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;
13 use XML::LibXML::XPathContext;
19 default => sub { Graph->new() },
27 isa => 'Text::Tradition::Collation::RelationshipStore',
29 relationships => 'relationships',
30 related_readings => 'related_readings',
31 get_relationship => 'get_relationship',
32 del_relationship => 'del_relationship',
34 writer => '_set_relations',
39 isa => 'Text::Tradition',
44 isa => 'HashRef[Text::Tradition::Collation::Reading]',
48 _add_reading => 'set',
49 del_reading => 'delete',
50 has_reading => 'exists',
53 default => sub { {} },
56 has 'wit_list_separator' => (
65 default => 'base text',
88 isa => 'Text::Tradition::Collation::Reading',
89 writer => '_set_start',
95 isa => 'Text::Tradition::Collation::Reading',
100 has 'cached_svg' => (
103 predicate => 'has_cached_svg',
104 clearer => 'wipe_svg',
107 has 'cached_table' => (
110 predicate => 'has_cached_table',
111 clearer => 'wipe_table',
114 has '_graphcalc_done' => (
122 Text::Tradition::Collation - a software model for a text collation
127 my $t = Text::Tradition->new(
128 'name' => 'this is a text',
130 'file' => '/path/to/tei_parallel_seg_file.xml' );
132 my $c = $t->collation;
133 my @readings = $c->readings;
134 my @paths = $c->paths;
135 my @relationships = $c->relationships;
137 my $svg_variant_graph = $t->collation->as_svg();
141 Text::Tradition is a library for representation and analysis of collated
142 texts, particularly medieval ones. The Collation is the central feature of
143 a Tradition, where the text, its sequence of readings, and its relationships
144 between readings are actually kept.
150 The constructor. Takes a hash or hashref of the following arguments:
154 =item * tradition - The Text::Tradition object to which the collation
157 =item * linear - Whether the collation should be linear; that is, whether
158 transposed readings should be treated as two linked readings rather than one,
159 and therefore whether the collation graph is acyclic. Defaults to true.
161 =item * baselabel - The default label for the path taken by a base text
162 (if any). Defaults to 'base text'.
164 =item * wit_list_separator - The string to join a list of witnesses for
165 purposes of making labels in display graphs. Defaults to ', '.
167 =item * ac_label - The extra label to tack onto a witness sigil when
168 representing another layer of path for the given witness - that is, when
169 a text has more than one possible reading due to scribal corrections or
170 the like. Defaults to ' (a.c.)'.
172 =item * wordsep - The string used to separate words in the original text.
183 =head2 wit_list_separator
191 Simple accessors for collation attributes.
195 The meta-reading at the start of every witness path.
199 The meta-reading at the end of every witness path.
203 Returns all Reading objects in the graph.
205 =head2 reading( $id )
207 Returns the Reading object corresponding to the given ID.
209 =head2 add_reading( $reading_args )
211 Adds a new reading object to the collation.
212 See L<Text::Tradition::Collation::Reading> for the available arguments.
214 =head2 del_reading( $object_or_id )
216 Removes the given reading from the collation, implicitly removing its
217 paths and relationships.
219 =head2 merge_readings( $main, $second, $concatenate, $with_str )
221 Merges the $second reading into the $main one. If $concatenate is true, then
222 the merged node will carry the text of both readings, concatenated with either
223 $with_str (if specified) or a sensible default (the empty string if the
224 appropriate 'join_*' flag is set on either reading, or else $self->wordsep.)
226 The first two arguments may be either readings or reading IDs.
228 =head2 has_reading( $id )
230 Predicate to see whether a given reading ID is in the graph.
232 =head2 reading_witnesses( $object_or_id )
234 Returns a list of sigils whose witnesses contain the reading.
238 Returns all reading paths within the document - that is, all edges in the
239 collation graph. Each path is an arrayref of [ $source, $target ] reading IDs.
241 =head2 add_path( $source, $target, $sigil )
243 Links the given readings in the collation in sequence, under the given witness
244 sigil. The readings may be specified by object or ID.
246 =head2 del_path( $source, $target, $sigil )
248 Links the given readings in the collation in sequence, under the given witness
249 sigil. The readings may be specified by object or ID.
251 =head2 has_path( $source, $target );
253 Returns true if the two readings are linked in sequence in any witness.
254 The readings may be specified by object or ID.
258 Returns all Relationship objects in the collation.
260 =head2 add_relationship( $reading, $other_reading, $options )
262 Adds a new relationship of the type given in $options between the two readings,
263 which may be specified by object or ID. Returns a value of ( $status, @vectors)
264 where $status is true on success, and @vectors is a list of relationship edges
265 that were ultimately added.
266 See L<Text::Tradition::Collation::Relationship> for the available options.
272 $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
273 $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
274 $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
277 ### Reading construct/destruct functions
280 my( $self, $reading ) = @_;
281 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
282 my %args = %$reading;
283 $reading = Text::Tradition::Collation::Reading->new(
284 'collation' => $self,
287 # First check to see if a reading with this ID exists.
288 if( $self->reading( $reading->id ) ) {
289 throw( "Collation already has a reading with id " . $reading->id );
291 $self->_graphcalc_done(0);
292 $self->_add_reading( $reading->id => $reading );
293 # Once the reading has been added, put it in both graphs.
294 $self->sequence->add_vertex( $reading->id );
295 $self->relations->add_reading( $reading->id );
299 around del_reading => sub {
304 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
307 # Remove the reading from the graphs.
