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 # Combine the text of the readings
413 my $joinstr = $combine_char;
414 unless( defined $joinstr ) {
415 $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior;
416 $joinstr = $self->wordsep unless defined $joinstr;
418 $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) );
419 $kept_obj->normal_form(
420 join( $joinstr, $kept_obj->normal_form, $del_obj->normal_form ) );
421 # Combine the lexemes present in the readings
422 if( $kept_obj->has_lexemes && $del_obj->has_lexemes ) {
423 $kept_obj->add_lexeme( $del_obj->lexemes );
426 $self->del_reading( $deleted );
430 # Helper function for manipulating the graph.
431 sub _stringify_args {
432 my( $self, $first, $second, @args ) = @_;
434 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
435 $second = $second->id
436 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
437 return( $first, $second, @args );
440 # Helper function for manipulating the graph.
441 sub _objectify_args {
442 my( $self, $first, $second, $arg ) = @_;
443 $first = $self->reading( $first )
444 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
445 $second = $self->reading( $second )
446 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
447 return( $first, $second, $arg );
454 # We only need the IDs for adding paths to the graph, not the reading
455 # objects themselves.
456 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
458 $self->_graphcalc_done(0);
459 # Connect the readings
460 unless( $self->sequence->has_edge( $source, $target ) ) {
461 $self->sequence->add_edge( $source, $target );
462 $self->relations->add_equivalence_edge( $source, $target );
464 # Note the witness in question
465 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
471 if( ref( $_[0] ) eq 'ARRAY' ) {
478 # We only need the IDs for adding paths to the graph, not the reading
479 # objects themselves.
480 my( $source, $target, $wit ) = $self->_stringify_args( @args );
482 $self->_graphcalc_done(0);
483 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
484 $self->sequence->delete_edge_attribute( $source, $target, $wit );
486 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
487 $self->sequence->delete_edge( $source, $target );
488 $self->relations->delete_equivalence_edge( $source, $target );
493 # Extra graph-alike utility
496 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
497 return undef unless $self->sequence->has_edge( $source, $target );
498 return $self->sequence->has_edge_attribute( $source, $target, $wit );
501 =head2 clear_witness( @sigil_list )
503 Clear the given witnesses out of the collation entirely, removing references
504 to them in paths, and removing readings that belong only to them. Should only
505 be called via $tradition->del_witness.
510 my( $self, @sigils ) = @_;
512 $self->_graphcalc_done(0);
513 # Clear the witness(es) out of the paths
514 foreach my $e ( $self->paths ) {
515 foreach my $sig ( @sigils ) {
516 $self->del_path( $e, $sig );
520 # Clear out the newly unused readings
521 foreach my $r ( $self->readings ) {
522 unless( $self->reading_witnesses( $r ) ) {
523 $self->del_reading( $r );
528 sub add_relationship {
530 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
531 my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts );
532 $self->_graphcalc_done(0);
536 around qw/ get_relationship del_relationship / => sub {
540 if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) {
543 my( $source, $target ) = $self->_stringify_args( @args );
544 $self->$orig( $source, $target );
547 =head2 reading_witnesses( $reading )
549 Return a list of sigils corresponding to the witnesses in which the reading appears.
553 sub reading_witnesses {
554 my( $self, $reading ) = @_;
555 # We need only check either the incoming or the outgoing edges; I have
556 # arbitrarily chosen "incoming". Thus, special-case the start node.
557 if( $reading eq $self->start ) {
558 return map { $_->sigil } $self->tradition->witnesses;
561 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
562 my $wits = $self->sequence->get_edge_attributes( @$e );
563 @all_witnesses{ keys %$wits } = 1;
565 my $acstr = $self->ac_label;
566 foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) {
567 delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit};
569 return keys %all_witnesses;
572 =head1 OUTPUT METHODS
574 =head2 as_svg( \%options )
