1 package Text::Tradition::Collation;
3 use Encode qw( decode_utf8 );
7 use IPC::Run qw( run binary );
9 use Text::Tradition::Collation::Reading;
10 use Text::Tradition::Collation::RelationshipStore;
11 use Text::Tradition::Error;
12 use XML::Easy::Syntax qw( $xml10_namestartchar_rx $xml10_namechar_rx );
14 use XML::LibXML::XPathContext;
20 default => sub { Graph->new() },
28 isa => 'Text::Tradition::Collation::RelationshipStore',
30 relationships => 'relationships',
31 related_readings => 'related_readings',
32 get_relationship => 'get_relationship',
33 del_relationship => 'del_relationship',
34 equivalence => 'equivalence',
35 equivalence_graph => 'equivalence_graph',
37 writer => '_set_relations',
42 isa => 'Text::Tradition',
43 writer => '_set_tradition',
48 isa => 'HashRef[Text::Tradition::Collation::Reading]',
52 _add_reading => 'set',
53 del_reading => 'delete',
54 has_reading => 'exists',
57 default => sub { {} },
60 has 'wit_list_separator' => (
69 default => 'base text',
92 isa => 'Text::Tradition::Collation::Reading',
93 writer => '_set_start',
99 isa => 'Text::Tradition::Collation::Reading',
100 writer => '_set_end',
104 has 'cached_svg' => (
107 predicate => 'has_cached_svg',
108 clearer => 'wipe_svg',
111 has 'cached_table' => (
114 predicate => 'has_cached_table',
115 clearer => 'wipe_table',
118 has '_graphcalc_done' => (
126 Text::Tradition::Collation - a software model for a text collation
131 my $t = Text::Tradition->new(
132 'name' => 'this is a text',
134 'file' => '/path/to/tei_parallel_seg_file.xml' );
136 my $c = $t->collation;
137 my @readings = $c->readings;
138 my @paths = $c->paths;
139 my @relationships = $c->relationships;
141 my $svg_variant_graph = $t->collation->as_svg();
145 Text::Tradition is a library for representation and analysis of collated
146 texts, particularly medieval ones. The Collation is the central feature of
147 a Tradition, where the text, its sequence of readings, and its relationships
148 between readings are actually kept.
154 The constructor. Takes a hash or hashref of the following arguments:
158 =item * tradition - The Text::Tradition object to which the collation
161 =item * linear - Whether the collation should be linear; that is, whether
162 transposed readings should be treated as two linked readings rather than one,
163 and therefore whether the collation graph is acyclic. Defaults to true.
165 =item * baselabel - The default label for the path taken by a base text
166 (if any). Defaults to 'base text'.
168 =item * wit_list_separator - The string to join a list of witnesses for
169 purposes of making labels in display graphs. Defaults to ', '.
171 =item * ac_label - The extra label to tack onto a witness sigil when
172 representing another layer of path for the given witness - that is, when
173 a text has more than one possible reading due to scribal corrections or
174 the like. Defaults to ' (a.c.)'.
176 =item * wordsep - The string used to separate words in the original text.
187 =head2 wit_list_separator
195 Simple accessors for collation attributes.
199 The meta-reading at the start of every witness path.
203 The meta-reading at the end of every witness path.
207 Returns all Reading objects in the graph.
209 =head2 reading( $id )
211 Returns the Reading object corresponding to the given ID.
213 =head2 add_reading( $reading_args )
215 Adds a new reading object to the collation.
216 See L<Text::Tradition::Collation::Reading> for the available arguments.
218 =head2 del_reading( $object_or_id )
220 Removes the given reading from the collation, implicitly removing its
221 paths and relationships.
223 =head2 merge_readings( $main, $second, $concatenate, $with_str )
225 Merges the $second reading into the $main one. If $concatenate is true, then
226 the merged node will carry the text of both readings, concatenated with either
227 $with_str (if specified) or a sensible default (the empty string if the
228 appropriate 'join_*' flag is set on either reading, or else $self->wordsep.)
230 The first two arguments may be either readings or reading IDs.
232 =head2 has_reading( $id )
234 Predicate to see whether a given reading ID is in the graph.
236 =head2 reading_witnesses( $object_or_id )
238 Returns a list of sigils whose witnesses contain the reading.
242 Returns all reading paths within the document - that is, all edges in the
243 collation graph. Each path is an arrayref of [ $source, $target ] reading IDs.
245 =head2 add_path( $source, $target, $sigil )
247 Links the given readings in the collation in sequence, under the given witness
248 sigil. The readings may be specified by object or ID.
250 =head2 del_path( $source, $target, $sigil )
252 Links the given readings in the collation in sequence, under the given witness
253 sigil. The readings may be specified by object or ID.
255 =head2 has_path( $source, $target );
257 Returns true if the two readings are linked in sequence in any witness.
258 The readings may be specified by object or ID.
262 Returns all Relationship objects in the collation.
264 =head2 add_relationship( $reading, $other_reading, $options )
266 Adds a new relationship of the type given in $options between the two readings,
267 which may be specified by object or ID. Returns a value of ( $status, @vectors)
268 where $status is true on success, and @vectors is a list of relationship edges
269 that were ultimately added.
270 See L<Text::Tradition::Collation::Relationship> for the available options.
276 $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
277 $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
278 $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
281 ### Reading construct/destruct functions
284 my( $self, $reading ) = @_;
285 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
286 my %args = %$reading;
287 if( $self->tradition->has_language && !exists $args{'language'} ) {
288 $args{'language'} = $self->tradition->language;
290 $reading = Text::Tradition::Collation::Reading->new(
291 'collation' => $self,
294 # First check to see if a reading with this ID exists.
295 if( $self->reading( $reading->id ) ) {
296 throw( "Collation already has a reading with id " . $reading->id );
298 $self->_graphcalc_done(0);
299 $self->_add_reading( $reading->id => $reading );
300 # Once the reading has been added, put it in both graphs.
301 $self->sequence->add_vertex( $reading->id );
302 $self->relations->add_reading( $reading->id );
306 around del_reading => sub {
311 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
314 # Remove the reading from the graphs.
