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 $reading = Text::Tradition::Collation::Reading->new(
288 'collation' => $self,
291 # First check to see if a reading with this ID exists.
292 if( $self->reading( $reading->id ) ) {
293 throw( "Collation already has a reading with id " . $reading->id );
295 $self->_graphcalc_done(0);
296 $self->_add_reading( $reading->id => $reading );
297 # Once the reading has been added, put it in both graphs.
298 $self->sequence->add_vertex( $reading->id );
299 $self->relations->add_reading( $reading->id );
303 around del_reading => sub {
308 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
311 # Remove the reading from the graphs.
312 $self->_graphcalc_done(0);
313 $self->_clear_cache; # Explicitly clear caches to GC the reading
314 $self->sequence->delete_vertex( $arg );
315 $self->relations->delete_reading( $arg );
318 $self->$orig( $arg );
325 my $cxfile = 't/data/Collatex-16.xml';
326 my $t = Text::Tradition->new(
328 'input' => 'CollateX',
331 my $c = $t->collation;
333 my $rno = scalar $c->readings;
334 # Split n21 for testing purposes
335 my $new_r = $c->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } );
336 my $old_r = $c->reading( 'n21' );
337 $old_r->alter_text( 'to' );
338 $c->del_path( 'n20', 'n21', 'A' );
339 $c->add_path( 'n20', 'n21p0', 'A' );
340 $c->add_path( 'n21p0', 'n21', 'A' );
342 ok( $c->reading( 'n21p0' ), "New reading exists" );
343 is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" );
345 # Combine n3 and n4 ( with his )
346 $c->merge_readings( 'n3', 'n4', 1 );
347 ok( !$c->reading('n4'), "Reading n4 is gone" );
348 is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" );
350 # Collapse n9 and n10 ( rood / root )
351 $c->merge_readings( 'n9', 'n10' );
352 ok( !$c->reading('n10'), "Reading n10 is gone" );
353 is( $c->reading('n9')->text, 'rood', "Reading n9 has an unchanged word" );
355 # Combine n21 and n21p0
356 my $remaining = $c->reading('n21');
357 $remaining ||= $c->reading('n22'); # one of these should still exist
358 $c->merge_readings( 'n21p0', $remaining, 1 );
359 ok( !$c->reading('n21'), "Reading $remaining is gone" );
360 is( $c->reading('n21p0')->text, 'unto', "Reading n21p0 merged correctly" );
369 # We only need the IDs for adding paths to the graph, not the reading
370 # objects themselves.
371 my( $kept, $deleted, $combine, $combine_char ) = $self->_stringify_args( @_ );
372 $self->_graphcalc_done(0);
374 # The kept reading should inherit the paths and the relationships
375 # of the deleted reading.
376 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
377 my @vector = ( $kept );
378 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
379 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
380 next if $vector[0] eq $vector[1]; # Don't add a self loop
381 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
382 $self->sequence->add_edge( @vector );
383 my $fwits = $self->sequence->get_edge_attributes( @vector );
384 @wits{keys %$fwits} = values %$fwits;
385 $self->sequence->set_edge_attributes( @vector, \%wits );
387 $self->relations->merge_readings( $kept, $deleted, $combine_char );
389 # Do the deletion deed.
391 my $kept_obj = $self->reading( $kept );
392 my $del_obj = $self->reading( $deleted );
393 my $joinstr = $combine_char;
394 unless( defined $joinstr ) {
395 $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior;
396 $joinstr = $self->wordsep unless defined $joinstr;
398 $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) );
400 $self->del_reading( $deleted );
404 # Helper function for manipulating the graph.
405 sub _stringify_args {
406 my( $self, $first, $second, @args ) = @_;
408 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
409 $second = $second->id
410 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
411 return( $first, $second, @args );
414 # Helper function for manipulating the graph.
415 sub _objectify_args {
416 my( $self, $first, $second, $arg ) = @_;
417 $first = $self->reading( $first )
418 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
419 $second = $self->reading( $second )
420 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
421 return( $first, $second, $arg );
428 # We only need the IDs for adding paths to the graph, not the reading
429 # objects themselves.
430 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
432 $self->_graphcalc_done(0);
433 # Connect the readings
434 unless( $self->sequence->has_edge( $source, $target ) ) {
435 $self->sequence->add_edge( $source, $target );
436 $self->relations->add_equivalence_edge( $source, $target );
438 # Note the witness in question
439 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
445 if( ref( $_[0] ) eq 'ARRAY' ) {
452 # We only need the IDs for adding paths to the graph, not the reading
453 # objects themselves.
454 my( $source, $target, $wit ) = $self->_stringify_args( @args );
456 $self->_graphcalc_done(0);
457 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
458 $self->sequence->delete_edge_attribute( $source, $target, $wit );
460 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
461 $self->sequence->delete_edge( $source, $target );
462 $self->relations->delete_equivalence_edge( $source, $target );
467 # Extra graph-alike utility
470 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
471 return undef unless $self->sequence->has_edge( $source, $target );
472 return $self->sequence->has_edge_attribute( $source, $target, $wit );
475 =head2 clear_witness( @sigil_list )
477 Clear the given witnesses out of the collation entirely, removing references
478 to them in paths, and removing readings that belong only to them. Should only
479 be called via $tradition->del_witness.