576 Returns an SVG string that represents the graph, via as_dot and graphviz.
577 See as_dot for a list of options. Must have GraphViz (dot) installed to run.
582 my( $self, $opts ) = @_;
583 throw( "Need GraphViz installed to output SVG" )
584 unless File::Which::which( 'dot' );
585 my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'};
586 $self->calculate_ranks()
587 unless( $self->_graphcalc_done || $opts->{'nocalc'} || !$self->linear );
588 if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) {
589 my @cmd = qw/dot -Tsvg/;
591 my $dotfile = File::Temp->new();
593 # $dotfile->unlink_on_destroy(0);
594 binmode $dotfile, ':utf8';
595 print $dotfile $self->as_dot( $opts );
596 push( @cmd, $dotfile->filename );
597 run( \@cmd, ">", binary(), \$svg );
598 $svg = decode_utf8( $svg );
599 $self->cached_svg( $svg ) unless $want_subgraph;
602 return $self->cached_svg;
607 =head2 as_dot( \%options )
609 Returns a string that is the collation graph expressed in dot
610 (i.e. GraphViz) format. Options include:
625 my( $self, $opts ) = @_;
626 my $startrank = $opts->{'from'} if $opts;
627 my $endrank = $opts->{'to'} if $opts;
628 my $color_common = $opts->{'color_common'} if $opts;
629 my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank
630 && $self->end->rank > 100;
631 $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs
633 # Check the arguments
635 return if $endrank && $startrank > $endrank;
636 return if $startrank > $self->end->rank;
638 if( defined $endrank ) {
639 return if $endrank < 0;
640 $endrank = undef if $endrank == $self->end->rank;
643 my $graph_name = $self->tradition->name;
644 $graph_name =~ s/[^\w\s]//g;
645 $graph_name = join( '_', split( /\s+/, $graph_name ) );
653 'fillcolor' => 'white',
658 'arrowhead' => 'open',
659 'color' => '#000000',
660 'fontcolor' => '#000000',
663 my $dot = sprintf( "digraph %s {\n", $graph_name );
664 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
665 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
667 # Output substitute start/end readings if necessary
669 $dot .= "\t\"__SUBSTART__\" [ label=\"...\",id=\"__START__\" ];\n";
672 $dot .= "\t\"__SUBEND__\" [ label=\"...\",id=\"__END__\" ];\n";
674 if( $STRAIGHTENHACK ) {
676 my $startlabel = $startrank ? '__SUBSTART__' : '__START__';
677 $dot .= "\tsubgraph { rank=same \"$startlabel\" \"#SILENT#\" }\n";
678 $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];"
680 my %used; # Keep track of the readings that actually appear in the graph
681 # Sort the readings by rank if we have ranks; this speeds layout.
682 my @all_readings = $self->end->has_rank
683 ? sort { $a->rank <=> $b->rank } $self->readings
685 # TODO Refrain from outputting lacuna nodes - just grey out the edges.
686 foreach my $reading ( @all_readings ) {
687 # Only output readings within our rank range.
688 next if $startrank && $reading->rank < $startrank;
689 next if $endrank && $reading->rank > $endrank;
690 $used{$reading->id} = 1;
691 # Need not output nodes without separate labels
692 next if $reading->id eq $reading->text;
694 my $label = $reading->text;
695 $label .= '-' if $reading->join_next;
696 $label = "-$label" if $reading->join_prior;
697 $label =~ s/\"/\\\"/g;
698 $rattrs->{'label'} = $label;
699 $rattrs->{'id'} = $reading->id;
700 $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
701 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
704 # Add the real edges. Need to weight one edge per rank jump, in a
706 # my $weighted = $self->_add_edge_weights;
707 my @edges = $self->paths;
708 my( %substart, %subend );
709 foreach my $edge ( @edges ) {
710 # Do we need to output this edge?
711 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
712 my $label = $self->_path_display_label( $self->path_witnesses( $edge ) );
713 my $variables = { %edge_attrs, 'label' => $label };
715 # Account for the rank gap if necessary
716 my $rank0 = $self->reading( $edge->[0] )->rank
717 if $self->reading( $edge->[0] )->has_rank;
718 my $rank1 = $self->reading( $edge->[1] )->rank
719 if $self->reading( $edge->[1] )->has_rank;
720 if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) {
721 $variables->{'minlen'} = $rank1 - $rank0;
724 # Add the calculated edge weights
725 # if( exists $weighted->{$edge->[0]}
726 # && $weighted->{$edge->[0]} eq $edge->[1] ) {
727 # # $variables->{'color'} = 'red';
728 # $variables->{'weight'} = 3.0;
731 # EXPERIMENTAL: make edge width reflect no. of witnesses
732 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
733 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
735 my $varopts = _dot_attr_string( $variables );
736 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
737 $edge->[0], $edge->[1], $varopts );
738 } elsif( $used{$edge->[0]} ) {
739 $subend{$edge->[0]} = $edge->[1];
740 } elsif( $used{$edge->[1]} ) {
741 $substart{$edge->[1]} = $edge->[0];
744 # Add substitute start and end edges if necessary
745 foreach my $node ( keys %substart ) {
746 my $witstr = $self->_path_display_label ( $self->path_witnesses( $substart{$node}, $node ) );
747 my $variables = { %edge_attrs, 'label' => $witstr };
748 my $nrdg = $self->reading( $node );
749 if( $nrdg->has_rank && $nrdg->rank > $startrank ) {
750 # Substart is actually one lower than $startrank
751 $variables->{'minlen'} = $nrdg->rank - ( $startrank - 1 );
753 my $varopts = _dot_attr_string( $variables );
754 $dot .= "\t\"__SUBSTART__\" -> \"$node\" $varopts;\n";
756 foreach my $node ( keys %subend ) {
757 my $witstr = $self->_path_display_label ( $self->path_witnesses( $node, $subend{$node} ) );
758 my $variables = { %edge_attrs, 'label' => $witstr };
759 my $varopts = _dot_attr_string( $variables );
760 $dot .= "\t\"$node\" -> \"__SUBEND__\" $varopts;\n";
763 if( $STRAIGHTENHACK ) {
764 my $endlabel = $endrank ? '__SUBEND__' : '__END__';
765 $dot .= "\t\"$endlabel\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
772 sub _dot_attr_string {
775 foreach my $k ( sort keys %$hash ) {
777 push( @attrs, $k.'="'.$v.'"' );
779 return( '[ ' . join( ', ', @attrs ) . ' ]' );
782 sub _add_edge_weights {
784 # Walk the graph from START to END, choosing the successor node with
785 # the largest number of witness paths each time.