315 $self->_graphcalc_done(0);
316 $self->_clear_cache; # Explicitly clear caches to GC the reading
317 $self->sequence->delete_vertex( $arg );
318 $self->relations->delete_reading( $arg );
321 $self->$orig( $arg );
328 my $cxfile = 't/data/Collatex-16.xml';
329 my $t = Text::Tradition->new(
331 'input' => 'CollateX',
334 my $c = $t->collation;
336 my $rno = scalar $c->readings;
337 # Split n21 for testing purposes
338 my $new_r = $c->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } );
339 my $old_r = $c->reading( 'n21' );
340 $old_r->alter_text( 'to' );
341 $c->del_path( 'n20', 'n21', 'A' );
342 $c->add_path( 'n20', 'n21p0', 'A' );
343 $c->add_path( 'n21p0', 'n21', 'A' );
345 ok( $c->reading( 'n21p0' ), "New reading exists" );
346 is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" );
348 # Combine n3 and n4 ( with his )
349 $c->merge_readings( 'n3', 'n4', 1 );
350 ok( !$c->reading('n4'), "Reading n4 is gone" );
351 is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" );
353 # Collapse n9 and n10 ( rood / root )
354 $c->merge_readings( 'n9', 'n10' );
355 ok( !$c->reading('n10'), "Reading n10 is gone" );
356 is( $c->reading('n9')->text, 'rood', "Reading n9 has an unchanged word" );
358 # Combine n21 and n21p0
359 my $remaining = $c->reading('n21');
360 $remaining ||= $c->reading('n22'); # one of these should still exist
361 $c->merge_readings( 'n21p0', $remaining, 1 );
362 ok( !$c->reading('n21'), "Reading $remaining is gone" );
363 is( $c->reading('n21p0')->text, 'unto', "Reading n21p0 merged correctly" );
372 # We only need the IDs for adding paths to the graph, not the reading
373 # objects themselves.
374 my( $kept, $deleted, $combine, $combine_char ) = $self->_stringify_args( @_ );
375 $self->_graphcalc_done(0);
377 # The kept reading should inherit the paths and the relationships
378 # of the deleted reading.
379 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
380 my @vector = ( $kept );
381 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
382 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
383 next if $vector[0] eq $vector[1]; # Don't add a self loop
384 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
385 $self->sequence->add_edge( @vector );
386 my $fwits = $self->sequence->get_edge_attributes( @vector );
387 @wits{keys %$fwits} = values %$fwits;
388 $self->sequence->set_edge_attributes( @vector, \%wits );
390 $self->relations->merge_readings( $kept, $deleted, $combine_char );
392 # Do the deletion deed.
394 my $kept_obj = $self->reading( $kept );
395 my $del_obj = $self->reading( $deleted );
396 my $joinstr = $combine_char;
397 unless( defined $joinstr ) {
398 $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior;
399 $joinstr = $self->wordsep unless defined $joinstr;
401 $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) );
403 $self->del_reading( $deleted );
407 # Helper function for manipulating the graph.
408 sub _stringify_args {
409 my( $self, $first, $second, @args ) = @_;
411 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
412 $second = $second->id
413 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
414 return( $first, $second, @args );
417 # Helper function for manipulating the graph.
418 sub _objectify_args {
419 my( $self, $first, $second, $arg ) = @_;
420 $first = $self->reading( $first )
421 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
422 $second = $self->reading( $second )
423 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
424 return( $first, $second, $arg );
431 # We only need the IDs for adding paths to the graph, not the reading
432 # objects themselves.
433 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
435 $self->_graphcalc_done(0);
436 # Connect the readings
437 unless( $self->sequence->has_edge( $source, $target ) ) {
438 $self->sequence->add_edge( $source, $target );
439 $self->relations->add_equivalence_edge( $source, $target );
441 # Note the witness in question
442 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
448 if( ref( $_[0] ) eq 'ARRAY' ) {
455 # We only need the IDs for adding paths to the graph, not the reading
456 # objects themselves.
457 my( $source, $target, $wit ) = $self->_stringify_args( @args );
459 $self->_graphcalc_done(0);
460 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
461 $self->sequence->delete_edge_attribute( $source, $target, $wit );
463 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
464 $self->sequence->delete_edge( $source, $target );
465 $self->relations->delete_equivalence_edge( $source, $target );
470 # Extra graph-alike utility
473 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
474 return undef unless $self->sequence->has_edge( $source, $target );
475 return $self->sequence->has_edge_attribute( $source, $target, $wit );
478 =head2 clear_witness( @sigil_list )
480 Clear the given witnesses out of the collation entirely, removing references
481 to them in paths, and removing readings that belong only to them. Should only
482 be called via $tradition->del_witness.
487 my( $self, @sigils ) = @_;
489 $self->_graphcalc_done(0);
490 # Clear the witness(es) out of the paths
491 foreach my $e ( $self->paths ) {
492 foreach my $sig ( @sigils ) {
493 $self->del_path( $e, $sig );
497 # Clear out the newly unused readings
498 foreach my $r ( $self->readings ) {
499 unless( $self->reading_witnesses( $r ) ) {
500 $self->del_reading( $r );
505 sub add_relationship {
507 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
508 my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts );
509 $self->_graphcalc_done(0);
513 around qw/ get_relationship del_relationship / => sub {
517 if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) {
520 my( $source, $target ) = $self->_stringify_args( @args );
521 $self->$orig( $source, $target );
524 =head2 reading_witnesses( $reading )
526 Return a list of sigils corresponding to the witnesses in which the reading appears.
530 sub reading_witnesses {
531 my( $self, $reading ) = @_;
532 # We need only check either the incoming or the outgoing edges; I have
533 # arbitrarily chosen "incoming". Thus, special-case the start node.
