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',
82 isa => 'Text::Tradition::Collation::Reading',
83 writer => '_set_start',
89 isa => 'Text::Tradition::Collation::Reading',
97 predicate => 'has_cached_svg',
98 clearer => 'wipe_svg',
101 has 'cached_table' => (
104 predicate => 'has_cached_table',
105 clearer => 'wipe_table',
108 has '_graphcalc_done' => (
116 Text::Tradition::Collation - a software model for a text collation
121 my $t = Text::Tradition->new(
122 'name' => 'this is a text',
124 'file' => '/path/to/tei_parallel_seg_file.xml' );
126 my $c = $t->collation;
127 my @readings = $c->readings;
128 my @paths = $c->paths;
129 my @relationships = $c->relationships;
131 my $svg_variant_graph = $t->collation->as_svg();
135 Text::Tradition is a library for representation and analysis of collated
136 texts, particularly medieval ones. The Collation is the central feature of
137 a Tradition, where the text, its sequence of readings, and its relationships
138 between readings are actually kept.
144 The constructor. Takes a hash or hashref of the following arguments:
148 =item * tradition - The Text::Tradition object to which the collation
151 =item * linear - Whether the collation should be linear; that is, whether
152 transposed readings should be treated as two linked readings rather than one,
153 and therefore whether the collation graph is acyclic. Defaults to true.
155 =item * baselabel - The default label for the path taken by a base text
156 (if any). Defaults to 'base text'.
158 =item * wit_list_separator - The string to join a list of witnesses for
159 purposes of making labels in display graphs. Defaults to ', '.
161 =item * ac_label - The extra label to tack onto a witness sigil when
162 representing another layer of path for the given witness - that is, when
163 a text has more than one possible reading due to scribal corrections or
164 the like. Defaults to ' (a.c.)'.
174 =head2 wit_list_separator
180 Simple accessors for collation attributes.
184 The meta-reading at the start of every witness path.
188 The meta-reading at the end of every witness path.
192 Returns all Reading objects in the graph.
194 =head2 reading( $id )
196 Returns the Reading object corresponding to the given ID.
198 =head2 add_reading( $reading_args )
200 Adds a new reading object to the collation.
201 See L<Text::Tradition::Collation::Reading> for the available arguments.
203 =head2 del_reading( $object_or_id )
205 Removes the given reading from the collation, implicitly removing its
206 paths and relationships.
208 =head2 merge_readings( $main, $second )
210 Merges the $second reading into the $main one.
211 The arguments may be either readings or reading IDs.
213 =head2 has_reading( $id )
215 Predicate to see whether a given reading ID is in the graph.
217 =head2 reading_witnesses( $object_or_id )
219 Returns a list of sigils whose witnesses contain the reading.
223 Returns all reading paths within the document - that is, all edges in the
224 collation graph. Each path is an arrayref of [ $source, $target ] reading IDs.
226 =head2 add_path( $source, $target, $sigil )
228 Links the given readings in the collation in sequence, under the given witness
229 sigil. The readings may be specified by object or ID.
231 =head2 del_path( $source, $target, $sigil )
233 Links the given readings in the collation in sequence, under the given witness
234 sigil. The readings may be specified by object or ID.
236 =head2 has_path( $source, $target );
238 Returns true if the two readings are linked in sequence in any witness.
239 The readings may be specified by object or ID.
243 Returns all Relationship objects in the collation.
245 =head2 add_relationship( $reading, $other_reading, $options )
247 Adds a new relationship of the type given in $options between the two readings,
248 which may be specified by object or ID. Returns a value of ( $status, @vectors)
249 where $status is true on success, and @vectors is a list of relationship edges
250 that were ultimately added.
251 See L<Text::Tradition::Collation::Relationship> for the available options.
257 $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
258 $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
259 $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
262 ### Reading construct/destruct functions
265 my( $self, $reading ) = @_;
266 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
267 my %args = %$reading;
268 $reading = Text::Tradition::Collation::Reading->new(
269 'collation' => $self,
272 # First check to see if a reading with this ID exists.
273 if( $self->reading( $reading->id ) ) {
274 throw( "Collation already has a reading with id " . $reading->id );
276 $self->_graphcalc_done(0);
277 $self->_add_reading( $reading->id => $reading );
278 # Once the reading has been added, put it in both graphs.
279 $self->sequence->add_vertex( $reading->id );
280 $self->relations->add_reading( $reading->id );
284 around del_reading => sub {
289 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
292 # Remove the reading from the graphs.
293 $self->_graphcalc_done(0);
294 $self->sequence->delete_vertex( $arg );
295 $self->relations->delete_reading( $arg );
298 $self->$orig( $arg );
301 # merge_readings( $main, $to_be_deleted );
306 # We only need the IDs for adding paths to the graph, not the reading
307 # objects themselves.
308 my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
309 $self->_graphcalc_done(0);
311 # The kept reading should inherit the paths and the relationships
312 # of the deleted reading.