484 my( $self, @sigils ) = @_;
486 $self->_graphcalc_done(0);
487 # Clear the witness(es) out of the paths
488 foreach my $e ( $self->paths ) {
489 foreach my $sig ( @sigils ) {
490 $self->del_path( $e, $sig );
494 # Clear out the newly unused readings
495 foreach my $r ( $self->readings ) {
496 unless( $self->reading_witnesses( $r ) ) {
497 $self->del_reading( $r );
502 sub add_relationship {
504 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
505 my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts );
506 $self->_graphcalc_done(0);
510 around qw/ get_relationship del_relationship / => sub {
514 if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) {
517 my( $source, $target ) = $self->_stringify_args( @args );
518 $self->$orig( $source, $target );
521 =head2 reading_witnesses( $reading )
523 Return a list of sigils corresponding to the witnesses in which the reading appears.
527 sub reading_witnesses {
528 my( $self, $reading ) = @_;
529 # We need only check either the incoming or the outgoing edges; I have
530 # arbitrarily chosen "incoming". Thus, special-case the start node.
531 if( $reading eq $self->start ) {
532 return map { $_->sigil } $self->tradition->witnesses;
535 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
536 my $wits = $self->sequence->get_edge_attributes( @$e );
537 @all_witnesses{ keys %$wits } = 1;
539 my $acstr = $self->ac_label;
540 foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) {
541 delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit};
543 return keys %all_witnesses;
546 =head1 OUTPUT METHODS
548 =head2 as_svg( \%options )
550 Returns an SVG string that represents the graph, via as_dot and graphviz.
551 See as_dot for a list of options. Must have GraphViz (dot) installed to run.
556 my( $self, $opts ) = @_;
557 throw( "Need GraphViz installed to output SVG" )
558 unless File::Which::which( 'dot' );
559 my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'};
560 $self->calculate_ranks() unless( $self->_graphcalc_done || $opts->{'nocalc'} );
561 if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) {
562 my @cmd = qw/dot -Tsvg/;
564 my $dotfile = File::Temp->new();
566 # $dotfile->unlink_on_destroy(0);
567 binmode $dotfile, ':utf8';
568 print $dotfile $self->as_dot( $opts );
569 push( @cmd, $dotfile->filename );
570 run( \@cmd, ">", binary(), \$svg );
571 $svg = decode_utf8( $svg );
572 $self->cached_svg( $svg ) unless $want_subgraph;
575 return $self->cached_svg;
580 =head2 as_dot( \%options )
582 Returns a string that is the collation graph expressed in dot
583 (i.e. GraphViz) format. Options include:
598 my( $self, $opts ) = @_;
599 my $startrank = $opts->{'from'} if $opts;
600 my $endrank = $opts->{'to'} if $opts;
601 my $color_common = $opts->{'color_common'} if $opts;
602 my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank
603 && $self->end->rank > 100;
604 $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs
606 # Check the arguments
608 return if $endrank && $startrank > $endrank;
609 return if $startrank > $self->end->rank;
611 if( defined $endrank ) {
612 return if $endrank < 0;
613 $endrank = undef if $endrank == $self->end->rank;
616 my $graph_name = $self->tradition->name;
617 $graph_name =~ s/[^\w\s]//g;
618 $graph_name = join( '_', split( /\s+/, $graph_name ) );
626 'fillcolor' => 'white',
631 'arrowhead' => 'open',
632 'color' => '#000000',
633 'fontcolor' => '#000000',
636 my $dot = sprintf( "digraph %s {\n", $graph_name );
637 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
638 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
640 # Output substitute start/end readings if necessary
642 $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
645 $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
647 if( $STRAIGHTENHACK ) {
649 my $startlabel = $startrank ? 'SUBSTART' : 'START';
650 $dot .= "\tsubgraph { rank=same \"#$startlabel#\" \"#SILENT#\" }\n";
651 $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];"
653 my %used; # Keep track of the readings that actually appear in the graph
654 # Sort the readings by rank if we have ranks; this speeds layout.
655 my @all_readings = $self->end->has_rank
656 ? sort { $a->rank <=> $b->rank } $self->readings
658 # TODO Refrain from outputting lacuna nodes - just grey out the edges.
659 foreach my $reading ( @all_readings ) {
660 # Only output readings within our rank range.
661 next if $startrank && $reading->rank < $startrank;
662 next if $endrank && $reading->rank > $endrank;
663 $used{$reading->id} = 1;
664 # Need not output nodes without separate labels
665 next if $reading->id eq $reading->text;
667 my $label = $reading->text;
668 $label .= '-' if $reading->join_next;
669 $label = "-$label" if $reading->join_prior;
670 $label =~ s/\"/\\\"/g;
671 $rattrs->{'label'} = $label;
672 $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
673 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
676 # Add the real edges. Need to weight one edge per rank jump, in a
678 # my $weighted = $self->_add_edge_weights;
679 my @edges = $self->paths;
680 my( %substart, %subend );
681 foreach my $edge ( @edges ) {
682 # Do we need to output this edge?