787 my $curr = $self->start->id;
788 my $ranked = $self->end->has_rank;
789 while( $curr ne $self->end->id ) {
790 my $rank = $ranked ? $self->reading( $curr )->rank : 0;
791 my @succ = sort { $self->path_witnesses( $curr, $a )
792 <=> $self->path_witnesses( $curr, $b ) }
793 $self->sequence->successors( $curr );
794 my $next = pop @succ;
795 my $nextrank = $ranked ? $self->reading( $next )->rank : 0;
796 # Try to avoid lacunae in the weighted path.
798 ( $self->reading( $next )->is_lacuna ||
799 $nextrank - $rank > 1 ) ){
802 $weighted->{$curr} = $next;
808 =head2 path_witnesses( $edge )
810 Returns the list of sigils whose witnesses are associated with the given edge.
811 The edge can be passed as either an array or an arrayref of ( $source, $target ).
816 my( $self, @edge ) = @_;
817 # If edge is an arrayref, cope.
818 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
822 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
826 # Helper function. Make a display label for the given witnesses, showing a.c.
827 # witnesses only where the main witness is not also in the list.
828 sub _path_display_label {
831 map { $wits{$_} = 1 } @_;
833 # If an a.c. wit is listed, remove it if the main wit is also listed.
834 # Otherwise keep it for explicit listing.
835 my $aclabel = $self->ac_label;
837 foreach my $w ( sort keys %wits ) {
838 if( $w =~ /^(.*)\Q$aclabel\E$/ ) {
839 if( exists $wits{$1} ) {
842 push( @disp_ac, $w );
847 # See if we are in a majority situation.
848 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
849 $maj = $maj > 5 ? $maj : 5;
850 if( scalar keys %wits > $maj ) {
851 unshift( @disp_ac, 'majority' );
852 return join( ', ', @disp_ac );
854 return join( ', ', sort keys %wits );
858 =head2 readings_at_rank( $rank )
860 Returns a list of readings at a given rank, taken from the alignment table.
864 sub readings_at_rank {
865 my( $self, $rank ) = @_;
866 my $table = $self->alignment_table;
867 # Table rank is real rank - 1.
868 my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}};
870 foreach my $e ( @elements ) {
871 next unless ref( $e ) eq 'HASH';
872 next unless exists $e->{'t'};
873 $readings{$e->{'t'}->id} = $e->{'t'};
875 return values %readings;
880 Returns a GraphML representation of the collation. The GraphML will contain
881 two graphs. The first expresses the attributes of the readings and the witness
882 paths that link them; the second expresses the relationships that link the
883 readings. This is the native transfer format for a tradition.
892 my $datafile = 't/data/florilegium_tei_ps.xml';
893 my $tradition = Text::Tradition->new( 'input' => 'TEI',
898 ok( $tradition, "Got a tradition object" );
899 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
900 ok( $tradition->collation, "Tradition has a collation" );
902 my $c = $tradition->collation;
903 is( scalar $c->readings, $READINGS, "Collation has all readings" );
904 is( scalar $c->paths, $PATHS, "Collation has all paths" );
905 is( scalar $c->relationships, 0, "Collation has all relationships" );
907 # Add a few relationships
908 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
909 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
910 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
912 # Now write it to GraphML and parse it again.
914 my $graphml = $c->as_graphml;
915 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
916 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
917 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
918 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
920 # Now add a stemma, write to GraphML, and parse again.
921 my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
922 is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" );
923 is( $tradition->stemmata, 1, "Tradition now has the stemma" );
924 $graphml = $c->as_graphml;
925 like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" );
932 my( $self, $options ) = @_;
933 $self->calculate_ranks unless $self->_graphcalc_done;
935 my $start = $options->{'from'}
936 ? $self->reading( $options->{'from'} ) : $self->start;
937 my $end = $options->{'to'}
938 ? $self->reading( $options->{'to'} ) : $self->end;
939 if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) {
940 throw( 'Start node must be before end node' );
942 # The readings need to be ranked for this to work.
943 $start = $self->start unless $start->has_rank;
944 $end = $self->end unless $end->has_rank;
946 unless( $start eq $self->start ) {
947 $rankoffset = $start->rank - 1;
952 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
953 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
954 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
955 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
957 # Create the document and root node
958 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
959 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
960 $graphml->setDocumentElement( $root );
961 $root->setNamespace( $xsi_ns, 'xsi', 0 );
962 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
964 # List of attribute types to save on our objects and their corresponding
970 'ReadingID' => 'string',
971 'RelationshipType' => 'string',
972 'RelationshipScope' => 'string',
975 # List of attribute names *not* to save on our objects.
