $n ne $self->start && $n ne $self->end &&
1088 ( $n->rank < $start->rank || $n->rank > $end->rank );
1089 $use_readings{$n->id} = 1;
1090 # Add to the main graph
1091 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
1092 my $node_xmlid = 'n' . $node_ctr++;
1093 $node_hash{ $n->id } = $node_xmlid;
1094 $node_el->setAttribute( 'id', $node_xmlid );
1095 foreach my $d ( keys %reading_attributes ) {
1097 # Custom serialization
1098 if( $d eq 'lexemes' ) {
1099 # If nval is a true value, we have lexemes so we need to
1100 # serialize them. Otherwise set nval to undef so that the
1101 # key is excluded from this reading.
1102 $nval = $nval ? $n->_serialize_lexemes : undef;
1103 } elsif( $d eq 'normal_form' && $n->normal_form eq $n->text ) {
1106 if( $rankoffset && $d eq 'rank' && $n ne $self->start ) {
1107 # Adjust the ranks within the subgraph.
1108 $nval = $n eq $self->end ? $end->rank - $rankoffset + 1
1109 : $nval - $rankoffset;
1111 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
1116 # Add the path edges to the sequence graph
1118 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
1119 # We add an edge in the graphml for every witness in $e.
1120 next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} );
1121 my @edge_wits = sort $self->path_witnesses( $e );
1122 $e->[0] = $self->start->id unless $use_readings{$e->[0]};
1123 $e->[1] = $self->end->id unless $use_readings{$e->[1]};
1124 # Skip any path from start to end; that witness is not in the subgraph.
1125 next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id );
1126 foreach my $wit ( @edge_wits ) {
1127 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
1128 $node_hash{ $e->[0] },
1129 $node_hash{ $e->[1] } );
1130 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
1131 $edge_el->setAttribute( 'source', $from );
1132 $edge_el->setAttribute( 'target', $to );
1133 $edge_el->setAttribute( 'id', $id );
1135 # It's a witness path, so add the witness
1137 my $key = $edge_data_keys{'witness'};
1138 # Is this an ante-corr witness?
1139 my $aclabel = $self->ac_label;
1140 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
1141 # Keep the base witness
1143 # ...and record that this is an 'extra' reading path
1144 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
1146 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
1150 # Report the actual number of nodes and edges that went in
1151 $sgraph->setAttribute( 'parse.edges', $edge_ctr );
1152 $sgraph->setAttribute( 'parse.nodes', $node_ctr );
1154 # Add the relationship graph to the XML
1155 map { delete $edge_data_keys{$_} } @path_attributes;
1156 $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
1157 $node_data_keys{'id'}, \%edge_data_keys );
1159 # Save and return the thing
1160 my $result = decode_utf8( $graphml->toString(1) );
1164 sub _add_graphml_data {
1165 my( $el, $key, $value ) = @_;
1166 return unless defined $value;
1167 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
1168 $data_el->setAttribute( 'key', $key );
1169 $data_el->appendText( $value );
1174 Returns a CSV alignment table representation of the collation graph, one
1175 row per witness (or witness uncorrected.)
1181 my $table = $self->alignment_table;
1182 my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } );
1184 # Make the header row
1185 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
1186 push( @result, decode_utf8( $csv->string ) );
1187 # Make the rest of the rows
1188 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1189 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
1190 my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs;
1191 $csv->combine( @row );
1192 push( @result, decode_utf8( $csv->string ) );
1194 return join( "\n", @result );
1197 =head2 alignment_table( $use_refs, $include_witnesses )
1199 Return a reference to an alignment table, in a slightly enhanced CollateX
1200 format which looks like this:
1202 $table = { alignment => [ { witness => "SIGIL",
1203 tokens => [ { t => "TEXT" }, ... ] },
1204 { witness => "SIG2",
1205 tokens => [ { t => "TEXT" }, ... ] },
1207 length => TEXTLEN };
1209 If $use_refs is set to 1, the reading object is returned in the table
1210 instead of READINGTEXT; if not, the text of the reading is returned.
1212 If $include_witnesses is set to a hashref, only the witnesses whose sigil
1213 keys have a true hash value will be included.