313 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
314 my @vector = ( $kept );
315 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
316 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
317 next if $vector[0] eq $vector[1]; # Don't add a self loop
318 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
319 $self->sequence->add_edge( @vector );
320 my $fwits = $self->sequence->get_edge_attributes( @vector );
321 @wits{keys %$fwits} = values %$fwits;
322 $self->sequence->set_edge_attributes( @vector, \%wits );
324 $self->relations->merge_readings( $kept, $deleted, $combine_char );
326 # Do the deletion deed.
327 if( $combine_char ) {
328 my $kept_obj = $self->reading( $kept );
329 my $new_text = join( $combine_char, $kept_obj->text,
330 $self->reading( $deleted )->text );
331 $kept_obj->alter_text( $new_text );
333 $self->del_reading( $deleted );
337 # Helper function for manipulating the graph.
338 sub _stringify_args {
339 my( $self, $first, $second, $arg ) = @_;
341 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
342 $second = $second->id
343 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
344 return( $first, $second, $arg );
347 # Helper function for manipulating the graph.
348 sub _objectify_args {
349 my( $self, $first, $second, $arg ) = @_;
350 $first = $self->reading( $first )
351 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
352 $second = $self->reading( $second )
353 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
354 return( $first, $second, $arg );
361 # We only need the IDs for adding paths to the graph, not the reading
362 # objects themselves.
363 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
365 $self->_graphcalc_done(0);
366 # Connect the readings
367 $self->sequence->add_edge( $source, $target );
368 # Note the witness in question
369 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
375 if( ref( $_[0] ) eq 'ARRAY' ) {
382 # We only need the IDs for adding paths to the graph, not the reading
383 # objects themselves.
384 my( $source, $target, $wit ) = $self->_stringify_args( @args );
386 $self->_graphcalc_done(0);
387 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
388 $self->sequence->delete_edge_attribute( $source, $target, $wit );
390 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
391 $self->sequence->delete_edge( $source, $target );
396 # Extra graph-alike utility
399 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
400 return undef unless $self->sequence->has_edge( $source, $target );
401 return $self->sequence->has_edge_attribute( $source, $target, $wit );
404 =head2 clear_witness( @sigil_list )
406 Clear the given witnesses out of the collation entirely, removing references
407 to them in paths, and removing readings that belong only to them. Should only
408 be called via $tradition->del_witness.
413 my( $self, @sigils ) = @_;
415 $self->_graphcalc_done(0);
416 # Clear the witness(es) out of the paths
417 foreach my $e ( $self->paths ) {
418 foreach my $sig ( @sigils ) {
419 $self->del_path( $e, $sig );
423 # Clear out the newly unused readings
424 foreach my $r ( $self->readings ) {
425 unless( $self->reading_witnesses( $r ) ) {
426 $self->del_reading( $r );
431 sub add_relationship {
433 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
434 my( @vectors ) = $self->relations->add_relationship( $source,
435 $self->reading( $source ), $target, $self->reading( $target ), $opts );
436 $self->_graphcalc_done(0);
440 around qw/ get_relationship del_relationship / => sub {
444 if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) {
447 my( $source, $target ) = $self->_stringify_args( @args );
448 $self->$orig( $source, $target );
451 =head2 reading_witnesses( $reading )
453 Return a list of sigils corresponding to the witnesses in which the reading appears.
457 sub reading_witnesses {
458 my( $self, $reading ) = @_;
459 # We need only check either the incoming or the outgoing edges; I have
460 # arbitrarily chosen "incoming". Thus, special-case the start node.
461 if( $reading eq $self->start ) {
462 return map { $_->sigil } $self->tradition->witnesses;
465 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
466 my $wits = $self->sequence->get_edge_attributes( @$e );
467 @all_witnesses{ keys %$wits } = 1;
469 my $acstr = $self->ac_label;
470 foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) {
471 delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit};
473 return keys %all_witnesses;
476 =head1 OUTPUT METHODS
478 =head2 as_svg( \%options )