976 # We will also not save any attribute beginning with _.
978 map { $skipsave{$_} = 1 } qw/ cached_svg /;
980 # Add the data keys for the graph. Include an extra key 'version' for the
981 # GraphML output version.
984 my %graph_attributes = ( 'version' => 'string' );
985 # Graph attributes include those of Tradition and those of Collation.
987 my $tmeta = $self->tradition->meta;
988 my $cmeta = $self->meta;
989 map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes;
990 map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes;
991 foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) {
992 next if $attr->name =~ /^_/;
993 next if $skipsave{$attr->name};
994 next unless $save_types{$attr->type_constraint->name};
995 $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
997 # Extra custom key for the tradition stemma(ta)
998 $graph_attributes{'stemmata'} = 'string';
1000 foreach my $datum ( sort keys %graph_attributes ) {
1001 $graph_data_keys{$datum} = 'dg'.$gdi++;
1002 my $key = $root->addNewChild( $graphml_ns, 'key' );
1003 $key->setAttribute( 'attr.name', $datum );
1004 $key->setAttribute( 'attr.type', $graph_attributes{$datum} );
1005 $key->setAttribute( 'for', 'graph' );
1006 $key->setAttribute( 'id', $graph_data_keys{$datum} );
1009 # Add the data keys for reading nodes
1010 my %reading_attributes;
1011 my $rmeta = Text::Tradition::Collation::Reading->meta;
1012 foreach my $attr( $rmeta->get_all_attributes ) {
1013 next if $attr->name =~ /^_/;
1014 next if $skipsave{$attr->name};
1015 next unless $save_types{$attr->type_constraint->name};
1016 $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
1018 # Extra custom key for the reading morphology
1019 $reading_attributes{'lexemes'} = 'string';
1023 foreach my $datum ( sort keys %reading_attributes ) {
1024 $node_data_keys{$datum} = 'dn'.$ndi++;
1025 my $key = $root->addNewChild( $graphml_ns, 'key' );
1026 $key->setAttribute( 'attr.name', $datum );
1027 $key->setAttribute( 'attr.type', $reading_attributes{$datum} );
1028 $key->setAttribute( 'for', 'node' );
1029 $key->setAttribute( 'id', $node_data_keys{$datum} );
1032 # Add the data keys for edges, that is, paths and relationships. Path
1033 # data does not come from a Moose class so is here manually.
1036 my %edge_attributes = (
1037 witness => 'string', # ID/label for a path
1038 extra => 'boolean', # Path key
1040 my @path_attributes = keys %edge_attributes; # track our manual additions
1041 my $pmeta = Text::Tradition::Collation::Relationship->meta;
1042 foreach my $attr( $pmeta->get_all_attributes ) {
1043 next if $attr->name =~ /^_/;
1044 next if $skipsave{$attr->name};
1045 next unless $save_types{$attr->type_constraint->name};
1046 $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
1048 foreach my $datum ( sort keys %edge_attributes ) {
1049 $edge_data_keys{$datum} = 'de'.$edi++;
1050 my $key = $root->addNewChild( $graphml_ns, 'key' );
1051 $key->setAttribute( 'attr.name', $datum );
1052 $key->setAttribute( 'attr.type', $edge_attributes{$datum} );
1053 $key->setAttribute( 'for', 'edge' );
1054 $key->setAttribute( 'id', $edge_data_keys{$datum} );
1057 # Add the collation graph itself. First, sanitize the name to a valid XML ID.
1058 my $xmlidname = $self->tradition->name;
1059 $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g;
1060 if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) {
1061 $xmlidname = '_'.$xmlidname;
1063 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
1064 $sgraph->setAttribute( 'edgedefault', 'directed' );
1065 $sgraph->setAttribute( 'id', $xmlidname );
1066 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
1067 $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later
1068 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
1069 $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later
1070 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
1072 # Tradition/collation attribute data
1073 foreach my $datum ( keys %graph_attributes ) {
1075 if( $datum eq 'version' ) {
1077 } elsif( $datum eq 'stemmata' ) {
1079 map { push( @stemstrs, $_->editable( {linesep => ''} ) ) }
1080 $self->tradition->stemmata;
1081 $value = join( "\n", @stemstrs );
1082 } elsif( $gattr_from{$datum} eq 'Tradition' ) {
1083 $value = $self->tradition->$datum;
1085 $value = $self->$datum;
1087 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
1092 # Add our readings to the graph
1093 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
1094 next if $n->has_rank && $n ne $self->start && $n ne $self->end &&
1095 ( $n->rank < $start->rank || $n->rank > $end->rank );
1096 $use_readings{$n->id} = 1;
1097 # Add to the main graph
1098 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
1099 my $node_xmlid = 'n' . $node_ctr++;
1100 $node_hash{ $n->id } = $node_xmlid;
1101 $node_el->setAttribute( 'id', $node_xmlid );
1102 foreach my $d ( keys %reading_attributes ) {
1104 # Custom serialization
1105 if( $d eq 'lexemes' ) {
1106 # If nval is a true value, we have lexemes so we need to
1107 # serialize them. Otherwise set nval to undef so that the
1108 # key is excluded from this reading.