683 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
684 my $label = $self->_path_display_label( $self->path_witnesses( $edge ) );
685 my $variables = { %edge_attrs, 'label' => $label };
687 # Account for the rank gap if necessary
688 my $rank0 = $self->reading( $edge->[0] )->rank
689 if $self->reading( $edge->[0] )->has_rank;
690 my $rank1 = $self->reading( $edge->[1] )->rank
691 if $self->reading( $edge->[1] )->has_rank;
692 if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) {
693 $variables->{'minlen'} = $rank1 - $rank0;
696 # Add the calculated edge weights
697 # if( exists $weighted->{$edge->[0]}
698 # && $weighted->{$edge->[0]} eq $edge->[1] ) {
699 # # $variables->{'color'} = 'red';
700 # $variables->{'weight'} = 3.0;
703 # EXPERIMENTAL: make edge width reflect no. of witnesses
704 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
705 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
707 my $varopts = _dot_attr_string( $variables );
708 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
709 $edge->[0], $edge->[1], $varopts );
710 } elsif( $used{$edge->[0]} ) {
711 $subend{$edge->[0]} = 1;
712 } elsif( $used{$edge->[1]} ) {
713 $substart{$edge->[1]} = 1;
716 # Add substitute start and end edges if necessary
717 foreach my $node ( keys %substart ) {
718 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
719 my $variables = { %edge_attrs, 'label' => $witstr };
720 my $varopts = _dot_attr_string( $variables );
721 $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;";
723 foreach my $node ( keys %subend ) {
724 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
725 my $variables = { %edge_attrs, 'label' => $witstr };
726 my $varopts = _dot_attr_string( $variables );
727 $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;";
730 if( $STRAIGHTENHACK ) {
731 my $endlabel = $endrank ? 'SUBEND' : 'END';
732 $dot .= "\t\"#$endlabel#\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
739 sub _dot_attr_string {
742 foreach my $k ( sort keys %$hash ) {
744 push( @attrs, $k.'="'.$v.'"' );
746 return( '[ ' . join( ', ', @attrs ) . ' ]' );
749 sub _add_edge_weights {
751 # Walk the graph from START to END, choosing the successor node with
752 # the largest number of witness paths each time.
754 my $curr = $self->start->id;
755 my $ranked = $self->end->has_rank;
756 while( $curr ne $self->end->id ) {
757 my $rank = $ranked ? $self->reading( $curr )->rank : 0;
758 my @succ = sort { $self->path_witnesses( $curr, $a )
759 <=> $self->path_witnesses( $curr, $b ) }
760 $self->sequence->successors( $curr );
761 my $next = pop @succ;
762 my $nextrank = $ranked ? $self->reading( $next )->rank : 0;
763 # Try to avoid lacunae in the weighted path.
765 ( $self->reading( $next )->is_lacuna ||
766 $nextrank - $rank > 1 ) ){
769 $weighted->{$curr} = $next;
775 =head2 path_witnesses( $edge )
777 Returns the list of sigils whose witnesses are associated with the given edge.
778 The edge can be passed as either an array or an arrayref of ( $source, $target ).
783 my( $self, @edge ) = @_;
784 # If edge is an arrayref, cope.
785 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
789 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
793 # Helper function. Make a display label for the given witnesses, showing a.c.
794 # witnesses only where the main witness is not also in the list.
795 sub _path_display_label {
798 map { $wits{$_} = 1 } @_;
800 # If an a.c. wit is listed, remove it if the main wit is also listed.
801 # Otherwise keep it for explicit listing.
802 my $aclabel = $self->ac_label;
804 foreach my $w ( sort keys %wits ) {
805 if( $w =~ /^(.*)\Q$aclabel\E$/ ) {
806 if( exists $wits{$1} ) {
809 push( @disp_ac, $w );
814 # See if we are in a majority situation.
815 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
816 if( scalar keys %wits > $maj ) {
817 unshift( @disp_ac, 'majority' );
818 return join( ', ', @disp_ac );
820 return join( ', ', sort keys %wits );
824 =head2 readings_at_rank( $rank )
826 Returns a list of readings at a given rank, taken from the alignment table.
830 sub readings_at_rank {
831 my( $self, $rank ) = @_;
832 my $table = $self->alignment_table;
833 # Table rank is real rank - 1.
834 my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}};
836 foreach my $e ( @elements ) {
837 next unless ref( $e ) eq 'HASH';
838 next unless exists $e->{'t'};
839 $readings{$e->{'t'}->id} = $e->{'t'};
841 return values %readings;
846 Returns a GraphML representation of the collation. The GraphML will contain
847 two graphs. The first expresses the attributes of the readings and the witness
848 paths that link them; the second expresses the relationships that link the
849 readings. This is the native transfer format for a tradition.
858 my $datafile = 't/data/florilegium_tei_ps.xml';
859 my $tradition = Text::Tradition->new( 'input' => 'TEI',
864 ok( $tradition, "Got a tradition object" );
865 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
866 ok( $tradition->collation, "Tradition has a collation" );
868 my $c = $tradition->collation;
869 is( scalar $c->readings, $READINGS, "Collation has all readings" );
870 is( scalar $c->paths, $PATHS, "Collation has all paths" );
871 is( scalar $c->relationships, 0, "Collation has all relationships" );
873 # Add a few relationships
874 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
875 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
876 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
878 # Now write it to GraphML and parse it again.
