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" );
373 my( $kept_obj, $del_obj, $combine, $combine_char ) = $self->_objectify_args( @_ );
374 my $mergemeta = $kept_obj->is_meta;
375 throw( "Cannot merge meta and non-meta reading" )
376 unless ( $mergemeta && $del_obj->is_meta )
377 || ( !$mergemeta && !$del_obj->is_meta );
379 throw( "Cannot merge with start or end node" )
380 if( $kept_obj eq $self->start || $kept_obj eq $self->end
381 || $del_obj eq $self->start || $del_obj eq $self->end );
383 # We only need the IDs for adding paths to the graph, not the reading
384 # objects themselves.
385 my $kept = $kept_obj->id;
386 my $deleted = $del_obj->id;
387 $self->_graphcalc_done(0);
389 # The kept reading should inherit the paths and the relationships
390 # of the deleted reading.
391 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
392 my @vector = ( $kept );
393 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
394 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
395 next if $vector[0] eq $vector[1]; # Don't add a self loop
396 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
397 $self->sequence->add_edge( @vector );
398 my $fwits = $self->sequence->get_edge_attributes( @vector );
399 @wits{keys %$fwits} = values %$fwits;
400 $self->sequence->set_edge_attributes( @vector, \%wits );
402 $self->relations->merge_readings( $kept, $deleted, $combine );
404 # Do the deletion deed.
406 my $joinstr = $combine_char;
407 unless( defined $joinstr ) {
408 $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior;
409 $joinstr = $self->wordsep unless defined $joinstr;
411 $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) );
413 $self->del_reading( $deleted );
417 # Helper function for manipulating the graph.
418 sub _stringify_args {
419 my( $self, $first, $second, @args ) = @_;
421 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
422 $second = $second->id
423 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
424 return( $first, $second, @args );
427 # Helper function for manipulating the graph.
428 sub _objectify_args {
429 my( $self, $first, $second, $arg ) = @_;
430 $first = $self->reading( $first )
431 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
432 $second = $self->reading( $second )
433 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
434 return( $first, $second, $arg );
441 # We only need the IDs for adding paths to the graph, not the reading
442 # objects themselves.
443 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
445 $self->_graphcalc_done(0);
446 # Connect the readings
447 unless( $self->sequence->has_edge( $source, $target ) ) {
448 $self->sequence->add_edge( $source, $target );
449 $self->relations->add_equivalence_edge( $source, $target );
451 # Note the witness in question
452 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
458 if( ref( $_[0] ) eq 'ARRAY' ) {
465 # We only need the IDs for adding paths to the graph, not the reading
466 # objects themselves.
467 my( $source, $target, $wit ) = $self->_stringify_args( @args );
469 $self->_graphcalc_done(0);
470 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
471 $self->sequence->delete_edge_attribute( $source, $target, $wit );
473 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
474 $self->sequence->delete_edge( $source, $target );
475 $self->relations->delete_equivalence_edge( $source, $target );
480 # Extra graph-alike utility
483 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
484 return undef unless $self->sequence->has_edge( $source, $target );
485 return $self->sequence->has_edge_attribute( $source, $target, $wit );
488 =head2 clear_witness( @sigil_list )
490 Clear the given witnesses out of the collation entirely, removing references
491 to them in paths, and removing readings that belong only to them. Should only
492 be called via $tradition->del_witness.
497 my( $self, @sigils ) = @_;
499 $self->_graphcalc_done(0);
500 # Clear the witness(es) out of the paths
501 foreach my $e ( $self->paths ) {
502 foreach my $sig ( @sigils ) {
503 $self->del_path( $e, $sig );
507 # Clear out the newly unused readings
508 foreach my $r ( $self->readings ) {
509 unless( $self->reading_witnesses( $r ) ) {
510 $self->del_reading( $r );
515 sub add_relationship {
517 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
518 my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts );
519 $self->_graphcalc_done(0);
523 around qw/ get_relationship del_relationship / => sub {
527 if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) {
530 my( $source, $target ) = $self->_stringify_args( @args );
531 $self->$orig( $source, $target );
534 =head2 reading_witnesses( $reading )
536 Return a list of sigils corresponding to the witnesses in which the reading appears.
540 sub reading_witnesses {
541 my( $self, $reading ) = @_;
542 # We need only check either the incoming or the outgoing edges; I have
543 # arbitrarily chosen "incoming". Thus, special-case the start node.