1109 $nval = $nval ? $n->_serialize_lexemes : undef;
1110 } elsif( $d eq 'normal_form' && $n->normal_form eq $n->text ) {
1113 if( $rankoffset && $d eq 'rank' && $n ne $self->start ) {
1114 # Adjust the ranks within the subgraph.
1115 $nval = $n eq $self->end ? $end->rank - $rankoffset + 1
1116 : $nval - $rankoffset;
1118 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
1123 # Add the path edges to the sequence graph
1125 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
1126 # We add an edge in the graphml for every witness in $e.
1127 next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} );
1128 my @edge_wits = sort $self->path_witnesses( $e );
1129 $e->[0] = $self->start->id unless $use_readings{$e->[0]};
1130 $e->[1] = $self->end->id unless $use_readings{$e->[1]};
1131 # Skip any path from start to end; that witness is not in the subgraph.
1132 next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id );
1133 foreach my $wit ( @edge_wits ) {
1134 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
1135 $node_hash{ $e->[0] },
1136 $node_hash{ $e->[1] } );
1137 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
1138 $edge_el->setAttribute( 'source', $from );
1139 $edge_el->setAttribute( 'target', $to );
1140 $edge_el->setAttribute( 'id', $id );
1142 # It's a witness path, so add the witness
1144 my $key = $edge_data_keys{'witness'};
1145 # Is this an ante-corr witness?
1146 my $aclabel = $self->ac_label;
1147 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
1148 # Keep the base witness
1150 # ...and record that this is an 'extra' reading path
1151 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
1153 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
1157 # Report the actual number of nodes and edges that went in
1158 $sgraph->setAttribute( 'parse.edges', $edge_ctr );
1159 $sgraph->setAttribute( 'parse.nodes', $node_ctr );
1161 # Add the relationship graph to the XML
1162 map { delete $edge_data_keys{$_} } @path_attributes;
1163 $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
1164 $node_data_keys{'id'}, \%edge_data_keys );
1166 # Save and return the thing
1167 my $result = decode_utf8( $graphml->toString(1) );
1171 sub _add_graphml_data {
1172 my( $el, $key, $value ) = @_;
1173 return unless defined $value;
1174 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
1175 $data_el->setAttribute( 'key', $key );
1176 $data_el->appendText( $value );
1181 Returns a CSV alignment table representation of the collation graph, one
1182 row per witness (or witness uncorrected.)
1188 my $table = $self->alignment_table;
1189 my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } );
1191 # Make the header row
1192 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
1193 push( @result, decode_utf8( $csv->string ) );
1194 # Make the rest of the rows
1195 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1196 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
1197 my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs;
1198 $csv->combine( @row );
1199 push( @result, decode_utf8( $csv->string ) );
1201 return join( "\n", @result );
1204 =head2 alignment_table( $use_refs, $include_witnesses )
1206 Return a reference to an alignment table, in a slightly enhanced CollateX
1207 format which looks like this:
1209 $table = { alignment => [ { witness => "SIGIL",
1210 tokens => [ { t => "TEXT" }, ... ] },
1211 { witness => "SIG2",
1212 tokens => [ { t => "TEXT" }, ... ] },
1214 length => TEXTLEN };
1216 If $use_refs is set to 1, the reading object is returned in the table
1217 instead of READINGTEXT; if not, the text of the reading is returned.
1219 If $include_witnesses is set to a hashref, only the witnesses whose sigil
1220 keys have a true hash value will be included.
1224 sub alignment_table {
1226 $self->calculate_ranks() unless $self->_graphcalc_done;
1227 return $self->cached_table if $self->has_cached_table;
1229 # Make sure we can do this
1230 throw( "Need a linear graph in order to make an alignment table" )
1231 unless $self->linear;
1232 $self->calculate_ranks unless $self->end->has_rank;
1234 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
1235 my @all_pos = ( 1 .. $self->end->rank - 1 );
1236 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
1237 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
1238 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1239 my @row = _make_witness_row( \@wit_path, \@all_pos );
1240 push( @{$table->{'alignment'}},
1241 { 'witness' => $wit->sigil, 'tokens' => \@row } );
1242 if( $wit->is_layered ) {
1243 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
1244 $wit->sigil.$self->ac_label );
1245 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
1246 push( @{$table->{'alignment'}},
1247 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
1250 $self->cached_table( $table );
1254 sub _make_witness_row {
1255 my( $path, $positions ) = @_;
1257 map { $char_hash{$_} = undef } @$positions;
1259 foreach my $rdg ( @$path ) {
1260 my $rtext = $rdg->text;
1261 $rtext = '#LACUNA#' if $rdg->is_lacuna;
1262 print STDERR "rank " . $rdg->rank . "\n" if $debug;
1263 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
1264 $char_hash{$rdg->rank} = { 't' => $rdg };
1266 my @row = map { $char_hash{$_} } @$positions;
1267 # Fill in lacuna markers for undef spots in the row
1268 my $last_el = shift @row;
1269 my @filled_row = ( $last_el );
1270 foreach my $el ( @row ) {
1271 # If we are using node reference, make the lacuna node appear many times
1272 # in the table. If not, use the lacuna tag.