880 my $graphml = $c->as_graphml;
881 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
882 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
883 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
884 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
891 my( $self, $options ) = @_;
892 $self->calculate_ranks unless $self->_graphcalc_done;
894 my $start = $options->{'from'}
895 ? $self->reading( $options->{'from'} ) : $self->start;
896 my $end = $options->{'to'}
897 ? $self->reading( $options->{'to'} ) : $self->end;
898 if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) {
899 throw( 'Start node must be before end node' );
901 # The readings need to be ranked for this to work.
902 $start = $self->start unless $start->has_rank;
903 $end = $self->end unless $end->has_rank;
905 unless( $start eq $self->start ) {
906 $rankoffset = $start->rank - 1;
911 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
912 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
913 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
914 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
916 # Create the document and root node
917 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
918 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
919 $graphml->setDocumentElement( $root );
920 $root->setNamespace( $xsi_ns, 'xsi', 0 );
921 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
923 # List of attribute types to save on our objects and their corresponding
929 'RelationshipType' => 'string',
930 'RelationshipScope' => 'string',
933 # List of attribute names *not* to save on our objects.
934 # We will also not save any attribute beginning with _.
936 map { $skipsave{$_} = 1 } qw/ cached_svg /;
938 # Add the data keys for the graph. Include an extra key 'version' for the
939 # GraphML output version.
942 my %graph_attributes = ( 'version' => 'string' );
943 # Graph attributes include those of Tradition and those of Collation.
945 my $tmeta = $self->tradition->meta;
946 my $cmeta = $self->meta;
947 map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes;
948 map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes;
949 foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) {
950 next if $attr->name =~ /^_/;
951 next if $skipsave{$attr->name};
952 next unless $save_types{$attr->type_constraint->name};
953 $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
956 foreach my $datum ( sort keys %graph_attributes ) {
957 $graph_data_keys{$datum} = 'dg'.$gdi++;
958 my $key = $root->addNewChild( $graphml_ns, 'key' );
959 $key->setAttribute( 'attr.name', $datum );
960 $key->setAttribute( 'attr.type', $graph_attributes{$datum} );
961 $key->setAttribute( 'for', 'graph' );
962 $key->setAttribute( 'id', $graph_data_keys{$datum} );
965 # Add the data keys for reading nodes
966 my %reading_attributes;
967 my $rmeta = Text::Tradition::Collation::Reading->meta;
968 foreach my $attr( $rmeta->get_all_attributes ) {
969 next if $attr->name =~ /^_/;
970 next if $skipsave{$attr->name};
971 next unless $save_types{$attr->type_constraint->name};
972 $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
976 foreach my $datum ( sort keys %reading_attributes ) {
977 $node_data_keys{$datum} = 'dn'.$ndi++;
978 my $key = $root->addNewChild( $graphml_ns, 'key' );
979 $key->setAttribute( 'attr.name', $datum );
980 $key->setAttribute( 'attr.type', $reading_attributes{$datum} );
981 $key->setAttribute( 'for', 'node' );
982 $key->setAttribute( 'id', $node_data_keys{$datum} );
985 # Add the data keys for edges, that is, paths and relationships. Path
986 # data does not come from a Moose class so is here manually.
989 my %edge_attributes = (
990 witness => 'string', # ID/label for a path
991 extra => 'boolean', # Path key
993 my @path_attributes = keys %edge_attributes; # track our manual additions
994 my $pmeta = Text::Tradition::Collation::Relationship->meta;
995 foreach my $attr( $pmeta->get_all_attributes ) {
996 next if $attr->name =~ /^_/;
997 next if $skipsave{$attr->name};
998 next unless $save_types{$attr->type_constraint->name};
999 $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
1001 foreach my $datum ( sort keys %edge_attributes ) {
1002 $edge_data_keys{$datum} = 'de'.$edi++;
1003 my $key = $root->addNewChild( $graphml_ns, 'key' );
1004 $key->setAttribute( 'attr.name', $datum );
1005 $key->setAttribute( 'attr.type', $edge_attributes{$datum} );
1006 $key->setAttribute( 'for', 'edge' );
1007 $key->setAttribute( 'id', $edge_data_keys{$datum} );
1010 # Add the collation graph itself. First, sanitize the name to a valid XML ID.
1011 my $xmlidname = $self->tradition->name;
1012 $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g;
1013 if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) {
1014 $xmlidname = '_'.$xmlidname;
1016 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
1017 $sgraph->setAttribute( 'edgedefault', 'directed' );
1018 $sgraph->setAttribute( 'id', $xmlidname );
1019 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
1020 $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later
1021 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
1022 $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later
1023 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
1025 # Collation attribute data
1026 foreach my $datum ( keys %graph_attributes ) {
1028 if( $datum eq 'version' ) {
1030 } elsif( $gattr_from{$datum} eq 'Tradition' ) {
1031 $value = $self->tradition->$datum;
1033 $value = $self->$datum;
1035 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
1040 # Add our readings to the graph
1041 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
1042 next if $n->has_rank && $n ne $self->start && $n ne $self->end &&
1043 ( $n->rank < $start->rank || $n->rank > $end->rank );
1044 $use_readings{$n->id} = 1;
1045 # Add to the main graph
1046 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
1047 my $node_xmlid = 'n' . $node_ctr++;
1048 $node_hash{ $n->id } = $node_xmlid;
1049 $node_el->setAttribute( 'id', $node_xmlid );
1050 foreach my $d ( keys %reading_attributes ) {
1052 if( $rankoffset && $d eq 'rank' && $n ne $self->start ) {
1053 # Adjust the ranks within the subgraph.