480 Returns an SVG string that represents the graph, via as_dot and graphviz.
481 See as_dot for a list of options. Must have GraphViz (dot) installed to run.
486 my( $self, $opts ) = @_;
487 throw( "Need GraphViz installed to output SVG" )
488 unless File::Which::which( 'dot' );
489 my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'};
490 $self->calculate_ranks() unless $self->_graphcalc_done;
491 if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) {
492 my @cmd = qw/dot -Tsvg/;
494 my $dotfile = File::Temp->new();
496 # $dotfile->unlink_on_destroy(0);
497 binmode $dotfile, ':utf8';
498 print $dotfile $self->as_dot( $opts );
499 push( @cmd, $dotfile->filename );
500 run( \@cmd, ">", binary(), \$svg );
501 $svg = decode_utf8( $svg );
502 $self->cached_svg( $svg ) unless $want_subgraph;
505 return $self->cached_svg;
510 =head2 as_dot( \%options )
512 Returns a string that is the collation graph expressed in dot
513 (i.e. GraphViz) format. Options include:
528 my( $self, $opts ) = @_;
529 my $startrank = $opts->{'from'} if $opts;
530 my $endrank = $opts->{'to'} if $opts;
531 my $color_common = $opts->{'color_common'} if $opts;
532 my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank
533 && $self->end->rank > 100;
535 # Check the arguments
537 return if $endrank && $startrank > $endrank;
538 return if $startrank > $self->end->rank;
540 if( defined $endrank ) {
541 return if $endrank < 0;
542 $endrank = undef if $endrank == $self->end->rank;
545 my $graph_name = $self->tradition->name;
546 $graph_name =~ s/[^\w\s]//g;
547 $graph_name = join( '_', split( /\s+/, $graph_name ) );
555 'fillcolor' => 'white',
560 'arrowhead' => 'open',
561 'color' => '#000000',
562 'fontcolor' => '#000000',
565 my $dot = sprintf( "digraph %s {\n", $graph_name );
566 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
567 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
569 # Output substitute start/end readings if necessary
571 $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
574 $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
576 if( $STRAIGHTENHACK ) {
578 $dot .= "\tsubgraph { rank=same \"#START#\" \"#SILENT#\" }\n";
579 $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];"
581 my %used; # Keep track of the readings that actually appear in the graph
582 # Sort the readings by rank if we have ranks; this speeds layout.
583 my @all_readings = $self->end->has_rank
584 ? sort { $a->rank <=> $b->rank } $self->readings
586 # TODO Refrain from outputting lacuna nodes - just grey out the edges.
587 foreach my $reading ( @all_readings ) {
588 # Only output readings within our rank range.
589 next if $startrank && $reading->rank < $startrank;
590 next if $endrank && $reading->rank > $endrank;
591 $used{$reading->id} = 1;
592 # Need not output nodes without separate labels
593 next if $reading->id eq $reading->text;
595 my $label = $reading->text;
596 $label .= '-' if $reading->join_next;
597 $label = "-$label" if $reading->join_prior;
598 $label =~ s/\"/\\\"/g;
599 $rattrs->{'label'} = $label;
600 $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
601 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
604 # Add the real edges. Need to weight one edge per rank jump, in a
606 # my $weighted = $self->_add_edge_weights;
607 my @edges = $self->paths;
608 my( %substart, %subend );
609 foreach my $edge ( @edges ) {
610 # Do we need to output this edge?
611 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
612 my $label = $self->_path_display_label( $self->path_witnesses( $edge ) );
613 my $variables = { %edge_attrs, 'label' => $label };
615 # Account for the rank gap if necessary
616 my $rank0 = $self->reading( $edge->[0] )->rank
617 if $self->reading( $edge->[0] )->has_rank;
618 my $rank1 = $self->reading( $edge->[1] )->rank
619 if $self->reading( $edge->[1] )->has_rank;
620 if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) {
621 $variables->{'minlen'} = $rank1 - $rank0;
624 # Add the calculated edge weights
625 # if( exists $weighted->{$edge->[0]}
626 # && $weighted->{$edge->[0]} eq $edge->[1] ) {
627 # # $variables->{'color'} = 'red';
628 # $variables->{'weight'} = 3.0;
631 # EXPERIMENTAL: make edge width reflect no. of witnesses
632 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
633 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
635 my $varopts = _dot_attr_string( $variables );
636 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
637 $edge->[0], $edge->[1], $varopts );
638 } elsif( $used{$edge->[0]} ) {
639 $subend{$edge->[0]} = 1;
640 } elsif( $used{$edge->[1]} ) {
641 $substart{$edge->[1]} = 1;
644 # Add substitute start and end edges if necessary
645 foreach my $node ( keys %substart ) {
646 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
647 my $variables = { %edge_attrs, 'label' => $witstr };
648 my $varopts = _dot_attr_string( $variables );
649 $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;";
651 foreach my $node ( keys %subend ) {
652 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
653 my $variables = { %edge_attrs, 'label' => $witstr };
654 my $varopts = _dot_attr_string( $variables );
655 $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;";
658 if( $STRAIGHTENHACK ) {
659 $dot .= "\t\"#END#\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
666 sub _dot_attr_string {
669 foreach my $k ( sort keys %$hash ) {
671 push( @attrs, $k.'="'.$v.'"' );
673 return( '[ ' . join( ', ', @attrs ) . ' ]' );
676 sub _add_edge_weights {
678 # Walk the graph from START to END, choosing the successor node with
679 # the largest number of witness paths each time.