308 $self->_graphcalc_done(0);
309 $self->_clear_cache; # Explicitly clear caches to GC the reading
310 $self->sequence->delete_vertex( $arg );
311 $self->relations->delete_reading( $arg );
314 $self->$orig( $arg );
321 my $cxfile = 't/data/Collatex-16.xml';
322 my $t = Text::Tradition->new(
324 'input' => 'CollateX',
327 my $c = $t->collation;
329 my $rno = scalar $c->readings;
330 # Split n21 for testing purposes
331 my $new_r = $c->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } );
332 my $old_r = $c->reading( 'n21' );
333 $old_r->alter_text( 'to' );
334 $c->del_path( 'n20', 'n21', 'A' );
335 $c->add_path( 'n20', 'n21p0', 'A' );
336 $c->add_path( 'n21p0', 'n21', 'A' );
338 ok( $c->reading( 'n21p0' ), "New reading exists" );
339 is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" );
341 # Combine n3 and n4 ( with his )
342 $c->merge_readings( 'n3', 'n4', 1 );
343 ok( !$c->reading('n4'), "Reading n4 is gone" );
344 is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" );
346 # Collapse n9 and n10 ( rood / root )
347 $c->merge_readings( 'n9', 'n10' );
348 ok( !$c->reading('n10'), "Reading n10 is gone" );
349 is( $c->reading('n9')->text, 'rood', "Reading n9 has an unchanged word" );
351 # Combine n21 and n21p0
352 my $remaining = $c->reading('n21');
353 $remaining ||= $c->reading('n22'); # one of these should still exist
354 $c->merge_readings( 'n21p0', $remaining, 1 );
355 ok( !$c->reading('n21'), "Reading $remaining is gone" );
356 is( $c->reading('n21p0')->text, 'unto', "Reading n21p0 merged correctly" );
365 # We only need the IDs for adding paths to the graph, not the reading
366 # objects themselves.
367 my( $kept, $deleted, $combine, $combine_char ) = $self->_stringify_args( @_ );
368 $self->_graphcalc_done(0);
370 # The kept reading should inherit the paths and the relationships
371 # of the deleted reading.
372 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
373 my @vector = ( $kept );
374 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
375 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
376 next if $vector[0] eq $vector[1]; # Don't add a self loop
377 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
378 $self->sequence->add_edge( @vector );
379 my $fwits = $self->sequence->get_edge_attributes( @vector );
380 @wits{keys %$fwits} = values %$fwits;
381 $self->sequence->set_edge_attributes( @vector, \%wits );
383 $self->relations->merge_readings( $kept, $deleted, $combine_char );
385 # Do the deletion deed.
387 my $kept_obj = $self->reading( $kept );
388 my $del_obj = $self->reading( $deleted );
389 my $joinstr = $combine_char;
390 unless( defined $joinstr ) {
391 $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior;
392 $joinstr = $self->wordsep unless defined $joinstr;
394 $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) );
396 $self->del_reading( $deleted );
400 # Helper function for manipulating the graph.
401 sub _stringify_args {
402 my( $self, $first, $second, @args ) = @_;
404 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
405 $second = $second->id
406 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
407 return( $first, $second, @args );
410 # Helper function for manipulating the graph.
411 sub _objectify_args {
412 my( $self, $first, $second, $arg ) = @_;
413 $first = $self->reading( $first )
414 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
415 $second = $self->reading( $second )
416 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
417 return( $first, $second, $arg );
424 # We only need the IDs for adding paths to the graph, not the reading
425 # objects themselves.
426 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
428 $self->_graphcalc_done(0);
429 # Connect the readings
430 $self->sequence->add_edge( $source, $target );
431 # Note the witness in question
432 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
438 if( ref( $_[0] ) eq 'ARRAY' ) {
445 # We only need the IDs for adding paths to the graph, not the reading
446 # objects themselves.
447 my( $source, $target, $wit ) = $self->_stringify_args( @args );
449 $self->_graphcalc_done(0);
450 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
451 $self->sequence->delete_edge_attribute( $source, $target, $wit );
453 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
454 $self->sequence->delete_edge( $source, $target );
459 # Extra graph-alike utility
462 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
463 return undef unless $self->sequence->has_edge( $source, $target );
464 return $self->sequence->has_edge_attribute( $source, $target, $wit );
467 =head2 clear_witness( @sigil_list )
469 Clear the given witnesses out of the collation entirely, removing references
470 to them in paths, and removing readings that belong only to them. Should only
471 be called via $tradition->del_witness.
476 my( $self, @sigils ) = @_;
478 $self->_graphcalc_done(0);
479 # Clear the witness(es) out of the paths
480 foreach my $e ( $self->paths ) {
481 foreach my $sig ( @sigils ) {
482 $self->del_path( $e, $sig );
486 # Clear out the newly unused readings
487 foreach my $r ( $self->readings ) {
488 unless( $self->reading_witnesses( $r ) ) {
489 $self->del_reading( $r );
494 sub add_relationship {
496 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
497 my( @vectors ) = $self->relations->add_relationship( $source,
498 $self->reading( $source ), $target, $self->reading( $target ), $opts );
499 $self->_graphcalc_done(0);
503 around qw/ get_relationship del_relationship / => sub {
507 if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) {
510 my( $source, $target ) = $self->_stringify_args( @args );
511 $self->$orig( $source, $target );
514 =head2 reading_witnesses( $reading )
516 Return a list of sigils corresponding to the witnesses in which the reading appears.
520 sub reading_witnesses {
521 my( $self, $reading ) = @_;
522 # We need only check either the incoming or the outgoing edges; I have
523 # arbitrarily chosen "incoming". Thus, special-case the start node.