1054 $nval = $n eq $self->end ? $end->rank - $rankoffset + 1
1055 : $nval - $rankoffset;
1057 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
1062 # Add the path edges to the sequence graph
1064 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
1065 # We add an edge in the graphml for every witness in $e.
1066 next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} );
1067 my @edge_wits = sort $self->path_witnesses( $e );
1068 $e->[0] = $self->start->id unless $use_readings{$e->[0]};
1069 $e->[1] = $self->end->id unless $use_readings{$e->[1]};
1070 # Skip any path from start to end; that witness is not in the subgraph.
1071 next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id );
1072 foreach my $wit ( @edge_wits ) {
1073 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
1074 $node_hash{ $e->[0] },
1075 $node_hash{ $e->[1] } );
1076 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
1077 $edge_el->setAttribute( 'source', $from );
1078 $edge_el->setAttribute( 'target', $to );
1079 $edge_el->setAttribute( 'id', $id );
1081 # It's a witness path, so add the witness
1083 my $key = $edge_data_keys{'witness'};
1084 # Is this an ante-corr witness?
1085 my $aclabel = $self->ac_label;
1086 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
1087 # Keep the base witness
1089 # ...and record that this is an 'extra' reading path
1090 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
1092 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
1096 # Report the actual number of nodes and edges that went in
1097 $sgraph->setAttribute( 'parse.edges', $edge_ctr );
1098 $sgraph->setAttribute( 'parse.nodes', $node_ctr );
1100 # Add the relationship graph to the XML
1101 map { delete $edge_data_keys{$_} } @path_attributes;
1102 $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
1103 $node_data_keys{'id'}, \%edge_data_keys );
1105 # Save and return the thing
1106 my $result = decode_utf8( $graphml->toString(1) );
1110 sub _add_graphml_data {
1111 my( $el, $key, $value ) = @_;
1112 return unless defined $value;
1113 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
1114 $data_el->setAttribute( 'key', $key );
1115 $data_el->appendText( $value );
1120 Returns a CSV alignment table representation of the collation graph, one
1121 row per witness (or witness uncorrected.)
1127 my $table = $self->alignment_table;
1128 my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } );
1130 # Make the header row
1131 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
1132 push( @result, decode_utf8( $csv->string ) );
1133 # Make the rest of the rows
1134 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1135 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
1136 my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs;
1137 $csv->combine( @row );
1138 push( @result, decode_utf8( $csv->string ) );
1140 return join( "\n", @result );
1143 =head2 alignment_table( $use_refs, $include_witnesses )
1145 Return a reference to an alignment table, in a slightly enhanced CollateX
1146 format which looks like this:
1148 $table = { alignment => [ { witness => "SIGIL",
1149 tokens => [ { t => "TEXT" }, ... ] },
1150 { witness => "SIG2",
1151 tokens => [ { t => "TEXT" }, ... ] },
1153 length => TEXTLEN };
1155 If $use_refs is set to 1, the reading object is returned in the table
1156 instead of READINGTEXT; if not, the text of the reading is returned.
1158 If $include_witnesses is set to a hashref, only the witnesses whose sigil
1159 keys have a true hash value will be included.
1163 sub alignment_table {
1165 $self->calculate_ranks() unless $self->_graphcalc_done;
1166 return $self->cached_table if $self->has_cached_table;
1168 # Make sure we can do this
1169 throw( "Need a linear graph in order to make an alignment table" )
1170 unless $self->linear;
1171 $self->calculate_ranks unless $self->end->has_rank;
1173 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
1174 my @all_pos = ( 1 .. $self->end->rank - 1 );
1175 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
1176 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
1177 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1178 my @row = _make_witness_row( \@wit_path, \@all_pos );
1179 push( @{$table->{'alignment'}},
1180 { 'witness' => $wit->sigil, 'tokens' => \@row } );
1181 if( $wit->is_layered ) {
1182 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
1183 $wit->sigil.$self->ac_label );
1184 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
1185 push( @{$table->{'alignment'}},
1186 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
1189 $self->cached_table( $table );
1193 sub _make_witness_row {
1194 my( $path, $positions ) = @_;
1196 map { $char_hash{$_} = undef } @$positions;
1198 foreach my $rdg ( @$path ) {
1199 my $rtext = $rdg->text;
1200 $rtext = '#LACUNA#' if $rdg->is_lacuna;
1201 print STDERR "rank " . $rdg->rank . "\n" if $debug;
1202 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
1203 $char_hash{$rdg->rank} = { 't' => $rdg };
1205 my @row = map { $char_hash{$_} } @$positions;
1206 # Fill in lacuna markers for undef spots in the row
1207 my $last_el = shift @row;
1208 my @filled_row = ( $last_el );
1209 foreach my $el ( @row ) {
1210 # If we are using node reference, make the lacuna node appear many times
1211 # in the table. If not, use the lacuna tag.