1273 if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) {
1276 push( @filled_row, $el );
1282 =head1 NAVIGATION METHODS
1284 =head2 reading_sequence( $first, $last, $sigil, $backup )
1286 Returns the ordered list of readings, starting with $first and ending
1287 with $last, for the witness given in $sigil. If a $backup sigil is
1288 specified (e.g. when walking a layered witness), it will be used wherever
1289 no $sigil path exists. If there is a base text reading, that will be
1290 used wherever no path exists for $sigil or $backup.
1294 # TODO Think about returning some lazy-eval iterator.
1295 # TODO Get rid of backup; we should know from what witness is whether we need it.
1297 sub reading_sequence {
1298 my( $self, $start, $end, $witness ) = @_;
1300 $witness = $self->baselabel unless $witness;
1301 my @readings = ( $start );
1304 while( $n && $n->id ne $end->id ) {
1305 if( exists( $seen{$n->id} ) ) {
1306 throw( "Detected loop for $witness at " . $n->id );
1310 my $next = $self->next_reading( $n, $witness );
1312 throw( "Did not find any path for $witness from reading " . $n->id );
1314 push( @readings, $next );
1317 # Check that the last reading is our end reading.
1318 my $last = $readings[$#readings];
1319 throw( "Last reading found from " . $start->text .
1320 " for witness $witness is not the end!" ) # TODO do we get this far?
1321 unless $last->id eq $end->id;
1326 =head2 next_reading( $reading, $sigil );
1328 Returns the reading that follows the given reading along the given witness
1334 # Return the successor via the corresponding path.
1336 my $answer = $self->_find_linked_reading( 'next', @_ );
1337 return undef unless $answer;
1338 return $self->reading( $answer );
1341 =head2 prior_reading( $reading, $sigil )
1343 Returns the reading that precedes the given reading along the given witness
1349 # Return the predecessor via the corresponding path.
1351 my $answer = $self->_find_linked_reading( 'prior', @_ );
1352 return $self->reading( $answer );
1355 sub _find_linked_reading {
1356 my( $self, $direction, $node, $path ) = @_;
1358 # Get a backup if we are dealing with a layered witness
1360 my $aclabel = $self->ac_label;
1361 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1365 my @linked_paths = $direction eq 'next'
1366 ? $self->sequence->edges_from( $node )
1367 : $self->sequence->edges_to( $node );
1368 return undef unless scalar( @linked_paths );
1370 # We have to find the linked path that contains all of the
1371 # witnesses supplied in $path.
1372 my( @path_wits, @alt_path_wits );
1373 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1374 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1377 foreach my $le ( @linked_paths ) {
1378 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1381 my @le_wits = sort $self->path_witnesses( $le );
1382 if( _is_within( \@path_wits, \@le_wits ) ) {
1383 # This is the right path.
1384 return $direction eq 'next' ? $le->[1] : $le->[0];
1385 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1389 # Got this far? Return the alternate path if it exists.
1390 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1393 # Got this far? Return the base path if it exists.
1394 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1397 # Got this far? We have no appropriate path.
1398 warn "Could not find $direction node from " . $node->id
1399 . " along path $path";
1405 my( $set1, $set2 ) = @_;
1406 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1407 foreach my $el ( @$set1 ) {
1408 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1413 # Return the string that joins together a list of witnesses for
1414 # display on a single path.
1415 sub _witnesses_of_label {
1416 my( $self, $label ) = @_;
1417 my $regex = $self->wit_list_separator;
1418 my @answer = split( /\Q$regex\E/, $label );
1422 =head2 common_readings
1424 Returns the list of common readings in the graph (i.e. those readings that are
1425 shared by all non-lacunose witnesses.)
1429 sub common_readings {
1431 my @common = grep { $_->is_common } $self->readings;
1435 =head2 path_text( $sigil, [, $start, $end ] )
1437 Returns the text of a witness (plus its backup, if we are using a layer)
1438 as stored in the collation. The text is returned as a string, where the
1439 individual readings are joined with spaces and the meta-readings (e.g.
1440 lacunae) are omitted. Optional specification of $start and $end allows
1441 the generation of a subset of the witness text.
1446 my( $self, $wit, $start, $end ) = @_;
1447 $start = $self->start unless $start;
1448 $end = $self->end unless $end;
1449 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1452 foreach my $r ( @path ) {
1453 unless ( $r->join_prior || !$last || $last->join_next ) {
1456 $pathtext .= $r->text;
1462 =head1 INITIALIZATION METHODS
1464 These are mostly for use by parsers.
1466 =head2 make_witness_path( $witness )
1468 Link the array of readings contained in $witness->path (and in
1469 $witness->uncorrected_path if it exists) into collation paths.