534 if( $reading eq $self->start ) {
535 return map { $_->sigil } $self->tradition->witnesses;
538 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
539 my $wits = $self->sequence->get_edge_attributes( @$e );
540 @all_witnesses{ keys %$wits } = 1;
542 my $acstr = $self->ac_label;
543 foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) {
544 delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit};
546 return keys %all_witnesses;
549 =head1 OUTPUT METHODS
551 =head2 as_svg( \%options )
553 Returns an SVG string that represents the graph, via as_dot and graphviz.
554 See as_dot for a list of options. Must have GraphViz (dot) installed to run.
559 my( $self, $opts ) = @_;
560 throw( "Need GraphViz installed to output SVG" )
561 unless File::Which::which( 'dot' );
562 my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'};
563 $self->calculate_ranks() unless( $self->_graphcalc_done || $opts->{'nocalc'} );
564 if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) {
565 my @cmd = qw/dot -Tsvg/;
567 my $dotfile = File::Temp->new();
569 # $dotfile->unlink_on_destroy(0);
570 binmode $dotfile, ':utf8';
571 print $dotfile $self->as_dot( $opts );
572 push( @cmd, $dotfile->filename );
573 run( \@cmd, ">", binary(), \$svg );
574 $svg = decode_utf8( $svg );
575 $self->cached_svg( $svg ) unless $want_subgraph;
578 return $self->cached_svg;
583 =head2 as_dot( \%options )
585 Returns a string that is the collation graph expressed in dot
586 (i.e. GraphViz) format. Options include:
601 my( $self, $opts ) = @_;
602 my $startrank = $opts->{'from'} if $opts;
603 my $endrank = $opts->{'to'} if $opts;
604 my $color_common = $opts->{'color_common'} if $opts;
605 my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank
606 && $self->end->rank > 100;
607 $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs
609 # Check the arguments
611 return if $endrank && $startrank > $endrank;
612 return if $startrank > $self->end->rank;
614 if( defined $endrank ) {
615 return if $endrank < 0;
616 $endrank = undef if $endrank == $self->end->rank;
619 my $graph_name = $self->tradition->name;
620 $graph_name =~ s/[^\w\s]//g;
621 $graph_name = join( '_', split( /\s+/, $graph_name ) );
629 'fillcolor' => 'white',
634 'arrowhead' => 'open',
635 'color' => '#000000',
636 'fontcolor' => '#000000',
639 my $dot = sprintf( "digraph %s {\n", $graph_name );
640 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
641 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
643 # Output substitute start/end readings if necessary
645 $dot .= "\t\"__SUBSTART__\" [ label=\"...\",id=\"__START__\" ];\n";
648 $dot .= "\t\"__SUBEND__\" [ label=\"...\",id=\"__END__\" ];\n";
650 if( $STRAIGHTENHACK ) {
652 my $startlabel = $startrank ? '__SUBSTART__' : '__START__';
653 $dot .= "\tsubgraph { rank=same \"$startlabel\" \"#SILENT#\" }\n";
654 $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];"
656 my %used; # Keep track of the readings that actually appear in the graph
657 # Sort the readings by rank if we have ranks; this speeds layout.
658 my @all_readings = $self->end->has_rank
659 ? sort { $a->rank <=> $b->rank } $self->readings
661 # TODO Refrain from outputting lacuna nodes - just grey out the edges.
662 foreach my $reading ( @all_readings ) {
663 # Only output readings within our rank range.
664 next if $startrank && $reading->rank < $startrank;
665 next if $endrank && $reading->rank > $endrank;
666 $used{$reading->id} = 1;
667 # Need not output nodes without separate labels
668 next if $reading->id eq $reading->text;
670 my $label = $reading->text;
671 $label .= '-' if $reading->join_next;
672 $label = "-$label" if $reading->join_prior;
673 $label =~ s/\"/\\\"/g;
674 $rattrs->{'label'} = $label;
675 $rattrs->{'id'} = $reading->id;
676 $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
677 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
680 # Add the real edges. Need to weight one edge per rank jump, in a
682 # my $weighted = $self->_add_edge_weights;
683 my @edges = $self->paths;
684 my( %substart, %subend );
685 foreach my $edge ( @edges ) {
686 # Do we need to output this edge?
687 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
688 my $label = $self->_path_display_label( $self->path_witnesses( $edge ) );
689 my $variables = { %edge_attrs, 'label' => $label };
691 # Account for the rank gap if necessary
692 my $rank0 = $self->reading( $edge->[0] )->rank
693 if $self->reading( $edge->[0] )->has_rank;
694 my $rank1 = $self->reading( $edge->[1] )->rank
695 if $self->reading( $edge->[1] )->has_rank;
696 if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) {
697 $variables->{'minlen'} = $rank1 - $rank0;
700 # Add the calculated edge weights
701 # if( exists $weighted->{$edge->[0]}
702 # && $weighted->{$edge->[0]} eq $edge->[1] ) {
703 # # $variables->{'color'} = 'red';
704 # $variables->{'weight'} = 3.0;
707 # EXPERIMENTAL: make edge width reflect no. of witnesses
708 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
709 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
711 my $varopts = _dot_attr_string( $variables );
712 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
713 $edge->[0], $edge->[1], $varopts );
714 } elsif( $used{$edge->[0]} ) {
715 $subend{$edge->[0]} = 1;
716 } elsif( $used{$edge->[1]} ) {
717 $substart{$edge->[1]} = 1;
720 # Add substitute start and end edges if necessary
721 foreach my $node ( keys %substart ) {
722 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
723 my $variables = { %edge_attrs, 'label' => $witstr };
724 my $varopts = _dot_attr_string( $variables );
725 $dot .= "\t\"__SUBSTART__\" -> \"$node\" $varopts;";
727 foreach my $node ( keys %subend ) {
728 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
729 my $variables = { %edge_attrs, 'label' => $witstr };
730 my $varopts = _dot_attr_string( $variables );
731 $dot .= "\t\"$node\" -> \"__SUBEND__\" $varopts;";
734 if( $STRAIGHTENHACK ) {
735 my $endlabel = $endrank ? '__SUBEND__' : '__END__';
736 $dot .= "\t\"$endlabel\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
743 sub _dot_attr_string {
746 foreach my $k ( sort keys %$hash ) {
748 push( @attrs, $k.'="'.$v.'"' );
750 return( '[ ' . join( ', ', @attrs ) . ' ]' );
753 sub _add_edge_weights {
755 # Walk the graph from START to END, choosing the successor node with
756 # the largest number of witness paths each time.