524 if( $reading eq $self->start ) {
525 return map { $_->sigil } $self->tradition->witnesses;
528 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
529 my $wits = $self->sequence->get_edge_attributes( @$e );
530 @all_witnesses{ keys %$wits } = 1;
532 my $acstr = $self->ac_label;
533 foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) {
534 delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit};
536 return keys %all_witnesses;
539 =head1 OUTPUT METHODS
541 =head2 as_svg( \%options )
543 Returns an SVG string that represents the graph, via as_dot and graphviz.
544 See as_dot for a list of options. Must have GraphViz (dot) installed to run.
549 my( $self, $opts ) = @_;
550 throw( "Need GraphViz installed to output SVG" )
551 unless File::Which::which( 'dot' );
552 my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'};
553 $self->calculate_ranks() unless $self->_graphcalc_done;
554 if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) {
555 my @cmd = qw/dot -Tsvg/;
557 my $dotfile = File::Temp->new();
559 # $dotfile->unlink_on_destroy(0);
560 binmode $dotfile, ':utf8';
561 print $dotfile $self->as_dot( $opts );
562 push( @cmd, $dotfile->filename );
563 run( \@cmd, ">", binary(), \$svg );
564 $svg = decode_utf8( $svg );
565 $self->cached_svg( $svg ) unless $want_subgraph;
568 return $self->cached_svg;
573 =head2 as_dot( \%options )
575 Returns a string that is the collation graph expressed in dot
576 (i.e. GraphViz) format. Options include:
591 my( $self, $opts ) = @_;
592 my $startrank = $opts->{'from'} if $opts;
593 my $endrank = $opts->{'to'} if $opts;
594 my $color_common = $opts->{'color_common'} if $opts;
595 my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank
596 && $self->end->rank > 100;
597 $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs
599 # Check the arguments
601 return if $endrank && $startrank > $endrank;
602 return if $startrank > $self->end->rank;
604 if( defined $endrank ) {
605 return if $endrank < 0;
606 $endrank = undef if $endrank == $self->end->rank;
609 my $graph_name = $self->tradition->name;
610 $graph_name =~ s/[^\w\s]//g;
611 $graph_name = join( '_', split( /\s+/, $graph_name ) );
619 'fillcolor' => 'white',
624 'arrowhead' => 'open',
625 'color' => '#000000',
626 'fontcolor' => '#000000',
629 my $dot = sprintf( "digraph %s {\n", $graph_name );
630 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
631 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
633 # Output substitute start/end readings if necessary
635 $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
638 $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
640 if( $STRAIGHTENHACK ) {
642 my $startlabel = $startrank ? 'SUBSTART' : 'START';
643 $dot .= "\tsubgraph { rank=same \"#$startlabel#\" \"#SILENT#\" }\n";
644 $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];"
646 my %used; # Keep track of the readings that actually appear in the graph
647 # Sort the readings by rank if we have ranks; this speeds layout.
648 my @all_readings = $self->end->has_rank
649 ? sort { $a->rank <=> $b->rank } $self->readings
651 # TODO Refrain from outputting lacuna nodes - just grey out the edges.
652 foreach my $reading ( @all_readings ) {
653 # Only output readings within our rank range.
654 next if $startrank && $reading->rank < $startrank;
655 next if $endrank && $reading->rank > $endrank;
656 $used{$reading->id} = 1;
657 # Need not output nodes without separate labels
658 next if $reading->id eq $reading->text;
660 my $label = $reading->text;
661 $label .= '-' if $reading->join_next;
662 $label = "-$label" if $reading->join_prior;
663 $label =~ s/\"/\\\"/g;
664 $rattrs->{'label'} = $label;
665 $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
666 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
669 # Add the real edges. Need to weight one edge per rank jump, in a
671 # my $weighted = $self->_add_edge_weights;
672 my @edges = $self->paths;
673 my( %substart, %subend );
674 foreach my $edge ( @edges ) {
675 # Do we need to output this edge?
676 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
677 my $label = $self->_path_display_label( $self->path_witnesses( $edge ) );
678 my $variables = { %edge_attrs, 'label' => $label };
680 # Account for the rank gap if necessary
681 my $rank0 = $self->reading( $edge->[0] )->rank
682 if $self->reading( $edge->[0] )->has_rank;
683 my $rank1 = $self->reading( $edge->[1] )->rank
684 if $self->reading( $edge->[1] )->has_rank;
685 if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) {
686 $variables->{'minlen'} = $rank1 - $rank0;
689 # Add the calculated edge weights
690 # if( exists $weighted->{$edge->[0]}
691 # && $weighted->{$edge->[0]} eq $edge->[1] ) {
692 # # $variables->{'color'} = 'red';
693 # $variables->{'weight'} = 3.0;
696 # EXPERIMENTAL: make edge width reflect no. of witnesses
697 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
698 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
700 my $varopts = _dot_attr_string( $variables );
701 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
702 $edge->[0], $edge->[1], $varopts );
703 } elsif( $used{$edge->[0]} ) {
704 $subend{$edge->[0]} = 1;
705 } elsif( $used{$edge->[1]} ) {
706 $substart{$edge->[1]} = 1;
709 # Add substitute start and end edges if necessary
710 foreach my $node ( keys %substart ) {
711 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
712 my $variables = { %edge_attrs, 'label' => $witstr };
713 my $varopts = _dot_attr_string( $variables );
714 $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;";
716 foreach my $node ( keys %subend ) {
717 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
718 my $variables = { %edge_attrs, 'label' => $witstr };
719 my $varopts = _dot_attr_string( $variables );
720 $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;";
723 if( $STRAIGHTENHACK ) {
724 my $endlabel = $endrank ? 'SUBEND' : 'END';
725 $dot .= "\t\"#$endlabel#\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
732 sub _dot_attr_string {
735 foreach my $k ( sort keys %$hash ) {
737 push( @attrs, $k.'="'.$v.'"' );
739 return( '[ ' . join( ', ', @attrs ) . ' ]' );
742 sub _add_edge_weights {
744 # Walk the graph from START to END, choosing the successor node with
745 # the largest number of witness paths each time.