544 if( $reading eq $self->start ) {
545 return map { $_->sigil } $self->tradition->witnesses;
548 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
549 my $wits = $self->sequence->get_edge_attributes( @$e );
550 @all_witnesses{ keys %$wits } = 1;
552 my $acstr = $self->ac_label;
553 foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) {
554 delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit};
556 return keys %all_witnesses;
559 =head1 OUTPUT METHODS
561 =head2 as_svg( \%options )
563 Returns an SVG string that represents the graph, via as_dot and graphviz.
564 See as_dot for a list of options. Must have GraphViz (dot) installed to run.
569 my( $self, $opts ) = @_;
570 throw( "Need GraphViz installed to output SVG" )
571 unless File::Which::which( 'dot' );
572 my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'};
573 $self->calculate_ranks()
574 unless( $self->_graphcalc_done || $opts->{'nocalc'} || !$self->linear );
575 if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) {
576 my @cmd = qw/dot -Tsvg/;
578 my $dotfile = File::Temp->new();
580 # $dotfile->unlink_on_destroy(0);
581 binmode $dotfile, ':utf8';
582 print $dotfile $self->as_dot( $opts );
583 push( @cmd, $dotfile->filename );
584 run( \@cmd, ">", binary(), \$svg );
585 $svg = decode_utf8( $svg );
586 $self->cached_svg( $svg ) unless $want_subgraph;
589 return $self->cached_svg;
594 =head2 as_dot( \%options )
596 Returns a string that is the collation graph expressed in dot
597 (i.e. GraphViz) format. Options include:
612 my( $self, $opts ) = @_;
613 my $startrank = $opts->{'from'} if $opts;
614 my $endrank = $opts->{'to'} if $opts;
615 my $color_common = $opts->{'color_common'} if $opts;
616 my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank
617 && $self->end->rank > 100;
618 $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs
620 # Check the arguments
622 return if $endrank && $startrank > $endrank;
623 return if $startrank > $self->end->rank;
625 if( defined $endrank ) {
626 return if $endrank < 0;
627 $endrank = undef if $endrank == $self->end->rank;
630 my $graph_name = $self->tradition->name;
631 $graph_name =~ s/[^\w\s]//g;
632 $graph_name = join( '_', split( /\s+/, $graph_name ) );
640 'fillcolor' => 'white',
645 'arrowhead' => 'open',
646 'color' => '#000000',
647 'fontcolor' => '#000000',
650 my $dot = sprintf( "digraph %s {\n", $graph_name );
651 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
652 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
654 # Output substitute start/end readings if necessary
656 $dot .= "\t\"__SUBSTART__\" [ label=\"...\",id=\"__START__\" ];\n";
659 $dot .= "\t\"__SUBEND__\" [ label=\"...\",id=\"__END__\" ];\n";
661 if( $STRAIGHTENHACK ) {
663 my $startlabel = $startrank ? '__SUBSTART__' : '__START__';
664 $dot .= "\tsubgraph { rank=same \"$startlabel\" \"#SILENT#\" }\n";
665 $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];"
667 my %used; # Keep track of the readings that actually appear in the graph
668 # Sort the readings by rank if we have ranks; this speeds layout.
669 my @all_readings = $self->end->has_rank
670 ? sort { $a->rank <=> $b->rank } $self->readings
672 # TODO Refrain from outputting lacuna nodes - just grey out the edges.
673 foreach my $reading ( @all_readings ) {
674 # Only output readings within our rank range.
675 next if $startrank && $reading->rank < $startrank;
676 next if $endrank && $reading->rank > $endrank;
677 $used{$reading->id} = 1;
678 # Need not output nodes without separate labels
679 next if $reading->id eq $reading->text;
681 my $label = $reading->text;
682 $label .= '-' if $reading->join_next;
683 $label = "-$label" if $reading->join_prior;
684 $label =~ s/\"/\\\"/g;
685 $rattrs->{'label'} = $label;
686 $rattrs->{'id'} = $reading->id;
687 $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
688 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
691 # Add the real edges. Need to weight one edge per rank jump, in a
693 # my $weighted = $self->_add_edge_weights;
694 my @edges = $self->paths;
695 my( %substart, %subend );
696 foreach my $edge ( @edges ) {
697 # Do we need to output this edge?
698 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
699 my $label = $self->_path_display_label( $self->path_witnesses( $edge ) );
700 my $variables = { %edge_attrs, 'label' => $label };
702 # Account for the rank gap if necessary
703 my $rank0 = $self->reading( $edge->[0] )->rank
704 if $self->reading( $edge->[0] )->has_rank;
705 my $rank1 = $self->reading( $edge->[1] )->rank
706 if $self->reading( $edge->[1] )->has_rank;
707 if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) {
708 $variables->{'minlen'} = $rank1 - $rank0;
711 # Add the calculated edge weights
712 # if( exists $weighted->{$edge->[0]}
713 # && $weighted->{$edge->[0]} eq $edge->[1] ) {
714 # # $variables->{'color'} = 'red';
715 # $variables->{'weight'} = 3.0;
718 # EXPERIMENTAL: make edge width reflect no. of witnesses
719 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
720 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
722 my $varopts = _dot_attr_string( $variables );
723 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
724 $edge->[0], $edge->[1], $varopts );
725 } elsif( $used{$edge->[0]} ) {
726 $subend{$edge->[0]} = 1;
727 } elsif( $used{$edge->[1]} ) {
728 $substart{$edge->[1]} = 1;
731 # Add substitute start and end edges if necessary
732 foreach my $node ( keys %substart ) {
733 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
734 my $variables = { %edge_attrs, 'label' => $witstr };
735 my $varopts = _dot_attr_string( $variables );
736 $dot .= "\t\"__SUBSTART__\" -> \"$node\" $varopts;";
738 foreach my $node ( keys %subend ) {
739 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
740 my $variables = { %edge_attrs, 'label' => $witstr };
741 my $varopts = _dot_attr_string( $variables );
742 $dot .= "\t\"$node\" -> \"__SUBEND__\" $varopts;";
745 if( $STRAIGHTENHACK ) {
746 my $endlabel = $endrank ? '__SUBEND__' : '__END__';
747 $dot .= "\t\"$endlabel\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
754 sub _dot_attr_string {
757 foreach my $k ( sort keys %$hash ) {
759 push( @attrs, $k.'="'.$v.'"' );
761 return( '[ ' . join( ', ', @attrs ) . ' ]' );
764 sub _add_edge_weights {
766 # Walk the graph from START to END, choosing the successor node with
767 # the largest number of witness paths each time.