758 my $curr = $self->start->id;
759 my $ranked = $self->end->has_rank;
760 while( $curr ne $self->end->id ) {
761 my $rank = $ranked ? $self->reading( $curr )->rank : 0;
762 my @succ = sort { $self->path_witnesses( $curr, $a )
763 <=> $self->path_witnesses( $curr, $b ) }
764 $self->sequence->successors( $curr );
765 my $next = pop @succ;
766 my $nextrank = $ranked ? $self->reading( $next )->rank : 0;
767 # Try to avoid lacunae in the weighted path.
769 ( $self->reading( $next )->is_lacuna ||
770 $nextrank - $rank > 1 ) ){
773 $weighted->{$curr} = $next;
779 =head2 path_witnesses( $edge )
781 Returns the list of sigils whose witnesses are associated with the given edge.
782 The edge can be passed as either an array or an arrayref of ( $source, $target ).
787 my( $self, @edge ) = @_;
788 # If edge is an arrayref, cope.
789 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
793 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
797 # Helper function. Make a display label for the given witnesses, showing a.c.
798 # witnesses only where the main witness is not also in the list.
799 sub _path_display_label {
802 map { $wits{$_} = 1 } @_;
804 # If an a.c. wit is listed, remove it if the main wit is also listed.
805 # Otherwise keep it for explicit listing.
806 my $aclabel = $self->ac_label;
808 foreach my $w ( sort keys %wits ) {
809 if( $w =~ /^(.*)\Q$aclabel\E$/ ) {
810 if( exists $wits{$1} ) {
813 push( @disp_ac, $w );
818 # See if we are in a majority situation.
819 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
820 if( scalar keys %wits > $maj ) {
821 unshift( @disp_ac, 'majority' );
822 return join( ', ', @disp_ac );
824 return join( ', ', sort keys %wits );
828 =head2 readings_at_rank( $rank )
830 Returns a list of readings at a given rank, taken from the alignment table.
834 sub readings_at_rank {
835 my( $self, $rank ) = @_;
836 my $table = $self->alignment_table;
837 # Table rank is real rank - 1.
838 my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}};
840 foreach my $e ( @elements ) {
841 next unless ref( $e ) eq 'HASH';
842 next unless exists $e->{'t'};
843 $readings{$e->{'t'}->id} = $e->{'t'};
845 return values %readings;
850 Returns a GraphML representation of the collation. The GraphML will contain
851 two graphs. The first expresses the attributes of the readings and the witness
852 paths that link them; the second expresses the relationships that link the
853 readings. This is the native transfer format for a tradition.
862 my $datafile = 't/data/florilegium_tei_ps.xml';
863 my $tradition = Text::Tradition->new( 'input' => 'TEI',
868 ok( $tradition, "Got a tradition object" );
869 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
870 ok( $tradition->collation, "Tradition has a collation" );
872 my $c = $tradition->collation;
873 is( scalar $c->readings, $READINGS, "Collation has all readings" );
874 is( scalar $c->paths, $PATHS, "Collation has all paths" );
875 is( scalar $c->relationships, 0, "Collation has all relationships" );
877 # Add a few relationships
878 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
879 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
880 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
882 # Now write it to GraphML and parse it again.
884 my $graphml = $c->as_graphml;
885 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
886 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
887 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
888 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
895 my( $self, $options ) = @_;
896 $self->calculate_ranks unless $self->_graphcalc_done;
898 my $start = $options->{'from'}
899 ? $self->reading( $options->{'from'} ) : $self->start;
900 my $end = $options->{'to'}
901 ? $self->reading( $options->{'to'} ) : $self->end;
902 if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) {
903 throw( 'Start node must be before end node' );
905 # The readings need to be ranked for this to work.
906 $start = $self->start unless $start->has_rank;
907 $end = $self->end unless $end->has_rank;
909 unless( $start eq $self->start ) {
910 $rankoffset = $start->rank - 1;
915 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
916 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
917 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
918 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
920 # Create the document and root node
921 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
922 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
923 $graphml->setDocumentElement( $root );
924 $root->setNamespace( $xsi_ns, 'xsi', 0 );
925 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
927 # List of attribute types to save on our objects and their corresponding
933 'ReadingID' => 'string',
934 'RelationshipType' => 'string',
935 'RelationshipScope' => 'string',
938 # List of attribute names *not* to save on our objects.
939 # We will also not save any attribute beginning with _.
941 map { $skipsave{$_} = 1 } qw/ cached_svg /;
943 # Add the data keys for the graph. Include an extra key 'version' for the
944 # GraphML output version.
947 my %graph_attributes = ( 'version' => 'string' );
948 # Graph attributes include those of Tradition and those of Collation.
950 my $tmeta = $self->tradition->meta;
951 my $cmeta = $self->meta;
952 map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes;
953 map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes;
954 foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) {
955 next if $attr->name =~ /^_/;
956 next if $skipsave{$attr->name};
957 next unless $save_types{$attr->type_constraint->name};
958 $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
961 foreach my $datum ( sort keys %graph_attributes ) {
962 $graph_data_keys{$datum} = 'dg'.$gdi++;
963 my $key = $root->addNewChild( $graphml_ns, 'key' );
964 $key->setAttribute( 'attr.name', $datum );
965 $key->setAttribute( 'attr.type', $graph_attributes{$datum} );
966 $key->setAttribute( 'for', 'graph' );
967 $key->setAttribute( 'id', $graph_data_keys{$datum} );
970 # Add the data keys for reading nodes
971 my %reading_attributes;
972 my $rmeta = Text::Tradition::Collation::Reading->meta;
973 foreach my $attr( $rmeta->get_all_attributes ) {
974 next if $attr->name =~ /^_/;
975 next if $skipsave{$attr->name};
976 next unless $save_types{$attr->type_constraint->name};
977 $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
979 # Extra custom key for the reading morphology
980 $reading_attributes{'lexemes'} = 'string';
984 foreach my $datum ( sort keys %reading_attributes ) {
985 $node_data_keys{$datum} = 'dn'.$ndi++;
986 my $key = $root->addNewChild( $graphml_ns, 'key' );
987 $key->setAttribute( 'attr.name', $datum );
988 $key->setAttribute( 'attr.type', $reading_attributes{$datum} );
989 $key->setAttribute( 'for', 'node' );
990 $key->setAttribute( 'id', $node_data_keys{$datum} );
993 # Add the data keys for edges, that is, paths and relationships. Path
994 # data does not come from a Moose class so is here manually.