747 my $curr = $self->start->id;
748 my $ranked = $self->end->has_rank;
749 while( $curr ne $self->end->id ) {
750 my $rank = $ranked ? $self->reading( $curr )->rank : 0;
751 my @succ = sort { $self->path_witnesses( $curr, $a )
752 <=> $self->path_witnesses( $curr, $b ) }
753 $self->sequence->successors( $curr );
754 my $next = pop @succ;
755 my $nextrank = $ranked ? $self->reading( $next )->rank : 0;
756 # Try to avoid lacunae in the weighted path.
758 ( $self->reading( $next )->is_lacuna ||
759 $nextrank - $rank > 1 ) ){
762 $weighted->{$curr} = $next;
768 =head2 path_witnesses( $edge )
770 Returns the list of sigils whose witnesses are associated with the given edge.
771 The edge can be passed as either an array or an arrayref of ( $source, $target ).
776 my( $self, @edge ) = @_;
777 # If edge is an arrayref, cope.
778 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
782 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
786 # Helper function. Make a display label for the given witnesses, showing a.c.
787 # witnesses only where the main witness is not also in the list.
788 sub _path_display_label {
791 map { $wits{$_} = 1 } @_;
793 # If an a.c. wit is listed, remove it if the main wit is also listed.
794 # Otherwise keep it for explicit listing.
795 my $aclabel = $self->ac_label;
797 foreach my $w ( sort keys %wits ) {
798 if( $w =~ /^(.*)\Q$aclabel\E$/ ) {
799 if( exists $wits{$1} ) {
802 push( @disp_ac, $w );
807 # See if we are in a majority situation.
808 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
809 if( scalar keys %wits > $maj ) {
810 unshift( @disp_ac, 'majority' );
811 return join( ', ', @disp_ac );
813 return join( ', ', sort keys %wits );
817 =head2 readings_at_rank( $rank )
819 Returns a list of readings at a given rank, taken from the alignment table.
823 sub readings_at_rank {
824 my( $self, $rank ) = @_;
825 my $table = $self->alignment_table;
826 # Table rank is real rank - 1.
827 my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}};
829 foreach my $e ( @elements ) {
830 next unless ref( $e ) eq 'HASH';
831 next unless exists $e->{'t'};
832 $readings{$e->{'t'}->id} = $e->{'t'};
834 return values %readings;
839 Returns a GraphML representation of the collation. The GraphML will contain
840 two graphs. The first expresses the attributes of the readings and the witness
841 paths that link them; the second expresses the relationships that link the
842 readings. This is the native transfer format for a tradition.
851 my $datafile = 't/data/florilegium_tei_ps.xml';
852 my $tradition = Text::Tradition->new( 'input' => 'TEI',
857 ok( $tradition, "Got a tradition object" );
858 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
859 ok( $tradition->collation, "Tradition has a collation" );
861 my $c = $tradition->collation;
862 is( scalar $c->readings, $READINGS, "Collation has all readings" );
863 is( scalar $c->paths, $PATHS, "Collation has all paths" );
864 is( scalar $c->relationships, 0, "Collation has all relationships" );
866 # Add a few relationships
867 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
868 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
869 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
871 # Now write it to GraphML and parse it again.
873 my $graphml = $c->as_graphml;
874 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
875 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
876 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
877 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
885 $self->calculate_ranks unless $self->_graphcalc_done;
888 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
889 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
890 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
891 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
893 # Create the document and root node
894 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
895 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
896 $graphml->setDocumentElement( $root );
897 $root->setNamespace( $xsi_ns, 'xsi', 0 );
898 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
900 # List of attribute types to save on our objects and their corresponding
906 'RelationshipType' => 'string',
907 'RelationshipScope' => 'string',
910 # List of attribute names *not* to save on our objects.
911 # We will also not save any attribute beginning with _.
913 map { $skipsave{$_} = 1 } qw/ cached_svg /;
915 # Add the data keys for the graph. Include an extra key 'version' for the
916 # GraphML output version.
919 my %graph_attributes = ( 'version' => 'string' );
920 # Graph attributes include those of Tradition and those of Collation.
922 my $tmeta = $self->tradition->meta;
923 my $cmeta = $self->meta;
924 map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes;
925 map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes;
926 foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) {
927 next if $attr->name =~ /^_/;
928 next if $skipsave{$attr->name};
929 next unless $save_types{$attr->type_constraint->name};
930 $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
933 foreach my $datum ( sort keys %graph_attributes ) {
934 $graph_data_keys{$datum} = 'dg'.$gdi++;
935 my $key = $root->addNewChild( $graphml_ns, 'key' );
936 $key->setAttribute( 'attr.name', $datum );
937 $key->setAttribute( 'attr.type', $graph_attributes{$datum} );
938 $key->setAttribute( 'for', 'graph' );
939 $key->setAttribute( 'id', $graph_data_keys{$datum} );
942 # Add the data keys for reading nodes
943 my %reading_attributes;
944 my $rmeta = Text::Tradition::Collation::Reading->meta;
945 foreach my $attr( $rmeta->get_all_attributes ) {
946 next if $attr->name =~ /^_/;
947 next if $skipsave{$attr->name};
948 next unless $save_types{$attr->type_constraint->name};
949 $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
953 foreach my $datum ( sort keys %reading_attributes ) {
954 $node_data_keys{$datum} = 'dn'.$ndi++;
955 my $key = $root->addNewChild( $graphml_ns, 'key' );
956 $key->setAttribute( 'attr.name', $datum );
957 $key->setAttribute( 'attr.type', $reading_attributes{$datum} );
958 $key->setAttribute( 'for', 'node' );
959 $key->setAttribute( 'id', $node_data_keys{$datum} );
962 # Add the data keys for edges, that is, paths and relationships. Path
963 # data does not come from a Moose class so is here manually.