1212 if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) {
1215 push( @filled_row, $el );
1221 =head1 NAVIGATION METHODS
1223 =head2 reading_sequence( $first, $last, $sigil, $backup )
1225 Returns the ordered list of readings, starting with $first and ending
1226 with $last, for the witness given in $sigil. If a $backup sigil is
1227 specified (e.g. when walking a layered witness), it will be used wherever
1228 no $sigil path exists. If there is a base text reading, that will be
1229 used wherever no path exists for $sigil or $backup.
1233 # TODO Think about returning some lazy-eval iterator.
1234 # TODO Get rid of backup; we should know from what witness is whether we need it.
1236 sub reading_sequence {
1237 my( $self, $start, $end, $witness ) = @_;
1239 $witness = $self->baselabel unless $witness;
1240 my @readings = ( $start );
1243 while( $n && $n->id ne $end->id ) {
1244 if( exists( $seen{$n->id} ) ) {
1245 throw( "Detected loop for $witness at " . $n->id );
1249 my $next = $self->next_reading( $n, $witness );
1251 throw( "Did not find any path for $witness from reading " . $n->id );
1253 push( @readings, $next );
1256 # Check that the last reading is our end reading.
1257 my $last = $readings[$#readings];
1258 throw( "Last reading found from " . $start->text .
1259 " for witness $witness is not the end!" ) # TODO do we get this far?
1260 unless $last->id eq $end->id;
1265 =head2 next_reading( $reading, $sigil );
1267 Returns the reading that follows the given reading along the given witness
1273 # Return the successor via the corresponding path.
1275 my $answer = $self->_find_linked_reading( 'next', @_ );
1276 return undef unless $answer;
1277 return $self->reading( $answer );
1280 =head2 prior_reading( $reading, $sigil )
1282 Returns the reading that precedes the given reading along the given witness
1288 # Return the predecessor via the corresponding path.
1290 my $answer = $self->_find_linked_reading( 'prior', @_ );
1291 return $self->reading( $answer );
1294 sub _find_linked_reading {
1295 my( $self, $direction, $node, $path ) = @_;
1297 # Get a backup if we are dealing with a layered witness
1299 my $aclabel = $self->ac_label;
1300 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1304 my @linked_paths = $direction eq 'next'
1305 ? $self->sequence->edges_from( $node )
1306 : $self->sequence->edges_to( $node );
1307 return undef unless scalar( @linked_paths );
1309 # We have to find the linked path that contains all of the
1310 # witnesses supplied in $path.
1311 my( @path_wits, @alt_path_wits );
1312 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1313 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1316 foreach my $le ( @linked_paths ) {
1317 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1320 my @le_wits = sort $self->path_witnesses( $le );
1321 if( _is_within( \@path_wits, \@le_wits ) ) {
1322 # This is the right path.
1323 return $direction eq 'next' ? $le->[1] : $le->[0];
1324 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1328 # Got this far? Return the alternate path if it exists.
1329 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1332 # Got this far? Return the base path if it exists.
1333 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1336 # Got this far? We have no appropriate path.
1337 warn "Could not find $direction node from " . $node->id
1338 . " along path $path";
1344 my( $set1, $set2 ) = @_;
1345 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1346 foreach my $el ( @$set1 ) {
1347 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1352 # Return the string that joins together a list of witnesses for
1353 # display on a single path.
1354 sub _witnesses_of_label {
1355 my( $self, $label ) = @_;
1356 my $regex = $self->wit_list_separator;
1357 my @answer = split( /\Q$regex\E/, $label );
1361 =head2 common_readings
1363 Returns the list of common readings in the graph (i.e. those readings that are
1364 shared by all non-lacunose witnesses.)
1368 sub common_readings {
1370 my @common = grep { $_->is_common } $self->readings;
1374 =head2 path_text( $sigil, [, $start, $end ] )
1376 Returns the text of a witness (plus its backup, if we are using a layer)
1377 as stored in the collation. The text is returned as a string, where the
1378 individual readings are joined with spaces and the meta-readings (e.g.
1379 lacunae) are omitted. Optional specification of $start and $end allows
1380 the generation of a subset of the witness text.
1385 my( $self, $wit, $start, $end ) = @_;
1386 $start = $self->start unless $start;
1387 $end = $self->end unless $end;
1388 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1389 return $self->_text_from_path( @path );
1392 # Utility function so that we can cheat and use it when we need both the path
1394 sub _text_from_path {
1395 my( $self, @path ) = @_;
1398 foreach my $r ( @path ) {
1399 if( $r->join_prior || !$last || $last->join_next ) {
1400 $pathtext .= $r->text;
1402 $pathtext .= ' ' . $r->text;
1409 =head1 INITIALIZATION METHODS
1411 These are mostly for use by parsers.
1413 =head2 make_witness_path( $witness )
1415 Link the array of readings contained in $witness->path (and in
1416 $witness->uncorrected_path if it exists) into collation paths.
1417 Clear out the arrays when finished.
1419 =head2 make_witness_paths
1421 Call make_witness_path for all witnesses in the tradition.
1425 # For use when a collation is constructed from a base text and an apparatus.
1426 # We have the sequences of readings and just need to add path edges.