997 my %edge_attributes = (
998 witness => 'string', # ID/label for a path
999 extra => 'boolean', # Path key
1001 my @path_attributes = keys %edge_attributes; # track our manual additions
1002 my $pmeta = Text::Tradition::Collation::Relationship->meta;
1003 foreach my $attr( $pmeta->get_all_attributes ) {
1004 next if $attr->name =~ /^_/;
1005 next if $skipsave{$attr->name};
1006 next unless $save_types{$attr->type_constraint->name};
1007 $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
1009 foreach my $datum ( sort keys %edge_attributes ) {
1010 $edge_data_keys{$datum} = 'de'.$edi++;
1011 my $key = $root->addNewChild( $graphml_ns, 'key' );
1012 $key->setAttribute( 'attr.name', $datum );
1013 $key->setAttribute( 'attr.type', $edge_attributes{$datum} );
1014 $key->setAttribute( 'for', 'edge' );
1015 $key->setAttribute( 'id', $edge_data_keys{$datum} );
1018 # Add the collation graph itself. First, sanitize the name to a valid XML ID.
1019 my $xmlidname = $self->tradition->name;
1020 $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g;
1021 if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) {
1022 $xmlidname = '_'.$xmlidname;
1024 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
1025 $sgraph->setAttribute( 'edgedefault', 'directed' );
1026 $sgraph->setAttribute( 'id', $xmlidname );
1027 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
1028 $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later
1029 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
1030 $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later
1031 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
1033 # Collation attribute data
1034 foreach my $datum ( keys %graph_attributes ) {
1036 if( $datum eq 'version' ) {
1038 } elsif( $gattr_from{$datum} eq 'Tradition' ) {
1039 $value = $self->tradition->$datum;
1041 $value = $self->$datum;
1043 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
1048 # Add our readings to the graph
1049 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
1050 next if $n->has_rank && $n ne $self->start && $n ne $self->end &&
1051 ( $n->rank < $start->rank || $n->rank > $end->rank );
1052 $use_readings{$n->id} = 1;
1053 # Add to the main graph
1054 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
1055 my $node_xmlid = 'n' . $node_ctr++;
1056 $node_hash{ $n->id } = $node_xmlid;
1057 $node_el->setAttribute( 'id', $node_xmlid );
1058 foreach my $d ( keys %reading_attributes ) {
1060 # Custom serialization
1061 if( $d eq 'lexemes' ) {
1062 # If nval is a true value, we have lexemes so we need to
1063 # serialize them. Otherwise set nval to undef so that the
1064 # key is excluded from this reading.
1065 $nval = $nval ? $n->_serialize_lexemes : undef;
1067 if( $rankoffset && $d eq 'rank' && $n ne $self->start ) {
1068 # Adjust the ranks within the subgraph.
1069 $nval = $n eq $self->end ? $end->rank - $rankoffset + 1
1070 : $nval - $rankoffset;
1072 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
1077 # Add the path edges to the sequence graph
1079 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
1080 # We add an edge in the graphml for every witness in $e.
1081 next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} );
1082 my @edge_wits = sort $self->path_witnesses( $e );
1083 $e->[0] = $self->start->id unless $use_readings{$e->[0]};
1084 $e->[1] = $self->end->id unless $use_readings{$e->[1]};
1085 # Skip any path from start to end; that witness is not in the subgraph.
1086 next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id );
1087 foreach my $wit ( @edge_wits ) {
1088 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
1089 $node_hash{ $e->[0] },
1090 $node_hash{ $e->[1] } );
1091 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
1092 $edge_el->setAttribute( 'source', $from );
1093 $edge_el->setAttribute( 'target', $to );
1094 $edge_el->setAttribute( 'id', $id );
1096 # It's a witness path, so add the witness
1098 my $key = $edge_data_keys{'witness'};
1099 # Is this an ante-corr witness?
1100 my $aclabel = $self->ac_label;
1101 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
1102 # Keep the base witness
1104 # ...and record that this is an 'extra' reading path
1105 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
1107 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
1111 # Report the actual number of nodes and edges that went in
1112 $sgraph->setAttribute( 'parse.edges', $edge_ctr );
1113 $sgraph->setAttribute( 'parse.nodes', $node_ctr );
1115 # Add the relationship graph to the XML
1116 map { delete $edge_data_keys{$_} } @path_attributes;
1117 $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
1118 $node_data_keys{'id'}, \%edge_data_keys );
1120 # Save and return the thing
1121 my $result = decode_utf8( $graphml->toString(1) );
1125 sub _add_graphml_data {
1126 my( $el, $key, $value ) = @_;
1127 return unless defined $value;
1128 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
1129 $data_el->setAttribute( 'key', $key );
1130 $data_el->appendText( $value );
1135 Returns a CSV alignment table representation of the collation graph, one
1136 row per witness (or witness uncorrected.)