966 my %edge_attributes = (
967 witness => 'string', # ID/label for a path
968 extra => 'boolean', # Path key
970 my @path_attributes = keys %edge_attributes; # track our manual additions
971 my $pmeta = Text::Tradition::Collation::Relationship->meta;
972 foreach my $attr( $pmeta->get_all_attributes ) {
973 next if $attr->name =~ /^_/;
974 next if $skipsave{$attr->name};
975 next unless $save_types{$attr->type_constraint->name};
976 $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
978 foreach my $datum ( sort keys %edge_attributes ) {
979 $edge_data_keys{$datum} = 'de'.$edi++;
980 my $key = $root->addNewChild( $graphml_ns, 'key' );
981 $key->setAttribute( 'attr.name', $datum );
982 $key->setAttribute( 'attr.type', $edge_attributes{$datum} );
983 $key->setAttribute( 'for', 'edge' );
984 $key->setAttribute( 'id', $edge_data_keys{$datum} );
987 # Add the collation graph itself
988 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
989 $sgraph->setAttribute( 'edgedefault', 'directed' );
990 $sgraph->setAttribute( 'id', $self->tradition->name );
991 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
992 $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
993 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
994 $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
995 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
997 # Collation attribute data
998 foreach my $datum ( keys %graph_attributes ) {
1000 if( $datum eq 'version' ) {
1002 } elsif( $gattr_from{$datum} eq 'Tradition' ) {
1003 $value = $self->tradition->$datum;
1005 $value = $self->$datum;
1007 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
1012 # Add our readings to the graph
1013 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
1014 # Add to the main graph
1015 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
1016 my $node_xmlid = 'n' . $node_ctr++;
1017 $node_hash{ $n->id } = $node_xmlid;
1018 $node_el->setAttribute( 'id', $node_xmlid );
1019 foreach my $d ( keys %reading_attributes ) {
1021 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
1026 # Add the path edges to the sequence graph
1028 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
1029 # We add an edge in the graphml for every witness in $e.
1030 foreach my $wit ( sort $self->path_witnesses( $e ) ) {
1031 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
1032 $node_hash{ $e->[0] },
1033 $node_hash{ $e->[1] } );
1034 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
1035 $edge_el->setAttribute( 'source', $from );
1036 $edge_el->setAttribute( 'target', $to );
1037 $edge_el->setAttribute( 'id', $id );
1039 # It's a witness path, so add the witness
1041 my $key = $edge_data_keys{'witness'};
1042 # Is this an ante-corr witness?
1043 my $aclabel = $self->ac_label;
1044 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
1045 # Keep the base witness
1047 # ...and record that this is an 'extra' reading path
1048 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
1050 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
1054 # Add the relationship graph to the XML
1055 map { delete $edge_data_keys{$_} } @path_attributes;
1056 $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
1057 $node_data_keys{'id'}, \%edge_data_keys );
1059 # Save and return the thing
1060 my $result = decode_utf8( $graphml->toString(1) );
1064 sub _add_graphml_data {
1065 my( $el, $key, $value ) = @_;
1066 return unless defined $value;
1067 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
1068 $data_el->setAttribute( 'key', $key );
1069 $data_el->appendText( $value );
1074 Returns a CSV alignment table representation of the collation graph, one
1075 row per witness (or witness uncorrected.)
1081 my $table = $self->alignment_table;
1082 my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } );
1084 # Make the header row
1085 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
1086 push( @result, decode_utf8( $csv->string ) );
1087 # Make the rest of the rows
1088 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1089 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
1090 my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs;
1091 $csv->combine( @row );
1092 push( @result, decode_utf8( $csv->string ) );
1094 return join( "\n", @result );
1097 =head2 alignment_table( $use_refs, $include_witnesses )
1099 Return a reference to an alignment table, in a slightly enhanced CollateX
1100 format which looks like this:
1102 $table = { alignment => [ { witness => "SIGIL",
1103 tokens => [ { t => "TEXT" }, ... ] },
1104 { witness => "SIG2",
1105 tokens => [ { t => "TEXT" }, ... ] },
1107 length => TEXTLEN };
1109 If $use_refs is set to 1, the reading object is returned in the table
1110 instead of READINGTEXT; if not, the text of the reading is returned.
1112 If $include_witnesses is set to a hashref, only the witnesses whose sigil
1113 keys have a true hash value will be included.