769 my $curr = $self->start->id;
770 my $ranked = $self->end->has_rank;
771 while( $curr ne $self->end->id ) {
772 my $rank = $ranked ? $self->reading( $curr )->rank : 0;
773 my @succ = sort { $self->path_witnesses( $curr, $a )
774 <=> $self->path_witnesses( $curr, $b ) }
775 $self->sequence->successors( $curr );
776 my $next = pop @succ;
777 my $nextrank = $ranked ? $self->reading( $next )->rank : 0;
778 # Try to avoid lacunae in the weighted path.
780 ( $self->reading( $next )->is_lacuna ||
781 $nextrank - $rank > 1 ) ){
784 $weighted->{$curr} = $next;
790 =head2 path_witnesses( $edge )
792 Returns the list of sigils whose witnesses are associated with the given edge.
793 The edge can be passed as either an array or an arrayref of ( $source, $target ).
798 my( $self, @edge ) = @_;
799 # If edge is an arrayref, cope.
800 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
804 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
808 # Helper function. Make a display label for the given witnesses, showing a.c.
809 # witnesses only where the main witness is not also in the list.
810 sub _path_display_label {
813 map { $wits{$_} = 1 } @_;
815 # If an a.c. wit is listed, remove it if the main wit is also listed.
816 # Otherwise keep it for explicit listing.
817 my $aclabel = $self->ac_label;
819 foreach my $w ( sort keys %wits ) {
820 if( $w =~ /^(.*)\Q$aclabel\E$/ ) {
821 if( exists $wits{$1} ) {
824 push( @disp_ac, $w );
829 # See if we are in a majority situation.
830 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
831 $maj = $maj > 5 ? $maj : 5;
832 if( scalar keys %wits > $maj ) {
833 unshift( @disp_ac, 'majority' );
834 return join( ', ', @disp_ac );
836 return join( ', ', sort keys %wits );
840 =head2 readings_at_rank( $rank )
842 Returns a list of readings at a given rank, taken from the alignment table.
846 sub readings_at_rank {
847 my( $self, $rank ) = @_;
848 my $table = $self->alignment_table;
849 # Table rank is real rank - 1.
850 my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}};
852 foreach my $e ( @elements ) {
853 next unless ref( $e ) eq 'HASH';
854 next unless exists $e->{'t'};
855 $readings{$e->{'t'}->id} = $e->{'t'};
857 return values %readings;
862 Returns a GraphML representation of the collation. The GraphML will contain
863 two graphs. The first expresses the attributes of the readings and the witness
864 paths that link them; the second expresses the relationships that link the
865 readings. This is the native transfer format for a tradition.
874 my $datafile = 't/data/florilegium_tei_ps.xml';
875 my $tradition = Text::Tradition->new( 'input' => 'TEI',
880 ok( $tradition, "Got a tradition object" );
881 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
882 ok( $tradition->collation, "Tradition has a collation" );
884 my $c = $tradition->collation;
885 is( scalar $c->readings, $READINGS, "Collation has all readings" );
886 is( scalar $c->paths, $PATHS, "Collation has all paths" );
887 is( scalar $c->relationships, 0, "Collation has all relationships" );
889 # Add a few relationships
890 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
891 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
892 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
894 # Now write it to GraphML and parse it again.
896 my $graphml = $c->as_graphml;
897 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
898 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
899 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
900 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
902 # Now add a stemma, write to GraphML, and parse again.
903 my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
904 is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" );
905 is( $tradition->stemmata, 1, "Tradition now has the stemma" );
906 $graphml = $c->as_graphml;
907 like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" );
914 my( $self, $options ) = @_;
915 $self->calculate_ranks unless $self->_graphcalc_done;
917 my $start = $options->{'from'}
918 ? $self->reading( $options->{'from'} ) : $self->start;
919 my $end = $options->{'to'}
920 ? $self->reading( $options->{'to'} ) : $self->end;
921 if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) {
922 throw( 'Start node must be before end node' );
924 # The readings need to be ranked for this to work.