1427 # When we are done, clear out the witness path attributes, as they are no
1429 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1431 sub make_witness_paths {
1433 foreach my $wit ( $self->tradition->witnesses ) {
1434 # print STDERR "Making path for " . $wit->sigil . "\n";
1435 $self->make_witness_path( $wit );
1439 sub make_witness_path {
1440 my( $self, $wit ) = @_;
1441 my @chain = @{$wit->path};
1442 my $sig = $wit->sigil;
1443 # Add start and end if necessary
1444 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1445 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1446 foreach my $idx ( 0 .. $#chain-1 ) {
1447 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1449 if( $wit->is_layered ) {
1450 @chain = @{$wit->uncorrected_path};
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 my $source = $chain[$idx];
1455 my $target = $chain[$idx+1];
1456 $self->add_path( $source, $target, $sig.$self->ac_label )
1457 unless $self->has_path( $source, $target, $sig );
1461 $wit->clear_uncorrected_path;
1464 =head2 calculate_ranks
1466 Calculate the reading ranks (that is, their aligned positions relative
1467 to each other) for the graph. This can only be called on linear collations.
1471 use Text::Tradition;
1473 my $cxfile = 't/data/Collatex-16.xml';
1474 my $t = Text::Tradition->new(
1476 'input' => 'CollateX',
1479 my $c = $t->collation;
1482 my $table = $c->alignment_table;
1483 ok( $c->has_cached_table, "Alignment table was cached" );
1484 is( $c->alignment_table, $table, "Cached table returned upon second call" );
1485 $c->calculate_ranks;
1486 is( $c->alignment_table, $table, "Cached table retained with no rank change" );
1487 $c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } );
1488 isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" );
1494 sub calculate_ranks {
1496 # Save the existing ranks, in case we need to invalidate the cached SVG.
1498 map { $existing_ranks{$_} = $_->rank } $self->readings;
1500 # Do the rankings based on the relationship equivalence graph, starting
1501 # with the start node.
1502 my $topo_start = $self->equivalence( $self->start->id );
1503 my $node_ranks = { $topo_start => 0 };
1504 my @curr_origin = ( $topo_start );
1505 # A little iterative function.
1506 while( @curr_origin ) {
1507 @curr_origin = _assign_rank( $self->equivalence_graph,
1508 $node_ranks, @curr_origin );
1510 # Transfer our rankings from the topological graph to the real one.
1511 foreach my $r ( $self->readings ) {
1512 if( defined $node_ranks->{$self->equivalence( $r->id )} ) {
1513 $r->rank( $node_ranks->{$self->equivalence( $r->id )} );
1515 # Die. Find the last rank we calculated.
1516 my @all_defined = sort { ( $node_ranks->{$self->equivalence( $a->id )}||-1 )
1517 <=> ( $node_ranks->{$self->equivalence( $b->id )}||-1 ) }
1519 my $last = pop @all_defined;
1520 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1523 # Do we need to invalidate the cached data?
1524 if( $self->has_cached_svg || $self->has_cached_table ) {
1525 foreach my $r ( $self->readings ) {
1526 next if defined( $existing_ranks{$r} )
1527 && $existing_ranks{$r} == $r->rank;
1528 # Something has changed, so clear the cache
1529 $self->_clear_cache;
1530 # ...and recalculate the common readings.
1531 $self->calculate_common_readings();
1535 # The graph calculation information is now up to date.
1536 $self->_graphcalc_done(1);
1540 my( $graph, $node_ranks, @current_nodes ) = @_;
1541 # Look at each of the children of @current_nodes. If all the child's
1542 # parents have a rank, assign it the highest rank + 1 and add it to
1543 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1544 # parent gets a rank.
1546 foreach my $c ( @current_nodes ) {
1547 warn "Current reading $c has no rank!"
1548 unless exists $node_ranks->{$c};
1549 # print STDERR "Looking at child of node $c, rank "
1550 # . $node_ranks->{$c} . "\n";
1551 foreach my $child ( $graph->successors( $c ) ) {
1552 next if exists $node_ranks->{$child};
1553 my $highest_rank = -1;
1555 foreach my $parent ( $graph->predecessors( $child ) ) {
1556 if( exists $node_ranks->{$parent} ) {
1557 $highest_rank = $node_ranks->{$parent}
1558 if $highest_rank <= $node_ranks->{$parent};
1565 my $c_rank = $highest_rank + 1;
1566 # print STDERR "Assigning rank $c_rank to node $child \n";
1567 $node_ranks->{$child} = $c_rank;
1568 push( @next_nodes, $child );
1576 $self->wipe_svg if $self->has_cached_svg;
1577 $self->wipe_table if $self->has_cached_table;
1581 =head2 flatten_ranks
1583 A convenience method for parsing collation data. Searches the graph for readings
1584 with the same text at the same rank, and merges any that are found.
1590 my %unique_rank_rdg;
1592 foreach my $rdg ( $self->readings ) {
1593 next unless $rdg->has_rank;
1594 my $key = $rdg->rank . "||" . $rdg->text;
1595 if( exists $unique_rank_rdg{$key} ) {
1597 # print STDERR "Combining readings at same rank: $key\n";
1599 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1600 # TODO see if this now makes a common point.
1602 $unique_rank_rdg{$key} = $rdg;
1605 # If we merged readings, the ranks are still fine but the alignment
1606 # table is wrong. Wipe it.