1117 sub alignment_table {
1119 $self->calculate_ranks() unless $self->_graphcalc_done;
1120 return $self->cached_table if $self->has_cached_table;
1122 # Make sure we can do this
1123 throw( "Need a linear graph in order to make an alignment table" )
1124 unless $self->linear;
1125 $self->calculate_ranks unless $self->end->has_rank;
1127 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
1128 my @all_pos = ( 1 .. $self->end->rank - 1 );
1129 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
1130 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
1131 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1132 my @row = _make_witness_row( \@wit_path, \@all_pos );
1133 push( @{$table->{'alignment'}},
1134 { 'witness' => $wit->sigil, 'tokens' => \@row } );
1135 if( $wit->is_layered ) {
1136 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
1137 $wit->sigil.$self->ac_label );
1138 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
1139 push( @{$table->{'alignment'}},
1140 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
1143 $self->cached_table( $table );
1147 sub _make_witness_row {
1148 my( $path, $positions ) = @_;
1150 map { $char_hash{$_} = undef } @$positions;
1152 foreach my $rdg ( @$path ) {
1153 my $rtext = $rdg->text;
1154 $rtext = '#LACUNA#' if $rdg->is_lacuna;
1155 print STDERR "rank " . $rdg->rank . "\n" if $debug;
1156 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
1157 $char_hash{$rdg->rank} = { 't' => $rdg };
1159 my @row = map { $char_hash{$_} } @$positions;
1160 # Fill in lacuna markers for undef spots in the row
1161 my $last_el = shift @row;
1162 my @filled_row = ( $last_el );
1163 foreach my $el ( @row ) {
1164 # If we are using node reference, make the lacuna node appear many times
1165 # in the table. If not, use the lacuna tag.
1166 if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) {
1169 push( @filled_row, $el );
1175 =head1 NAVIGATION METHODS
1177 =head2 reading_sequence( $first, $last, $sigil, $backup )
1179 Returns the ordered list of readings, starting with $first and ending
1180 with $last, for the witness given in $sigil. If a $backup sigil is
1181 specified (e.g. when walking a layered witness), it will be used wherever
1182 no $sigil path exists. If there is a base text reading, that will be
1183 used wherever no path exists for $sigil or $backup.
1187 # TODO Think about returning some lazy-eval iterator.
1188 # TODO Get rid of backup; we should know from what witness is whether we need it.
1190 sub reading_sequence {
1191 my( $self, $start, $end, $witness ) = @_;
1193 $witness = $self->baselabel unless $witness;
1194 my @readings = ( $start );
1197 while( $n && $n->id ne $end->id ) {
1198 if( exists( $seen{$n->id} ) ) {
1199 throw( "Detected loop for $witness at " . $n->id );
1203 my $next = $self->next_reading( $n, $witness );
1205 throw( "Did not find any path for $witness from reading " . $n->id );
1207 push( @readings, $next );
1210 # Check that the last reading is our end reading.
1211 my $last = $readings[$#readings];
1212 throw( "Last reading found from " . $start->text .
1213 " for witness $witness is not the end!" ) # TODO do we get this far?
1214 unless $last->id eq $end->id;
1219 =head2 next_reading( $reading, $sigil );
1221 Returns the reading that follows the given reading along the given witness
1227 # Return the successor via the corresponding path.
1229 my $answer = $self->_find_linked_reading( 'next', @_ );
1230 return undef unless $answer;
1231 return $self->reading( $answer );
1234 =head2 prior_reading( $reading, $sigil )
1236 Returns the reading that precedes the given reading along the given witness
1242 # Return the predecessor via the corresponding path.
1244 my $answer = $self->_find_linked_reading( 'prior', @_ );
1245 return $self->reading( $answer );
1248 sub _find_linked_reading {
1249 my( $self, $direction, $node, $path ) = @_;
1251 # Get a backup if we are dealing with a layered witness
1253 my $aclabel = $self->ac_label;
1254 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1258 my @linked_paths = $direction eq 'next'
1259 ? $self->sequence->edges_from( $node )
1260 : $self->sequence->edges_to( $node );
1261 return undef unless scalar( @linked_paths );
1263 # We have to find the linked path that contains all of the
1264 # witnesses supplied in $path.
1265 my( @path_wits, @alt_path_wits );
1266 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1267 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1270 foreach my $le ( @linked_paths ) {
1271 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1274 my @le_wits = sort $self->path_witnesses( $le );
1275 if( _is_within( \@path_wits, \@le_wits ) ) {
1276 # This is the right path.
1277 return $direction eq 'next' ? $le->[1] : $le->[0];
1278 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1282 # Got this far? Return the alternate path if it exists.
1283 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1286 # Got this far? Return the base path if it exists.
1287 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1290 # Got this far? We have no appropriate path.
1291 warn "Could not find $direction node from " . $node->id
1292 . " along path $path";
1298 my( $set1, $set2 ) = @_;
1299 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1300 foreach my $el ( @$set1 ) {
1301 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1306 # Return the string that joins together a list of witnesses for
1307 # display on a single path.
1308 sub _witnesses_of_label {
1309 my( $self, $label ) = @_;
1310 my $regex = $self->wit_list_separator;
1311 my @answer = split( /\Q$regex\E/, $label );
1315 =head2 common_readings
1317 Returns the list of common readings in the graph (i.e. those readings that are
1318 shared by all non-lacunose witnesses.)
1322 sub common_readings {
1324 my @common = grep { $_->is_common } $self->readings;
1328 =head2 path_text( $sigil, [, $start, $end ] )
1330 Returns the text of a witness (plus its backup, if we are using a layer)
1331 as stored in the collation. The text is returned as a string, where the
1332 individual readings are joined with spaces and the meta-readings (e.g.
1333 lacunae) are omitted. Optional specification of $start and $end allows
1334 the generation of a subset of the witness text.
1339 my( $self, $wit, $start, $end ) = @_;
1340 $start = $self->start unless $start;
1341 $end = $self->end unless $end;
1342 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1345 foreach my $r ( @path ) {
1346 if( $r->join_prior || !$last || $last->join_next ) {
1347 $pathtext .= $r->text;
1349 $pathtext .= ' ' . $r->text;
1356 =head1 INITIALIZATION METHODS
1358 These are mostly for use by parsers.
1360 =head2 make_witness_path( $witness )
1362 Link the array of readings contained in $witness->path (and in
1363 $witness->uncorrected_path if it exists) into collation paths.