925 $start = $self->start unless $start->has_rank;
926 $end = $self->end unless $end->has_rank;
928 unless( $start eq $self->start ) {
929 $rankoffset = $start->rank - 1;
934 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
935 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
936 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
937 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
939 # Create the document and root node
940 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
941 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
942 $graphml->setDocumentElement( $root );
943 $root->setNamespace( $xsi_ns, 'xsi', 0 );
944 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
946 # List of attribute types to save on our objects and their corresponding
952 'ReadingID' => 'string',
953 'RelationshipType' => 'string',
954 'RelationshipScope' => 'string',
957 # List of attribute names *not* to save on our objects.
958 # We will also not save any attribute beginning with _.
960 map { $skipsave{$_} = 1 } qw/ cached_svg /;
962 # Add the data keys for the graph. Include an extra key 'version' for the
963 # GraphML output version.
966 my %graph_attributes = ( 'version' => 'string' );
967 # Graph attributes include those of Tradition and those of Collation.
969 my $tmeta = $self->tradition->meta;
970 my $cmeta = $self->meta;
971 map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes;
972 map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes;
973 foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) {
974 next if $attr->name =~ /^_/;
975 next if $skipsave{$attr->name};
976 next unless $save_types{$attr->type_constraint->name};
977 $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
979 # Extra custom key for the tradition stemma(ta)
980 $graph_attributes{'stemmata'} = 'string';
982 foreach my $datum ( sort keys %graph_attributes ) {
983 $graph_data_keys{$datum} = 'dg'.$gdi++;
984 my $key = $root->addNewChild( $graphml_ns, 'key' );
985 $key->setAttribute( 'attr.name', $datum );
986 $key->setAttribute( 'attr.type', $graph_attributes{$datum} );
987 $key->setAttribute( 'for', 'graph' );
988 $key->setAttribute( 'id', $graph_data_keys{$datum} );
991 # Add the data keys for reading nodes
992 my %reading_attributes;
993 my $rmeta = Text::Tradition::Collation::Reading->meta;
994 foreach my $attr( $rmeta->get_all_attributes ) {
995 next if $attr->name =~ /^_/;
996 next if $skipsave{$attr->name};
997 next unless $save_types{$attr->type_constraint->name};
998 $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
1000 # Extra custom key for the reading morphology
1001 $reading_attributes{'lexemes'} = 'string';
1005 foreach my $datum ( sort keys %reading_attributes ) {
1006 $node_data_keys{$datum} = 'dn'.$ndi++;
1007 my $key = $root->addNewChild( $graphml_ns, 'key' );
1008 $key->setAttribute( 'attr.name', $datum );
1009 $key->setAttribute( 'attr.type', $reading_attributes{$datum} );
1010 $key->setAttribute( 'for', 'node' );
1011 $key->setAttribute( 'id', $node_data_keys{$datum} );
1014 # Add the data keys for edges, that is, paths and relationships. Path
1015 # data does not come from a Moose class so is here manually.
1018 my %edge_attributes = (
1019 witness => 'string', # ID/label for a path
1020 extra => 'boolean', # Path key
1022 my @path_attributes = keys %edge_attributes; # track our manual additions
1023 my $pmeta = Text::Tradition::Collation::Relationship->meta;
1024 foreach my $attr( $pmeta->get_all_attributes ) {
1025 next if $attr->name =~ /^_/;
1026 next if $skipsave{$attr->name};
1027 next unless $save_types{$attr->type_constraint->name};
1028 $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
1030 foreach my $datum ( sort keys %edge_attributes ) {
1031 $edge_data_keys{$datum} = 'de'.$edi++;
1032 my $key = $root->addNewChild( $graphml_ns, 'key' );
1033 $key->setAttribute( 'attr.name', $datum );
1034 $key->setAttribute( 'attr.type', $edge_attributes{$datum} );
1035 $key->setAttribute( 'for', 'edge' );
1036 $key->setAttribute( 'id', $edge_data_keys{$datum} );
1039 # Add the collation graph itself. First, sanitize the name to a valid XML ID.
1040 my $xmlidname = $self->tradition->name;
1041 $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g;
1042 if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) {
1043 $xmlidname = '_'.$xmlidname;
1045 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
1046 $sgraph->setAttribute( 'edgedefault', 'directed' );
1047 $sgraph->setAttribute( 'id', $xmlidname );
1048 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
1049 $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later
1050 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
1051 $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later
1052 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
1054 # Tradition/collation attribute data
1055 foreach my $datum ( keys %graph_attributes ) {
1057 if( $datum eq 'version' ) {
1059 } elsif( $datum eq 'stemmata' ) {
1061 map { push( @stemstrs, $_->editable( {linesep => ''} ) ) }
1062 $self->tradition->stemmata;
1063 $value = join( "\n", @stemstrs );
1064 } elsif( $gattr_from{$datum} eq 'Tradition' ) {
1065 $value = $self->tradition->$datum;
1067 $value = $self->$datum;
1069 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
1074 # Add our readings to the graph
1075 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
1076 next if $n->has_rank && $n ne $self->start && $n ne $self->end &&
1077 ( $n->rank < $start->rank || $n->rank > $end->rank );
1078 $use_readings{$n->id} = 1;
1079 # Add to the main graph
1080 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
1081 my $node_xmlid = 'n' . $node_ctr++;
1082 $node_hash{ $n->id } = $node_xmlid;
1083 $node_el->setAttribute( 'id', $node_xmlid );
1084 foreach my $d ( keys %reading_attributes ) {
1086 # Custom serialization
1087 if( $d eq 'lexemes' ) {
1088 # If nval is a true value, we have lexemes so we need to
1089 # serialize them. Otherwise set nval to undef so that the
1090 # key is excluded from this reading.