1142 my $table = $self->alignment_table;
1143 my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } );
1145 # Make the header row
1146 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
1147 push( @result, decode_utf8( $csv->string ) );
1148 # Make the rest of the rows
1149 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1150 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
1151 my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs;
1152 $csv->combine( @row );
1153 push( @result, decode_utf8( $csv->string ) );
1155 return join( "\n", @result );
1158 =head2 alignment_table( $use_refs, $include_witnesses )
1160 Return a reference to an alignment table, in a slightly enhanced CollateX
1161 format which looks like this:
1163 $table = { alignment => [ { witness => "SIGIL",
1164 tokens => [ { t => "TEXT" }, ... ] },
1165 { witness => "SIG2",
1166 tokens => [ { t => "TEXT" }, ... ] },
1168 length => TEXTLEN };
1170 If $use_refs is set to 1, the reading object is returned in the table
1171 instead of READINGTEXT; if not, the text of the reading is returned.
1173 If $include_witnesses is set to a hashref, only the witnesses whose sigil
1174 keys have a true hash value will be included.
1178 sub alignment_table {
1180 $self->calculate_ranks() unless $self->_graphcalc_done;
1181 return $self->cached_table if $self->has_cached_table;
1183 # Make sure we can do this
1184 throw( "Need a linear graph in order to make an alignment table" )
1185 unless $self->linear;
1186 $self->calculate_ranks unless $self->end->has_rank;
1188 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
1189 my @all_pos = ( 1 .. $self->end->rank - 1 );
1190 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
1191 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
1192 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1193 my @row = _make_witness_row( \@wit_path, \@all_pos );
1194 push( @{$table->{'alignment'}},
1195 { 'witness' => $wit->sigil, 'tokens' => \@row } );
1196 if( $wit->is_layered ) {
1197 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
1198 $wit->sigil.$self->ac_label );
1199 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
1200 push( @{$table->{'alignment'}},
1201 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
1204 $self->cached_table( $table );
1208 sub _make_witness_row {
1209 my( $path, $positions ) = @_;
1211 map { $char_hash{$_} = undef } @$positions;
1213 foreach my $rdg ( @$path ) {
1214 my $rtext = $rdg->text;
1215 $rtext = '#LACUNA#' if $rdg->is_lacuna;
1216 print STDERR "rank " . $rdg->rank . "\n" if $debug;
1217 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
1218 $char_hash{$rdg->rank} = { 't' => $rdg };
1220 my @row = map { $char_hash{$_} } @$positions;
1221 # Fill in lacuna markers for undef spots in the row
1222 my $last_el = shift @row;
1223 my @filled_row = ( $last_el );
1224 foreach my $el ( @row ) {
1225 # If we are using node reference, make the lacuna node appear many times
1226 # in the table. If not, use the lacuna tag.
1227 if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) {
1230 push( @filled_row, $el );
1236 =head1 NAVIGATION METHODS
1238 =head2 reading_sequence( $first, $last, $sigil, $backup )
1240 Returns the ordered list of readings, starting with $first and ending
1241 with $last, for the witness given in $sigil. If a $backup sigil is
1242 specified (e.g. when walking a layered witness), it will be used wherever
1243 no $sigil path exists. If there is a base text reading, that will be
1244 used wherever no path exists for $sigil or $backup.
1248 # TODO Think about returning some lazy-eval iterator.
1249 # TODO Get rid of backup; we should know from what witness is whether we need it.
1251 sub reading_sequence {
1252 my( $self, $start, $end, $witness ) = @_;
1254 $witness = $self->baselabel unless $witness;
1255 my @readings = ( $start );
1258 while( $n && $n->id ne $end->id ) {
1259 if( exists( $seen{$n->id} ) ) {
1260 throw( "Detected loop for $witness at " . $n->id );
1264 my $next = $self->next_reading( $n, $witness );
1266 throw( "Did not find any path for $witness from reading " . $n->id );
1268 push( @readings, $next );
1271 # Check that the last reading is our end reading.
1272 my $last = $readings[$#readings];
1273 throw( "Last reading found from " . $start->text .
1274 " for witness $witness is not the end!" ) # TODO do we get this far?
1275 unless $last->id eq $end->id;
1280 =head2 next_reading( $reading, $sigil );
1282 Returns the reading that follows the given reading along the given witness
1288 # Return the successor via the corresponding path.
1290 my $answer = $self->_find_linked_reading( 'next', @_ );
1291 return undef unless $answer;
1292 return $self->reading( $answer );
1295 =head2 prior_reading( $reading, $sigil )
1297 Returns the reading that precedes the given reading along the given witness
1303 # Return the predecessor via the corresponding path.
1305 my $answer = $self->_find_linked_reading( 'prior', @_ );
1306 return $self->reading( $answer );
1309 sub _find_linked_reading {
1310 my( $self, $direction, $node, $path ) = @_;
1312 # Get a backup if we are dealing with a layered witness
1314 my $aclabel = $self->ac_label;
1315 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1319 my @linked_paths = $direction eq 'next'
1320 ? $self->sequence->edges_from( $node )
1321 : $self->sequence->edges_to( $node );
1322 return undef unless scalar( @linked_paths );
1324 # We have to find the linked path that contains all of the
1325 # witnesses supplied in $path.
1326 my( @path_wits, @alt_path_wits );
1327 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1328 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1331 foreach my $le ( @linked_paths ) {
1332 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1335 my @le_wits = sort $self->path_witnesses( $le );
1336 if( _is_within( \@path_wits, \@le_wits ) ) {
1337 # This is the right path.
1338 return $direction eq 'next' ? $le->[1] : $le->[0];
1339 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1343 # Got this far? Return the alternate path if it exists.
1344 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1347 # Got this far? Return the base path if it exists.
1348 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1351 # Got this far? We have no appropriate path.
1352 warn "Could not find $direction node from " . $node->id
1353 . " along path $path";
1359 my( $set1, $set2 ) = @_;
1360 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1361 foreach my $el ( @$set1 ) {
1362 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1367 # Return the string that joins together a list of witnesses for
1368 # display on a single path.
1369 sub _witnesses_of_label {
1370 my( $self, $label ) = @_;
1371 my $regex = $self->wit_list_separator;
1372 my @answer = split( /\Q$regex\E/, $label );
1376 =head2 common_readings
1378 Returns the list of common readings in the graph (i.e. those readings that are
1379 shared by all non-lacunose witnesses.)