681 my $curr = $self->start->id;
682 my $ranked = $self->end->has_rank;
683 while( $curr ne $self->end->id ) {
684 my $rank = $ranked ? $self->reading( $curr )->rank : 0;
685 my @succ = sort { $self->path_witnesses( $curr, $a )
686 <=> $self->path_witnesses( $curr, $b ) }
687 $self->sequence->successors( $curr );
688 my $next = pop @succ;
689 my $nextrank = $ranked ? $self->reading( $next )->rank : 0;
690 # Try to avoid lacunae in the weighted path.
692 ( $self->reading( $next )->is_lacuna ||
693 $nextrank - $rank > 1 ) ){
696 $weighted->{$curr} = $next;
702 =head2 path_witnesses( $edge )
704 Returns the list of sigils whose witnesses are associated with the given edge.
705 The edge can be passed as either an array or an arrayref of ( $source, $target ).
710 my( $self, @edge ) = @_;
711 # If edge is an arrayref, cope.
712 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
716 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
720 sub _path_display_label {
723 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
724 if( scalar @wits > $maj ) {
725 # TODO break out a.c. wits
728 return join( ', ', @wits );
732 =head2 witnesses_at_rank
734 Returns a list of witnesses that are not lacunose, for a given rank.
738 sub witnesses_at_rank {
739 my( $self, $rank ) = @_;
744 Returns a GraphML representation of the collation. The GraphML will contain
745 two graphs. The first expresses the attributes of the readings and the witness
746 paths that link them; the second expresses the relationships that link the
747 readings. This is the native transfer format for a tradition.
756 my $datafile = 't/data/florilegium_tei_ps.xml';
757 my $tradition = Text::Tradition->new( 'input' => 'TEI',
762 ok( $tradition, "Got a tradition object" );
763 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
764 ok( $tradition->collation, "Tradition has a collation" );
766 my $c = $tradition->collation;
767 is( scalar $c->readings, $READINGS, "Collation has all readings" );
768 is( scalar $c->paths, $PATHS, "Collation has all paths" );
769 is( scalar $c->relationships, 0, "Collation has all relationships" );
771 # Add a few relationships
772 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
773 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
774 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
776 # Now write it to GraphML and parse it again.
778 my $graphml = $c->as_graphml;
779 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
780 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
781 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
782 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
790 $self->calculate_ranks unless $self->_graphcalc_done;
793 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
794 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
795 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
796 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
798 # Create the document and root node
799 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
800 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
801 $graphml->setDocumentElement( $root );
802 $root->setNamespace( $xsi_ns, 'xsi', 0 );
803 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
805 # Add the data keys for the graph
808 my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
809 foreach my $datum ( @graph_attributes ) {
810 $graph_data_keys{$datum} = 'dg'.$gdi++;
811 my $key = $root->addNewChild( $graphml_ns, 'key' );
812 $key->setAttribute( 'attr.name', $datum );
813 $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
814 $key->setAttribute( 'for', 'graph' );
815 $key->setAttribute( 'id', $graph_data_keys{$datum} );
818 # Add the data keys for nodes
825 is_start => 'boolean',
827 is_lacuna => 'boolean',
828 is_common => 'boolean',
829 join_prior => 'boolean',
830 join_next => 'boolean',
832 foreach my $datum ( keys %node_data ) {
833 $node_data_keys{$datum} = 'dn'.$ndi++;
834 my $key = $root->addNewChild( $graphml_ns, 'key' );
835 $key->setAttribute( 'attr.name', $datum );
836 $key->setAttribute( 'attr.type', $node_data{$datum} );
837 $key->setAttribute( 'for', 'node' );
838 $key->setAttribute( 'id', $node_data_keys{$datum} );
841 # Add the data keys for edges, i.e. witnesses
845 class => 'string', # Class, deprecated soon
846 witness => 'string', # ID/label for a path
847 relationship => 'string', # ID/label for a relationship
848 extra => 'boolean', # Path key
849 scope => 'string', # Relationship key
850 annotation => 'string', # Relationship key
851 non_correctable => 'boolean', # Relationship key
852 non_independent => 'boolean', # Relationship key
854 foreach my $datum ( keys %edge_data ) {
855 $edge_data_keys{$datum} = 'de'.$edi++;
856 my $key = $root->addNewChild( $graphml_ns, 'key' );
857 $key->setAttribute( 'attr.name', $datum );
858 $key->setAttribute( 'attr.type', $edge_data{$datum} );
859 $key->setAttribute( 'for', 'edge' );
860 $key->setAttribute( 'id', $edge_data_keys{$datum} );
863 # Add the collation graph itself
864 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
865 $sgraph->setAttribute( 'edgedefault', 'directed' );
866 $sgraph->setAttribute( 'id', $self->tradition->name );
867 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
868 $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
869 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
870 $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
871 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
873 # Collation attribute data
874 foreach my $datum ( @graph_attributes ) {
875 my $value = $datum eq 'version' ? '3.0' : $self->$datum;
876 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
881 # Add our readings to the graph
882 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
883 # Add to the main graph
884 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
885 my $node_xmlid = 'n' . $node_ctr++;
886 $node_hash{ $n->id } = $node_xmlid;
887 $node_el->setAttribute( 'id', $node_xmlid );
888 foreach my $d ( keys %node_data ) {
890 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
895 # Add the path edges to the sequence graph
897 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
898 # We add an edge in the graphml for every witness in $e.