1091 $nval = $nval ? $n->_serialize_lexemes : undef;
1092 } elsif( $d eq 'normal_form' && $n->normal_form eq $n->text ) {
1095 if( $rankoffset && $d eq 'rank' && $n ne $self->start ) {
1096 # Adjust the ranks within the subgraph.
1097 $nval = $n eq $self->end ? $end->rank - $rankoffset + 1
1098 : $nval - $rankoffset;
1100 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
1105 # Add the path edges to the sequence graph
1107 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
1108 # We add an edge in the graphml for every witness in $e.
1109 next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} );
1110 my @edge_wits = sort $self->path_witnesses( $e );
1111 $e->[0] = $self->start->id unless $use_readings{$e->[0]};
1112 $e->[1] = $self->end->id unless $use_readings{$e->[1]};
1113 # Skip any path from start to end; that witness is not in the subgraph.
1114 next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id );
1115 foreach my $wit ( @edge_wits ) {
1116 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
1117 $node_hash{ $e->[0] },
1118 $node_hash{ $e->[1] } );
1119 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
1120 $edge_el->setAttribute( 'source', $from );
1121 $edge_el->setAttribute( 'target', $to );
1122 $edge_el->setAttribute( 'id', $id );
1124 # It's a witness path, so add the witness
1126 my $key = $edge_data_keys{'witness'};
1127 # Is this an ante-corr witness?
1128 my $aclabel = $self->ac_label;
1129 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
1130 # Keep the base witness
1132 # ...and record that this is an 'extra' reading path
1133 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
1135 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
1139 # Report the actual number of nodes and edges that went in
1140 $sgraph->setAttribute( 'parse.edges', $edge_ctr );
1141 $sgraph->setAttribute( 'parse.nodes', $node_ctr );
1143 # Add the relationship graph to the XML
1144 map { delete $edge_data_keys{$_} } @path_attributes;
1145 $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
1146 $node_data_keys{'id'}, \%edge_data_keys );
1148 # Save and return the thing
1149 my $result = decode_utf8( $graphml->toString(1) );
1153 sub _add_graphml_data {
1154 my( $el, $key, $value ) = @_;
1155 return unless defined $value;
1156 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
1157 $data_el->setAttribute( 'key', $key );
1158 $data_el->appendText( $value );
1163 Returns a CSV alignment table representation of the collation graph, one
1164 row per witness (or witness uncorrected.)
1170 my $table = $self->alignment_table;
1171 my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } );
1173 # Make the header row
1174 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
1175 push( @result, decode_utf8( $csv->string ) );
1176 # Make the rest of the rows
1177 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1178 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
1179 my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs;
1180 $csv->combine( @row );
1181 push( @result, decode_utf8( $csv->string ) );
1183 return join( "\n", @result );
1186 =head2 alignment_table( $use_refs, $include_witnesses )
1188 Return a reference to an alignment table, in a slightly enhanced CollateX
1189 format which looks like this:
1191 $table = { alignment => [ { witness => "SIGIL",
1192 tokens => [ { t => "TEXT" }, ... ] },
1193 { witness => "SIG2",
1194 tokens => [ { t => "TEXT" }, ... ] },
1196 length => TEXTLEN };
1198 If $use_refs is set to 1, the reading object is returned in the table
1199 instead of READINGTEXT; if not, the text of the reading is returned.
1201 If $include_witnesses is set to a hashref, only the witnesses whose sigil
1202 keys have a true hash value will be included.
1206 sub alignment_table {
1208 $self->calculate_ranks() unless $self->_graphcalc_done;
1209 return $self->cached_table if $self->has_cached_table;
1211 # Make sure we can do this
1212 throw( "Need a linear graph in order to make an alignment table" )
1213 unless $self->linear;
1214 $self->calculate_ranks unless $self->end->has_rank;
1216 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
1217 my @all_pos = ( 1 .. $self->end->rank - 1 );
1218 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
1219 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
1220 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1221 my @row = _make_witness_row( \@wit_path, \@all_pos );
1222 push( @{$table->{'alignment'}},
1223 { 'witness' => $wit->sigil, 'tokens' => \@row } );
1224 if( $wit->is_layered ) {
1225 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
1226 $wit->sigil.$self->ac_label );
1227 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
1228 push( @{$table->{'alignment'}},
1229 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
1232 $self->cached_table( $table );
1236 sub _make_witness_row {
1237 my( $path, $positions ) = @_;
1239 map { $char_hash{$_} = undef } @$positions;
1241 foreach my $rdg ( @$path ) {
1242 my $rtext = $rdg->text;
1243 $rtext = '#LACUNA#' if $rdg->is_lacuna;
1244 print STDERR "rank " . $rdg->rank . "\n" if $debug;
1245 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
1246 $char_hash{$rdg->rank} = { 't' => $rdg };
1248 my @row = map { $char_hash{$_} } @$positions;
1249 # Fill in lacuna markers for undef spots in the row
1250 my $last_el = shift @row;
1251 my @filled_row = ( $last_el );
1252 foreach my $el ( @row ) {
1253 # If we are using node reference, make the lacuna node appear many times
1254 # in the table. If not, use the lacuna tag.