1383 sub common_readings {
1385 my @common = grep { $_->is_common } $self->readings;
1389 =head2 path_text( $sigil, [, $start, $end ] )
1391 Returns the text of a witness (plus its backup, if we are using a layer)
1392 as stored in the collation. The text is returned as a string, where the
1393 individual readings are joined with spaces and the meta-readings (e.g.
1394 lacunae) are omitted. Optional specification of $start and $end allows
1395 the generation of a subset of the witness text.
1400 my( $self, $wit, $start, $end ) = @_;
1401 $start = $self->start unless $start;
1402 $end = $self->end unless $end;
1403 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1406 foreach my $r ( @path ) {
1407 unless ( $r->join_prior || !$last || $last->join_next ) {
1410 $pathtext .= $r->text;
1416 =head1 INITIALIZATION METHODS
1418 These are mostly for use by parsers.
1420 =head2 make_witness_path( $witness )
1422 Link the array of readings contained in $witness->path (and in
1423 $witness->uncorrected_path if it exists) into collation paths.
1424 Clear out the arrays when finished.
1426 =head2 make_witness_paths
1428 Call make_witness_path for all witnesses in the tradition.
1432 # For use when a collation is constructed from a base text and an apparatus.
1433 # We have the sequences of readings and just need to add path edges.
1434 # When we are done, clear out the witness path attributes, as they are no
1436 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1438 sub make_witness_paths {
1440 foreach my $wit ( $self->tradition->witnesses ) {
1441 # print STDERR "Making path for " . $wit->sigil . "\n";
1442 $self->make_witness_path( $wit );
1446 sub make_witness_path {
1447 my( $self, $wit ) = @_;
1448 my @chain = @{$wit->path};
1449 my $sig = $wit->sigil;
1450 # Add start and end if necessary
1451 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1452 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1453 foreach my $idx ( 0 .. $#chain-1 ) {
1454 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1456 if( $wit->is_layered ) {
1457 @chain = @{$wit->uncorrected_path};
1458 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1459 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1460 foreach my $idx( 0 .. $#chain-1 ) {
1461 my $source = $chain[$idx];
1462 my $target = $chain[$idx+1];
1463 $self->add_path( $source, $target, $sig.$self->ac_label )
1464 unless $self->has_path( $source, $target, $sig );
1468 $wit->clear_uncorrected_path;
1471 =head2 calculate_ranks
1473 Calculate the reading ranks (that is, their aligned positions relative
1474 to each other) for the graph. This can only be called on linear collations.
1478 use Text::Tradition;
1480 my $cxfile = 't/data/Collatex-16.xml';
1481 my $t = Text::Tradition->new(
1483 'input' => 'CollateX',
1486 my $c = $t->collation;
1489 my $table = $c->alignment_table;
1490 ok( $c->has_cached_table, "Alignment table was cached" );
1491 is( $c->alignment_table, $table, "Cached table returned upon second call" );
1492 $c->calculate_ranks;
1493 is( $c->alignment_table, $table, "Cached table retained with no rank change" );
1494 $c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } );
1495 isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" );
1501 sub calculate_ranks {
1503 # Save the existing ranks, in case we need to invalidate the cached SVG.
1505 map { $existing_ranks{$_} = $_->rank } $self->readings;
1507 # Do the rankings based on the relationship equivalence graph, starting
1508 # with the start node.
1509 my $topo_start = $self->equivalence( $self->start->id );
1510 my $node_ranks = { $topo_start => 0 };
1511 my @curr_origin = ( $topo_start );
1512 # A little iterative function.
1513 while( @curr_origin ) {
1514 @curr_origin = _assign_rank( $self->equivalence_graph,
1515 $node_ranks, @curr_origin );
1517 # Transfer our rankings from the topological graph to the real one.
1518 foreach my $r ( $self->readings ) {
1519 if( defined $node_ranks->{$self->equivalence( $r->id )} ) {
1520 $r->rank( $node_ranks->{$self->equivalence( $r->id )} );
1522 # Die. Find the last rank we calculated.
1523 my @all_defined = sort { ( $node_ranks->{$self->equivalence( $a->id )}||-1 )
1524 <=> ( $node_ranks->{$self->equivalence( $b->id )}||-1 ) }
1526 my $last = pop @all_defined;
1527 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1530 # Do we need to invalidate the cached data?
1531 if( $self->has_cached_svg || $self->has_cached_table ) {
1532 foreach my $r ( $self->readings ) {
1533 next if defined( $existing_ranks{$r} )
1534 && $existing_ranks{$r} == $r->rank;
1535 # Something has changed, so clear the cache
1536 $self->_clear_cache;
1537 # ...and recalculate the common readings.
1538 $self->calculate_common_readings();
1542 # The graph calculation information is now up to date.
1543 $self->_graphcalc_done(1);
1547 my( $graph, $node_ranks, @current_nodes ) = @_;
1548 # Look at each of the children of @current_nodes. If all the child's
1549 # parents have a rank, assign it the highest rank + 1 and add it to
1550 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1551 # parent gets a rank.
1553 foreach my $c ( @current_nodes ) {
1554 warn "Current reading $c has no rank!"
1555 unless exists $node_ranks->{$c};
1556 # print STDERR "Looking at child of node $c, rank "
1557 # . $node_ranks->{$c} . "\n";
1558 foreach my $child ( $graph->successors( $c ) ) {
1559 next if exists $node_ranks->{$child};
1560 my $highest_rank = -1;
1562 foreach my $parent ( $graph->predecessors( $child ) ) {
1563 if( exists $node_ranks->{$parent} ) {
1564 $highest_rank = $node_ranks->{$parent}
1565 if $highest_rank <= $node_ranks->{$parent};
1572 my $c_rank = $highest_rank + 1;
1573 # print STDERR "Assigning rank $c_rank to node $child \n";
1574 $node_ranks->{$child} = $c_rank;
1575 push( @next_nodes, $child );
1583 $self->wipe_svg if $self->has_cached_svg;
1584 $self->wipe_table if $self->has_cached_table;
1588 =head2 flatten_ranks
1590 A convenience method for parsing collation data. Searches the graph for readings
1591 with the same text at the same rank, and merges any that are found.