1217 sub alignment_table {
1219 $self->calculate_ranks() unless $self->_graphcalc_done;
1220 return $self->cached_table if $self->has_cached_table;
1222 # Make sure we can do this
1223 throw( "Need a linear graph in order to make an alignment table" )
1224 unless $self->linear;
1225 $self->calculate_ranks unless $self->end->has_rank;
1227 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
1228 my @all_pos = ( 1 .. $self->end->rank - 1 );
1229 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
1230 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
1231 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1232 my @row = _make_witness_row( \@wit_path, \@all_pos );
1233 push( @{$table->{'alignment'}},
1234 { 'witness' => $wit->sigil, 'tokens' => \@row } );
1235 if( $wit->is_layered ) {
1236 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
1237 $wit->sigil.$self->ac_label );
1238 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
1239 push( @{$table->{'alignment'}},
1240 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
1243 $self->cached_table( $table );
1247 sub _make_witness_row {
1248 my( $path, $positions ) = @_;
1250 map { $char_hash{$_} = undef } @$positions;
1252 foreach my $rdg ( @$path ) {
1253 my $rtext = $rdg->text;
1254 $rtext = '#LACUNA#' if $rdg->is_lacuna;
1255 print STDERR "rank " . $rdg->rank . "\n" if $debug;
1256 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
1257 $char_hash{$rdg->rank} = { 't' => $rdg };
1259 my @row = map { $char_hash{$_} } @$positions;
1260 # Fill in lacuna markers for undef spots in the row
1261 my $last_el = shift @row;
1262 my @filled_row = ( $last_el );
1263 foreach my $el ( @row ) {
1264 # If we are using node reference, make the lacuna node appear many times
1265 # in the table. If not, use the lacuna tag.
1266 if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) {
1269 push( @filled_row, $el );
1275 =head1 NAVIGATION METHODS
1277 =head2 reading_sequence( $first, $last, $sigil, $backup )
1279 Returns the ordered list of readings, starting with $first and ending
1280 with $last, for the witness given in $sigil. If a $backup sigil is
1281 specified (e.g. when walking a layered witness), it will be used wherever
1282 no $sigil path exists. If there is a base text reading, that will be
1283 used wherever no path exists for $sigil or $backup.
1287 # TODO Think about returning some lazy-eval iterator.
1288 # TODO Get rid of backup; we should know from what witness is whether we need it.
1290 sub reading_sequence {
1291 my( $self, $start, $end, $witness ) = @_;
1293 $witness = $self->baselabel unless $witness;
1294 my @readings = ( $start );
1297 while( $n && $n->id ne $end->id ) {
1298 if( exists( $seen{$n->id} ) ) {
1299 throw( "Detected loop for $witness at " . $n->id );
1303 my $next = $self->next_reading( $n, $witness );
1305 throw( "Did not find any path for $witness from reading " . $n->id );
1307 push( @readings, $next );
1310 # Check that the last reading is our end reading.
1311 my $last = $readings[$#readings];
1312 throw( "Last reading found from " . $start->text .
1313 " for witness $witness is not the end!" ) # TODO do we get this far?
1314 unless $last->id eq $end->id;
1319 =head2 next_reading( $reading, $sigil );
1321 Returns the reading that follows the given reading along the given witness
1327 # Return the successor via the corresponding path.
1329 my $answer = $self->_find_linked_reading( 'next', @_ );
1330 return undef unless $answer;
1331 return $self->reading( $answer );
1334 =head2 prior_reading( $reading, $sigil )
1336 Returns the reading that precedes the given reading along the given witness
1342 # Return the predecessor via the corresponding path.
1344 my $answer = $self->_find_linked_reading( 'prior', @_ );
1345 return $self->reading( $answer );
1348 sub _find_linked_reading {
1349 my( $self, $direction, $node, $path ) = @_;
1351 # Get a backup if we are dealing with a layered witness
1353 my $aclabel = $self->ac_label;
1354 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1358 my @linked_paths = $direction eq 'next'
1359 ? $self->sequence->edges_from( $node )
1360 : $self->sequence->edges_to( $node );
1361 return undef unless scalar( @linked_paths );
1363 # We have to find the linked path that contains all of the
1364 # witnesses supplied in $path.