1255 if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) {
1258 push( @filled_row, $el );
1264 =head1 NAVIGATION METHODS
1266 =head2 reading_sequence( $first, $last, $sigil, $backup )
1268 Returns the ordered list of readings, starting with $first and ending
1269 with $last, for the witness given in $sigil. If a $backup sigil is
1270 specified (e.g. when walking a layered witness), it will be used wherever
1271 no $sigil path exists. If there is a base text reading, that will be
1272 used wherever no path exists for $sigil or $backup.
1276 # TODO Think about returning some lazy-eval iterator.
1277 # TODO Get rid of backup; we should know from what witness is whether we need it.
1279 sub reading_sequence {
1280 my( $self, $start, $end, $witness ) = @_;
1282 $witness = $self->baselabel unless $witness;
1283 my @readings = ( $start );
1286 while( $n && $n->id ne $end->id ) {
1287 if( exists( $seen{$n->id} ) ) {
1288 throw( "Detected loop for $witness at " . $n->id );
1292 my $next = $self->next_reading( $n, $witness );
1294 throw( "Did not find any path for $witness from reading " . $n->id );
1296 push( @readings, $next );
1299 # Check that the last reading is our end reading.
1300 my $last = $readings[$#readings];
1301 throw( "Last reading found from " . $start->text .
1302 " for witness $witness is not the end!" ) # TODO do we get this far?
1303 unless $last->id eq $end->id;
1308 =head2 next_reading( $reading, $sigil );
1310 Returns the reading that follows the given reading along the given witness
1316 # Return the successor via the corresponding path.
1318 my $answer = $self->_find_linked_reading( 'next', @_ );
1319 return undef unless $answer;
1320 return $self->reading( $answer );
1323 =head2 prior_reading( $reading, $sigil )
1325 Returns the reading that precedes the given reading along the given witness
1331 # Return the predecessor via the corresponding path.
1333 my $answer = $self->_find_linked_reading( 'prior', @_ );
1334 return $self->reading( $answer );
1337 sub _find_linked_reading {
1338 my( $self, $direction, $node, $path ) = @_;
1340 # Get a backup if we are dealing with a layered witness
1342 my $aclabel = $self->ac_label;
1343 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1347 my @linked_paths = $direction eq 'next'
1348 ? $self->sequence->edges_from( $node )
1349 : $self->sequence->edges_to( $node );
1350 return undef unless scalar( @linked_paths );
1352 # We have to find the linked path that contains all of the
1353 # witnesses supplied in $path.
1354 my( @path_wits, @alt_path_wits );
1355 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1356 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1359 foreach my $le ( @linked_paths ) {
1360 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1363 my @le_wits = sort $self->path_witnesses( $le );
1364 if( _is_within( \@path_wits, \@le_wits ) ) {
1365 # This is the right path.
1366 return $direction eq 'next' ? $le->[1] : $le->[0];
1367 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1371 # Got this far? Return the alternate path if it exists.
1372 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1375 # Got this far? Return the base path if it exists.
1376 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1379 # Got this far? We have no appropriate path.
1380 warn "Could not find $direction node from " . $node->id
1381 . " along path $path";
1387 my( $set1, $set2 ) = @_;
1388 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1389 foreach my $el ( @$set1 ) {
1390 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1395 # Return the string that joins together a list of witnesses for
1396 # display on a single path.
1397 sub _witnesses_of_label {
1398 my( $self, $label ) = @_;
1399 my $regex = $self->wit_list_separator;
1400 my @answer = split( /\Q$regex\E/, $label );
1404 =head2 common_readings
1406 Returns the list of common readings in the graph (i.e. those readings that are
1407 shared by all non-lacunose witnesses.)
1411 sub common_readings {
1413 my @common = grep { $_->is_common } $self->readings;
1417 =head2 path_text( $sigil, [, $start, $end ] )
1419 Returns the text of a witness (plus its backup, if we are using a layer)
1420 as stored in the collation. The text is returned as a string, where the
1421 individual readings are joined with spaces and the meta-readings (e.g.
1422 lacunae) are omitted. Optional specification of $start and $end allows
1423 the generation of a subset of the witness text.
1428 my( $self, $wit, $start, $end ) = @_;
1429 $start = $self->start unless $start;
1430 $end = $self->end unless $end;
1431 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1434 foreach my $r ( @path ) {
1435 unless ( $r->join_prior || !$last || $last->join_next ) {
1438 $pathtext .= $r->text;
1444 =head1 INITIALIZATION METHODS
1446 These are mostly for use by parsers.
1448 =head2 make_witness_path( $witness )
1450 Link the array of readings contained in $witness->path (and in
1451 $witness->uncorrected_path if it exists) into collation paths.