1597 my %unique_rank_rdg;
1599 foreach my $rdg ( $self->readings ) {
1600 next unless $rdg->has_rank;
1601 my $key = $rdg->rank . "||" . $rdg->text;
1602 if( exists $unique_rank_rdg{$key} ) {
1604 # print STDERR "Combining readings at same rank: $key\n";
1606 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1607 # TODO see if this now makes a common point.
1609 $unique_rank_rdg{$key} = $rdg;
1612 # If we merged readings, the ranks are still fine but the alignment
1613 # table is wrong. Wipe it.
1614 $self->wipe_table() if $changed;
1618 =head2 calculate_common_readings
1620 Goes through the graph identifying the readings that appear in every witness
1621 (apart from those with lacunae at that spot.) Marks them as common and returns
1626 use Text::Tradition;
1628 my $cxfile = 't/data/Collatex-16.xml';
1629 my $t = Text::Tradition->new(
1631 'input' => 'CollateX',
1634 my $c = $t->collation;
1636 my @common = $c->calculate_common_readings();
1637 is( scalar @common, 8, "Found correct number of common readings" );
1638 my @marked = sort $c->common_readings();
1639 is( scalar @common, 8, "All common readings got marked as such" );
1640 my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /;
1641 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1647 sub calculate_common_readings {
1650 map { $_->is_common( 0 ) } $self->readings;
1651 # Implicitly calls calculate_ranks
1652 my $table = $self->alignment_table;
1653 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1654 my @row = map { $_->{'tokens'}->[$idx]
1655 ? $_->{'tokens'}->[$idx]->{'t'} : '' }
1656 @{$table->{'alignment'}};
1658 foreach my $r ( @row ) {
1660 $hash{$r->id} = $r unless $r->is_meta;
1662 $hash{'UNDEF'} = $r;
1665 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1666 my( $r ) = values %hash;
1668 push( @common, $r );
1674 =head2 text_from_paths
1676 Calculate the text array for all witnesses from the path, for later consistency
1677 checking. Only to be used if there is no non-graph-based way to know the
1682 sub text_from_paths {
1684 foreach my $wit ( $self->tradition->witnesses ) {
1685 my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1687 foreach my $r ( @readings ) {
1688 next if $r->is_meta;
1689 push( @text, $r->text );
1691 $wit->text( \@text );
1692 if( $wit->is_layered ) {
1693 my @ucrdgs = $self->reading_sequence( $self->start, $self->end,
1694 $wit->sigil.$self->ac_label );
1696 foreach my $r ( @ucrdgs ) {
1697 next if $r->is_meta;
1698 push( @uctext, $r->text );
1700 $wit->layertext( \@uctext );
1705 =head1 UTILITY FUNCTIONS
1707 =head2 common_predecessor( $reading_a, $reading_b )
1709 Find the last reading that occurs in sequence before both the given readings.
1710 At the very least this should be $self->start.
1712 =head2 common_successor( $reading_a, $reading_b )
1714 Find the first reading that occurs in sequence after both the given readings.
1715 At the very least this should be $self->end.
1719 use Text::Tradition;
1721 my $cxfile = 't/data/Collatex-16.xml';
1722 my $t = Text::Tradition->new(
1724 'input' => 'CollateX',
1727 my $c = $t->collation;
1729 is( $c->common_predecessor( 'n24', 'n23' )->id,
1730 'n20', "Found correct common predecessor" );
1731 is( $c->common_successor( 'n24', 'n23' )->id,
1732 '__END__', "Found correct common successor" );
1734 is( $c->common_predecessor( 'n19', 'n17' )->id,
1735 'n16', "Found correct common predecessor for readings on same path" );
1736 is( $c->common_successor( 'n21', 'n10' )->id,
1737 '__END__', "Found correct common successor for readings on same path" );
1743 ## Return the closest reading that is a predecessor of both the given readings.
1744 sub common_predecessor {
1746 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1747 return $self->_common_in_path( $r1, $r2, 'predecessors' );
1750 sub common_successor {
1752 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1753 return $self->_common_in_path( $r1, $r2, 'successors' );
1757 # TODO think about how to do this without ranks...
1758 sub _common_in_path {
1759 my( $self, $r1, $r2, $dir ) = @_;
1760 my $iter = $self->end->rank;
1762 my @last_r1 = ( $r1 );
1763 my @last_r2 = ( $r2 );
1764 # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' );
1766 # print STDERR "Finding common $dir for $r1, $r2\n";
1767 while( !@candidates ) {
1768 last unless $iter--; # Avoid looping infinitely
1769 # Iterate separately down the graph from r1 and r2
1770 my( @new_lc1, @new_lc2 );
1771 foreach my $lc ( @last_r1 ) {
1772 foreach my $p ( $lc->$dir ) {
1773 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) {
1774 # print STDERR "Path candidate $p from $lc\n";
1775 push( @candidates, $p );
1776 } elsif( !$all_seen{$p->id} ) {
1777 $all_seen{$p->id} = 'r1';
1778 push( @new_lc1, $p );
1782 foreach my $lc ( @last_r2 ) {
1783 foreach my $p ( $lc->$dir ) {
1784 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) {
1785 # print STDERR "Path candidate $p from $lc\n";
1786 push( @candidates, $p );
1787 } elsif( !$all_seen{$p->id} ) {
1788 $all_seen{$p->id} = 'r2';
1789 push( @new_lc2, $p );
1793 @last_r1 = @new_lc1;
1794 @last_r2 = @new_lc2;
1796 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1797 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1801 Text::Tradition::Error->throw(
1802 'ident' => 'Collation error',
1808 __PACKAGE__->meta->make_immutable;
1812 This package is free software and is provided "as is" without express
1813 or implied warranty. You can redistribute it and/or modify it under
1814 the same terms as Perl itself.
1818 Tara L Andrews E<lt>aurum@cpan.orgE<gt>