899 foreach my $wit ( sort $self->path_witnesses( $e ) ) {
900 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
901 $node_hash{ $e->[0] },
902 $node_hash{ $e->[1] } );
903 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
904 $edge_el->setAttribute( 'source', $from );
905 $edge_el->setAttribute( 'target', $to );
906 $edge_el->setAttribute( 'id', $id );
908 # It's a witness path, so add the witness
910 my $key = $edge_data_keys{'witness'};
911 # Is this an ante-corr witness?
912 my $aclabel = $self->ac_label;
913 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
914 # Keep the base witness
916 # ...and record that this is an 'extra' reading path
917 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
919 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
920 _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
924 # Add the relationship graph to the XML
925 $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
926 $node_data_keys{'id'}, \%edge_data_keys );
928 # Save and return the thing
929 my $result = decode_utf8( $graphml->toString(1) );
933 sub _add_graphml_data {
934 my( $el, $key, $value ) = @_;
935 return unless defined $value;
936 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
937 $data_el->setAttribute( 'key', $key );
938 $data_el->appendText( $value );
943 Returns a CSV alignment table representation of the collation graph, one
944 row per witness (or witness uncorrected.)
950 my $table = $self->alignment_table;
951 my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
953 # Make the header row
954 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
955 push( @result, decode_utf8( $csv->string ) );
956 # Make the rest of the rows
957 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
958 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
959 my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs;
960 $csv->combine( @row );
961 push( @result, decode_utf8( $csv->string ) );
963 return join( "\n", @result );
966 =head2 alignment_table( $use_refs, $include_witnesses )
968 Return a reference to an alignment table, in a slightly enhanced CollateX
969 format which looks like this:
971 $table = { alignment => [ { witness => "SIGIL",
972 tokens => [ { t => "TEXT" }, ... ] },
974 tokens => [ { t => "TEXT" }, ... ] },
978 If $use_refs is set to 1, the reading object is returned in the table
979 instead of READINGTEXT; if not, the text of the reading is returned.
981 If $include_witnesses is set to a hashref, only the witnesses whose sigil
982 keys have a true hash value will be included.
986 sub alignment_table {
988 $self->calculate_ranks() unless $self->_graphcalc_done;
989 return $self->cached_table if $self->has_cached_table;
991 # Make sure we can do this
992 throw( "Need a linear graph in order to make an alignment table" )
993 unless $self->linear;
994 $self->calculate_ranks unless $self->end->has_rank;
996 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
997 my @all_pos = ( 1 .. $self->end->rank - 1 );
998 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
999 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
1000 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
1001 my @row = _make_witness_row( \@wit_path, \@all_pos );
1002 push( @{$table->{'alignment'}},
1003 { 'witness' => $wit->sigil, 'tokens' => \@row } );
1004 if( $wit->is_layered ) {
1005 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
1006 $wit->sigil.$self->ac_label );
1007 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
1008 push( @{$table->{'alignment'}},
1009 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
1012 $self->cached_table( $table );
1016 sub _make_witness_row {
1017 my( $path, $positions ) = @_;
1019 map { $char_hash{$_} = undef } @$positions;
1021 foreach my $rdg ( @$path ) {
1022 my $rtext = $rdg->text;
1023 $rtext = '#LACUNA#' if $rdg->is_lacuna;
1024 print STDERR "rank " . $rdg->rank . "\n" if $debug;
1025 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
1026 $char_hash{$rdg->rank} = { 't' => $rdg };
1028 my @row = map { $char_hash{$_} } @$positions;
1029 # Fill in lacuna markers for undef spots in the row
1030 my $last_el = shift @row;
1031 my @filled_row = ( $last_el );
1032 foreach my $el ( @row ) {
1033 # If we are using node reference, make the lacuna node appear many times
1034 # in the table. If not, use the lacuna tag.
1035 if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) {
1038 push( @filled_row, $el );
1044 =head1 NAVIGATION METHODS
1046 =head2 reading_sequence( $first, $last, $sigil, $backup )
1048 Returns the ordered list of readings, starting with $first and ending
1049 with $last, for the witness given in $sigil. If a $backup sigil is
1050 specified (e.g. when walking a layered witness), it will be used wherever
1051 no $sigil path exists. If there is a base text reading, that will be
1052 used wherever no path exists for $sigil or $backup.
1056 # TODO Think about returning some lazy-eval iterator.
1057 # TODO Get rid of backup; we should know from what witness is whether we need it.