1364 Clear out the arrays when finished.
1366 =head2 make_witness_paths
1368 Call make_witness_path for all witnesses in the tradition.
1372 # For use when a collation is constructed from a base text and an apparatus.
1373 # We have the sequences of readings and just need to add path edges.
1374 # When we are done, clear out the witness path attributes, as they are no
1376 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1378 sub make_witness_paths {
1380 foreach my $wit ( $self->tradition->witnesses ) {
1381 # print STDERR "Making path for " . $wit->sigil . "\n";
1382 $self->make_witness_path( $wit );
1386 sub make_witness_path {
1387 my( $self, $wit ) = @_;
1388 my @chain = @{$wit->path};
1389 my $sig = $wit->sigil;
1390 # Add start and end if necessary
1391 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1392 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1393 foreach my $idx ( 0 .. $#chain-1 ) {
1394 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1396 if( $wit->is_layered ) {
1397 @chain = @{$wit->uncorrected_path};
1398 unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
1399 push( @chain, $self->end ) unless $chain[-1] eq $self->end;
1400 foreach my $idx( 0 .. $#chain-1 ) {
1401 my $source = $chain[$idx];
1402 my $target = $chain[$idx+1];
1403 $self->add_path( $source, $target, $sig.$self->ac_label )
1404 unless $self->has_path( $source, $target, $sig );
1408 $wit->clear_uncorrected_path;
1411 =head2 calculate_ranks
1413 Calculate the reading ranks (that is, their aligned positions relative
1414 to each other) for the graph. This can only be called on linear collations.
1418 use Text::Tradition;
1420 my $cxfile = 't/data/Collatex-16.xml';
1421 my $t = Text::Tradition->new(
1423 'input' => 'CollateX',
1426 my $c = $t->collation;
1429 my $table = $c->alignment_table;
1430 ok( $c->has_cached_table, "Alignment table was cached" );
1431 is( $c->alignment_table, $table, "Cached table returned upon second call" );
1432 $c->calculate_ranks;
1433 is( $c->alignment_table, $table, "Cached table retained with no rank change" );
1434 $c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } );
1435 isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" );
1441 sub calculate_ranks {
1443 # Save the existing ranks, in case we need to invalidate the cached SVG.
1445 # Walk a version of the graph where every node linked by a relationship
1446 # edge is fundamentally the same node, and do a topological ranking on
1447 # the nodes in this graph.
1448 my $topo_graph = Graph->new();
1452 foreach my $r ( $self->readings ) {
1453 next if exists $rel_containers{$r->id};
1454 my @rels = $r->related_readings( 'colocated' );
1456 # Make a relationship container.
1458 my $rn = 'rel_container_' . $rel_ctr++;
1459 $topo_graph->add_vertex( $rn );
1461 $rel_containers{$_->id} = $rn;
1464 # Add a new node to mirror the old node.
1465 $rel_containers{$r->id} = $r->id;
1466 $topo_graph->add_vertex( $r->id );
1471 foreach my $r ( $self->readings ) {
1472 $existing_ranks{$r} = $r->rank;
1473 foreach my $n ( $self->sequence->successors( $r->id ) ) {
1474 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
1475 $rel_containers{$n} );
1476 # $DB::single = 1 unless $tfrom && $tto;
1477 $topo_graph->add_edge( $tfrom, $tto );
1481 # Now do the rankings, starting with the start node.
1482 my $topo_start = $rel_containers{$self->start->id};
1483 my $node_ranks = { $topo_start => 0 };
1484 my @curr_origin = ( $topo_start );
1485 # A little iterative function.
1486 while( @curr_origin ) {
1487 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
1489 # Transfer our rankings from the topological graph to the real one.
1490 foreach my $r ( $self->readings ) {
1491 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
1492 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1494 # Die. Find the last rank we calculated.
1495 my @all_defined = sort { $node_ranks->{$rel_containers{$a->id}}
1496 <=> $node_ranks->{$rel_containers{$b->id}} }
1498 my $last = pop @all_defined;
1499 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1502 # Do we need to invalidate the cached data?
1503 if( $self->has_cached_svg || $self->has_cached_table ) {
1504 foreach my $r ( $self->readings ) {
1505 next if defined( $existing_ranks{$r} )
1506 && $existing_ranks{$r} == $r->rank;
1507 # Something has changed, so clear the cache
1508 $self->_clear_cache;
1509 # ...and recalculate the common readings.
1510 $self->calculate_common_readings();
1514 # The graph calculation information is now up to date.
1515 $self->_graphcalc_done(1);
1519 my( $graph, $node_ranks, @current_nodes ) = @_;
1520 # Look at each of the children of @current_nodes. If all the child's
1521 # parents have a rank, assign it the highest rank + 1 and add it to
1522 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1523 # parent gets a rank.
1525 foreach my $c ( @current_nodes ) {
1526 warn "Current reading $c has no rank!"