1365 my( @path_wits, @alt_path_wits );
1366 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1367 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1370 foreach my $le ( @linked_paths ) {
1371 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1374 my @le_wits = sort $self->path_witnesses( $le );
1375 if( _is_within( \@path_wits, \@le_wits ) ) {
1376 # This is the right path.
1377 return $direction eq 'next' ? $le->[1] : $le->[0];
1378 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1382 # Got this far? Return the alternate path if it exists.
1383 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1386 # Got this far? Return the base path if it exists.
1387 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1390 # Got this far? We have no appropriate path.
1391 warn "Could not find $direction node from " . $node->id
1392 . " along path $path";
1398 my( $set1, $set2 ) = @_;
1399 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1400 foreach my $el ( @$set1 ) {
1401 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1406 # Return the string that joins together a list of witnesses for
1407 # display on a single path.
1408 sub _witnesses_of_label {
1409 my( $self, $label ) = @_;
1410 my $regex = $self->wit_list_separator;
1411 my @answer = split( /\Q$regex\E/, $label );
1415 =head2 common_readings
1417 Returns the list of common readings in the graph (i.e. those readings that are
1418 shared by all non-lacunose witnesses.)
1422 sub common_readings {
1424 my @common = grep { $_->is_common } $self->readings;
1428 =head2 path_text( $sigil, [, $start, $end ] )
1430 Returns the text of a witness (plus its backup, if we are using a layer)
1431 as stored in the collation. The text is returned as a string, where the
1432 individual readings are joined with spaces and the meta-readings (e.g.
1433 lacunae) are omitted. Optional specification of $start and $end allows
1434 the generation of a subset of the witness text.
1439 my( $self, $wit, $start, $end ) = @_;
1440 $start = $self->start unless $start;
1441 $end = $self->end unless $end;
1442 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1445 foreach my $r ( @path ) {
1446 unless ( $r->join_prior || !$last || $last->join_next ) {
1449 $pathtext .= $r->text;
1455 =head1 INITIALIZATION METHODS
1457 These are mostly for use by parsers.
1459 =head2 make_witness_path( $witness )
1461 Link the array of readings contained in $witness->path (and in
1462 $witness->uncorrected_path if it exists) into collation paths.
1463 Clear out the arrays when finished.
1465 =head2 make_witness_paths
1467 Call make_witness_path for all witnesses in the tradition.
1471 # For use when a collation is constructed from a base text and an apparatus.
1472 # We have the sequences of readings and just need to add path edges.
1473 # When we are done, clear out the witness path attributes, as they are no
1475 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1477 sub make_witness_paths {
1479 foreach my $wit ( $self->tradition->witnesses ) {
1480 # print STDERR "Making path for " . $wit->sigil . "\n";
1481 $self->make_witness_path( $wit );
1485 sub make_witness_path {
1486 my( $self, $wit ) = @_;
1487 my @chain = @{$wit->path};
1488 my $sig = $wit->sigil;
1489 # Add start and end if necessary
1490 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1491 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1492 foreach my $idx ( 0 .. $#chain-1 ) {
1493 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1495 if( $wit->is_layered ) {
1496 @chain = @{$wit->uncorrected_path};
1497 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1498 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1499 foreach my $idx( 0 .. $#chain-1 ) {
1500 my $source = $chain[$idx];
1501 my $target = $chain[$idx+1];
1502 $self->add_path( $source, $target, $sig.$self->ac_label )
1503 unless $self->has_path( $source, $target, $sig );
1507 $wit->clear_uncorrected_path;
1510 =head2 calculate_ranks
1512 Calculate the reading ranks (that is, their aligned positions relative
1513 to each other) for the graph. This can only be called on linear collations.
1517 use Text::Tradition;
1519 my $cxfile = 't/data/Collatex-16.xml';
1520 my $t = Text::Tradition->new(
1522 'input' => 'CollateX',
1525 my $c = $t->collation;
1528 my $table = $c->alignment_table;
1529 ok( $c->has_cached_table, "Alignment table was cached" );
1530 is( $c->alignment_table, $table, "Cached table returned upon second call" );
1531 $c->calculate_ranks;
1532 is( $c->alignment_table, $table, "Cached table retained with no rank change" );
1533 $c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } );
1534 isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" );
1540 sub calculate_ranks {
1542 # Save the existing ranks, in case we need to invalidate the cached SVG.