1470 Clear out the arrays when finished.
1472 =head2 make_witness_paths
1474 Call make_witness_path for all witnesses in the tradition.
1478 # For use when a collation is constructed from a base text and an apparatus.
1479 # We have the sequences of readings and just need to add path edges.
1480 # When we are done, clear out the witness path attributes, as they are no
1482 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1484 sub make_witness_paths {
1486 foreach my $wit ( $self->tradition->witnesses ) {
1487 # print STDERR "Making path for " . $wit->sigil . "\n";
1488 $self->make_witness_path( $wit );
1492 sub make_witness_path {
1493 my( $self, $wit ) = @_;
1494 my @chain = @{$wit->path};
1495 my $sig = $wit->sigil;
1496 # Add start and end if necessary
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 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1502 if( $wit->is_layered ) {
1503 @chain = @{$wit->uncorrected_path};
1504 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1505 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1506 foreach my $idx( 0 .. $#chain-1 ) {
1507 my $source = $chain[$idx];
1508 my $target = $chain[$idx+1];
1509 $self->add_path( $source, $target, $sig.$self->ac_label )
1510 unless $self->has_path( $source, $target, $sig );
1514 $wit->clear_uncorrected_path;
1517 =head2 calculate_ranks
1519 Calculate the reading ranks (that is, their aligned positions relative
1520 to each other) for the graph. This can only be called on linear collations.
1524 use Text::Tradition;
1526 my $cxfile = 't/data/Collatex-16.xml';
1527 my $t = Text::Tradition->new(
1529 'input' => 'CollateX',
1532 my $c = $t->collation;
1535 my $table = $c->alignment_table;
1536 ok( $c->has_cached_table, "Alignment table was cached" );
1537 is( $c->alignment_table, $table, "Cached table returned upon second call" );
1538 $c->calculate_ranks;
1539 is( $c->alignment_table, $table, "Cached table retained with no rank change" );
1540 $c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } );
1541 isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" );
1547 sub calculate_ranks {
1549 # Save the existing ranks, in case we need to invalidate the cached SVG.
1551 map { $existing_ranks{$_} = $_->rank } $self->readings;
1553 # Do the rankings based on the relationship equivalence graph, starting
1554 # with the start node.
1555 my ( $node_ranks, $rank_nodes ) = $self->relations->equivalence_ranks();
1557 # Transfer our rankings from the topological graph to the real one.
1558 foreach my $r ( $self->readings ) {
1559 if( defined $node_ranks->{$self->equivalence( $r->id )} ) {
1560 $r->rank( $node_ranks->{$self->equivalence( $r->id )} );
1562 # Die. Find the last rank we calculated.
1563 my @all_defined = sort { ( $node_ranks->{$self->equivalence( $a->id )}||-1 )
1564 <=> ( $node_ranks->{$self->equivalence( $b->id )}||-1 ) }
1566 my $last = pop @all_defined;
1567 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1570 # Do we need to invalidate the cached data?
1571 if( $self->has_cached_svg || $self->has_cached_table ) {
1572 foreach my $r ( $self->readings ) {
1573 next if defined( $existing_ranks{$r} )
1574 && $existing_ranks{$r} == $r->rank;
1575 # Something has changed, so clear the cache
1576 $self->_clear_cache;
1577 # ...and recalculate the common readings.
1578 $self->calculate_common_readings();
1582 # The graph calculation information is now up to date.
1583 $self->_graphcalc_done(1);
1588 $self->wipe_svg if $self->has_cached_svg;
1589 $self->wipe_table if $self->has_cached_table;
1593 =head2 flatten_ranks
1595 A convenience method for parsing collation data. Searches the graph for readings
1596 with the same text at the same rank, and merges any that are found.
1602 my %unique_rank_rdg;
1604 foreach my $rdg ( $self->readings ) {
1605 next unless $rdg->has_rank;
1606 my $key = $rdg->rank . "||" . $rdg->text;
1607 if( exists $unique_rank_rdg{$key} ) {
1608 # Make sure they don't have different grammatical forms
1609 my $ur = $unique_rank_rdg{$key};
1610 if( $rdg->disambiguated && $ur->disambiguated ) {
1611 my $rform = join( '//', map { $_->form->to_string } $rdg->lexemes );
1612 my $uform = join( '//', map { $_->form->to_string } $ur->lexemes );
1613 next unless $rform eq $uform;
1614 } elsif( $rdg->disambiguated xor $ur->disambiguated ) {
1618 #print STDERR "Combining readings at same rank: $key\n";
1620 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1621 # TODO see if this now makes a common point.
1623 $unique_rank_rdg{$key} = $rdg;
1626 # If we merged readings, the ranks are still fine but the alignment
1627 # table is wrong. Wipe it.