1527 unless exists $node_ranks->{$c};
1528 # print STDERR "Looking at child of node $c, rank "
1529 # . $node_ranks->{$c} . "\n";
1530 foreach my $child ( $graph->successors( $c ) ) {
1531 next if exists $node_ranks->{$child};
1532 my $highest_rank = -1;
1534 foreach my $parent ( $graph->predecessors( $child ) ) {
1535 if( exists $node_ranks->{$parent} ) {
1536 $highest_rank = $node_ranks->{$parent}
1537 if $highest_rank <= $node_ranks->{$parent};
1544 my $c_rank = $highest_rank + 1;
1545 # print STDERR "Assigning rank $c_rank to node $child \n";
1546 $node_ranks->{$child} = $c_rank;
1547 push( @next_nodes, $child );
1555 $self->wipe_svg if $self->has_cached_svg;
1556 $self->wipe_table if $self->has_cached_table;
1560 =head2 flatten_ranks
1562 A convenience method for parsing collation data. Searches the graph for readings
1563 with the same text at the same rank, and merges any that are found.
1569 my %unique_rank_rdg;
1571 foreach my $rdg ( $self->readings ) {
1572 next unless $rdg->has_rank;
1573 my $key = $rdg->rank . "||" . $rdg->text;
1574 if( exists $unique_rank_rdg{$key} ) {
1576 # print STDERR "Combining readings at same rank: $key\n";
1578 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1579 # TODO see if this now makes a common point.
1581 $unique_rank_rdg{$key} = $rdg;
1584 # If we merged readings, the ranks are still fine but the alignment
1585 # table is wrong. Wipe it.
1586 $self->wipe_table() if $changed;
1590 =head2 calculate_common_readings
1592 Goes through the graph identifying the readings that appear in every witness
1593 (apart from those with lacunae at that spot.) Marks them as common and returns
1598 use Text::Tradition;
1600 my $cxfile = 't/data/Collatex-16.xml';
1601 my $t = Text::Tradition->new(
1603 'input' => 'CollateX',
1606 my $c = $t->collation;
1608 my @common = $c->calculate_common_readings();
1609 is( scalar @common, 8, "Found correct number of common readings" );
1610 my @marked = sort $c->common_readings();
1611 is( scalar @common, 8, "All common readings got marked as such" );
1612 my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /;
1613 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1619 sub calculate_common_readings {
1622 map { $_->is_common( 0 ) } $self->readings;
1623 # Implicitly calls calculate_ranks
1624 my $table = $self->alignment_table;
1625 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1626 my @row = map { $_->{'tokens'}->[$idx]
1627 ? $_->{'tokens'}->[$idx]->{'t'} : '' }
1628 @{$table->{'alignment'}};
1630 foreach my $r ( @row ) {
1632 $hash{$r->id} = $r unless $r->is_meta;
1634 $hash{'UNDEF'} = $r;
1637 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1638 my( $r ) = values %hash;
1640 push( @common, $r );
1646 =head2 text_from_paths
1648 Calculate the text array for all witnesses from the path, for later consistency
1649 checking. Only to be used if there is no non-graph-based way to know the
1654 sub text_from_paths {
1656 foreach my $wit ( $self->tradition->witnesses ) {
1657 my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1659 foreach my $r ( @readings ) {
1660 next if $r->is_meta;
1661 push( @text, $r->text );
1663 $wit->text( \@text );
1664 if( $wit->is_layered ) {
1665 my @ucrdgs = $self->reading_sequence( $self->start, $self->end,
1666 $wit->sigil.$self->ac_label );
1668 foreach my $r ( @ucrdgs ) {
1669 next if $r->is_meta;
1670 push( @uctext, $r->text );
1672 $wit->layertext( \@uctext );
1677 =head1 UTILITY FUNCTIONS
1679 =head2 common_predecessor( $reading_a, $reading_b )
1681 Find the last reading that occurs in sequence before both the given readings.
1683 =head2 common_successor( $reading_a, $reading_b )
1685 Find the first reading that occurs in sequence after both the given readings.
1689 use Text::Tradition;
1691 my $cxfile = 't/data/Collatex-16.xml';
1692 my $t = Text::Tradition->new(
1694 'input' => 'CollateX',
1697 my $c = $t->collation;
1699 is( $c->common_predecessor( 'n24', 'n23' )->id,
1700 'n20', "Found correct common predecessor" );
1701 is( $c->common_successor( 'n24', 'n23' )->id,
1702 '#END#', "Found correct common successor" );
1704 is( $c->common_predecessor( 'n19', 'n17' )->id,
1705 'n16', "Found correct common predecessor for readings on same path" );
1706 is( $c->common_successor( 'n21', 'n10' )->id,
1707 '#END#', "Found correct common successor for readings on same path" );
1713 ## Return the closest reading that is a predecessor of both the given readings.
1714 sub common_predecessor {
1716 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1717 return $self->_common_in_path( $r1, $r2, 'predecessors' );
1720 sub common_successor {
1722 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1723 return $self->_common_in_path( $r1, $r2, 'successors' );
1726 sub _common_in_path {
1727 my( $self, $r1, $r2, $dir ) = @_;
1728 my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
1729 $iter = $self->end->rank - $iter if $dir eq 'successors';
1731 my @last_checked = ( $r1, $r2 );
1733 while( !@candidates ) {
1735 foreach my $lc ( @last_checked ) {
1736 foreach my $p ( $lc->$dir ) {
1737 if( $all_seen{$p->id} ) {
1738 push( @candidates, $p );
1740 $all_seen{$p->id} = 1;
1741 push( @new_lc, $p );
1745 @last_checked = @new_lc;
1747 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1748 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1752 Text::Tradition::Error->throw(
1753 'ident' => 'Collation error',
1759 __PACKAGE__->meta->make_immutable;
1763 This package is free software and is provided "as is" without express
1764 or implied warranty. You can redistribute it and/or modify it under
1765 the same terms as Perl itself.
1769 Tara L Andrews E<lt>aurum@cpan.orgE<gt>