1544 map { $existing_ranks{$_} = $_->rank } $self->readings;
1546 # Do the rankings based on the relationship equivalence graph, starting
1547 # with the start node.
1548 my ( $node_ranks, $rank_nodes ) = $self->relations->equivalence_ranks();
1550 # Transfer our rankings from the topological graph to the real one.
1551 foreach my $r ( $self->readings ) {
1552 if( defined $node_ranks->{$self->equivalence( $r->id )} ) {
1553 $r->rank( $node_ranks->{$self->equivalence( $r->id )} );
1555 # Die. Find the last rank we calculated.
1556 my @all_defined = sort { ( $node_ranks->{$self->equivalence( $a->id )}||-1 )
1557 <=> ( $node_ranks->{$self->equivalence( $b->id )}||-1 ) }
1559 my $last = pop @all_defined;
1560 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1563 # Do we need to invalidate the cached data?
1564 if( $self->has_cached_svg || $self->has_cached_table ) {
1565 foreach my $r ( $self->readings ) {
1566 next if defined( $existing_ranks{$r} )
1567 && $existing_ranks{$r} == $r->rank;
1568 # Something has changed, so clear the cache
1569 $self->_clear_cache;
1570 # ...and recalculate the common readings.
1571 $self->calculate_common_readings();
1575 # The graph calculation information is now up to date.
1576 $self->_graphcalc_done(1);
1581 $self->wipe_svg if $self->has_cached_svg;
1582 $self->wipe_table if $self->has_cached_table;
1586 =head2 flatten_ranks
1588 A convenience method for parsing collation data. Searches the graph for readings
1589 with the same text at the same rank, and merges any that are found.
1595 my %unique_rank_rdg;
1597 foreach my $rdg ( $self->readings ) {
1598 next unless $rdg->has_rank;
1599 my $key = $rdg->rank . "||" . $rdg->text;
1600 if( exists $unique_rank_rdg{$key} ) {
1601 # Make sure they don't have different grammatical forms
1602 my $ur = $unique_rank_rdg{$key};
1603 if( $rdg->disambiguated && $ur->disambiguated ) {
1604 my $rform = join( '//', map { $_->form->to_string } $rdg->lexemes );
1605 my $uform = join( '//', map { $_->form->to_string } $ur->lexemes );
1606 next unless $rform eq $uform;
1607 } elsif( $rdg->disambiguated xor $ur->disambiguated ) {
1611 #print STDERR "Combining readings at same rank: $key\n";
1613 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1614 # TODO see if this now makes a common point.
1616 $unique_rank_rdg{$key} = $rdg;
1619 # If we merged readings, the ranks are still fine but the alignment
1620 # table is wrong. Wipe it.
1621 $self->wipe_table() if $changed;
1625 =head2 calculate_common_readings
1627 Goes through the graph identifying the readings that appear in every witness
1628 (apart from those with lacunae at that spot.) Marks them as common and returns
1633 use Text::Tradition;
1635 my $cxfile = 't/data/Collatex-16.xml';
1636 my $t = Text::Tradition->new(
1638 'input' => 'CollateX',
1641 my $c = $t->collation;
1643 my @common = $c->calculate_common_readings();
1644 is( scalar @common, 8, "Found correct number of common readings" );
1645 my @marked = sort $c->common_readings();
1646 is( scalar @common, 8, "All common readings got marked as such" );
1647 my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /;
1648 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1654 sub calculate_common_readings {
1657 map { $_->is_common( 0 ) } $self->readings;
1658 # Implicitly calls calculate_ranks
1659 my $table = $self->alignment_table;
1660 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1661 my @row = map { $_->{'tokens'}->[$idx]
1662 ? $_->{'tokens'}->[$idx]->{'t'} : '' }
1663 @{$table->{'alignment'}};
1665 foreach my $r ( @row ) {
1667 $hash{$r->id} = $r unless $r->is_meta;
1669 $hash{'UNDEF'} = $r;
1672 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1673 my( $r ) = values %hash;
1675 push( @common, $r );
1681 =head2 text_from_paths
1683 Calculate the text array for all witnesses from the path, for later consistency
1684 checking. Only to be used if there is no non-graph-based way to know the
1689 sub text_from_paths {
1691 foreach my $wit ( $self->tradition->witnesses ) {
1692 my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1694 foreach my $r ( @readings ) {
1695 next if $r->is_meta;
1696 push( @text, $r->text );
1698 $wit->text( \@text );
1699 if( $wit->is_layered ) {
1700 my @ucrdgs = $self->reading_sequence( $self->start, $self->end,
1701 $wit->sigil.$self->ac_label );
1703 foreach my $r ( @ucrdgs ) {
1704 next if $r->is_meta;
1705 push( @uctext, $r->text );
1707 $wit->layertext( \@uctext );
1712 =head1 UTILITY FUNCTIONS
1714 =head2 common_predecessor( $reading_a, $reading_b )