1607 $self->wipe_table() if $changed;
1611 =head2 calculate_common_readings
1613 Goes through the graph identifying the readings that appear in every witness
1614 (apart from those with lacunae at that spot.) Marks them as common and returns
1619 use Text::Tradition;
1621 my $cxfile = 't/data/Collatex-16.xml';
1622 my $t = Text::Tradition->new(
1624 'input' => 'CollateX',
1627 my $c = $t->collation;
1629 my @common = $c->calculate_common_readings();
1630 is( scalar @common, 8, "Found correct number of common readings" );
1631 my @marked = sort $c->common_readings();
1632 is( scalar @common, 8, "All common readings got marked as such" );
1633 my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /;
1634 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1640 sub calculate_common_readings {
1643 map { $_->is_common( 0 ) } $self->readings;
1644 # Implicitly calls calculate_ranks
1645 my $table = $self->alignment_table;
1646 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1647 my @row = map { $_->{'tokens'}->[$idx]
1648 ? $_->{'tokens'}->[$idx]->{'t'} : '' }
1649 @{$table->{'alignment'}};
1651 foreach my $r ( @row ) {
1653 $hash{$r->id} = $r unless $r->is_meta;
1655 $hash{'UNDEF'} = $r;
1658 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1659 my( $r ) = values %hash;
1661 push( @common, $r );
1667 =head2 text_from_paths
1669 Calculate the text array for all witnesses from the path, for later consistency
1670 checking. Only to be used if there is no non-graph-based way to know the
1675 sub text_from_paths {
1677 foreach my $wit ( $self->tradition->witnesses ) {
1678 my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1680 foreach my $r ( @readings ) {
1681 next if $r->is_meta;
1682 push( @text, $r->text );
1684 $wit->text( \@text );
1685 if( $wit->is_layered ) {
1686 my @ucrdgs = $self->reading_sequence( $self->start, $self->end,
1687 $wit->sigil.$self->ac_label );
1689 foreach my $r ( @ucrdgs ) {
1690 next if $r->is_meta;
1691 push( @uctext, $r->text );
1693 $wit->layertext( \@uctext );
1698 =head1 UTILITY FUNCTIONS
1700 =head2 common_predecessor( $reading_a, $reading_b )
1702 Find the last reading that occurs in sequence before both the given readings.
1703 At the very least this should be $self->start.
1705 =head2 common_successor( $reading_a, $reading_b )
1707 Find the first reading that occurs in sequence after both the given readings.
1708 At the very least this should be $self->end.
1712 use Text::Tradition;
1714 my $cxfile = 't/data/Collatex-16.xml';
1715 my $t = Text::Tradition->new(
1717 'input' => 'CollateX',
1720 my $c = $t->collation;
1722 is( $c->common_predecessor( 'n24', 'n23' )->id,
1723 'n20', "Found correct common predecessor" );
1724 is( $c->common_successor( 'n24', 'n23' )->id,
1725 '#END#', "Found correct common successor" );
1727 is( $c->common_predecessor( 'n19', 'n17' )->id,
1728 'n16', "Found correct common predecessor for readings on same path" );
1729 is( $c->common_successor( 'n21', 'n10' )->id,
1730 '#END#', "Found correct common successor for readings on same path" );
1736 ## Return the closest reading that is a predecessor of both the given readings.
1737 sub common_predecessor {
1739 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1740 return $self->_common_in_path( $r1, $r2, 'predecessors' );
1743 sub common_successor {
1745 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1746 return $self->_common_in_path( $r1, $r2, 'successors' );
1750 # TODO think about how to do this without ranks...
1751 sub _common_in_path {
1752 my( $self, $r1, $r2, $dir ) = @_;
1753 my $iter = $self->end->rank;
1755 my @last_r1 = ( $r1 );
1756 my @last_r2 = ( $r2 );
1757 # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' );
1759 # print STDERR "Finding common $dir for $r1, $r2\n";
1760 while( !@candidates ) {
1761 last unless $iter--; # Avoid looping infinitely
1762 # Iterate separately down the graph from r1 and r2
1763 my( @new_lc1, @new_lc2 );
1764 foreach my $lc ( @last_r1 ) {
1765 foreach my $p ( $lc->$dir ) {
1766 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) {
1767 # print STDERR "Path candidate $p from $lc\n";
1768 push( @candidates, $p );
1769 } elsif( !$all_seen{$p->id} ) {
1770 $all_seen{$p->id} = 'r1';
1771 push( @new_lc1, $p );
1775 foreach my $lc ( @last_r2 ) {
1776 foreach my $p ( $lc->$dir ) {
1777 if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) {
1778 # print STDERR "Path candidate $p from $lc\n";
1779 push( @candidates, $p );
1780 } elsif( !$all_seen{$p->id} ) {
1781 $all_seen{$p->id} = 'r2';
1782 push( @new_lc2, $p );
1786 @last_r1 = @new_lc1;
1787 @last_r2 = @new_lc2;
1789 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1790 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1794 Text::Tradition::Error->throw(
1795 'ident' => 'Collation error',
1801 __PACKAGE__->meta->make_immutable;
1805 This package is free software and is provided "as is" without express
1806 or implied warranty. You can redistribute it and/or modify it under
1807 the same terms as Perl itself.
1811 Tara L Andrews E<lt>aurum@cpan.orgE<gt>