1059 sub reading_sequence {
1060 my( $self, $start, $end, $witness ) = @_;
1062 $witness = $self->baselabel unless $witness;
1063 my @readings = ( $start );
1066 while( $n && $n->id ne $end->id ) {
1067 if( exists( $seen{$n->id} ) ) {
1068 throw( "Detected loop for $witness at " . $n->id );
1072 my $next = $self->next_reading( $n, $witness );
1074 throw( "Did not find any path for $witness from reading " . $n->id );
1076 push( @readings, $next );
1079 # Check that the last reading is our end reading.
1080 my $last = $readings[$#readings];
1081 throw( "Last reading found from " . $start->text .
1082 " for witness $witness is not the end!" ) # TODO do we get this far?
1083 unless $last->id eq $end->id;
1088 =head2 next_reading( $reading, $sigil );
1090 Returns the reading that follows the given reading along the given witness
1096 # Return the successor via the corresponding path.
1098 my $answer = $self->_find_linked_reading( 'next', @_ );
1099 return undef unless $answer;
1100 return $self->reading( $answer );
1103 =head2 prior_reading( $reading, $sigil )
1105 Returns the reading that precedes the given reading along the given witness
1111 # Return the predecessor via the corresponding path.
1113 my $answer = $self->_find_linked_reading( 'prior', @_ );
1114 return $self->reading( $answer );
1117 sub _find_linked_reading {
1118 my( $self, $direction, $node, $path ) = @_;
1120 # Get a backup if we are dealing with a layered witness
1122 my $aclabel = $self->ac_label;
1123 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1127 my @linked_paths = $direction eq 'next'
1128 ? $self->sequence->edges_from( $node )
1129 : $self->sequence->edges_to( $node );
1130 return undef unless scalar( @linked_paths );
1132 # We have to find the linked path that contains all of the
1133 # witnesses supplied in $path.
1134 my( @path_wits, @alt_path_wits );
1135 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1136 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1139 foreach my $le ( @linked_paths ) {
1140 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1143 my @le_wits = sort $self->path_witnesses( $le );
1144 if( _is_within( \@path_wits, \@le_wits ) ) {
1145 # This is the right path.
1146 return $direction eq 'next' ? $le->[1] : $le->[0];
1147 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1151 # Got this far? Return the alternate path if it exists.
1152 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1155 # Got this far? Return the base path if it exists.
1156 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1159 # Got this far? We have no appropriate path.
1160 warn "Could not find $direction node from " . $node->id
1161 . " along path $path";
1167 my( $set1, $set2 ) = @_;
1168 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1169 foreach my $el ( @$set1 ) {
1170 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1175 # Return the string that joins together a list of witnesses for
1176 # display on a single path.
1177 sub _witnesses_of_label {
1178 my( $self, $label ) = @_;
1179 my $regex = $self->wit_list_separator;
1180 my @answer = split( /\Q$regex\E/, $label );
1184 =head2 common_readings
1186 Returns the list of common readings in the graph (i.e. those readings that are
1187 shared by all non-lacunose witnesses.)
1191 sub common_readings {
1193 my @common = grep { $_->is_common } $self->readings;
1197 =head2 path_text( $sigil, $mainsigil [, $start, $end ] )
1199 Returns the text of a witness (plus its backup, if we are using a layer)
1200 as stored in the collation. The text is returned as a string, where the
1201 individual readings are joined with spaces and the meta-readings (e.g.
1202 lacunae) are omitted. Optional specification of $start and $end allows
1203 the generation of a subset of the witness text.
1208 my( $self, $wit, $start, $end ) = @_;
1209 $start = $self->start unless $start;
1210 $end = $self->end unless $end;
1211 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1214 foreach my $r ( @path ) {
1215 if( $r->join_prior || !$last || $last->join_next ) {
1216 $pathtext .= $r->text;
1218 $pathtext .= ' ' . $r->text;
1225 =head1 INITIALIZATION METHODS
1227 These are mostly for use by parsers.
1229 =head2 make_witness_path( $witness )
1231 Link the array of readings contained in $witness->path (and in
1232 $witness->uncorrected_path if it exists) into collation paths.
1233 Clear out the arrays when finished.
1235 =head2 make_witness_paths
1237 Call make_witness_path for all witnesses in the tradition.
1241 # For use when a collation is constructed from a base text and an apparatus.
1242 # We have the sequences of readings and just need to add path edges.
1243 # When we are done, clear out the witness path attributes, as they are no
1245 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1247 sub make_witness_paths {
1249 foreach my $wit ( $self->tradition->witnesses ) {
1250 # print STDERR "Making path for " . $wit->sigil . "\n";
1251 $self->make_witness_path( $wit );
1255 sub make_witness_path {
1256 my( $self, $wit ) = @_;
1257 my @chain = @{$wit->path};
1258 my $sig = $wit->sigil;
1259 foreach my $idx ( 0 .. $#chain-1 ) {
1260 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1262 if( $wit->is_layered ) {
1263 @chain = @{$wit->uncorrected_path};
1264 foreach my $idx( 0 .. $#chain-1 ) {
1265 my $source = $chain[$idx];
1266 my $target = $chain[$idx+1];
1267 $self->add_path( $source, $target, $sig.$self->ac_label )
1268 unless $self->has_path( $source, $target, $sig );
1272 $wit->clear_uncorrected_path;
1275 =head2 calculate_ranks
1277 Calculate the reading ranks (that is, their aligned positions relative
1278 to each other) for the graph. This can only be called on linear collations.