1716 Find the last reading that occurs in sequence before both the given readings.
1717 At the very least this should be $self->start.
1719 =head2 common_successor( $reading_a, $reading_b )
1721 Find the first reading that occurs in sequence after both the given readings.
1722 At the very least this should be $self->end.
1726 use Text::Tradition;
1728 my $cxfile = 't/data/Collatex-16.xml';
1729 my $t = Text::Tradition->new(
1731 'input' => 'CollateX',
1734 my $c = $t->collation;
1736 is( $c->common_predecessor( 'n24', 'n23' )->id,
1737 'n20', "Found correct common predecessor" );
1738 is( $c->common_successor( 'n24', 'n23' )->id,
1739 '__END__', "Found correct common successor" );
1741 is( $c->common_predecessor( 'n19', 'n17' )->id,
1742 'n16', "Found correct common predecessor for readings on same path" );
1743 is( $c->common_successor( 'n21', 'n10' )->id,
1744 '__END__', "Found correct common successor for readings on same path" );
1750 ## Return the closest reading that is a predecessor of both the given readings.
1751 sub common_predecessor {
1753 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1754 return $self->_common_in_path( $r1, $r2, 'predecessors' );
1757 sub common_successor {
1759 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1760 return $self->_common_in_path( $r1, $r2, 'successors' );
1764 # TODO think about how to do this without ranks...
1765 sub _common_in_path {
1766 my( $self, $r1, $r2, $dir ) = @_;
1767 my $iter = $self->end->rank;
1769 my @last_r1 = ( $r1 );
1770 my @last_r2 = ( $r2 );
1771 # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' );
1773 # print STDERR "Finding common $dir for $r1, $r2\n";
1774 while( !@candidates ) {
1775 last unless $iter--; # Avoid looping infinitely
1776 # Iterate separately down the graph from r1 and r2
1777 my( @new_lc1, @new_lc2 );
1778 foreach my $lc ( @last_r1 ) {
1779 foreach my $p ( $lc->$dir ) {
1780 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) {
1781 # print STDERR "Path candidate $p from $lc\n";
1782 push( @candidates, $p );
1783 } elsif( !$all_seen{$p->id} ) {
1784 $all_seen{$p->id} = 'r1';
1785 push( @new_lc1, $p );
1789 foreach my $lc ( @last_r2 ) {
1790 foreach my $p ( $lc->$dir ) {
1791 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) {
1792 # print STDERR "Path candidate $p from $lc\n";
1793 push( @candidates, $p );
1794 } elsif( !$all_seen{$p->id} ) {
1795 $all_seen{$p->id} = 'r2';
1796 push( @new_lc2, $p );
1800 @last_r1 = @new_lc1;
1801 @last_r2 = @new_lc2;
1803 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1804 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1808 Text::Tradition::Error->throw(
1809 'ident' => 'Collation error',
1815 __PACKAGE__->meta->make_immutable;
1819 This package is free software and is provided "as is" without express
1820 or implied warranty. You can redistribute it and/or modify it under
1821 the same terms as Perl itself.
1825 Tara L Andrews E<lt>aurum@cpan.orgE<gt>