1628 $self->wipe_table() if $changed;
1632 =head2 calculate_common_readings
1634 Goes through the graph identifying the readings that appear in every witness
1635 (apart from those with lacunae at that spot.) Marks them as common and returns
1640 use Text::Tradition;
1642 my $cxfile = 't/data/Collatex-16.xml';
1643 my $t = Text::Tradition->new(
1645 'input' => 'CollateX',
1648 my $c = $t->collation;
1650 my @common = $c->calculate_common_readings();
1651 is( scalar @common, 8, "Found correct number of common readings" );
1652 my @marked = sort $c->common_readings();
1653 is( scalar @common, 8, "All common readings got marked as such" );
1654 my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /;
1655 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1661 sub calculate_common_readings {
1664 map { $_->is_common( 0 ) } $self->readings;
1665 # Implicitly calls calculate_ranks
1666 my $table = $self->alignment_table;
1667 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1668 my @row = map { $_->{'tokens'}->[$idx]
1669 ? $_->{'tokens'}->[$idx]->{'t'} : '' }
1670 @{$table->{'alignment'}};
1672 foreach my $r ( @row ) {
1674 $hash{$r->id} = $r unless $r->is_meta;
1676 $hash{'UNDEF'} = $r;
1679 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1680 my( $r ) = values %hash;
1682 push( @common, $r );
1688 =head2 text_from_paths
1690 Calculate the text array for all witnesses from the path, for later consistency
1691 checking. Only to be used if there is no non-graph-based way to know the
1696 sub text_from_paths {
1698 foreach my $wit ( $self->tradition->witnesses ) {
1699 my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1701 foreach my $r ( @readings ) {
1702 next if $r->is_meta;
1703 push( @text, $r->text );
1705 $wit->text( \@text );
1706 if( $wit->is_layered ) {
1707 my @ucrdgs = $self->reading_sequence( $self->start, $self->end,
1708 $wit->sigil.$self->ac_label );
1710 foreach my $r ( @ucrdgs ) {
1711 next if $r->is_meta;
1712 push( @uctext, $r->text );
1714 $wit->layertext( \@uctext );
1719 =head1 UTILITY FUNCTIONS
1721 =head2 common_predecessor( $reading_a, $reading_b )
1723 Find the last reading that occurs in sequence before both the given readings.
1724 At the very least this should be $self->start.
1726 =head2 common_successor( $reading_a, $reading_b )
1728 Find the first reading that occurs in sequence after both the given readings.
1729 At the very least this should be $self->end.
1733 use Text::Tradition;
1735 my $cxfile = 't/data/Collatex-16.xml';
1736 my $t = Text::Tradition->new(
1738 'input' => 'CollateX',
1741 my $c = $t->collation;
1743 is( $c->common_predecessor( 'n24', 'n23' )->id,
1744 'n20', "Found correct common predecessor" );
1745 is( $c->common_successor( 'n24', 'n23' )->id,
1746 '__END__', "Found correct common successor" );
1748 is( $c->common_predecessor( 'n19', 'n17' )->id,
1749 'n16', "Found correct common predecessor for readings on same path" );
1750 is( $c->common_successor( 'n21', 'n10' )->id,
1751 '__END__', "Found correct common successor for readings on same path" );
1757 ## Return the closest reading that is a predecessor of both the given readings.
1758 sub common_predecessor {
1760 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1761 return $self->_common_in_path( $r1, $r2, 'predecessors' );
1764 sub common_successor {
1766 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1767 return $self->_common_in_path( $r1, $r2, 'successors' );
1771 # TODO think about how to do this without ranks...
1772 sub _common_in_path {
1773 my( $self, $r1, $r2, $dir ) = @_;
1774 my $iter = $self->end->rank;
1776 my @last_r1 = ( $r1 );
1777 my @last_r2 = ( $r2 );
1778 # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' );
1780 # print STDERR "Finding common $dir for $r1, $r2\n";
1781 while( !@candidates ) {
1782 last unless $iter--; # Avoid looping infinitely
1783 # Iterate separately down the graph from r1 and r2
1784 my( @new_lc1, @new_lc2 );
1785 foreach my $lc ( @last_r1 ) {
1786 foreach my $p ( $lc->$dir ) {
1787 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) {
1788 # print STDERR "Path candidate $p from $lc\n";
1789 push( @candidates, $p );
1790 } elsif( !$all_seen{$p->id} ) {
1791 $all_seen{$p->id} = 'r1';
1792 push( @new_lc1, $p );
1796 foreach my $lc ( @last_r2 ) {
1797 foreach my $p ( $lc->$dir ) {
1798 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) {
1799 # print STDERR "Path candidate $p from $lc\n";
1800 push( @candidates, $p );
1801 } elsif( !$all_seen{$p->id} ) {
1802 $all_seen{$p->id} = 'r2';
1803 push( @new_lc2, $p );
1807 @last_r1 = @new_lc1;
1808 @last_r2 = @new_lc2;
1810 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1811 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1815 Text::Tradition::Error->throw(
1816 'ident' => 'Collation error',
1822 __PACKAGE__->meta->make_immutable;
1826 This package is free software and is provided "as is" without express
1827 or implied warranty. You can redistribute it and/or modify it under
1828 the same terms as Perl itself.
1832 Tara L Andrews E<lt>aurum@cpan.orgE<gt>