1452 Clear out the arrays when finished.
1454 =head2 make_witness_paths
1456 Call make_witness_path for all witnesses in the tradition.
1460 # For use when a collation is constructed from a base text and an apparatus.
1461 # We have the sequences of readings and just need to add path edges.
1462 # When we are done, clear out the witness path attributes, as they are no
1464 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1466 sub make_witness_paths {
1468 foreach my $wit ( $self->tradition->witnesses ) {
1469 # print STDERR "Making path for " . $wit->sigil . "\n";
1470 $self->make_witness_path( $wit );
1474 sub make_witness_path {
1475 my( $self, $wit ) = @_;
1476 my @chain = @{$wit->path};
1477 my $sig = $wit->sigil;
1478 # Add start and end if necessary
1479 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1480 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1481 foreach my $idx ( 0 .. $#chain-1 ) {
1482 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1484 if( $wit->is_layered ) {
1485 @chain = @{$wit->uncorrected_path};
1486 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1487 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1488 foreach my $idx( 0 .. $#chain-1 ) {
1489 my $source = $chain[$idx];
1490 my $target = $chain[$idx+1];
1491 $self->add_path( $source, $target, $sig.$self->ac_label )
1492 unless $self->has_path( $source, $target, $sig );
1496 $wit->clear_uncorrected_path;
1499 =head2 calculate_ranks
1501 Calculate the reading ranks (that is, their aligned positions relative
1502 to each other) for the graph. This can only be called on linear collations.
1506 use Text::Tradition;
1508 my $cxfile = 't/data/Collatex-16.xml';
1509 my $t = Text::Tradition->new(
1511 'input' => 'CollateX',
1514 my $c = $t->collation;
1517 my $table = $c->alignment_table;
1518 ok( $c->has_cached_table, "Alignment table was cached" );
1519 is( $c->alignment_table, $table, "Cached table returned upon second call" );
1520 $c->calculate_ranks;
1521 is( $c->alignment_table, $table, "Cached table retained with no rank change" );
1522 $c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } );
1523 isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" );
1529 sub calculate_ranks {
1531 # Save the existing ranks, in case we need to invalidate the cached SVG.
1533 map { $existing_ranks{$_} = $_->rank } $self->readings;
1535 # Do the rankings based on the relationship equivalence graph, starting
1536 # with the start node.
1537 my ( $node_ranks, $rank_nodes ) = $self->relations->equivalence_ranks();
1539 # Transfer our rankings from the topological graph to the real one.
1540 foreach my $r ( $self->readings ) {
1541 if( defined $node_ranks->{$self->equivalence( $r->id )} ) {
1542 $r->rank( $node_ranks->{$self->equivalence( $r->id )} );
1544 # Die. Find the last rank we calculated.
1545 my @all_defined = sort { ( $node_ranks->{$self->equivalence( $a->id )}||-1 )
1546 <=> ( $node_ranks->{$self->equivalence( $b->id )}||-1 ) }
1548 my $last = pop @all_defined;
1549 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1552 # Do we need to invalidate the cached data?
1553 if( $self->has_cached_svg || $self->has_cached_table ) {
1554 foreach my $r ( $self->readings ) {
1555 next if defined( $existing_ranks{$r} )
1556 && $existing_ranks{$r} == $r->rank;
1557 # Something has changed, so clear the cache
1558 $self->_clear_cache;
1559 # ...and recalculate the common readings.
1560 $self->calculate_common_readings();
1564 # The graph calculation information is now up to date.
1565 $self->_graphcalc_done(1);
1570 $self->wipe_svg if $self->has_cached_svg;
1571 $self->wipe_table if $self->has_cached_table;
1575 =head2 flatten_ranks
1577 A convenience method for parsing collation data. Searches the graph for readings
1578 with the same text at the same rank, and merges any that are found.
1584 my %unique_rank_rdg;
1586 foreach my $rdg ( $self->readings ) {
1587 next unless $rdg->has_rank;
1588 my $key = $rdg->rank . "||" . $rdg->text;
1589 if( exists $unique_rank_rdg{$key} ) {
1590 # Make sure they don't have different grammatical forms
1591 my $ur = $unique_rank_rdg{$key};
1592 if( $rdg->disambiguated && $ur->disambiguated ) {
1593 my $rform = join( '//', map { $_->form->to_string } $rdg->lexemes );
1594 my $uform = join( '//', map { $_->form->to_string } $ur->lexemes );
1595 next unless $rform eq $uform;
1596 } elsif( $rdg->disambiguated xor $ur->disambiguated ) {
1600 #print STDERR "Combining readings at same rank: $key\n";
1602 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1603 # TODO see if this now makes a common point.
1605 $unique_rank_rdg{$key} = $rdg;
1608 # If we merged readings, the ranks are still fine but the alignment
1609 # table is wrong. Wipe it.