1282 use Text::Tradition;
1284 my $cxfile = 't/data/Collatex-16.xml';
1285 my $t = Text::Tradition->new(
1287 'input' => 'CollateX',
1290 my $c = $t->collation;
1293 my $table = $c->alignment_table;
1294 ok( $c->has_cached_table, "Alignment table was cached" );
1295 is( $c->alignment_table, $table, "Cached table returned upon second call" );
1296 $c->calculate_ranks;
1297 is( $c->alignment_table, $table, "Cached table retained with no rank change" );
1298 $c->add_relationship( 'n9', 'n23', { 'type' => 'spelling' } );
1299 isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" );
1305 sub calculate_ranks {
1307 # Save the existing ranks, in case we need to invalidate the cached SVG.
1309 # Walk a version of the graph where every node linked by a relationship
1310 # edge is fundamentally the same node, and do a topological ranking on
1311 # the nodes in this graph.
1312 my $topo_graph = Graph->new();
1316 foreach my $r ( $self->readings ) {
1317 next if exists $rel_containers{$r->id};
1318 my @rels = $r->related_readings( 'colocated' );
1320 # Make a relationship container.
1322 my $rn = 'rel_container_' . $rel_ctr++;
1323 $topo_graph->add_vertex( $rn );
1325 $rel_containers{$_->id} = $rn;
1328 # Add a new node to mirror the old node.
1329 $rel_containers{$r->id} = $r->id;
1330 $topo_graph->add_vertex( $r->id );
1335 foreach my $r ( $self->readings ) {
1336 $existing_ranks{$r} = $r->rank;
1337 foreach my $n ( $self->sequence->successors( $r->id ) ) {
1338 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
1339 $rel_containers{$n} );
1340 # $DB::single = 1 unless $tfrom && $tto;
1341 $topo_graph->add_edge( $tfrom, $tto );
1345 # Now do the rankings, starting with the start node.
1346 my $topo_start = $rel_containers{$self->start->id};
1347 my $node_ranks = { $topo_start => 0 };
1348 my @curr_origin = ( $topo_start );
1349 # A little iterative function.
1350 while( @curr_origin ) {
1351 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
1353 # Transfer our rankings from the topological graph to the real one.
1354 foreach my $r ( $self->readings ) {
1355 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
1356 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1358 # Die. Find the last rank we calculated.
1359 my @all_defined = sort { $node_ranks->{$rel_containers{$a->id}}
1360 <=> $node_ranks->{$rel_containers{$b->id}} }
1362 my $last = pop @all_defined;
1363 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1366 # Do we need to invalidate the cached data?
1367 if( $self->has_cached_svg || $self->has_cached_table ) {
1368 foreach my $r ( $self->readings ) {
1369 next if defined( $existing_ranks{$r} )
1370 && $existing_ranks{$r} == $r->rank;
1371 # Something has changed, so clear the cache
1372 $self->_clear_cache;
1373 # ...and recalculate the common readings.
1374 $self->calculate_common_readings();
1378 # The graph calculation information is now up to date.
1379 $self->_graphcalc_done(1);
1383 my( $graph, $node_ranks, @current_nodes ) = @_;
1384 # Look at each of the children of @current_nodes. If all the child's
1385 # parents have a rank, assign it the highest rank + 1 and add it to
1386 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1387 # parent gets a rank.
1389 foreach my $c ( @current_nodes ) {
1390 warn "Current reading $c has no rank!"
1391 unless exists $node_ranks->{$c};
1392 # print STDERR "Looking at child of node $c, rank "
1393 # . $node_ranks->{$c} . "\n";
1394 foreach my $child ( $graph->successors( $c ) ) {
1395 next if exists $node_ranks->{$child};
1396 my $highest_rank = -1;
1398 foreach my $parent ( $graph->predecessors( $child ) ) {
1399 if( exists $node_ranks->{$parent} ) {
1400 $highest_rank = $node_ranks->{$parent}
1401 if $highest_rank <= $node_ranks->{$parent};
1408 my $c_rank = $highest_rank + 1;
1409 # print STDERR "Assigning rank $c_rank to node $child \n";
1410 $node_ranks->{$child} = $c_rank;
1411 push( @next_nodes, $child );
1419 $self->wipe_svg if $self->has_cached_svg;
1420 $self->wipe_table if $self->has_cached_table;
1424 =head2 flatten_ranks
1426 A convenience method for parsing collation data. Searches the graph for readings
1427 with the same text at the same rank, and merges any that are found.
1433 my %unique_rank_rdg;
1434 foreach my $rdg ( $self->readings ) {
1435 next unless $rdg->has_rank;
1436 my $key = $rdg->rank . "||" . $rdg->text;
1437 if( exists $unique_rank_rdg{$key} ) {
1439 # print STDERR "Combining readings at same rank: $key\n";
1440 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1441 # TODO see if this now makes a common point.
1443 $unique_rank_rdg{$key} = $rdg;
1449 =head2 calculate_common_readings
1451 Goes through the graph identifying the readings that appear in every witness
1452 (apart from those with lacunae at that spot.) Marks them as common and returns
1457 use Text::Tradition;
1459 my $cxfile = 't/data/Collatex-16.xml';
1460 my $t = Text::Tradition->new(
1462 'input' => 'CollateX',
1465 my $c = $t->collation;
1467 my @common = $c->calculate_common_readings();
1468 is( scalar @common, 8, "Found correct number of common readings" );
1469 my @marked = sort $c->common_readings();
1470 is( scalar @common, 8, "All common readings got marked as such" );
1471 my @expected = qw/ n1 n12 n16 n19 n20 n5 n6 n7 /;
1472 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1478 sub calculate_common_readings {
1481 map { $_->is_common( 0 ) } $self->readings;
1482 # Implicitly calls calculate_ranks
1483 my $table = $self->alignment_table;
1484 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1485 my @row = map { $_->{'tokens'}->[$idx]
1486 ? $_->{'tokens'}->[$idx]->{'t'} : '' }
1487 @{$table->{'alignment'}};
1489 foreach my $r ( @row ) {
1491 $hash{$r->id} = $r unless $r->is_meta;
1493 $hash{'UNDEF'} = $r;
1496 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1497 my( $r ) = values %hash;
1499 push( @common, $r );
1505 =head2 text_from_paths
1507 Calculate the text array for all witnesses from the path, for later consistency
1508 checking. Only to be used if there is no non-graph-based way to know the
1513 sub text_from_paths {
1515 foreach my $wit ( $self->tradition->witnesses ) {
1516 my @text = split( /\s+/,
1517 $self->reading_sequence( $self->start, $self->end, $wit->sigil ) );
1518 $wit->text( \@text );
1519 if( $wit->is_layered ) {
1520 my @uctext = split( /\s+/,
1521 $self->reading_sequence( $self->start, $self->end,
1522 $wit->sigil.$self->ac_label ) );
1523 $wit->text( \@uctext );
1528 =head1 UTILITY FUNCTIONS
1530 =head2 common_predecessor( $reading_a, $reading_b )
1532 Find the last reading that occurs in sequence before both the given readings.
1534 =head2 common_successor( $reading_a, $reading_b )
1536 Find the first reading that occurs in sequence after both the given readings.
1540 use Text::Tradition;
1542 my $cxfile = 't/data/Collatex-16.xml';
1543 my $t = Text::Tradition->new(
1545 'input' => 'CollateX',
1548 my $c = $t->collation;
1550 is( $c->common_predecessor( 'n9', 'n23' )->id,
1551 'n20', "Found correct common predecessor" );
1552 is( $c->common_successor( 'n9', 'n23' )->id,
1553 '#END#', "Found correct common successor" );
1555 is( $c->common_predecessor( 'n19', 'n17' )->id,
1556 'n16', "Found correct common predecessor for readings on same path" );
1557 is( $c->common_successor( 'n21', 'n26' )->id,
1558 '#END#', "Found correct common successor for readings on same path" );
1564 ## Return the closest reading that is a predecessor of both the given readings.
1565 sub common_predecessor {
1567 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1568 return $self->_common_in_path( $r1, $r2, 'predecessors' );
1571 sub common_successor {
1573 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1574 return $self->_common_in_path( $r1, $r2, 'successors' );
1577 sub _common_in_path {
1578 my( $self, $r1, $r2, $dir ) = @_;
1579 my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
1580 $iter = $self->end->rank - $iter if $dir eq 'successors';
1582 my @last_checked = ( $r1, $r2 );
1584 while( !@candidates ) {
1586 foreach my $lc ( @last_checked ) {
1587 foreach my $p ( $lc->$dir ) {
1588 if( $all_seen{$p->id} ) {
1589 push( @candidates, $p );
1591 $all_seen{$p->id} = 1;
1592 push( @new_lc, $p );
1596 @last_checked = @new_lc;
1598 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1599 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1603 Text::Tradition::Error->throw(
1604 'ident' => 'Collation error',
1610 __PACKAGE__->meta->make_immutable;
1614 This package is free software and is provided "as is" without express
1615 or implied warranty. You can redistribute it and/or modify it under
1616 the same terms as Perl itself.
1620 Tara L Andrews E<lt>aurum@cpan.orgE<gt>