1610 $self->wipe_table() if $changed;
1614 =head2 calculate_common_readings
1616 Goes through the graph identifying the readings that appear in every witness
1617 (apart from those with lacunae at that spot.) Marks them as common and returns
1622 use Text::Tradition;
1624 my $cxfile = 't/data/Collatex-16.xml';
1625 my $t = Text::Tradition->new(
1627 'input' => 'CollateX',
1630 my $c = $t->collation;
1632 my @common = $c->calculate_common_readings();
1633 is( scalar @common, 8, "Found correct number of common readings" );
1634 my @marked = sort $c->common_readings();
1635 is( scalar @common, 8, "All common readings got marked as such" );
1636 my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /;
1637 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1643 sub calculate_common_readings {
1646 map { $_->is_common( 0 ) } $self->readings;
1647 # Implicitly calls calculate_ranks
1648 my $table = $self->alignment_table;
1649 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1650 my @row = map { $_->{'tokens'}->[$idx]
1651 ? $_->{'tokens'}->[$idx]->{'t'} : '' }
1652 @{$table->{'alignment'}};
1654 foreach my $r ( @row ) {
1656 $hash{$r->id} = $r unless $r->is_meta;
1658 $hash{'UNDEF'} = $r;
1661 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1662 my( $r ) = values %hash;
1664 push( @common, $r );
1670 =head2 text_from_paths
1672 Calculate the text array for all witnesses from the path, for later consistency
1673 checking. Only to be used if there is no non-graph-based way to know the
1678 sub text_from_paths {
1680 foreach my $wit ( $self->tradition->witnesses ) {
1681 my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1683 foreach my $r ( @readings ) {
1684 next if $r->is_meta;
1685 push( @text, $r->text );
1687 $wit->text( \@text );
1688 if( $wit->is_layered ) {
1689 my @ucrdgs = $self->reading_sequence( $self->start, $self->end,
1690 $wit->sigil.$self->ac_label );
1692 foreach my $r ( @ucrdgs ) {
1693 next if $r->is_meta;
1694 push( @uctext, $r->text );
1696 $wit->layertext( \@uctext );
1701 =head1 UTILITY FUNCTIONS
1703 =head2 common_predecessor( $reading_a, $reading_b )
1705 Find the last reading that occurs in sequence before both the given readings.
1706 At the very least this should be $self->start.
1708 =head2 common_successor( $reading_a, $reading_b )
1710 Find the first reading that occurs in sequence after both the given readings.
1711 At the very least this should be $self->end.
1715 use Text::Tradition;
1717 my $cxfile = 't/data/Collatex-16.xml';
1718 my $t = Text::Tradition->new(
1720 'input' => 'CollateX',
1723 my $c = $t->collation;
1725 is( $c->common_predecessor( 'n24', 'n23' )->id,
1726 'n20', "Found correct common predecessor" );
1727 is( $c->common_successor( 'n24', 'n23' )->id,
1728 '__END__', "Found correct common successor" );
1730 is( $c->common_predecessor( 'n19', 'n17' )->id,
1731 'n16', "Found correct common predecessor for readings on same path" );
1732 is( $c->common_successor( 'n21', 'n10' )->id,
1733 '__END__', "Found correct common successor for readings on same path" );
1739 ## Return the closest reading that is a predecessor of both the given readings.
1740 sub common_predecessor {
1742 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1743 return $self->_common_in_path( $r1, $r2, 'predecessors' );
1746 sub common_successor {
1748 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1749 return $self->_common_in_path( $r1, $r2, 'successors' );
1753 # TODO think about how to do this without ranks...
1754 sub _common_in_path {
1755 my( $self, $r1, $r2, $dir ) = @_;
1756 my $iter = $self->end->rank;
1758 my @last_r1 = ( $r1 );
1759 my @last_r2 = ( $r2 );
1760 # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' );
1762 # print STDERR "Finding common $dir for $r1, $r2\n";
1763 while( !@candidates ) {
1764 last unless $iter--; # Avoid looping infinitely
1765 # Iterate separately down the graph from r1 and r2
1766 my( @new_lc1, @new_lc2 );
1767 foreach my $lc ( @last_r1 ) {
1768 foreach my $p ( $lc->$dir ) {
1769 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) {
1770 # print STDERR "Path candidate $p from $lc\n";
1771 push( @candidates, $p );
1772 } elsif( !$all_seen{$p->id} ) {
1773 $all_seen{$p->id} = 'r1';
1774 push( @new_lc1, $p );
1778 foreach my $lc ( @last_r2 ) {
1779 foreach my $p ( $lc->$dir ) {
1780 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) {
1781 # print STDERR "Path candidate $p from $lc\n";
1782 push( @candidates, $p );
1783 } elsif( !$all_seen{$p->id} ) {
1784 $all_seen{$p->id} = 'r2';
1785 push( @new_lc2, $p );
1789 @last_r1 = @new_lc1;
1790 @last_r2 = @new_lc2;
1792 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1793 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1797 Text::Tradition::Error->throw(
1798 'ident' => 'Collation error',
1804 __PACKAGE__->meta->make_immutable;
1808 This package is free software and is provided "as is" without express
1809 or implied warranty. You can redistribute it and/or modify it under
1810 the same terms as Perl itself.
1814 Tara L Andrews E<lt>aurum@cpan.orgE<gt>